3.6: Nucleic Acids
By the end of this section, you will be able to:
- Describe the structure of nucleic acids and define the two types of nucleic acids
- Explain the structure and role of DNA
- Explain the structure and roles of RNA
Nucleic acids are the most important macromolecules for the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) . DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is found in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope.
The entire genetic content of a cell is known as its genome, and the study of genomes is genomics. In eukaryotic cells but not in prokaryotes, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes. A chromosome may contain tens of thousands of genes. Many genes contain the information to make protein products; other genes code for RNA products. DNA controls all of the cellular activities by turning the genes “on” or “off.”
The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA (mRNA) . Other types of RNA—like rRNA, tRNA, and microRNA—are involved in protein synthesis and its regulation.
DNA and RNA are made up of monomers known as nucleotides . The nucleotides combine with each other to form a polynucleotide , DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group (Figure \(\PageIndex{1}\)). Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.
The nitrogenous bases, important components of nucleotides, are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus, decreases the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).
Adenine and guanine are classified as purines . The primary structure of a purine is two carbon-nitrogen rings. Cytosine, thymine, and uracil are classified as pyrimidines which have a single carbon-nitrogen ring as their primary structure (Figure \(\PageIndex{1}\)). Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, the nitrogenous bases are simply known by their symbols A, T, G, C, and U. DNA contains A, T, G, and C whereas RNA contains A, U, G, and C.
The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose (Figure \(\PageIndex{1}\)). The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). The phosphate residue is attached to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′–3′ phosphodiester linkage. The phosphodiester linkage is not formed by simple dehydration reaction like the other linkages connecting monomers in macromolecules: its formation involves the removal of two phosphate groups. A polynucleotide may have thousands of such phosphodiester linkages.
DNA Double-Helix Structure
DNA has a double-helix structure (Figure \(\PageIndex{2}\)). The sugar and phosphate lie on the outside of the helix, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase, in pairs; the pairs are bound to each other by hydrogen bonds. Every base pair in the double helivx is separated from the next base pair by 0.34 nm. The two strands of the helix run in opposite directions, meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand. (This is referred to as antiparallel orientation and is important to DNA replication and in many nucleic acid interactions.)
Only certain types of base pairing are allowed. For example, a certain purine can only pair with a certain pyrimidine. This means A can pair with T, and G can pair with C, as shown in Figure \(\PageIndex{3}\). This is known as the base complementary rule. In other words, the DNA strands are complementary to each other. If the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG. During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand.
RNA
Ribonucleic acid, or RNA, is mainly involved in the process of protein synthesis under the direction of DNA. RNA is usually single-stranded and is made of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and the phosphate group.
There are four major types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and microRNA (miRNA). The first, mRNA, carries the message from DNA, which controls all of the cellular activities in a cell. If a cell requires a certain protein to be synthesized, the gene for this product is turned “on” and the messenger RNA is synthesized in the nucleus. The RNA base sequence is complementary to the coding sequence of the DNA from which it has been copied. However, in RNA, the base T is absent and U is present instead. If the DNA strand has a sequence AATTGCGC, the sequence of the complementary RNA is UUAACGCG. In the cytoplasm, the mRNA interacts with ribosomes and other cellular machinery (Figure \(\PageIndex{4}\)).
The mRNA is read in sets of three bases known as codons. Each codon codes for a single amino acid. In this way, the mRNA is read and the protein product is made. Ribosomal RNA (rRNA) is a major constituent of ribosomes on which the mRNA binds. The rRNA ensures the proper alignment of the mRNA and the ribosomes; the rRNA of the ribosome also has an enzymatic activity (peptidyl transferase) and catalyzes the formation of the peptide bonds between two aligned amino acids. Transfer RNA (tRNA) is one of the smallest of the four types of RNA, usually 70–90 nucleotides long. It carries the correct amino acid to the site of protein synthesis. It is the base pairing between the tRNA and mRNA that allows for the correct amino acid to be inserted in the polypeptide chain. microRNAs are the smallest RNA molecules and their role involves the regulation of gene expression by interfering with the expression of certain mRNA messages. Table \(\PageIndex{1}\) below summarizes features of DNA and RNA.
Table \(\PageIndex{1}\): Features of DNA and RNA.
| Features of DNA and RNA | ||
|---|---|---|
| DNA | RNA | |
| Function | Carries genetic information | Involved in protein synthesis |
| Location | Remains in the nucleus | Leaves the nucleus |
| Structure | Double helix | Usually single-stranded |
| Sugar | Deoxyribose | Ribose |
| Pyrimidines | Cytosine, thymine | Cytosine, uracil |
| Purines | Adenine, guanine | Adenine, guanine |
Even though the RNA is single stranded, most RNA types show extensive intramolecular base pairing between complementary sequences, creating a predictable three-dimensional structure essential for their function.
As you have learned, information flow in an organism takes place from DNA to RNA to protein. DNA dictates the structure of mRNA in a process known as transcription , and RNA dictates the structure of protein in a process known as translation . This is known as the Central Dogma of Life, which holds true for all organisms; however, exceptions to the rule occur in connection with viral infections.
To learn more about DNA, explore the Howard Hughes Medical Institute BioInteractive animations on the topic of DNA .
Summary
Nucleic acids are molecules made up of nucleotides that direct cellular activities such as cell division and protein synthesis.  There are two types of nucleic acids: DNA and RNA. DNA carries the genetic blueprint of the cell and is passed on from parents to offspring (in the form of chromosomes). It has a double-helical structure with the two strands running in opposite directions, connected by hydrogen bonds, and complementary to each other. RNA is single-stranded and is made of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is involved in protein synthesis and its regulation. Messenger RNA (mRNA) is copied from the DNA, is exported from the nucleus to the cytoplasm, and contains information for the construction of proteins. Ribosomal RNA (rRNA) is a part of the ribosomes at the site of protein synthesis, whereas transfer RNA (tRNA) carries the amino acid to the site of protein synthesis. microRNA regulates the use of mRNA for protein synthesis.
Review Questions
A nucleotide of DNA may contain ________.
A. ribose, uracil, and a phosphate group
B. deoxyribose, uracil, and a phosphate group
C. deoxyribose, thymine, and a phosphate group
D. ribose, thymine, and a phosphate group
- Answer
-
Answer: C
The building blocks of nucleic acids are ________.
A. sugars
B. nitrogenous bases
C. peptides
D. nucleotides
- Answer
-
Answer: D
Free Response
What are the structural differences between RNA and DNA?
- Answer
-
Answer: DNA has a double-helix structure. The sugar and the phosphate are on the outside of the helix and the nitrogenous bases are in the interior. The monomers of DNA are nucleotides containing deoxyribose, one of the four nitrogenous bases (A, T, G and C), and a phosphate group. RNA is usually single-stranded and is made of ribonucleotides that are linked by phosphodiester linkages. A ribonucleotide contains ribose (the pentose sugar), one of the four nitrogenous bases (A,U, G, and C), and the phosphate group.
What are the four types of RNA and how do they function?
- Answer
-
Answer: The four types of RNA are messenger RNA, ribosomal RNA, transfer RNA, and microRNA. Messenger RNA carries the information from the DNA that controls all cellular activities. The mRNA binds to the ribosomes that are constructed of proteins and rRNA, and tRNA transfers the correct amino acid to the site of protein synthesis. microRNA regulates the availability of mRNA for translation.
Study Figure \(\PageIndex{3}\). A mutation occurs, and cytosine is replaced with adenine. What impact do you think this will have on the DNA structure?
- Answer
-
Answer: Adenine is larger than cytosine and will not be able to base pair properly with the guanine on the opposing strand. This will cause the DNA to bulge. DNA repair enzymes may recognize the bulge and replace the incorrect nucleotide.
Glossary
- deoxyribonucleic acid (DNA)
- double-helical molecule that carries the hereditary information of the cell
- messenger RNA (mRNA)
- RNA that carries information from DNA to ribosomes during protein synthesis
- nucleic acid
- biological macromolecule that carries the genetic blueprint of a cell and carries instructions for the functioning of the cell
- nucleotide
- monomer of nucleic acids; contains a pentose sugar, one or more phosphate groups, and a nitrogenous base
- phosphodiester
- linkage covalent chemical bond that holds together the polynucleotide chains with a phosphate group linking two pentose sugars of neighboring nucleotides
- polynucleotide
- long chain of nucleotides
- purine
- type of nitrogenous base in DNA and RNA; adenine and guanine are purines
- pyrimidine
- type of nitrogenous base in DNA and RNA; cytosine, thymine, and uracil are pyrimidines
- ribonucleic acid (RNA)
- single-stranded, often internally base paired, molecule that is involved in protein synthesis
- ribosomal RNA (rRNA)
- RNA that ensures the proper alignment of the mRNA and the ribosomes during protein synthesis and catalyzes the formation of the peptide linkage
- transcription
- process through which messenger RNA forms on a template of DNA
- transfer RNA (tRNA)
- RNA that carries activated amino acids to the site of protein synthesis on the ribosome
- translation
- process through which RNA directs the formation of protein
Contributors and Attributions
-
Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski (Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY 4.0; Download for free at<EMAIL_ADDRESS>).


1.3: Scale of the Cosmos
Perhaps you have heard the phrase that a large number is astronomical . Astronomical comes from the fact that the size of the Universe is so big, it is often hard to comprehend. Even distances between the planets and the Sun in our own Solar System are numbers we are not custom to using. To understand the scale of the Cosmos, we will start with several examples in our Solar System. First, the distance between the Earth and Moon is about 230,000 miles. The closest distance between Earth and Mars is about 32,000,000 miles. The distance between the Earth and Sun is about 93,000,000 miles. The distance between Mercury – the closest planet to the Sun – and the Sun is about 36,000,000 miles. The distance between Neptune – the farthest planet from the Sun – and the Sun is about 2,797,770,000 miles. It is often useful to make a scale model of large systems. Some cities, museums, and parks will create a scale Solar System, based on something like 1 foot equals 1 million miles.
To simplify distance in our Solar System, astronomers use the Astronomical Unit (1 AU), which equals 93,000,000 miles or the average distance from Earth to the Sun.
As for other numbers, these are the diameters of three Solar System bodies. First, our Earth’s diameter is just less than 8,000 miles. Jupiter’s diameter – the largest planet in our Solar System – is around 88,000 miles. And the Sun’s diameter is about 850,000 miles.
