Biochemistry

Oxidoreductases

Oxidoreductases

Catalyze oxidation-reduction reactions (transfer of electrons); Often have electron-carrying cofactor like NAD+ or NADP+; Enzymes with dehydrogenase or reductase in their names

Transferases

Catalyze the movement of a functional group from one molecule to another; I.e. Kinases (transfer of a phosphate group)

Hydrolases

Catalyze the breaking of a compound into two molecules using the addition of water; Many named for their substrate; I.e. Phosphatase cleaves a phosphate group from another molecule

Lyases

Catalyze the cleavage of a single molecule into two products; AKA synthases when catalyze reverse reaction

Isomerases

Catalyze the rearrangement of bonds within a molecule; Catalyze reactions between stereoisomers and constitutional isomers

Ligases

Catalyze addition or synthesis reactions, generally between large similar molecules, and often require ATP; Nucleic acid synthesis and repair

Endergonic Reaction

Requires energy input

Exergonic Reaction

Energy is given off

Cofactors (Coenzymes)

Nonprotein molecules that tend to be small in size so they can bind to the active site of the enzyme and participate in the catalysis of the reaction, usually by carrying charge through ionization, protonation, or deprotonation

Apoenzymes

Enzymes without their cofactors

Holoenzymes

Enzymes containing their cofactors

Prosthetic Groups

Tightly bound cofactors or coenzymes that are necessary for enzyme function

Michaelis-Menten Plot

Michaelis-Menten Equation (and V_max)

V_max = [E]k_cat

Catalytic Efficiency

k_cat/K_m

Lineweaver-Burk Plot

Positive Cooperativity

Hill’s coefficient > 1; I.e. After one ligand is bound the affinity of the enzyme for further ligands increases

Negative Cooperativity

Hill’s coefficient < 1; I.e. After one ligand is bound the affinity of the enzyme for further ligands decreases

Competitive Inhibition

Inhibitor binds to enzyme active site; Overcome by adding more substrate so that the substrate-to-inhibitor ratio is higher; No effect on Vmax, increases Km

Noncompetitive Inhibition

Binds to an allosteric site on the enzyme to induce a change in enzyme conformation; Binds equally well to the enzyme and ES complex; Decreases Vmax, no effect on Km

Mixed Inhibition

When an inhibitor can bind to either the enzyme or the ES complex, but has a different affinity for each; Bind at an allosteric site; Alters Km, decreases Vmax

Uncompetitive Inhibition

Bind only to the ES complex and essentially lock the substrate in the enzyme, preventing its release; Bind at an allosteric site; Lowers Km and Vmax

Allosteric Enzymes

Alternate between an active and an inactive form that cannot carry out the enzymatic reaction

Collagen

Structural protein that has characteristic trihelical fiber and makes up most of the extracellular matrix of connective tissue; Found throughout the body and is important in providing strength and flexibility

Elastin

Structural protein that is an important component of the extracellular matrix of connective tissue; Primary role is to stretch and then recoil like a spring, which restores the original shape of the tissue

Keratins

Structural intermediate filament proteins found in epithelial cells; Contribute to the mechanical integrity of the cell and also function as regulatory proteins; Primary protein that makes up hair and nails

Actin

Structural protein that makes up microfilaments and the thin filaments in myofibrils; The most abundant protein in eukaryotic cells; Have a positive and a negative side, which allow motor proteins to travel unidirectionally along this protein, like a one-way street

Tubulin

The structural protein that makes up microtubules, which are important for providing structure, chromosome separation in mitosis and meiosis, and intracellular transport with kinesin and dynein; Has a negative end usually located adjacent to the nucleus, whereas the positive end is usually in the periphery of a cell

Myosin

Primary motor protein that interacts with actin; The thick filament in a myofibril; Can be involved in cellular transport; Each subunit has a single head and neck; Movement at the neck is responsible for the power stroke of sarcomere contraction

Kinesin

One of two motor proteins associated with microtubules; Has two heads, one head attached to tubulin at all times; Plays a key role in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis; Brings vesicles toward the positive end of the microtubule

Dynein

One of two motor proteins associated with microtubules; Has two heads, one head attached to tubulin at all times; Involved in the sliding movement of cilia and flagella; Brings vesicles toward the negative end of the microtubule

Binding Proteins

Proteins that transport or sequester molecules by binding to them; Hemoglobin, calcium-binding proteins, DNA-binding proteins, etc.; Has an affinity curve for its molecule of interest

Cell Adhesion Molecules (CAMs)

Proteins found on the surface of most cells and aid in binding the cell to the extracellular matrix or other cells; All are integral membrane proteins; Three types: Cadherins, integrins, and selectins

Cadherins

Group of glycoproteins that mediate calcium-dependent cell adhesion; Often hold similar cell types together; Type of CAM

