MCAT B/B - Biochemistry

ch.1 - ch.12

Chiral Amino Acids

All are L-amino acids and (S) absolute configuration, except Cysteine (R).

Achiral Amino Acid

Glycine (has a hydrogen atom as its R-group).

Nonpolar Aliphatic R-Groups

Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Methionine.

Aromatic R-Groups

Phenylalanine, Tyrosine, Tryptophan.

Polar Uncharged R-Groups

Serine, Threonine, Asparagine, Glutamine, Cysteine.

Negatively Charged (Acidic) R-Groups

Aspartic acid (aspartate), Glutamic acid (glutamate).

Positively Charged (Basic) R-Groups

Arginine, Lysine, Histidine.

Zwitterion

A molecule containing both positive and negative charges, resulting in a net neutral charge.

Isoelectric Point (pI)

The pH at which an amino acid exists completely as a neutral zwitterion.

Peptide Bond Formation

Condensation/dehydration reaction; nucleophilic amino group attacks electrophilic carbonyl carbon.

Primary Structure

Linear sequence of amino acids stabilized by covalent peptide bonds.

Secondary Structure

Local structure (α-helices and β-pleated sheets) stabilized by backbone hydrogen bonds.

Tertiary Structure

Three-dimensional shape driven by hydrophobic interactions, acid-base salt bridges, and disulfide bonds.

Quaternary Structure

Interaction between multiple polypeptide subunits (e.g., hemoglobin).

Denaturation

Loss of tertiary/quaternary structure, usually due to heat or solute concentrations.

Oxidoreductases

Enzymes that catalyze oxidation-reduction reactions (transfer of electrons).

Transferases

Enzymes that move a functional group from one molecule to another.

Hydrolases

Enzymes that catalyze cleavage of a molecule with the addition of water.

Lyases

Enzymes that split a molecule without water or electron transfer (often form cyclic or double bonds).

Isomerases

Enzymes that catalyze the rearrangement of bonds within a molecule.

Ligases

Enzymes that use ATP to join two large biological molecules together.

Induced Fit Model

Substrate binding induces a conformational change in both enzyme active site and substrate.

Cofactors & Coenzymes

Metal ions (cofactors) or small organic groups (coenzymes) required for enzyme activity.

Apoenzyme vs. Holoenzyme

Apoenzyme is catalytically inactive (lacks cofactor); Holoenzyme is active (contains cofactor).

Structural Proteins

Collagen, elastin, keratin, actin, tubulin; usually fibrous.

Motor Proteins

Myosin, kinesin, dynein; utilize ATP to generate mechanical force along cytoskeletal tracks.

Cell Adhesion Molecules (CAMs)

Cadherins, integrins, selectins; anchor cells to things or to each other.

Antibodies (Immunoglobulins)

Y-shaped binding proteins produced by B-cells with two identical heavy chains and two light chains.

Native PAGE

Electrophoresis technique separating proteins by size and charge in their native state.

SDS-PAGE

Electrophoresis using detergent to denature proteins, sorting them strictly by molecular mass.

Isoelectric Focusing

Separates proteins in a pH gradient gel based on their specific isoelectric point (pI).

Chromatography Types

Column (size/polarity), Ion-Exchange (charge), Size-Exclusion (gel filtration/pore size), Affinity (receptor-ligand binding).

Edman Degradation

Sequences proteins by sequentially cleaving and identifying N-terminal amino acids.

Michaelis-Menten Equation

v = (Vmax * [S]) / (Km + [S]).

Km (Michaelis Constant)

Substrate concentration at 1/2 Vmax; inversely proportional to enzyme-substrate affinity.

Catalytic Efficiency

Kcat / Km.

Lineweaver-Burk Plot

Double reciprocal plot; x-intercept = -1/Km, y-intercept = 1/Vmax.

Competitive Inhibition

Binds active site; increases Km, Vmax remains unchanged.

Noncompetitive Inhibition

Binds allosteric site equally to E and ES; Km unchanged, decreases Vmax.

Mixed Inhibition

Binds allosteric site unequally to E and ES; alters Km, decreases Vmax.

Uncompetitive Inhibition

Binds only the enzyme-substrate (ES) complex; decreases both Km and Vmax.

Hill Coefficient

1 is positive cooperativity, <1 is negative cooperativity, =1 is non-cooperative.

D- vs L- Sugars

Determined by highest-numbered chiral carbon; D-sugars have the -OH group on the right.

Epimers

Diastereomers that differ in configuration at exactly one chiral center.

Anomers

Epimers that form at ring-closing carbon (anomeric carbon); α- (trans to CH2OH) vs β- (cis to CH2OH).

Mutarotation

Spontaneous shifting between α and β anomeric configurations in solution.

Reducing Sugar

Any monosaccharide with a free aldehyde or ketone group capable of oxidation (Tollens' / Benedict's positive).

Sucrose

Glucose + Fructose (linked via α-1,2-glycosidic bond).

Lactose

Galactose + Glucose (linked via β-1,4-glycosidic bond).

Maltose

Glucose + Glucose (linked via α-1,4-glycosidic bond).

Glycogen & Starch

Storage polysaccharides; contain α-1,4 linkages for chains and α-1,6 linkages for branch points.

Cellulose

Structural plant polysaccharide; unbranched β-1,4-glycosidic linkages (indigestible by humans).

Phospholipids

Glycerol backbone + 2 fatty acid tails + 1 polar phosphate head group.

Sphingolipids

Contain a sphingosine backbone instead of glycerol; structural role in myelin sheaths.