The idea here is not to memorize size and distance; rather, it is to appreciate the grand scale of the Universe within which we live.
Going beyond our Solar System, the closest star is Proxima Centauri, part of the Alpha Centauri triple star system. It is about 24,340,000,000,000 miles (that is 24 trillion, 340 billion miles) away or about 270,000 times more distant than Earth to the Sun. And that is the closest star beyond our Sun. Because of these great distances, astronomers will use another measure: the distance light travels in one year, or the light year. This sounds like a time measure, but it is not.
Light travels 186,000 miles in one second, or 2. 99 x 108 meters per second. That is 5,869,713,600,000 miles in a year. So the Sun is about 8 light minutes from Earth and Proxima Centauri about 4. 24 light years distant.


Understand Kohlberg’s theory on preconventional, conventional, and postconventional moral development
Lawrence Kohlberg (1963) built on the work of Piaget and was interested in finding out how our moral reasoning changes as we get older. He wanted to find out how people decide what is right and what is wrong. In order to explore this area, he read a story containing a moral dilemma to boys of different age groups (also known as the Heinz dilemma). In the story, a man is trying to obtain an expensive drug that his wife needs in order to treat her cancer. The man has no money and no one will loan him the money he requires. He begs the pharmacist to reduce the price, but the pharmacist refuses. So, the man decides to break into the pharmacy to steal the drug. Then Kohlberg asked the children to decide whether the man was right or wrong in his choice. Kohlberg was not interested in whether they said the man was right or wrong, he was interested in finding out how they arrived at such a decision. He wanted to know what they thought made something right or wrong.
Pre-conventional Moral Development
The youngest subjects seemed to answer based on what would happen to the man as a result of the act. For example, they might say the man should not break into the pharmacy because the pharmacist might find him and beat him, or they might say that the man should break in and steal the drug and his wife will give him a big kiss. Right or wrong, both decisions were based on what would physically happen to the man as a result of the act. This is a self-centered approach to moral decision-making. He called this most superficial understanding of right and wrong pre-conventional moral development.
Pre-conventional development covers stages one and two in Kohlberg’s theory. In stage one, the focus is on the direct consequences of their actions. Their main concern is avoiding punishment and being obedient. In stage two, the focus is more “what’s in it for me”? A stage two mentality is self-interest driven.
Conventional Moral Development
Middle childhood boys seemed to base their answers on what other people would think of the man as a result of his act. For instance, they might say he should break into the store, and then everyone would think he was a good husband. Or, he shouldn’t because it is against the law. In either case, right and wrong is determined by what other people think. Because what other people think is usually a function of socially accepted morality, this view is often thought of as applying society’s standards. A good decision is one that gains the approval of others or one that complies with the law. This is conventional moral development.
The conventional moral development covers stages three and four. In stage three, the focus is on what society deems okay or good in order to gain approval from others. In stage four, the focus is on maintaining social order. The person has an understanding that laws and social conventions are created to maintain a properly functioning society.
Post-conventional Moral Development
Older children were the only ones to appreciate the fact that the Heinz dilemma has different levels of right and wrong. Right and wrong are based on social contracts established for the good of everyone or on universal principles of right and wrong that transcend the self and social convention. For example, the man should break into the store because, even if it is against the law, the wife needs the drug and her life is more important than the consequences the man might face for breaking the law. Or, the man should not violate the principle of the right of property because this rule is essential for social order. In either case, the person’s judgment goes beyond what happens to the self. It is based on a concern for others, for society as a whole, or for an ethical standard rather than a legal standard. This level is called post-conventional moral development because it goes beyond convention or what other people think to a higher, universal ethical principle of conduct that may or may not be reflected in the law. Notice that such thinking (the kind supreme justices do all day in deliberating whether a law is moral or ethical, etc.) requires being able to think abstractly. Often this is not accomplished until a person reaches adolescence or adulthood.
Post conventional moral development covers stages five and six. In stage five, the person realizes that not everything is black and white. The person realizes that there are many different ways of thinking about what is good and what is right. Further, just because there is a law does not mean that the law is necessarily good for everyone. In stage five, then, the idea is to do the most good for the most people. Kohlberg’s sixth stage is interesting in that it does not seem that people make it to this stage and stay. Indeed, many researchers have failed to identify people who operate within a stage six mentality at all, while others have identified a very few people who operate within stage six on occasion. Why might this be the case? Stage six is a way of thinking about the question of morality in a way that is not personal. Instead, a person tries to empathize with other people and to see the world from the other person’s perspective before making a decision. While this sounds easy, very few people are capable of doing this well, and even fewer are capable of doing it consistently. Further, the idea of universal justice is involved in stage six. Indeed, a person in stage six is ready to disobey unjust laws. The focus is on doing the right thing, regardless of the personal consequences.
Watch It
The Heinz dilemma is a frequently used example used to help us understand Kohlberg’s stages of moral development. It is described in the following video:
A link to an interactive elements can be found at the bottom of this page.
From a theoretical point of view, it is not important what the participant thinks that Heinz should do. Kohlberg’s theory holds that the justification the participant offers is what is significant, the form of their response. Below are some of many examples of possible arguments that belong to the six stages:
Stage one (obedience): Heinz should not steal the medicine because he will consequently be put in prison which will mean he is a bad person. OR Heinz should steal the medicine because it is only worth $200 and not how much the druggist wanted for it; Heinz had even offered to pay for it and was not stealing anything else.
Stage two (self-interest): Heinz should steal the medicine because he will be much happier if he saves his wife, even if he will have to serve a prison sentence. OR Heinz should not steal the medicine because prison is an awful place, and he would more likely languish in a jail cell than over his wife’s death.
Stage three (conformity): Heinz should steal the medicine because his wife expects it; he wants to be a good husband. OR Heinz should not steal the drug because stealing is bad and he is not a criminal; he has tried to do everything he can without breaking the law, you cannot blame him.
Stage four (law-and-order): Heinz should not steal the medicine because the law prohibits stealing, making it illegal. OR Heinz should steal the drug for his wife but also take the prescribed punishment for the crime as well as paying the druggist what he is owed. Criminals cannot just run around without regard for the law; actions have consequences.
Stage five (social contract orientation): Heinz should steal the medicine because everyone has a right to choose life, regardless of the law. OR Heinz should not steal the medicine because the scientist has a right to fair compensation. Even if his wife is sick, it does not make his actions right.
Stage six (universal human ethics): Heinz should steal the medicine, because saving a human life is a more fundamental value than the property rights of another person. OR Heinz should not steal the medicine, because others may need the medicine just as badly, and their lives are equally significant.
Modern Views of Moral Development
Kohlberg continued to explore his theory after the initial theory was researched. He theorized that there could be other stages and that there could be transitions into each stage. One thing that Kohlberg never fully addressed was his use of nearly all male samples. Men and women tend to have very different styles of moral decision making; men tend to be very justice oriented while women tend to be more compassion oriented. In terms of Kohlberg’s stages, women tend to be in lower stages than men because of their compassion orientation.
Carol Gilligan was one of Kohlberg’s research assistants. She believed that Kohlberg’s theory was inherently biased against women. Gilligan suggests that the biggest reason that there is a gender bias in Kohlberg’s theory is because males tend to focus on logic and rules while women focus on caring for others and relationships. She suggests, then, that in order to truly measure women’s moral development, it was necessary to create a measure specifically for women. Gilligan was clear that she did not believe neither male nor female moral development was better, but rather that they were equally important.
Consider your own decision-making processes. What guides your decisions? Are you primarily concerned with your personal well-being? Do you make choices based on what other people will think about your decision? Or are you guided by other principles? To what extent is this approach guided by your culture?
Glossary
conventional moral development
stages 3 and 4 of moral development where morality is internalized, and the concern is on society norms
pre-conventional moral development
first 2 stages of moral development where morality comes from outside the person, and the concern is on physical consequences of actions
post-conventional moral development
stages 5 and 6 of moral development where morality comes from personal understanding of rights and justice, regardless of whether that understanding matches societal norms
Contributors and Attributions
CC licensed content, Original
Modification, adaptation, and original content.
Authored by
: Stephanie Loalada for Lumen Learning.
Provided by
: Lumen Learning.
License
:
CC BY-SA: Attribution-ShareAlike
Heinz Dilemma - Kohlberg's stages of Moral Development (Interactive Animation).
Provided by
: RebelMangoTv.
Located at
:
https://www.youtube.com/watch?v=5czp9S4u26M
.
License
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Other
.
License Terms
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American Indian Movement
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a social and political organization with many local chapters around the United States of activist Native people focused on confronting the federal and state governments over racist policies and actions. AIM was most active in the 1970s and 1980s.
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animistic
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of or relating to a spiritual belief that everything in the world has its own living spirit.
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assimilation
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the process of changing the culture of a person or group of people to some other culture, through socialization or education.
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basketry
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an art form of many Indigenous peoples, created from woven plant matter. Each tribe has its own traditions and styles, with some tribes using many styles.
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blood quantum
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a term first applied by the US federal government to determine which people had rights to services and land at reservations. The term has become a characteristic to define who is eligible for citizenship in a tribe, with membership open only to those who have a minimum blood quantum of Indigenous genealogical ancestry.
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boarding schools
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educational institutions established by federal authorities to efficiently educate and assimilate Indigenous children through an immersive environment.
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Indian Claims
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a series of more than 700 lawsuits brought by tribal nations in the 20th century against the US federal government to demand repayment for failures in the administration of a variety of responsibilities.
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Indian mascots
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characterizations of a Native person or group used to represent athletic teams, often portraying savage or cartoonish stereotypes. The practice is considered highly racist toward Native peoples.
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Indians
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a commonly used term for Native Americans first applied by Christopher Columbus, who mistakenly thought the Indigenous peoples he encountered were people of India.
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Indigenous peoples
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the original populations of a land and those who carry culture and experiences from an Indigenous culture. Indigenous peoples may also be referred to as Native peoples, tribal peoples, tribes, First Nations peoples, Aboriginal peoples, or American Indians or Native Americans.
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Maori
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the Indigenous peoples of New Zealand.
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Marshall court trilogy
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three Supreme Court decisions—
Johnson v. M’Intosh
(1823),
Cherokee Nation v. Georgia
(1831), and
Worcester v. Georgia
(1832)—that determined that tribal nations are domestic sovereign nations within the United States and dependent on the federal government to guarantee their sovereignty.
