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.
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Conceptual Vocabulary for Amino Acids & Protein Structure
Amino Acids & Protein Structure
Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
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.
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.
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.
The tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.
The quaternary structure of a protein is the arrangement of multiple folded protein molecules in a multi-subunit complex.
Globular proteins, or spheroproteins are one of the two main protein classes, comprising globelike proteins that are more or less soluble in aqueous solutions.
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.
The secondary structure of a protein is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids.
The active site of an enzyme contains the catalytic and binding sites.
Negative feedback feeds part of a system's output, inverted, into the system's input; generally with the result that fluctuations are attenuated.
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 is the study of the rates of chemical reactions that are catalysed by enzymes.
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.
A side chain in organic chemistry and biochemistry is a part of a molecule that is attached to a core structure.
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.
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 is the physical process by which a polypeptide arranges into its characteristic three-dimensional structure.
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 is the catalysis of chemical reactions by proteins.
A substrate is a molecule upon which an enzyme acts.
A protein complex is a group of two or more associated proteins formed by protein-protein interaction that is stable over time.
Phosphorylation is the addition of a phosphate group to a protein molecule or a small molecule.
Proteomics is the large-scale study of proteins.
Enzyme inhibitors are molecules that bind to enzymes and decrease their activity.
Enzyme activators are molecules that bind to enzymes and increase their activity.
A protease is any enzyme that conducts proteolysis, that is, begins protein catabolism by hydrolysis of the peptide bonds that link amino acids together in the polypeptide chain.
A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids.
A disulfide bond is a single covalent bond derived from the coupling of thiol groups.
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 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.
Collagen is the main protein of connective tissue in animals and the most abundant protein in mammals, making up about 25% of the total protein content.
The term proteome refers all the expressed proteins in an organism at a given time point under defined conditions.
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.
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 (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.
The term salt bridge denotes a relatively weak ionic bond between positively and negatively charged side-chains of proteins.
A protein kinase is an enzyme that modifies other proteins by chemically adding phosphate groups to them, ie. phosphorylation.
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 or sorting is the mechanisms by which a cell transports proteins to the appropriate positions in the cell or outside of it.
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.
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.
Lysozyme is an enzyme that damages bacterial cell walls by catalyzing hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins.
Mixed inhibition refers to a combination of two different types of reversible enzyme inhibition - competitive inhibition and uncompetitive inhibition.
Enzyme assays are laboratory methods for measuring enzymatic activity, which are vital for the study of enzyme kinetics and enzyme inhibition.
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.
Elastin is a protein in connective tissue that is elastic and allows many tissues in the body to resume their shape after stretching or contracting.
Iron-sulfur proteins are proteins characterized by the presence of polymetallic systems containing sulfide ions, in which the iron ions have variable oxidation states.
A Ramachandran plot is a way to visualize dihedral angles phi against psi of amino acid residues in protein structure.
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.
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.
The TIM barrel is a conserved protein fold consisting of eight alpha-helices and eight parallel beta-strands that alternate along the peptide backbone.
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.
A helix bundle is a small protein fold composed of three or four alpha helices and held together by nonlocal hydrophobic interactions.
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.
The homeodomain fold is a protein structural domain that binds DNA and is thus commonly found in transcription factors.
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.
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.
A beta-propeller domain is an all-beta protein fold characterized by 4-8 blade-shaped beta sheets arranged toroidally around a central axis.
A leucine-rich repeat is a protein structural motif that forms an alpha/beta horseshoe fold.
The thioredoxin fold is a protein fold common to enzymes that catalyze disulfide bond formation and isomerization.
A ferredoxin fold is a common alpha-beta protein fold with a signature beta-alpha-beta-beta-alpha-beta secondary structure along its backbone.