MCAT Biochemistry Review

Which amino acids are positively charged at physiological pH?

Lysine (K), Arginine (R), Histidine (H)

Which amino acids are negatively charged at physiological pH?

Aspartate (D), Glutamate (E)

Which amino acid contains sulfur and can form disulfide bonds?

Cysteine

Which amino acid is most commonly phosphorylated?

Serine (also threonine and tyrosine)

What amino acid is often found in turns of proteins due to its rigid structure?

Proline

What does increasing enzyme concentration do to Vmax?

Increases Vmax

What does increasing enzyme concentration do to Km?

No effect

How does competitive inhibition affect Vmax and Km?

Vmax unchanged; Km increases

How does noncompetitive inhibition affect Vmax and Km?

Vmax decreases; Km unchanged

What is the Michaelis constant (Km)?

Substrate concentration at which enzyme velocity equals half Vmax

What is the rate-limiting enzyme of glycolysis?

Phosphofructokinase-1 (PFK-1)

What is the rate-limiting enzyme of gluconeogenesis?

Fructose-1,6-bisphosphatase

What is the rate-limiting enzyme of the TCA cycle?

Isocitrate dehydrogenase

Where does beta-oxidation occur?

Mitochondrial matrix

How much ATP is produced from one NADH?

~2.5 ATP

How much ATP is produced from one FADH₂?

~1.5 ATP

3° Structure

The 3-D shape of a single polypeptide chain, stabilized by hydrophobic interactions, acid-base interactions, H-bonds, and disulfide bonds.

Hydrophobic Interactions

A process that pushes hydrophobic R groups to the interior of a protein, which increases entropy of the surrounding water molecules and creates a negative Gibbs free energy ($\Delta G$).

Disulfide Bonds

Covalent bonds formed between the thiol groups of two cysteine molecules through oxidation, creating cystine.

4° Structure

The interaction between peptides in proteins that contain multiple subunits.

Prosthetic Group

The attached molecule in a conjugated protein, which can be a metal ion, vitamin, lipid, carbohydrate, or nucleic acid.

Denaturation

The loss of 3-D structure caused by heat or solute concentration, involving the breaking of non-covalent interactions like H-bonds and hydrophobic interactions.

Amphoteric

The property of amino acids that allows them to act as either a base or an acid.

pKa

The pH at which half of the species is deprotonated, where $[HA] = [A^-]$.

Isoelectric Point (pI)

The pH at which an amino acid is in zwitterion form and the charges cancel out to make a neutral molecule.

pI Formula (Neutral Side Chain)

$$pI = \frac{1}{2} (pK_{a1} + pK_{a2})$$

Oligopeptides

Peptide chains with less than 20 residues.

Amide Bonds

The C-N bond of a peptide bond, which is rigid due to resonance.

1° Structure

The linear sequence of amino acids in a peptide, stabilized by peptide bonds and written N-terminus to C-terminus.

2° Structure

The local structure of neighboring amino acids, stabilized by hydrogen bonding between amino groups and nonadjacent carboxyl groups.

$\alpha$-helices

A common 2° structure formed by clockwise coils around a central axis.

$\beta$-pleated sheets

A common 2° structure consisting of rippled strands that can be parallel or antiparallel.

Competitive Inhibition

Occurs when an inhibitor similar to the substrate binds at the active site; it can be overcome by adding more substrate, leaving $V_{max}$ unchanged while increasing $K_m$.

Uncompetitive Inhibition

Occurs when the inhibitor binds only with the enzyme-substrate complex, causing both $V_{max}$ and $K_m$ to decrease.

Noncompetitive Inhibition

Occurs when the inhibitor binds with equal affinity to the enzyme and the enzyme-substrate complex, causing $V_{max}$ to decrease while $K_m$ remains unchanged.

Mixed Inhibition

Occurs when the inhibitor binds with unequal affinity to the enzyme and the enzyme-complex; $V_{max}$ decreases, and $K_m$ increases or decreases based on affinity.