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mestizo
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Latin American term for a person of mixed heritage, normally Indigenous and Spanish or Indigenous and another White ethnicity.
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Métis
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Canadian term for a person of partial Indigenous heritage. A Métis person has different rights from a First Nations person.
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Native studies
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an educational discipline that originated from the critiques of studies of tribal communities by non-Native scholars. Native studies programs seek to center Indigenous knowledge and experience in studies of Indigenous peoples and societies.
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noble savages
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a romanticist term used to suggest that Native peoples were uncivilized and primitive, living in harmony with nature.
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oral histories
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spoken, rather than written, narratives of past events.
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oral tradition
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cultural knowledge that is passed on through oral, rather than written, form.
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petroglyphs
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images carved into stone and sometimes painted.
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pictographs
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drawings on the wall of a cave or rock shelter or on animal hide.
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public anthropologists
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anthropologists who work to make their research, analysis, and products available to the public through publication and presentation of their work in public, easily accessible places.
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termination
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a US federal policy adopted in 1953 that involved voiding the treaty agreements between the federal government and Native peoples, enabling the government to repossess and sell property that had been part of reservations in a process called liquidation. Terminated tribal peoples are no longer federally recognized Native peoples and have no rights to ask for federal services or assistance. Between 1954 and the 1970s, 109 tribes underwent termination. Most were federally restored between the 1970s and the 1990s.
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Trade and Intercourse Acts
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federal laws that administer trade between states and across federal borders. The law affects the ability of Native nations to establish industries and sell products or services beyond their borders.
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treaties
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agreements between sovereign entities, in this context Native nations and the United States.
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urban Indian
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a Native person who lives in an urban environment; sometimes a negative title used by those living on reservations to refer to Native people who are assumed to have willingly given up their culture, land, and Native identities.


2.MM: Molecular Models
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After completing this section, you should be able to
You will have noticed that we have given two names for most of the compounds discussed up to this point. In general we shall be using systematic (i.e., IUPAC—International Union of Pure and Applied Chemistry) names throughout the course. However, simple compounds are often known by their common names, which may be more familiar than their IUPAC counterparts. We shall address the subject of nomenclature (naming) in Chapter 3.
ethanol
formaldehyde (methanal),
acetone (propanone),
acetic (ethanoic) acid,
If your instructor is having you work with molecular models in class, they may use this section for you to practice creating specific structures.
Hint: Use the curved sticks to form the multiple bonds and the straight sticks for single bonds.


16.1: Hooke’s Law - Stress and Strain Revisited
Learning Objectives
By the end of this section, you will be able to:
- Explain Newton’s third law of motion with respect to stress and deformation.
- Describe the restoration of force and displacement.
- Calculate the energy in Hook’s Law of deformation, and the stored energy in a string.
Newton’s first law implies that an object oscillating back and forth is experiencing forces. Without force, the object would move in a straight line at a constant speed rather than oscillate. Consider, for example, plucking a plastic ruler to the left as shown in Figure \(\PageIndex{1}\). The deformation of the ruler creates a force in the opposite direction, known as a restoring force . Once released, the restoring force causes the ruler to move back toward its stable equilibrium position, where the net force on it is zero. However, by the time the ruler gets there, it gains momentum and continues to move to the right, producing the opposite deformation. It is then forced to the left, back through equilibrium, and the process is repeated until dissipative forces dampen the motion. These forces remove mechanical energy from the system, gradually reducing the motion until the ruler comes to rest.
The simplest oscillations occur when the restoring force is directly proportional to displacement. When stress and strain were covered in Newton’s Third Law of Motion , the name was given to this relationship between force and displacement was Hooke’s law:
\[F = -kx\]
Here, \(F\) is the restoring force, \(x\) is the displacement from equilibrium or deformation , and \(k\) is a constant related to the difficulty in deforming the system. The minus sign indicates the restoring force is in the direction opposite to the displacement.
The force constant \(k\) is related to the rigidity (or stiffness) of a system—the larger the force constant, the greater the restoring force, and the stiffer the system. The units of \(k\) are newtons per meter (N/m). For example, \(k\) is directly related to Young’s modulus when we stretch a string. Figure \(\PageIndex{3}\) shows a graph of the absolute value of the restoring force versus the displacement for a system that can be described by Hooke’s law—a simple spring in this case. The slope of the graph equals the force constant \(k\) in newtons per meter. A common physics laboratory exercise is to measure restoring forces created by springs, determine if they follow Hooke’s law, and calculate their force constants if they do.
Example \(\PageIndex{1}\): How Stiff Are Car Springs?
What is the force constant for the suspension system of a car that settles 1.20 cm when an 80.0-kg person gets in?
Strategy
Consider the car to be in its equilibrium position \(x = 0\) before the person gets in. The car then settles down 1.20 cm, which means it is displaced to a position \(x = -1.20 \times 10^{-2} m\). At that point, the springs supply a restoring force \(F\) equal to the person’s weight \(w = mg = (80.0 \, kg)(9.80 \, m/s^2) = 784 \, N.\) We take this force to be \(F\) in Hooke's law. Knowing \(F\) and \(x\), we can then solve the force constant \(k\).
Solution
1. Solve Hooke’s law, \(F = -kx\), for \(k\):
\[k = -\dfrac{F}{x}. \nonumber\]
2. Substitute known values and solve \(k\):
\[\begin{align*} k &= -\dfrac{784 \, N}{-1.20 \times 10^{-2}m} \\[5pt] &=6.53 \times 10^4 \, N/m.\end{align*}\]
Discussion
Note that \(F\) and \(x\) have opposite signs because they are in opposite directions—the restoring force is up, and the displacement is down. Also, note that the car would oscillate up and down when the person got in if it were not for damping (due to frictional forces) provided by shock absorbers. Bouncing cars are a sure sign of bad shock absorbers.
Energy in Hooke’s Law of Deformation
In order to produce a deformation, work must be done. That is, a force must be exerted through a distance, whether you pluck a guitar string or compress a car spring. If the only result is deformation, and no work goes into thermal, sound, or kinetic energy, then all the work is initially stored in the deformed object as some form of potential energy. The potential energy stored in a spring is \(PE_{el} = \dfrac{1}{2}kx^2\). Here, we generalize the idea to elastic potential energy for a deformation of any system that can be described by Hooke’s law. Hence,
\[PE_{el} = \dfrac{1}{2}kx^2,\]
where \(PR_{el}\) is the elastic potential energy stored in any deformed system that obeys Hooke’s law and has a displacement \(x\) from equilibrium and a force constant \(k\).
It is possible to find the work done in deforming a system in order to find the energy stored. This work is performed by an applied force \(F_{app}\). The applied force is exactly opposite to the restoring force (action-reaction), and so \(F_{app} = kx\). Figure \(\PageIndex{5}\) shows a graph of the applied force versus deformation \(x\) for a system that can be described by Hooke’s law. Work done on the system is force multiplied by distance, which equals the area under the curve or \(\dfrac{1}{2} kx^2\) (Method A in the figure). Another way to determine the work is to note that the force increases linearly from 0 to \(kx\), so that the average force is \((1/2)kx\), the distance moved is \(x\), and thus \(W = F_{app} d = [(1/2)kx](x) = (1/2)kx^2\) (Method B in the figure).
Example \(\PageIndex{2}\): Calculating Stored Energy: A Tranquilizer Gun Spring
We can use a toy gun’s spring mechanism to ask and answer two simple questions:
- How much energy is stored in the spring of a tranquilizer gun that has a force constant of 50.0 N/m and is compressed 0.150 m?
- If you neglect friction and the mass of the spring, at what speed will a 2.00-g projectile be ejected from the gun?
Strategy for a
(a): The energy stored in the spring can be found directly from elastic potential energy equation, because \(k\) and \(x\) are given.
Solution for a
Entering the given values for \(k\) and \(x\) yields
\[PE_{el} = \dfrac{1}{2}kx^2 = \dfrac{1}{2}(50.0 \, N/m)(0.150 \, m)^2 = 0.563 \, N \cdot m = 0.563 \, J\]
Strategy for b
Because there is no friction, the potential energy is converted entirely into kinetic energy. The expression for kinetic energy can be solved for the projectile’s speed.
Solution for b
- Identify known quantities:
\[ KE_f = PE_{el} \, or \, 1/2 mv^2 = (1/2)kx^2 = PE_{el} = 0.563 \, J\]
2. Solve for \(v\):
\[ v = \left[\dfrac{2PE_{el}}{m}\right] = \left[\dfrac{2(0.563 \, J)}{0.002 \, kg}\right] = 23.7(J/K)^{1/2}\]
3. Convert units: \(23.7 \, m/s\)
Discussion
(a) and (b): This projectile speed is impressive for a tranquilizer gun (more than 80 km/h). The numbers in this problem seem reasonable. The force needed to compress the spring is small enough for an adult to manage, and the energy imparted to the dart is small enough to limit the damage it might do. Yet, the speed of the dart is great enough for it to travel an acceptable distance.
Exercise \(\PageIndex{1}\): Check your Understanding
Envision holding the end of a ruler with one hand and deforming it with the other. When you let go, you can see the oscillations of the ruler. In what way could you modify this simple experiment to increase the rigidity of the system?
- Answer
-
You could hold the ruler at its midpoint so that the part of the ruler that oscillates is half as long as in the original experiment.
Exercise \(\PageIndex{2}\): Check your Understanding
If you apply a deforming force on an object and let it come to equilibrium, what happened to the work you did on the system?
- Answer
-
It was stored in the object as potential energy.
Summary
- An oscillation is a back and forth motion of an object between two points of deformation.
- An oscillation may create a wave, which is a disturbance that propagates from where it was created.
- The simplest type of oscillations and waves are related to systems that can be described by Hooke’s law: \( F = -kx\) where \(F\) is the \(x\) restoring force, \(PE_{el}\) is the displacement from equilibrium or deformation, and \(PE_{el} = (1/2)kx^2.\)
Glossary
- deformation
- displacement from equilibrium
- elastic potential energy
- potential energy stored as a result of deformation of an elastic object, such as the stretching of a spring
- force constant
- a constant related to the rigidity of a system: the larger the force constant, the more rigid the system; the force constant is represented by k
- restoring force
- force acting in opposition to the force caused by a deformation


12.1: Citation Styles
Background
The Ethical and Legal Use of Information chapter covered why you need to cite, and how citations allow you to use other people’s ideas in an ethical way. As the video in that chapter discussed, there are many different citation styles and the one you will use depends on your specific course, instructor, and assignment instructions.