Integrins

Group of proteins that all have two membrane-spanning chains called α and β which are important in binding to and communicating with the extracellular matrix, as well as in cellular signaling and can greatly impact cellular function by promoting cell division, apoptosis, or other processes; Type of CAM

Selectins

CAMs that bind to carbohydrate molecules that project from other cell surfaces (these are the weakest CAM bonds); Expressed on white blood cells and the endothelial cells that line blood vessels; Play important role in host defense

Opsonization

When antibodies mark a pathogen for immediate destruction by other white blood cells

Agglutinating

When an antigen and an antibody clump together into large insoluble protein complexes that can be phagocytized and digested by macrophages

Ion Channels

Proteins that create specific pathways for charged molecules; Used for molecules that are impermeable to the membrane (large, polar, or charged); Three types: Ungated, voltage-gated, and ligand-gated

Facilitated Diffusion

A type of passive transport where the diffusion of molecules down a concentration gradient through a pore in the membrane is created by a transmembrane protein ion channel; Used for molecules that are impermeable to the membrane (large, polar, or charged)

Ungated Channels

Have no gates and are therefore unregulated; I.e. Ungated potassium channels allow potassium transport until potassium has reach equilibrium

Voltage-Gated Channels

The gate is regulated by the membrane potential change near the channel; I.e. Sodium channels that are opened during membrane depolarization

Ligand-Gated Channels

The binding of a specific substance or ligand to the channel causes it to open or close; I.e. GABA binds to chloride channel to open it

Enzyme-Linked Receptors

Membrane receptors that display catalytic activity in response to ligand binding; Three primary protein domains: a membrane-spanning domain, a ligand-binding domain, and a catalytic domain

Membrane-Spanning Domain

In enzyme-linked receptors, this anchors the receptor in the cell membrane

Ligand-Binding Domain

In enzyme-linked receptors, this is stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain

Second Messenger Cascade

A series of events that transmit signals from the outside of a cell to its interior, triggering physiological changes; Caused by the ligand-biding domain inducing a conformational change that activates the catalytic domain

G Protein-Coupled Receptors (GPCR)

A large family of integral membrane proteins involved in signal transduction; Have seven membrane-spanning α-helices; Receptors found on the extracellular surface of the cell; Use a heterotrimeric G protein to transmit signals to an effector in the cell

(Heterotrimeric) G Protein

Used by GPCRs to transmit signals to an effector in the cell; Named for their intracellular link to guanine nucleotides (GDP and GTP)

The binding of a ligand increases the affinity of the receptor for the G protein. The binding of the G protein represents a switch to the active state and affects the intracellular signaling pathway.

Three Types: G_s, G_i, and G_q

G_s

Stimulates adenylate cyclase, with increases levels of cAMP in the cell

G_i

Inhibits adenylate cyclase, which decreases levels of cAMP in the cell

G_q

Activates phospholipase C, which cleaves a phospholipid from the membrane to form PIP₂. PIP₂ is then cleaved into DAG and IP₃; IP₃ can open calcium channels in the ER, increasing calcium levels in the cell.

Trimeric G Protein Cycle

In its inactive form, the α subunit binds GDP and is in a complex with the β and γ subunits. When a ligand binds to the GPCR, the receptor becomes activated and, in turn, engages the corresponding G protein (Step 1). Once GDP is replaced with GTP, the α subunit is able to dissociate from the β and γ subunits (Step 2). The activated α subunit alters the activity of adenylate cyclase. If the α subunit is α_s, then the enzyme is activated; if the α subunit is α_i, then the enzyme is inhibited. Once GTP on the activated α subunit is dephosphorylated to GDP (Step 3), the α subunit will rebind to the β and γ subunits (Step 4), rendering the G protein inactive

Electrophoresis

Works by subjecting compounds to an electric field, which moves them according to their net charge and size. Negatively charged compounds will migrate toward the positively charged anode, and vice versa.

Migration Velocity: v = Ez/f

• E = Electric Field Strength

• z = Net charge on the molecule

• f = Frictional coefficient

Polyacrylamide Gel

The standard medium for protein electrophoresis. Proteins travel through gel in relation to their size and charge, with smaller particles passing through easily while large particles get stuck. Slow molecules: Large and electrically neutral

Polyacrylamide Gel Electrophoresis (PAGE)

Method for analyzing proteins by mass-to-charge and mass-to-size ratios; Functional native protein can be recovered from the gel after electrophoresis (before staining); Useful to compare the molecular size or charge of proteins known to be similar in size from other analytic methods

SDS-PAGE

Separates proteins on the basis of relative molecular mass alone; SDS is a detergent that disrupts all noncovalent interactions and binds to proteins to create large chains with net negative charges, thereby neutralizing the protein’s original charge and denaturing the protein; As proteins move through gel, only affected by electric field strength and friction (depends on mass)

Isoelectric Focusing

Exploits the acidic and basic properties of amino acids by separating on the basis of pI; Protein mixture placed in a gel with a pH gradient (acidic at positive anode and basic at negative cathode) and positively-charged proteins will migrate towards cathode, and vice versa. As the protein reaches the portion of the gel where the pH is equal to the protein’s pI, the protein takes on a neutral charge and will stop moving.

