Side view of an ?-helix of alanine residues in atomic detail. Two hydrogen bonds to the same peptide group are highlighted in magenta; the oxygen-hydrogen distance is 2.08 Å (208 pm). The protein chain runs upwards, i.e., its N-terminus is at the bottom and its C-terminus at the top of the figure. Note that the sidechains point slightly downwards, i.e., towards the N-terminus.

Side view of an α-helix.

Treatment of biochemistry begins with discussion of amino acids & protein structure. If biochemistry were a language, then the amino acids would be the vocabulary of the language. Each amino acid has a different personality. After you become familiar with the chemical properties of each amino acid as you progress in biochemistry review begin always looking for instances in where you can broaden your understanding of how each individual amino acid behaves in unique ways in enzyme activity or as intermediates in biochemical pathways. It's important for effective learning to develop themes that can give structure to your biochemical knowledge base. Seeing each particular amino acid as a learning project in itself can be really helpful.

WikiPremed Resources


Proteins Images

Question Drill for Amino Acids & Protein Structure
Conceptual Vocabulary Self-Test

Basic Terms Crossword Puzzle

Basic Puzzle Solution

Learning Goals


Understand how to distinguish amino acids based on the chemical properties of their side chains, i.e. whether the side chain is acidic or basic, hydrophobic or hydrophilic.

Be able to distinguish L and D amino acids. (All naturally occurring proteins from living organisms consist of L amino acids.)

Have a good familiarity with the ionization states of amino acids including an understanding of amino acid titration curves and the isoelectric point.

Understand how steric considerations of peptide bonds play a role in determining protein structure.

Be able to distinguish primary, secondary, tertiary, and quaternary protein structure articulate the significance of the (limited) reversibility of protein denaturation.

Be prepared to describe the basic organic chemistry reactions in peptide bond formation and hydrolysis of peptide bonds.

Be able to describe how 'salting out' methods of protein precipitation work.

Recognize the various types of post-translational modifications of proteins.

Understand and contextualize various protein functions at the cellular, tissue, physiological levels including enzyme activity, transport & storage, structure, immunity, and signalling.

Point to several examples of structural proteins, transport proteins, signalling proteins, and proteins involved in immunity.

Suggested Assignments

Disciplined work with MCAT Masters becomes more important at this stage in the course as we move into Biology where there is quite a large conceptual vocabulary. Practice using the question server. Complete the fundamental terms crossword puzzle. Here is the solution to the puzzle.

Read pp. 110-112 in ExamKrackers Chemistry. Perform practice items 65-72 on pp. 116-117 (practice items for carbohydrates, proteins, lipids & nucleic acids).

Read pp. 12-20 and pp. 22-26 in ExamKrackers Biology I. Perform practice items 9-16 on pg. 21 and practice items 17-24 on pg. 27.

Work carefully through the web resources for amino acids & protein structure.