Two Connected Parts
All citation styles include two parts that work together:
- An in-text citation , which is a brief notation (usually within a paragraph, at the end of a sentence) acknowledging that information came from another source. In MLA and APA style, an in-text citation is contained inside parentheses (and sometimes called a “parenthetical citation”). Citation styles that use footnotes or endnotes (such as Chicago or Turabian) may use a superscript in the same way.
- At the end of the paper or assignment, there will be a list of more detailed bibliographic information that enables the reader to find the sources that were used. Every in-text citation must have a matching entry in this list. Depending on what citation style you are using, his list may be called “works cited,” “references,” or “bibliography.” Different citation styles will require you to format these citations in different ways, but they all include similar information, like the author’s name, title of the publication, date, URL, and/or page numbers.
The next section on When to Cite Sources addresses how to incorporate in-text citations and the MLA and APA sections will focus on how to create the full citations for various information source types.


3.4: Research and Other Types of Source-based Writing
Some high school and first-year college writing courses use the term “research paper” or “research writing” to apply to any situation in which students use information from an outside source in writing a paper. The logic behind this is that if the writer has to go find information from a source, that action of going and finding information is similar to research, so it is convenient to call that kind of writing task a “research paper.” However, it is only true research if it starts from a QUESTION to which the writer genuinely doesn’t know the answer and if the writer then develops or builds the answer to the question through gathering and processing information.
To help keep that difference in mind, this module will use “ research ” to refer to the goal-directed process of gathering information and building the answer to a research question, and “ source-based writing ” to refer to the many other types of information gathering and source-based writing one might do.
One important indicator of the difference between research and other source-based writing tasks is when in the process you develop the thesis (main point) of your paper. In a research project, you begin with a question, gather the data from which you will derive or build the answer to the question, build the answer, and then state your answer in a single sentence. This one-sentence statement of your answer to your research question then becomes your thesis statement and serves as the main point of your paper. In the research writing process, therefore, stating your thesis happens at the pivot point between research and writing (so roughly half or two thirds of the way through the project, depending on the amount of time spent gathering and processing information).
Any assignment you begin by developing a thesis that you then go out and gather information to support is source-based writing, but it is not technically “research” because it begins from the answer instead of the question.
Being aware of this distinction is essential to your successful completion of both research projects and other source-based writing tasks. The work processes that lead to efficiency and success with research projects are very different from the work processes you may have used successfully for other types of source-based papers. Both offer valuable learning experiences, but it is important to understand which type of assignment you are being asked to do so that you can adjust your expectations accordingly.
Think of the most recent writing project you have done that required sources. Based on this definition, was it a research project or a source-based writing project?
Contributors and Attributions
- Composition II. Authored by : Janet Zepernick. Provided by : Pittsburg State University. Located at : http://www.pittstate.edu/ . Project : Kaleidoscope Open Course Initiative. License : CC BY: Attribution
- Image of man using computer. Authored by : World Bank Photo Collection. Located at : https://flic.kr/p/cvL28d . License : CC BY-NC-ND: Attribution-NonCommercial-NoDerivatives
- Image of man with question mark. Authored by : Seth Capitulo. Located at : https://flic.kr/p/fnN1SJ . License : CC BY: Attribution


12.16: History of Odd Pricing
Learning Objectives
- Explain the concept of KVC and KVI and their impact on retail pricing strategy
One of the latest pricing strategies used by retailers is based on the concept of KVCs and KVIs. Key Value Categories and Key Value Items are a holistic method of pricing that do not rely exclusively on cost, demand or competition to make pricing decisions.
In the 1970s and 1980s, mass merchants developed the concept of “Key Items.” Key Items were identified by retailers during the planning phase of an upcoming season as a way to ensure that products perceived to be most important to the customer base are given extra attention by the retailer. For retail management, it was a way to cull broad assortments of products to ensure investment in the “right” products, and lists of roughly 200–300 Key Items were developed so that all areas of the business could work together on a common objective—maximizing the sales revenue of Key Items.
Key item strategy involved several pieces working together:
- Management inspection of buying plans to ensure proper product quantities, flow, and replenishment
- Product development departments developing the appropriate supply chain to ensure consistent quality and source of supply
- Store presentation guidelines (plan-o-grams) that would be consistent in every location to leverage impact and “market basket” benefits
- Promotion plans to take advantage of deep quantities and store presentations
- Pricing to be either especially sharp against competition or premium pricing to reflect the retailer’s strong position in the key item product
What is an example of a Key Item? They vary depending on the retail market, but most have one thing in common—they tend to be a basic or staple item in the retailer inventory. One of the earliest examples of a Key Item in apparel retailing was the basic pocket t-shirt in the 1980s at Gap Stores. What made it special was the unique high-quality of the product and that it was displayed in twenty colors (most competition at the time would carry 3 to 4 colors of that item). A more current example would be supermarkets displaying cases of soda in such quantity that they are displayed in the form of castles so as not to be missed.
Over time, as more retailers have embraced this strategy, the Key Item terminology evolved into Key Value Items or KVIs. And further, to take advantage of the extra transactions KVIs stimulated in related products, Key Value Categories or KVCs became another area of focus for the retailer. Both KVI and KVC lists have expanded due to the advances in data analytics, allowing retailers to maintain scrutiny of over 1,000 products. Commercial software applications have been developed exclusively to help retailers plan and track KVIs and KVCs.
KVIs and KVCs are probably the best example of how retail pricing strategies directly support high-level business objectives. In addition, retailers gain more leverage and a bit more control to make pricing decisions based on their priorities instead of reacting to purely external forces.
Practice Questions
Contributors and Attributions
- History of Odd Pricing. Authored by : Bob Danielson. Provided by : Lumen Learning. License : CC BY: Attribution
- Walmart Coke and Bud Displays. Authored by : Rusty Clark. Provided by : Flickr. Located at : https://www.flickr.com/photos/rusty_clark/6522222397 . License : CC BY: Attribution


20.3: Structure and Properties of Carboxylic Acids
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Objectives
After completing this section, you should be able to
- describe the geometry and electronic structure of a simple carboxylic acid; for example, acetic acid.
- describe the hydrogen bonding that occurs between carboxylic acid molecules, and hence account for the relatively high boiling points of these compounds.
- write an expression for the dissociation constant of a given carboxylic acid, and use it to calculate dissociation constants, percentage dissociation, etc.
- identify carboxylic acids as being weaker acids than mineral acids, such as hydrochloric acid, but stronger acids than alcohols.
- use the concept of resonance to explain why carboxylic acids are stronger acids than alcohols.
- draw an orbital picture of a carboxylate anion to show the equivalence of the two oxygen atoms.
- explain why the two carbon‑oxygen bond lengths are identical in sodium carboxylate, but different in carboxylic acid.
- write an equation for the reaction of a carboxylic acid with a base, such as sodium hydroxide.
Study Notes
You might wish to review Sections 2.7, “Acids and Bases: The Brønsted‑Lowry Definition” and 6.7, “Describing a Reaction: Equilibria, Rates, and Energy Changes” in conjunction with this section.
In the reading, the discussion of the role of resonance in the acidity of a carboxylic acid explains that the two carbon‑oxygen bonds in the delocalized carboxylate anion are identical (both 1.27 Å). However, in the structure of a carboxylic acid the \(\ce{C-O}\) bond (1.20 Å) is shorter than the \(\ce{C-OH}\) bond (1.34 Å).
Structure of the carboxyl acid group
Carboxylic acids are organic compounds which incorporate a carboxyl functional group, CO 2 H. The name carboxyl comes from the fact that a carbonyl and a hydroxyl group are attached to the same carbon.
The carbon and oxygen in the carbonyl are both sp 2 hybridized which gives a carboxylic acid a trigonal planar shape (around the carbonyl carbon) making the bond angles roughly 120 o . A resonance structure exists where one of the lone pairs of the hydroxyl oxygen (OH) is conjugated with the pi bond system of the carbonyl group. The conjugation can be represented by the resonance structure shown below which holds all the atoms in the carboxylic acid in a co-planar arrangement.
The effects of conjugation in a carboxylic acid can be seen when comparing the electrostatic potential maps of ethanol and acetic acid. Conjugation creates a greater polarization in the O-H bond in acetic acid, as shown by its darker blue color, which subsequently leads to a greater acidity in carboxylic acids.
Acidity of Carboxylic Acids
Carboxylic acids are named such because they tend to be more acidic than other functional groups in organic chemistry. In dilute aqueous solutions, they act as Brønsted–Lowry acids and partially dissociate to produce the corresponding carboxylate ion and hydronium (H 3 O + ).
The extent of this dissociation is described by the \(K_a\) value of the carboxylic acid. In a 0.1 M solution of acetic acid (\(K_a = 1.75 \times 10^{-5}\) @ 25 °C) only about 0.1% of the molecules are dissociated.
\[\begin{align*} K_{eq} &= K_a \\[4pt] &= \dfrac{[\ce{RCOO^{-}}][\ce{H3O^{+}}]}{[\ce{RCOOH}]} \\[4pt] &= 1.75 \times 10^{-5} \end{align*} \]
with \(pK_a = -\log K_a\).
The pK a 's of some typical carboxylic acids are listed in Table \(\PageIndex{1}\). The factors which affect the acidity of different carboxylic acids will be discussed in the next section of this text.
| Compound | K a | pK a |
|---|---|---|
| F 3 CCO 2 H | 0.59 | 0.23 |
| Cl 3 CCO 2 H | 0.22 | 0.66 |
| p-O 2 NC 6 H 4 CO 2 H | 3.39 X 10 -4 | 3.47 |
| HCO 2 H | 1.78 X 10 -4 | 3.75 |
| C 6 H 5 CO 2 H | 6.31 X 10 -5 | 4.20 |
| p-CH 3 OC 6 H 4 CO 2 H | 3.55 X 10 -5 | 4.45 |
| CH 3 CO 2 H | 1.75 X 10 -5 | 4.76 |
| CH 3 CH 2 CH 2 CO 2 H | 1.51 X 10 -5 | 4.82 |
The acidity of carboxylic acids comes about, in part, due to resonance stabilization of the carboxylate conjugate base. A classic example compares the relative acidity of ethanol and acetic acid, but the conclusions we reach will be equally valid for all alcohol and carboxylic acid groups. Despite the fact that they are both oxygen acids, the pK a values of ethanol and acetic acid are very different (acetic acid is more than 10 11 times more acidic than ethanol). In both species, the negative charge on the conjugate base is held by an oxygen so electronegativity does not explain the difference in acidity.