Edman Degradation

Uses cleavage to sequence proteins of up to 50 to 70 amino acids; Selectively and sequentially removes the N-terminal amino acid of the protein, which can be analyzed via mass spectroscopy

Bradford Protein Assay

Mixes a protein in solution with Coomassie Brilliant Blue dye. The dye gives up protons upon binding to amino acid groups, turning blue in the process. Ionic attractions between the dye and the protein then stabilize this blue form of the dye; thus, increased protein concentrations correspond to a larger concentration of blue dye in solution; Very important that only one protein is present

Aldoses

Carbohydrates that contain an aldehyde group as their most oxidized functional group

Ketoses

Carbohydrates that contain a ketone group as their most oxidized functional group

Glycosidic Linkages

A covalent bond that joins a carbohydrate molecule to another group, such as another carbohydrate or an alcohol; Sugars acting as substituents via this linkage are called glycosyl residues

_D-Fructose

_D-Glucose

_D-Galactose

_D-Mannose

Number of Possible Stereoisomers

Number of stereoisomers with a common backbone = 2^{^n}

n = Number of chiral carbons in the molecule

_L- vs. _D-Sugars (Fischer Projection)

All _D-sugars have the hydroxide of their highest-numbered chiral center on the right, and all _L-sugars have that hydroxide on the left (enantiomers)

Epimers

A type of diastereomer that differs in configuration at exactly one chiral center

Hemiacetals

Cyclic molecules formed from aldoses

Hemiketals

Cyclic molecules formed from ketoses

Anomeric Carbon

A carbon atom in a cyclic sugar that was once the carbonyl carbon in the open-chain form of the sugar

Anomers

Two sugars in ring formation that differ at the anomeric carbon

α-anomer

In glucose, this has the -OH group of C-1 trans to the -CH₂OH substituent (axial and down)

β-anomer

In glucose, this as the -OH group of C-1 cis to the -CH₂OH substituent (equatorial and up)

Mutarotation

In hemiacetal rings the single bond between C-1 and C-2 can rotate freely, and either the α- or β-anomer can spontaneously form; Occurs more rapidly when catalyzed with an acid or base; In solution, the α-anomeric configuration is less favored because the hydroxyl group of the anomeric carbon is axial, adding to the steric strain of the molecule

Aldonic Acids

Oxidized aldoses; Often oxidized by the human body in order to yield energy (reducing agents)

Reducing Sugar

Any monosaccharide with a hemiacetal ring

Lactone

Product of the oxidation of an aldose in ring form; A cyclic ester with a carbonyl group persisting on the anomeric carbon; Essential role in human body

Tollens’ Reagent

Produces a silvery mirror when the aldehyde group is readily available; Ketoses also test positive due to tautomerization under basic conditions to form a carboxylic acid

Benedicts’ Reagent

The aldehyde group of an aldose is readily oxidized, creating red Cu₂O; Ketoses also test positive due to tautomerization under basic conditions to form a carboxylic acid

Tautomerization

The rearrangement of bonds in a compound, usually by moving a hydrogen and forming a double bond

Enol

A compound with a double bond and an alcohol group

Alditol

When the aldehyde group of an aldose is reduced to an alcohol

Deoxy Sugar

Contains a hydrogen that replaces a hydroxyl group on a sugar; Ex. _D-2-deoxyribose

Esterification of Carbohydrates

Hexokinase

Catalyzes the phosphorylation of glucose important to metabolic reaction of glycolysis in which a phosphate group is transferred from ATP to glucose

Acetals

Formed when hemiacetals react with alcohols; The anomeric hydroxyl group is transformed into an alkoxy group, creating α- and β-acetals; Creates glycosides formed by glycosidic bonds

Furanosides

Glycosides derived from furanose (5-member carb) rings

Pyranosides

Glycosides derived from pyranose (six-member carb) rings

Sucrose

Lactose

Glucose + Galactose

Maltose

Homopolysaccharide

A polysaccharide composed entirely of glucose (or any other monosaccharide)

Heteropolysaccharide

A polymer made up of more than one type of monosaccharide

Cellulose

The main structural component of plants; Homopolysaccharide composed of β-_D-glucose molecules linked by β-1,4 glycosidic bonds, with hydrogen bonds holding the actual polymer chains together for support

Starches

Polysaccharides that are more digestible by humans because they are linked α-1,4 glycosidic bonds; Can be broken down by enzymes and used as a source of energy

Amylose

A linear glucose polymer linked via α-1,4 glycosidic bonds; How plants predominantly store starch

Amylopectin

Type of starch similar to amylose but contains branches via α-1,6 glycosidic bonds