Triacylglycerols

Three fatty acids esterified to a glycerol backbone; primary long-term energy storage form.

Saturated vs Unsaturated Fats

Saturated have no double bonds (solid at room temp); Unsaturated have double bonds (liquid).

Saponification

Ester hydrolysis of triacylglycerols using a strong base (NaOH) to form soap.

Micelles

Spherical aggregates of amphipathic lipids in water with hydrophobic cores and hydrophilic shells.

Steroid Structure

Four fused rings: three cyclohexane rings and one cyclopentane ring.

Fat-Soluble Vitamins

Vitamins A (vision), D (calcium balance), E (antioxidant), K (coagulation).

Terpenes

Steroid precursors built from five-carbon isoprene units (C5H8).

Nucleoside vs Nucleotide

Nucleoside is a sugar + base; Nucleotide is a sugar + base + phosphate group.

Watson-Crick Model

Antiparallel double helix; A-T (2 hydrogen bonds), G-C (3 hydrogen bonds); sugar-phosphate backbone outside.

Purines vs Pyrimidines

Purines (double ring: A, G); Pyrimidines (single ring: C, T, U). "CUT the PY".

Histones

Proteins (H2A, H2B, H3, H4) that DNA winds around to form nucleosomes. H1 locks it in place.

Heterochromatin vs Euchromatin

Heterochromatin is dense, silent, dark; Euchromatin is loose, transcriptionally active, light.

Telomeres

GC-rich caps at chromosome ends that protect against degradation.

Replication Enzymes

Helicase (unwinds), Primase (RNA primers), DNA Polymerase (synthesizes DNA), Ligase (joins Okazaki fragments).

Prokaryotic vs Eukaryotic Polymerases

Prokaryotes use DNA Pol III (synthesis) and Pol I (primer removal); Eukaryotes use Pol α, δ, ε (synthesis) and RNase H (primer removal).

PCR Steps

Denaturation (heat), Annealing (cool for primers), Extension (Taq polymerase synthesizes).

DNA Libraries

Genomic libraries contain introns and exons; cDNA libraries contain only coding exons (made via reverse transcription).

Central Dogma

DNA -> RNA -> Protein.

Degenerate Mnemonic/Wobble

The third base in a codon is flexible, protecting against mutation effects.

Start Codon

AUG (Methionine).

Stop Codons

UAA, UGA, UAG ("U Are Annoying, U Go Away, U Are Gone").

Silent Mutation

Base change that codes for the exact same amino acid.

Missense Mutation

Base change that results in a different amino acid.

Nonsense Mutation

Base change that introduces a premature stop codon.

Frameshift Mutation

Insertion or deletion of nucleotides altering the reading frame.

RNA Polymerase II

Main transcription enzyme in eukaryotes; binds the TATA box in the promoter.

Post-Transcriptional Processing

5' cap (7-methylguanosine), 3' poly-A tail, and splicing (snRNA/spliceosome removes introns).

Alternative Splicing

Splicing different combinations of exons together to yield multiple distinct protein variants from one gene.

Ribosome Sites

A site (aminoacyl-tRNA binds), P site (peptidyl-tRNA holds growing peptide chain), E site (exit site for uncharged tRNA).

Fluid Mosaic Model

Plasma membrane behaves as a fluid lipid bilayer embedded with carbohydrates, proteins, and cholesterols.

Membrane Cholesterol

Maintains membrane fluidity: increases fluidity at low temperatures, decreases fluidity at high temperatures.

Flugases (Flippases)

Enzymes that move lipids between membrane leaflets (outer to inner or vice versa).

Integral vs Peripheral Proteins

Integral span the membrane (transmembrane); Peripheral stick to the inner or outer surface.

Simple Diffusion

Passive transport down a concentration gradient directly across the lipid bilayer (small, nonpolar molecules).

Osmosis

Simple diffusion of water from low solute concentration (hypotonic) to high solute concentration (hypertonic).

Facilitated Diffusion

Passive transport down a concentration gradient utilizing a carrier protein or channel (polar or large molecules).

Active Transport

Primary uses ATP directly; Secondary uses an existing electrochemical gradient created by primary active transport (symport/antiport).

Sodium-Potassium Pump (Na+/K+ ATPase)

Pumps 3 Na+ ions out of the cell and 2 K+ ions into the cell per ATP molecule cleaved.

Glycolysis Rate-Limiting Enzyme

Phosphofructokinase-1 (PFK-1); inhibited by ATP/citrate, activated by AMP/fructose 2,6-bisphosphate.

Hexokinase vs Glucokinase

Hexokinase is in most tissues (low Km, feedback inhibited by G6P); Glucokinase is in liver/pancreas (high Km, induced by insulin).

Glyceraldehyde-3-Phosphate Dehydrogenase

Produces NADH during glycolysis.

Substrate-Level Phosphorylation Enzymes

Phosphoglycerate kinase and pyruvate kinase; produce ATP directly from ADP in glycolysis.

Pyruvate Dehydrogenase Complex (PDH)

Converts pyruvate to acetyl-CoA inside the mitochondria; inhibited by acetyl-CoA and NADH.

Fermentation Rate-Limiting Enzyme

Lactate dehydrogenase; reduces pyruvate to lactate to regenerate cytosolic NAD+ for glycolysis.

Galactokinase & Galactose-1-Phosphate Uridyltransferase

Enzymes that trap and convert galactose into glucose-1-phosphate.

Fructose-1,6-Bisphosphatase

Bypasses PFK-1 in gluconeogenesis; rate-limiting step.