For acetic acid, however, there is a key difference: a resonance contributor can be drawn in which the negative charge is localized on the second oxygen of the group. The two resonance forms for the conjugate base are equal in energy allowing for the the negative charge on the acetate ion to be equally shared between two oxygens. In the ethoxide anion, by contrast, the negative charge is ‘locked’ on the single oxygen. This stabilization leads to a marked increase in stability of the acetate anion, as illustrated by the energy diagram shown below. The increased stabilization of the acetate anion conjugate base promotes the acidity of acetic acid.
The delocalization of charge by resonance has a very powerful effect on the reactivity of organic molecules, enough to account for the difference of over 11 pK a units between ethanol and acetic acid (and remember, pK a is a log expression, so this represents a difference of over 10 11 between the acidity constants for the two molecules). The acetate anion is that much more stable than the ethoxide anion, all due to the effects of resonance delocalization.
X-ray crystallographic studies provide experimental evidence of the acetate anion resonance hybrid. Both C-O bonds in acetate are 126 pm which is roughly the average of C=O double bond (123 pm) and the C-O single bond (132 pm) of acetic acid. Both of the C-O bonds in the acetate anion are considered to have a bond order of 1 1/2. The negative charge is equally spread between the two oxygens giving them each a charge of -1/2.
Resonance structures and resonance hybrid of acetate ion.
Physical Properties of Some Carboxylic Acids
Carboxylic acids tend to have higher boiling points when compared to ethers, alcohols, aldehydes, or ketones with a similar molecular weight. For example acetic acid and ethanol have boiling points of 117.9 o C and 78.3 o C respectively despite the fact that they both contain two carbons. Because carboxylic acids and alcohols both contain an O-H bond they are strongly associated by a hydrogen-bonding intermolecular force. The difference is that for carboxylic acids, two molecules of a carboxylic acid form two hydrogen bonds with each other to create a cyclic dimer (pair of molecules). Two alcohol molecules can only form one hydrogen bond between each other. Thus, carboxylic acids have stronger intermolecular forces and higher boiling points than their corresponding alcohols.
| Formula | Common Name | Source | IUPAC Name | Melting Point | Boiling Point |
|---|---|---|---|---|---|
| HCO 2 H | formic acid | ants (L. formica) | methanoic acid | 8.4 ºC | 101 ºC |
| CH 3 CO 2 H | acetic acid | vinegar (L. acetum) | ethanoic acid | 16.6 ºC | 118 ºC |
| CH 3 CH 2 CO 2 H | propionic acid | milk (Gk. protus prion) | propanoic acid | -20.8 ºC | 141 ºC |
| CH 3 (CH 2 ) 2 CO 2 H | butyric acid | butter (L. butyrum) | butanoic acid | -5.5 ºC | 164 ºC |
| CH 3 (CH 2 ) 3 CO 2 H | valeric acid | valerian root | pentanoic acid | -34.5 ºC | 186 ºC |
| CH 3 (CH 2 ) 4 CO 2 H | caproic acid | goats (L. caper) | hexanoic acid | -4.0 ºC | 205 ºC |
| CH 3 (CH 2 ) 5 CO 2 H | enanthic acid | vines (Gk. oenanthe) | heptanoic acid | -7.5 ºC | 223 ºC |
| CH 3 (CH 2 ) 6 CO 2 H | caprylic acid | goats (L. caper) | octanoic acid | 16.3 ºC | 239 ºC |
| CH 3 (CH 2 ) 7 CO 2 H | pelargonic acid | pelargonium (an herb) | nonanoic acid | 12.0 ºC | 253 ºC |
| CH 3 (CH 2 ) 8 CO 2 H | capric acid | goats (L. caper) | decanoic acid | 31.0 ºC | 219 ºC |
Water Solubility of Carboxylic Acids
The ability to form hydrogen bonds gives carboxylic acids with low molecular weights some measure of solubility in water. Carboxylic acids with six or more carbons tend to only be slightly soluble in water. However, conversion to the corresponding carboxylate anion tends to immensely increase water solubility due to the creation of an ion-dipole intermolecular force. Typically a strong base is used to deprotonate a carboxylic acid and drive this reaction to completion as shown below.
This property of carboxylic acids allows many carboxylic acids to be purified by a technique called acid/base extraction. The figure below shows how a carboxylic acid (benzoic acid) can easily be separated from non-acidic water insoluble compounds (cyclohexanone) using an acid/base extraction. First, the two compounds are dissolved in an organic solvent immiscible with water (ether). Then a basic aqueous solution (5% NaOH) is added and two liquid layers are formed. As the layers are mixed, benzoic acid reacts with the basic solution to become sodium benzoate. Because sodium benzoate is soluble in water it is extracted into the aqueous layer while the non-acidic cyclohexanone remains in the organic layer. The two layers can be separated using a separatory funnel effectually removing the cyclohexanone. The aqueous layer can then be acidified with a strong acid causing sodium benzoate to become protonated, reforming benzoic acid. Because benzoic acid is insoluble in water it will form a precipitate which can easily be filtered off.
Exercise \(\PageIndex{1}\)
Use acid-base chemistry and differences in water solubility to separate 1-octanol from octanoic acid using the following solutions: 1 M NaOH, ether, and 6 M HCl and any lab equipment.
- Answer
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Exercise \(\PageIndex{2}\)
What percentage of propanoic acid (CH 3 CH 2 COOH) is dissociated into its conjugate base in a 0.20 M aqueous solution? K a = 1.32 x 10⁻⁵
- Answer
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From the acid equilibrium expression we get that:
[CH₃CH₂COO⁻][H 3 O⁺]/[CH₃CH₂COOH] = K a = 1.32 x 10⁻⁵
[X][X]/[0.20 M - X] = 1.32 x 10⁻⁵
Assume X is small compared to 0.20 M
[X] 2 /[0.20 M] = 1.32 x 10⁻⁵
X = [CH₃CH₂COO⁻] = 1.62 x 10⁻ 3 M
[CH₃CH₂COO⁻] / [CH₃CH₂COOH] X 100 = %Disassociation
1.62 x 10⁻ 3 M / 0.20 M X 100 = 0.812%


4.1: Characteristics of Eukaryotic Cells
- Identify and describe structures and organelles unique to eukaryotic cells
- Compare and contrast similar structures found in prokaryotic and eukaryotic cells
Eukaryotic organisms include protozoans, algae, fungi, plants, and animals. Some eukaryotic cells are independent, single-celled microorganisms, whereas others are part of multicellular organisms. The cells of eukaryotic organisms have several distinguishing characteristics. Above all, eukaryotic cells are defined by the presence of a nucleus surrounded by a complex nuclear membrane. Also, eukaryotic cells are characterized by the presence of membrane-bound organelles in the cytoplasm. Organelles such as mitochondria, the endoplasmic reticulum (ER), Golgi apparatus, lysosomes, and peroxisomes are held in place by the cytoskeleton, an internal network that supports transport of intracellular components and helps maintain cell shape (Figure \(\PageIndex{1}\)). The genome of eukaryotic cells is packaged in multiple, rod-shaped chromosomes as opposed to the single, circular-shaped chromosome that characterizes most prokaryotic cells. Table \(\PageIndex{1}\) compares the characteristics of eukaryotic cell structures with those of bacteria and archaea.
| Cell Structure | Prokaryotes | Eukaryotes | |
|---|---|---|---|
| Bacteria | Archaea | ||
| Size | ~0.5–1 μM | ~0.5–1 μM | ~5–20 μM |
| Surface area-to-volume ratio | High | High | Low |
| Nucleus | No | No | Yes |
| Genome characteristics |
|
|
|
| Cell division | Binary fission | Binary fission | Mitosis, meiosis |
| Membrane lipid composition |
|
|
|
| Cell wall composition |
|
|
|
| Motility structures | Rigid spiral flagella composed of flagellin | Rigid spiral flagella composed of archaeal flagellins | Flexible flagella and cilia composed of microtubules, membrane-bound |
| Membrane-bound organelles | No | No | Yes |
| Endomembrane system | No | No | Yes (ER, Golgi, lysosomes) |
| Ribosomes | 70S | 70S |
|
Identify two differences between eukaryotic and prokaryotic cell.
Upon arriving home from school, 7-year-old Sarah complains that a large spot on her arm will not stop itching. She keeps scratching at it, drawing the attention of her parents. Looking more closely, they see that it is a red circular spot with a raised red edge (Figure \(\PageIndex{2}\)).
Figure \(\PageIndex{2}\): Ringworm presents as a raised, red ring on the skin. (credit: Centers for Disease Control and Prevention)
The next day, Sarah’s parents take her to their doctor, who examines the spot using a Wood’s lamp. A Wood’s lamp produces ultraviolet light that causes the spot on Sarah’s arm to fluoresce, which confirms what the doctor already suspected: Sarah has a case of ringworm. Sarah’s mother is mortified to hear that her daughter has a “worm.” How could this happen?
What are some likely ways that Sarah might have contracted ringworm?
Inside the cell:
Nucleus
Unlike prokaryotic cells, in which DNA is loosely contained in the nucleoid region, eukaryotic cells possess a nucleus (plural = nuclei), which is surrounded by a complex nuclear membrane that houses the DNA genome (Figure \(\PageIndex{3}\)). By containing the cell’s DNA, the nucleus ultimately controls all activities of the cell and also serves an essential role in reproduction and heredity. Eukaryotic cells typically have their DNA organized into multiple linear chromosomes. The DNA within the nucleus is highly organized and condensed to fit inside the nucleus, which is accomplished by wrapping the DNA around proteins called histones.
Although most eukaryotic cells have only one nucleus, exceptions exist. For example, protozoans of the genus Paramecium typically have two complete nuclei: a small nucleus that is used for reproduction (micronucleus) and a large nucleus that directs cellular metabolism (macronucleus).  Cells whose nuclei divide, but whose cytoplasm does not, are called coenocytes.