Conceptual Vocabulary for Amino Acids & Protein Structure

Amino Acids & Protein Structure

Amino acid
An amino acid is a molecule that contains both amine and carboxyl functional groups. In biochemistry, this term is often used to refer to the select group of specific forms that serve as the building blocks of proteins.
Enzymes are proteins that catalyze chemical reactions.
Peptide bond
A peptide bond is a chemical bond that is formed between two amino acids when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water.
Primary structure
The primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms, including stereochemistry.
Peptides are short polymers formed from the linking, in a defined order, of alpha-amino acids.
Tertiary structure
Quaternary structure
The quaternary structure of a protein is the arrangement of multiple folded protein molecules in a multi-subunit complex.
Globular protein
Globular proteins, or spheroproteins are one of the two main protein classes, comprising globelike proteins that are more or less soluble in aqueous solutions.
Alpha helix
The alpha helix is a common motif in the secondary structure of proteins, a right-handed coiled conformation, resembling a spring, in which every backbone N-H group donates a hydrogen bond to the backbone carbonyl group of the amino acid four residues earlier.
Secondary structure
The secondary structure of a protein is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids.
Active site
The active site of an enzyme contains the catalytic and binding sites.
Negative feedback
Competitive inhibition
Competitive inhibition is a form of enzyme inhibition where binding of the inhibitor to the enzyme prevents binding of the substrate and vice versa.
Enzyme kinetics
Enzyme kinetics is the study of the rates of chemical reactions that are catalysed by enzymes.
Membrane transport protein
A membrane transport protein is a protein involved in the movement of ions, small molecules, or macromolecules, such as another protein across a biological membrane.
Glycoproteins are proteins that contain oligosaccharide chains covalently attached to their polypeptide backbones.
Side chain
A side chain in organic chemistry and biochemistry is a part of a molecule that is attached to a core structure.
Essential amino acid
An essential amino acid or indispensable amino acid is an amino acid that cannot be synthesized de novo, and therefore must be supplied in the diet.
Isoelectric point
The isoelectric point is the pH at which a particular molecule or surface carries no net electrical charge.
A zwitterion is a chemical compound that is electrically neutral but carries formal positive and negative charges on different atoms.
Protein folding
Protein folding is the physical process by which a polypeptide arranges into its characteristic three-dimensional structure.
Beta sheet
The beta-pleated sheet is a major form of regular secondary structure in proteins along with the alpha helix. This form of secondary structure consists of strands connected laterally by three or more hydrogen bonds, forming a generally twisted, pleated sheet.
Enzyme catalysis
Enzyme catalysis is the catalysis of chemical reactions by proteins.
A substrate is a molecule upon which an enzyme acts.
Protein complex
A protein complex is a group of two or more associated proteins formed by protein-protein interaction that is stable over time.
Proteomics is the large-scale study of proteins.
Enzyme inhibitor
Enzyme inhibitors are molecules that bind to enzymes and decrease their activity.
Enzyme activator
Enzyme activators are molecules that bind to enzymes and increase their activity.
Disulfide bond
A disulfide bond is a single covalent bond derived from the coupling of thiol groups.
Non-competitive inhibition
Non-competitive inhibition is a type of inhibition that reduces the maximum rate of a chemical reaction without changing the apparent binding affinity of the catalyst for the substrate.
Fibrous protein
Fibrous proteins, also called scleroproteins, are long filamentous protein molecules that form one of the two main classes of tertiary structure protein, the other being globular proteins.
The term proteome refers all the expressed proteins in an organism at a given time point under defined conditions.
Post-translational modification
Post-translational modification is the chemical modification of a protein after its initial synthesis on a ribosome. It is one of the later steps in protein biosynthesis for many proteins.
Native state
The native state of a protein is its operative or functional form.
The N- or amino-terminus refers to the end of a protein or polypeptide terminated by an amino acid with a free amine group.
The C- or carboxyl-terminus of a protein or polypeptide is the end of the amino acid chain terminated by a free carboxyl group.
Linus Pauling
Linus Pauling (1901 - 1994) was an American quantum chemist and biochemist who pioneered the application of quantum mechanics to chemistry in describing the nature of chemical bonds. He also made important contributions to crystal and protein structure determination.
Salt bridge
The term salt bridge denotes a relatively weak ionic bond between positively and negatively charged side-chains of proteins.
Protein kinase
A protein kinase is an enzyme that modifies other proteins by chemically adding phosphate groups to them, ie. phosphorylation.
Michaelis-Menten kinetics
Describing the kinetics of many enzymes, the Michaelis-Menten model is valid only when the concentration of enzyme is much less than the concentration of substrate and when the enzyme is not allosteric.
Protein targeting
Protein targeting or sorting is the mechanisms by which a cell transports proteins to the appropriate positions in the cell or outside of it.
Signal patch
A protein signal patch contains information to send a given protein to the indicated location in the cell. It is made up of amino acid residues that are distant to one another in the primary sequence, but come close to each other in the tertiary structure of the folded protein.
Signal peptide
A signal peptide is a short peptide chain that directs the post-translational transport of a protein.
Proteoglycans represent a special class of glycoproteins that are heavily glycosylated.
Mixed inhibition
Mixed inhibition refers to a combination of two different types of reversible enzyme inhibition - competitive inhibition and uncompetitive inhibition.
Enzyme assay
Enzyme assays are laboratory methods for measuring enzymatic activity, which are vital for the study of enzyme kinetics and enzyme inhibition.
Carrier protein
Carrier proteins are proteins that transport a specific substance or group of substances across intracellular compartments or in extracellular fluids or else across the cell membrane.
Keratins are a family of fibrous structural proteins which are tough and insoluble, forming the hard but nonmineralized structures found in reptiles, birds, amphibians and mammals.
Iron-sulfur protein
Iron-sulfur proteins are proteins characterized by the presence of polymetallic systems containing sulfide ions, in which the iron ions have variable oxidation states.
Ramachandran plot
A Ramachandran plot is a way to visualize dihedral angles phi against psi of amino acid residues in protein structure.
Levinthal paradox
The Levinthal paradox is a thought experiment postulating that if a protein is to attain its correctly folded configuration by sequentially sampling all the possible conformations, it would require a time longer than the age of the universe to arrive at its correct native conformation.
Molten globule
A molten globule is a stable, partially folded protein state found in mildly denaturing conditions such as low pH, mild denaturant, or high temperature.
Prenylation is the addition of hydrophobic molecules to a protein.
TIM barrel
The TIM barrel is a conserved protein fold consisting of eight alpha-helices and eight parallel beta-strands that alternate along the peptide backbone.
Beta barrel
A beta barrel is a large beta-sheet that twists and coils to form a closed structure in which the first strand is hydrogen bonded to the last.
Helix bundle
A helix bundle is a small protein fold composed of three or four alpha helices and held together by nonlocal hydrophobic interactions.
Globin fold
The globin fold is a common three-dimensional fold in proteins typically consisting of eight alpha helices, although some proteins have additional helix extensions at their termini.
Homeodomain fold
The homeodomain fold is a protein structural domain that binds DNA and is thus commonly found in transcription factors.
Alpha solenoid
An alpha solenoid is a protein fold found in the protein subunits of light-harvesting complexes, particularly in the peridinin chlorophyll proteins of dinoflagellates, and as domains of larger eukaryotic proteins that make up the nuclear pore complex.
Immunoglobulin fold
An immunoglobulin fold is a common all-beta protein fold that consists of a 2-layer sandwich of approximately 7 antiparallel beta-strands arranged in two beta-sheets.
Beta-propeller domain
A beta-propeller domain is an all-beta protein fold characterized by 4-8 blade-shaped beta sheets arranged toroidally around a central axis.
Leucine-rich repeat
A leucine-rich repeat is a protein structural motif that forms an alpha/beta horseshoe fold.
Thioredoxin fold
The thioredoxin fold is a protein fold common to enzymes that catalyze disulfide bond formation and isomerization.
Ferredoxin fold
A ferredoxin fold is a common alpha-beta protein fold with a signature beta-alpha-beta-beta-alpha-beta secondary structure along its backbone.