The nucleus is bound by a complex nuclear membrane, often called the nuclear envelope, that consists of two distinct lipid bilayers that are contiguous with each other (Figure \(\PageIndex{4}\)). Despite these connections between the inner and outer membranes, each membrane contains unique lipids and proteins on its inner and outer surfaces. The nuclear envelope contains nuclear pores, which are large, rosette-shaped protein complexes that control the movement of materials into and out of the nucleus. The overall shape of the nucleus is determined by the nuclear lamina, a meshwork of intermediate filaments found just inside the nuclear envelope membranes. Outside the nucleus, additional intermediate filaments form a looser mesh and serve to anchor the nucleus in position within the cell.
Nucleolus
The nucleolus is a dense region within the nucleus where ribosomal RNA (rRNA) biosynthesis occurs. In addition, the nucleolus is also the site where assembly of ribosomes begins. How does it do this? Some chromosomes have sections of DNA that encode ribosomal RNA. Pre-ribosomal complexes are assembled from rRNA and proteins into the ribosomal subunits in the nucleolus; these are then transported out to the cytoplasm, where ribosome assembly is completed (Figure \(\PageIndex{5}\)).
Chromatin and Chromosomes
Between the nucleolus and the nuclear envelope is the chromatin. To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the nucleus that are made up of DNA, the hereditary material, and carry information (genes) that are required. You may remember that in prokaryotes, DNA is organized into a single circular chromosome. Eukaryotic chromosomes are typically linear, and eukaryotic cells contain multiple distinct chromosomes. Many eukaryotic cells contain two copies of each chromosome and, therefore, are diploid. The length of a even a single chromosome greatly exceeds the length of the cell, so a chromosome needs to be packaged into a very small space to fit within the cell. For example, the combined length of all of the DNA of the human genome would measure approximately 2 meters if completely stretched out, and some eukaryotic genomes are many times larger than the human genome. Every eukaryotic species has a specific number of chromosomes in the nuclei of its body’s cells. For example, in humans, the chromosome number is 46, while in fruit flies, it is eight. Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. When the cell is in the growth and maintenance phases of its life cycle, proteins are attached to chromosomes, and they resemble an unwound, jumbled bunch of threads. These unwound protein-chromosome complexes are called chromatin (Figure \(\PageIndex{6}\)); chromatin describes the material that makes up the chromosomes both when condensed and decondensed.
Figure \(\PageIndex{6}\): (a) This image shows various levels of the organization of chromatin (DNA and protein). (b) This image shows paired chromosomes. (credit b: modification of work by NIH; scale-bar data from Matt Russell)
Ribosomes
Cytoplasmic ribosomes in eukaryotic cells are 80S ribosomes, composed of a 40S small subunit and a 60S large subunit. In terms of size and composition, this makes them distinct from the ribosomes of prokaryotic cells. The two types of cytoplasmic eukaryotic ribosomes are defined by their location in the cell: free ribosomes and membrane-bound ribosomes. Free ribosomes are found floating in the cytoplasm and serve to synthesize water-soluble proteins; membrane-bound ribosomes are found attached to the cytoplasmic side of the rough endoplasmic reticulum and make proteins for insertion into the cell membrane or proteins destined for export from the cell.
In contrast, ribosomes found in eukaryotic organelles such as mitochondria or chloroplasts have 70S ribosomes—the same size as prokaryotic ribosomes. The differences between eukaryotic and prokaryotic ribosomes are clinically relevant because certain antibiotic drugs are designed to target one or the other. For example, cycloheximide targets eukaryotic action, whereas chloramphenicol targets prokaryotic ribosomes. 1 Since human cells are eukaryotic, they generally are not harmed by antibiotics that destroy the prokaryotic ribosomes in bacteria. However, sometimes negative side effects may occur because mitochondria in human cells contain prokaryotic ribosomes.
Endomembrane System
The endomembrane system, unique to eukaryotic cells, is a series of membranous tubules, sacs, and flattened disks that synthesize many cell components and move materials around within the cell (Figure \(\PageIndex{7}\)). Because of their larger cell size, eukaryotic cells require this system to transport materials that cannot be dispersed by diffusion alone. The endomembrane system comprises several organelles and connections between them, including the endoplasmic reticulum, Golgi apparatus, lysosomes, and vesicles.
Endoplasmic Reticulum
The endoplasmic reticulum (ER) is an interconnected array of tubules and cisternae (flattened sacs) with a single lipid bilayer (Figure \(\PageIndex{7}\)). The spaces inside of the cisternae are called lumen of the ER. There are two types of ER, rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER). These two different types of ER are sites for the synthesis of distinctly different types of molecules. RER is studded with ribosomes bound on the cytoplasmic side of the membrane. These ribosomes make proteins destined for the plasma membrane (Figure \(\PageIndex{8}\)). Following synthesis, these proteins are inserted into the membrane of the RER. Small sacs of the RER containing these newly synthesized proteins then bud off and move either to the Golgi apparatus for further processing, directly to the plasma membrane, to the membrane of another organelle, or out of the cell. SER does not have ribosomes and, therefore, appears “smooth.” It is involved in biosynthesis of lipids, carbohydrate synthesis and degradation, and detoxification of medications and poisons; and storage of calcium ions.
Golgi Apparatus
The Golgi apparatus was discovered within the endomembrane system in 1898 by Italian scientist Camillo Golgi (1843–1926), who developed a novel staining technique that showed stacked membrane structures within the cells of Plasmodium , the causative agent of malaria. The Golgi apparatus is composed of a series of membranous disks called dictyosomes, each having a single lipid bilayer, that are stacked together (Figure \(\PageIndex{9}\)).
Modification, sorting, tagging, packaging, and distribution of lipids and proteins takes place in the Golgi apparatus. Enzymes in the Golgi apparatus modify lipids and proteins transported from the ER to the Golgi, often adding carbohydrate components to them, producing glycolipids, glycoproteins, or proteoglycans. Glycolipids and glycoproteins are often inserted into the plasma membrane and are important for signal recognition by other cells or infectious particles. Different types of cells can be distinguished from one another by the structure and arrangement of the glycolipids and glycoproteins contained in their plasma membranes. These glycolipids and glycoproteins commonly also serve as cell surface receptors.
Vesicles and Vacuoles
Vesicles and vacuoles are single-lipid, bilayer, membranous spheres with hollow interiors that function in storage and transport. Other than the fact that vacuoles are somewhat larger than vesicles, there is a very subtle distinction between them: The membranes of vesicles can fuse with either the plasma membrane or other membrane systems within the cell. Additionally, some agents such as enzymes within plant vacuoles break down macromolecules. The membrane of a vacuole does not fuse with the membranes of other cellular components making them great storage units.
Transport vesicles leaving the ER with proteins, carbohydrates and other goods or waste fuse with a Golgi apparatus on its receiving, or cis , face. The proteins are processed within the Golgi apparatus, and then additional transport vesicles containing the modified proteins and lipids pinch off from the Golgi apparatus on its outgoing, or trans , face. These outgoing vesicles move to and fuse with the plasma membrane (through exocytosis) or the membrane of other organelles (Figure \(\PageIndex{9}\)).
Lysosomes
In the 1960s, Belgian scientist Christian de Duve (1917–2013) discovered lysosomes, membrane-bound organelles of the endomembrane system that contain digestive enzymes. Certain types of eukaryotic cells use lysosomes to break down various particles, such as food, damaged organelles or cellular debris, microorganisms, or immune complexes. Compartmentalization of the digestive enzymes within the lysosome allows the cell to efficiently digest matter without harming the cytoplasmic components of the cell.
Name the components of the endomembrane system and describe the function of each component.
Peroxisomes
Christian de Duve is also credited with the discovery of peroxisomes, membrane-bound organelles that are not part of the endomembrane system (Figure \(\PageIndex{10}\)). Peroxisomes form independently in the cytoplasm from the synthesis of peroxin proteins by free ribosomes and the incorporation of these peroxin proteins into existing peroxisomes. Growing peroxisomes then divide by a process similar to binary fission.
Peroxisomes were first named for their ability to produce hydrogen peroxide, a highly reactive molecule that helps to break down molecules such as uric acid, amino acids, and fatty acids. Peroxisomes also possess the enzyme catalase, which can degrade hydrogen peroxide. Along with the SER, peroxisomes also play a role in lipid biosynthesis. Like lysosomes, the compartmentalization of these degradative molecules within an organelle helps protect the cytoplasmic contents from unwanted damage.
The peroxisomes of certain organisms are specialized to meet their particular functional needs. For example, glyoxysomes are modified peroxisomes of yeasts and plant cells that perform several metabolic functions, including the production of sugar molecules. Similarly, glycosomes are modified peroxisomes made by certain trypanosomes, the pathogenic protozoans that cause Chagas disease and African sleeping sickness.
Cytoskeleton
Eukaryotic cells have an internal cytoskeleton made of microfilaments, intermediate filaments, and microtubules. This matrix of fibers and tubes provides structural support as well as a network over which materials can be transported within the cell and on which organelles can be anchored (Figure \(\PageIndex{11}\)). For example, the process of exocytosis involves the movement of a vesicle via the cytoskeletal network to the plasma membrane, where it can release its contents.
Microfilaments are composed of two intertwined strands of actin, each composed of actin monomers forming filamentous cables 6 nm in diameter 2 (Figure \(\PageIndex{11}\)). The actin filaments work together with motor proteins, like myosin, to effect muscle contraction in animals or the amoeboid movement of some eukaryotic microbes. In ameboid organisms, actin can be found in two forms: a stiffer, polymerized, gel form and a more fluid, unpolymerized soluble form. Actin in the gel form creates stability in the ectoplasm, the gel-like area of cytoplasm just inside the plasma membrane of ameboid protozoans. Temporary extensions of the cytoplasmic membrane called pseudopodia (meaning “false feet”) are produced through the forward flow of soluble actin filaments into the pseudopodia, followed by the gel-sol cycling of the actin filaments, resulting in cell motility. Once the cytoplasm extends outward, forming a pseudopodium, the remaining cytoplasm flows up to join the leading edge, thereby creating forward locomotion. Beyond amoeboid movement, microfilaments are also involved in a variety of other processes in eukaryotic cells, including cytoplasmic streaming (the movement or circulation of cytoplasm within the cell), cleavage furrow formation during cell division, and muscle movement in animals (Figure \(\PageIndex{12}\)). These functions are the result of the dynamic nature of microfilaments, which can polymerize and depolymerize relatively easily in response to cellular signals, and their interactions with molecular motors in different types of eukaryotic cells.
Intermediate filaments (Figure \(\PageIndex{13}\)) are a diverse group of cytoskeletal filaments that act as cables within the cell. They are termed “intermediate” because their 10-nm diameter is thicker than that of actin but thinner than that of microtubules. 3 They are composed of several strands of polymerized subunits that, in turn, are made up of a wide variety of monomers. Intermediate filaments tend to be more permanent in the cell and maintain the position of the nucleus. They also form the nuclear lamina (lining or layer) just inside the nuclear envelope. Additionally, intermediate filaments play a role in anchoring cells together in animal tissues. The intermediate filament protein desmin is found in desmosomes, the protein structures that join muscle cells together and help them resist external physical forces. The intermediate filament protein keratin is a structural protein found in hair, skin, and nails.
Microtubules (Figure \(\PageIndex{14}\)) are a third type of cytoskeletal fiber composed of tubulin dimers (α tubulin and β tubulin). These form hollow tubes 23 nm in diameter that are used as girders within the cytoskeleton. 4 Like microfilaments, microtubules are dynamic and have the ability to rapidly assemble and disassemble. Microtubules also work with motor proteins (such as dynein and kinesin) to move organelles and vesicles around within the cytoplasm. Additionally, microtubules are the main components of eukaryotic flagella and cilia, composing both the filament and the basal body components (Figure \(\PageIndex{21}\)). Microtubules are also involved in cell division, forming the mitotic spindle that serves to separate chromosomes during mitosis and meiosis. The mitotic spindle is produced by two centrosomes, which are essentially microtubule-organizing centers, at opposite ends of the cell.
Compare and contrast the three types of cytoskeletal structures described in this section.
Endosymbiotic Theory
As scientists were making progress toward understanding the role of cells in plant and animal tissues, others were examining the structures within the cells themselves. In 1831, Scottish botanist Robert Brown (1773–1858) was the first to describe observations of nuclei, which he observed in plant cells. Then, in the early 1880s, German botanist Andreas Schimper (1856–1901) was the first to describe the chloroplasts of plant cells, identifying their role in starch formation during photosynthesis and noting that they divided independent of the nucleus.
Based upon the chloroplasts’ ability to reproduce independently, Russian botanist Konstantin Mereschkowski (1855–1921) suggested in 1905 that chloroplasts may have originated from ancestral photosynthetic bacteria living symbiotically inside a eukaryotic cell. He proposed a similar origin for the nucleus of plant cells. This was the first articulation of the endosymbiotic hypothesis, and would explain how eukaryotic cells evolved from ancestral bacteria.
Mereschkowski’s endosymbiotic hypothesis was furthered by American anatomist Ivan Wallin (1883–1969), who began to experimentally examine the similarities between mitochondria, chloroplasts, and bacteria—in other words, to put the endosymbiotic hypothesis to the test using objective investigation. Wallin published a series of papers in the 1920s supporting the endosymbiotic hypothesis, including a 1926 publication co-authored with Mereschkowski. Wallin claimed he could culture mitochondria outside of their eukaryotic host cells. Many scientists dismissed his cultures of mitochondria as resulting from bacterial contamination. Modern genome sequencing work supports the dissenting scientists by showing that much of the genome of mitochondria had been transferred to the host cell’s nucleus, preventing the mitochondria from being able to live on their own. 6 7
Wallin’s ideas regarding the endosymbiotic hypothesis were largely ignored for the next 50 years because scientists were unaware that these organelles contained their own DNA. However, with the discovery of mitochondrial and chloroplast DNA in the 1960s, the endosymbiotic hypothesis was resurrected. Lynn Margulis (1938–2011), an American geneticist, published her ideas regarding the endosymbiotic hypothesis of the origins of mitochondria and chloroplasts in 1967. 8 In the decade leading up to her publication, advances in microscopy had allowed scientists to differentiate prokaryotic cells from eukaryotic cells. In her publication, Margulis reviewed the literature and argued that the eukaryotic organelles such as mitochondria and chloroplasts are of prokaryotic origin. She presented a growing body of microscopic, genetic, molecular biology, fossil, and geological data to support her claims.
Again, this hypothesis was not initially popular, but mounting genetic evidence due to the advent of DNA sequencing supported the endosymbiotic theory, which is now defined as the theory that mitochondria and chloroplasts arose as a result of prokaryotic cells establishing a symbiotic relationship within a eukaryotic host (Figure \(\PageIndex{15}\)). With Margulis’ initial endosymbiotic theory gaining wide acceptance, she expanded on the theory in her 1981 book Symbiosis in Cell Evolution. In it, she explains how endosymbiosis is a major driving factor in the evolution of organisms. More recent genetic sequencing and phylogenetic analysis show that mitochondrial DNA and chloroplast DNA are highly related to their bacterial counterparts, both in DNA sequence and chromosome structure. However, mitochondrial DNA and chloroplast DNA are reduced compared with nuclear DNA because many of the genes have moved from the organelles into the host cell’s nucleus. Additionally, mitochondrial and chloroplast ribosomes are structurally similar to bacterial ribosomes, rather than to the eukaryotic ribosomes of their hosts. Last, the binary fission of these organelles strongly resembles the binary fission of bacteria, as compared with mitosis performed by eukaryotic cells. Since Margulis’ original proposal, scientists have observed several examples of bacterial endosymbionts in modern-day eukaryotic cells. Examples include the endosymbiotic bacteria found within the guts of certain insects, such as cockroaches,9 and photosynthetic bacteria-like organelles found in protists. 10
- What does the modern endosymbiotic theory state?
- What evidence supports the endosymbiotic theory?
Mitochondria
Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. ATP represents the short-term stored energy of the cell. Cellular respiration is the process of making ATP using the chemical energy found in glucose and other nutrients. In mitochondria, this process uses oxygen and produces carbon dioxide as a waste product. In fact, the carbon dioxide that you exhale with every breath comes from the cellular reactions that produce carbon dioxide as a byproduct (Figure \(\PageIndex{16}\)). The term “mitochondrion” was first coined by German microbiologist Carl Benda in 1898 and was later connected with the process of respiration by Otto Warburg in 1913.
Each mitochondrion has two lipid membranes. The outer membrane is a remnant of the original host cell’s membrane structures. The inner membrane was derived from the bacterial plasma membrane. The electron transport chain for aerobic respiration uses integral proteins embedded in the inner membrane. The mitochondrial matrix, corresponding to the location of the original bacterium’s cytoplasm, is the current location of many metabolic enzymes. It also contains mitochondrial DNA and 70S ribosomes. Invaginations of the inner membrane, called cristae, evolved to increase surface area for the location of biochemical reactions. The folding patterns of the cristae differ among various types of eukaryotic cells and are used to distinguish different eukaryotic organisms from each other.
Figure \(\PageIndex{16}\): Each mitochondrion is surrounded by two membranes, the inner of which is extensively folded into cristae and is the site of the intermembrane space. The mitochondrial matrix contains the mitochondrial DNA, ribosomes, and metabolic enzymes. The transmission electron micrograph of a mitochondrion, on the right, shows both membranes, including cristae and the mitochondrial matrix. (credit “micrograph”: modification of work by Matthew Britton; scale-bar data from Matt Russell)
Chloroplasts
Plant cells and algal cells contain chloroplasts, the organelles in which photosynthesis occurs (Figure \(\PageIndex{17}\)). Photosynthesis is the series of reactions that use carbon dioxide, water, and light energy to make glucose and oxygen. All chloroplasts have at least three membrane systems: the outer membrane, the inner membrane, and the thylakoid membrane system. Inside the outer and inner membranes is the chloroplast stroma, a gel-like fluid that makes up much of a chloroplast’s volume, and in which the thylakoid system floats. The thylakoid system is a highly dynamic collection of folded membrane sacs. It is where the green photosynthetic pigment chlorophyll is found and the light reactions of photosynthesis occur. In most plant chloroplasts, the thylakoids are arranged in stacks called grana (singular: granum), whereas in some algal chloroplasts, the thylakoids are free floating.
Figure \(\PageIndex{17}\): Photosynthesis takes place in chloroplasts, which have an outer membrane and an inner membrane. Stacks of thylakoids called grana form a third membrane layer.
Other organelles similar to mitochondria have arisen in other types of eukaryotes, but their roles differ. Hydrogenosomes are found in some anaerobic eukaryotes and serve as the location of anaerobic hydrogen production. Hydrogenosomes typically lack their own DNA and ribosomes. Kinetoplasts are a variation of the mitochondria found in some eukaryotic pathogens. In these organisms, each cell has a single, long, branched mitochondrion in which kinetoplast DNA, organized as multiple circular pieces of DNA, is found concentrated at one pole of the cell.
Many protozoans, including several protozoan parasites that cause infections in humans, can be identified by their unusual appearance. Distinguishing features may include complex cell morphologies, the presence of unique organelles, or the absence of common organelles. The protozoan parasites Giardia lamblia and Trichomonas vaginalis are two examples.
G. lamblia , a frequent cause of diarrhea in humans and many other animals, is an anaerobic parasite that possesses two nuclei and several flagella. Its Golgi apparatus and endoplasmic reticulum are greatly reduced, and it lacks mitochondria completely. However, it does have organelles known as mitosomes, double-membrane-bound organelles that appear to be severely reduced mitochondria. This has led scientists to believe that G. lamblia ’s ancestors once possessed mitochondria that evolved to become mitosomes. T. vaginalis , which causes the sexually transmitted infection vaginitis, is another protozoan parasite that lacks conventional mitochondria. Instead, it possesses hydrogenosomes, mitochondrial-related, double-membrane-bound organelles that produce molecular hydrogen used in cellular metabolism. Scientists believe that hydrogenosomes, like mitosomes, also evolved from mitochondria. 5
The Boundary Layer: the Cellular Envelope
Plasma Membrane
The plasma membrane structure of most bacterial and eukaryotic cell types is a bilayer composed mainly of phospholipids formed with ester linkages and proteins. Proteins on the cell’s surface are important for a variety of functions. (review chapter 3 section 3 for more detail, will be described more in chapter 8) Unlike the prokaryotic membrane, eukaryotic membranes contain sterols, including cholesterol, that alter membrane fluidity. Additionally, many eukaryotic cells contain some specialized lipids, including sphingolipids, which are thought to play a role in maintaining membrane stability as well as being involved in signal transduction pathways and cell-to-cell communication.
Cell Wall
In addition to a plasma membrane, some eukaryotic cells have a cell wall. Cells of fungi, algae, plants, and even some protists have cell walls. Depending upon the type of eukaryotic cell, cell walls can be made of a wide range of materials, including cellulose (fungi and plants); biogenic silica, calcium carbonate, agar, and carrageenan (protists and algae); or chitin (fungi). In general, all cell walls provide structural stability for the cell and protection from environmental stresses such as desiccation, changes in osmotic pressure, and traumatic injury. 6
Outside the Cell
Extracellular Matrix
Cells of animals and some protozoans do not have cell walls to help maintain shape and provide structural stability. Instead, many of these types of eukaryotic cells produce an extracellular matrix for this purpose. They secrete a sticky mass of carbohydrates and proteins into the spaces between adjacent cells (Figure \(\PageIndex{18}\)). Some protein components assemble into a basement membrane to which the remaining extracellular matrix components adhere. Proteoglycans typically form the bulky mass of the extracellular matrix while fibrous proteins, like collagen, provide strength. Both proteoglycans and collagen are attached to fibronectin proteins, which, in turn, are attached to integrin proteins. These integrin proteins interact with transmembrane proteins in the plasma membranes of eukaryotic cells that lack cell walls. This makes them both similar and different to the glycocalyx found in prokaryote cells.
In animal cells, the extracellular matrix allows cells within tissues to withstand external stresses and transmits signals from the outside of the cell to the inside. The amount of extracellular matrix is quite extensive in various types of connective tissues, and variations in the extracellular matrix can give different types of tissues their distinct properties. In addition, a host cell’s extracellular matrix is often the site where microbial pathogens attach themselves to establish infection. For example, Streptococcus pyogenes, the bacterium that causes strep throat and various other infections, binds to fibronectin in the extracellular matrix of the cells lining the oropharynx (upper region of the throat).
Flagella and Cilia
Some eukaryotic cells use flagella for locomotion; however, eukaryotic flagella are structurally distinct from those found in prokaryotic cells. Whereas the prokaryotic flagellum is a stiff, rotating structure, a eukaryotic flagellum is more like a flexible whip composed of nine parallel pairs of microtubules surrounding a central pair of microtubules. This arrangement is referred to as a 9+2 array (Figure \(\PageIndex{19}\)). The parallel microtubules use dynein motor proteins to move relative to each other, causing the flagellum to bend.
Cilia (singular: cilium) are a similar external structure found in some eukaryotic cells. Unique to eukaryotes, cilia are shorter than flagella and often cover the entire surface of a cell; however, they are structurally similar to flagella (a 9+2 array of microtubules) and use the same mechanism for movement. A structure called a basal body is found at the base of each cilium and flagellum. The basal body, which helps connect the cilium or flagellum to the cell, is composed of an array of triplet microtubules similar to that of a centriole but embedded in the plasma membrane. Because of their shorter length, cilia use a rapid, flexible, waving motion. In addition to motility, cilia may have other functions such as sweeping particles past or into cells. For example, ciliated protozoans use the sweeping of cilia to move food particles into their mouthparts, and ciliated cells in the mammalian respiratory tract beat in synchrony to sweep mucus and debris up and out of the lungs (Figure \(\PageIndex{19}\)).
- Explain how the cellular envelope of eukaryotic cells compares to that of prokaryotic cells.
- Explain the difference between eukaryotic and prokaryotic flagella.
Key Concepts and Summary
- Eukaryotic cells are defined by the presence of a nucleus containing the DNA genome and bound by a nuclear membrane (or nuclear envelope ) composed of two lipid bilayers that regulate transport of materials into and out of the nucleus through nuclear pores.
- Eukaryotic cell morphologies vary greatly and may be maintained by various structures, including the cytoskeleton, the cell membrane, and/or the cell wall
- The nucleolus , located in the nucleus of eukaryotic cells, is the site of ribosomal synthesis and the first stages of ribosome assembly.
- Eukaryotic cells contain 80S ribosomes in the rough endoplasmic reticulum ( membrane bound-ribosomes ) and cytoplasm ( free ribosomes ). They contain 70s ribosomes in mitochondria and chloroplasts.
- Eukaryotic cells have evolved an endomembrane system, containing membrane-bound organelles involved in transport. These include vesicles, the endoplasmic reticulum, and the Golgi apparatus.
- The smooth endoplasmic reticulum plays a role in lipid biosynthesis, carbohydrate metabolism, and detoxification of toxic compounds. The rough endoplasmic reticulum contains membrane-bound 80S ribosomes that synthesize proteins destined for the cell membrane
- The Golgi apparatus processes proteins and lipids, typically through the addition of sugar molecules, producing glycoproteins or glycolipids, components of the plasma membrane that are used in cell-to-cell communication.
- Lysosomes contain digestive enzymes that break down small particles ingested by endocytosis , large particles or cells ingested by phagocytosis , and damaged intracellular components.
- The cytoskeleton , composed of microfilaments , intermediate filaments , and microtubules , provides structural support in eukaryotic cells and serves as a network for transport of intracellular materials.
- Centrosomes are microtubule-organizing centers important in the formation of the mitotic spindle in mitosis.
- Endosymbiotic theory states that mitochondria and chloroplasts, organelles found in many types of organisms, have their origins in bacteria. Significant structural and genetic information support this theory.
- Mitochondria are the site of cellular respiration. They have two membranes: an outer membrane and an inner membrane with cristae. The mitochondrial matrix, within the inner membrane, contains the mitochondrial DNA, 70S ribosomes, and metabolic enzymes.
- Chloroplasts are used by plants and some protists to help collect solar energy and transform it into sugars for food, structural components or other uses.
- The plasma membrane of eukaryotic cells is structurally similar to that found in prokaryotic cells, and membrane components move according to the fluid mosaic model. However, eukaryotic membranes contain sterols, which alter membrane fluidity, as well as glycoproteins and glycolipids, which help the cell recognize other cells and infectious particles
- Cells of fungi, algae, plants, and some protists have a cell wall, whereas cells of animals and some protozoans have a sticky extracellular matrix that provides structural support and mediates cellular signaling.
- Eukaryotic flagella are structurally distinct from prokaryotic flagella but serve a similar purpose (locomotion). Cilia are structurally similar to eukaryotic flagella, but shorter; they may be used for locomotion, feeding, or movement of extracellular particles.
Footnotes
- A.E. Barnhill, M.T. Brewer, S.A. Carlson. “Adverse Effects of Antimicrobials via Predictable or Idiosyncratic Inhibition of Host Mitochondrial Components.” Antimicrobial Agents and Chemotherapy 56 no. 8 (2012):4046–4051.
- Fuchs E, Cleveland DW. “A Structural Scaffolding of Intermediate Filaments in Health and Disease.” Science 279 no. 5350 (1998):514–519.
- E. Fuchs, D.W. Cleveland. “A Structural Scaffolding of Intermediate Filaments in Health and Disease.” Science 279 no. 5350 (1998):514–519.
- E. Fuchs, D.W. Cleveland. “A Structural Scaffolding of Intermediate Filaments in Health and Disease.” Science 279 no. 5350 (1998):514–519.
- N. Yarlett, J.H.P. Hackstein. “Hydrogenosomes: One Organelle, Multiple Origins.” BioScience 55 no. 8 (2005):657–658.
- M. Dudzick. “Protists.” OpenStax CNX. November 27, 2013. http://cnx.org/contents/f7048bb6-e46...ef291cf7049c@1
- J.M. Jaynes, L.P. Vernon. “The Cyanelle of Cyanophora paradoxa : Almost a Cyanobacterial Chloroplast.” Trends in Biochemical Sciences 7 no. 1 (1982):22–24.
Contributor
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Nina Parker, (Shenandoah University), Mark Schneegurt (Wichita State University), Anh-Hue Thi Tu (Georgia Southwestern State University), Philip Lister (Central New Mexico Community College), and Brian M. Forster (Saint Joseph’s University) with many contributing authors. Original content via Openstax (CC BY 4.0; Access for free at https://openstax.org/books/microbiology/pages/1-introduction )


6.9: Discussion
Over coffee, Bob said that he really liked this chapter. “This material was full of cases of very concrete procedures for doing useful things. I like that.” Yolanda offered a somewhat different perspective “On the other hand, this last procedure only seems to work with interval orders and we still don't have a clue as to how to find the width of a poset in the general case. This might be very difficult—like the graph coloring problems discussed in the last chapter.” Dave weighed in with “Somehow I think there's going to be a fairly efficient process that works for all posets. We may not have all the tools yet, but let's wait a bit.”
Not much was said for a while and after a pause, Carlos ventured that there were probably a lot of combinatorial problems for posets that had analogous versions for graphs and in those cases, the poset version would be a bit more complicated, sometime a little bit and sometimes a very big bit. Zori was quiet but she was thinking. These poset structures might even be useful, as she could imagine many settings in which a linear order was impossible or impractical. Maybe there were ways here to earn a few dollars.


5.1: Introduction to Intervals
5.1 Introduction to Intervals
Intervals are the building blocks of scales, chords (or harmonies), and melodies. Intervals are a measurement between two pitches, either vertically or horizontally. When measuring vertically, we refer to harmonic intervals because the two notes sound simultaneously. When measuring horizontally, we refer to melodic intervals because the notes occur one after the other.
When you measure from the tonic up to each scale degree of a major scale, you find the following intervals:
All intervals in the example above are either “perfect” or “major.”
5.1.1 Numeric Size of Interval
There are two elements to naming intervals: the quality and the number (for example, “major sixth,” abbreviated as “M6”). Let us first focus on the numeric size of intervals. Odd-numbered intervals will always be a line to a line or a space to a space.
Even-numbered intervals will always be a space to a line or a line to a space.
5.1.2 Interval Quality: Perfect versus Major/Minor
Intervals such as the unison, fourth, fifth, and octave can be classified as “ perfect ” but never “major” or “minor”. Conversely, the intervals of the second, third, sixth, and seventh can be major or minor but never perfect in quality.
| Perfect Intervals : | Unison, 4th, 5th, 8ve |
| Major or Minor Intervals : | 2nd, 3rd, 6th, 7th |
Perfect intervals are always natural to natural, sharp to sharp, and flat to flat except for the fourths and fifths between BB and FF, which involve BB to FF♯ and BB♭ to FF.
Minor intervals are one half step smaller than major intervals.