Suicide Inhibitor

A substrate analogue that binds irreversibly to the active site via a covalent bond.

Homotropic Effector

An allosteric regulator that is also the substrate, such as $O_2$ for hemoglobin.

Zymogens

Inactive precursors to an enzyme that are activated by cleavage.

Lock & Key Theory

A theory suggesting the enzyme and substrate are exactly complementary and fit together like a key into a lock.

Induced Fit Theory

A theory suggesting that the enzyme and substrate undergo conformational changes to interact fully.

Oxidoreductases

Enzymes that catalyze REDOX reactions involving the transfer of electrons.

Hydrolases

Enzymes that catalyze cleavage of molecules with the addition of $H_2O$.

Lyases

Enzymes that catalyze cleavage without the addition of $H_2O$ and without electron transfer.

Kinases

A type of transferase that adds a phosphate group to a molecule.

Km

The substrate concentration at which an enzyme runs at half its $V_{max}$. Formula: $K_m = \frac{k_{-1} + k_2}{k_1}$.

Michaelis-Menten Equation

$$v = \frac{V_{max} [S]}{K_m + [S]}$$

Ion Channels

Proteins used for regulating ion flow, categorized as ungated, voltage-gated, or ligand-gated.

G Protein-Coupled Receptors (GPCR)

Receptors with $\alpha$, $\beta$, and $\gamma$ subunits where a 1st messenger ligand initiates a 2nd messenger cascade response.

Cell Adhesion Molecules (CAM)

Proteins including cadherins, integrins, and selectins that allow cells to bind to other cells or surfaces.

Antibodies (Ig)

Immunoglobulins used by the immune system to target antigens, with a variable region responsible for binding.

SDS-PAGE

An electrophoresis method that denatures proteins and masks native charge to allow accurate size comparison.

Isoelectric Focusing

Separates proteins by their pI; the protein migrates until it reaches a region where $pH = pI$.

Beer-Lambert Law

$Absorbance = \epsilon C l$, where $\epsilon$ is the extinction coefficient, $C$ is concentration, and $l$ is path length.

Anomeric Carbon

The new chiral center formed in carbohydrate ring closure; the carbonyl carbon in straight-chain form.

$\alpha$-anomers

Carbohydrate rings where the -OH on the anomeric carbon is trans to the free $-CH_2OH$ group.

Mutarotation

The spontaneous shift from one anomeric form to another via a straight-chain intermediate.

Epimers

A subtype of diastereomers that differ at exactly one chiral carbon.

Anomers

A subtype of epimers that differ specifically at the anomeric carbon.

Cellulose

The main structural component for plant cell walls and the main source of fiber in the human diet.

Amphipathic

A molecule containing both a hydrophilic (polar) head and hydrophobic (nonpolar) tails, such as a phospholipid.

Sphingomyelins

A major class of sphingophospholipids containing a phosphatidylcholine or phosphatidylethanolamine head group; part of the myelin sheath.

Gangliosides

Lipids containing oligosaccharides with at least 1 terminal N-acetylneuraminic acid (NANA).

Saponification

The ester hydrolysis of triacylglycerols using a strong base like sodium or KOH to form soaps.

Micelle

A water-soluble sphere with a lipid-soluble interior used to dissolve lipid-soluble molecules.

Terpenes

Odiferous steroid precursors made from isoprene units ($C_5H_8$).

Prostaglandins

Autocrine and paracrine signaling molecules that regulate cAMP levels and affect smooth muscle contraction and body temperature.

Vitamin K

Includes phylloquinone and menaquinones; essential for forming prothrombin, a clotting factor.

Oncogenes

Mutated proto-oncogenes that promote cell cycling; described as 'stepping on the gas pedal.'

Tumor Suppressor Genes

Genes coding for proteins that reduce cell cycling or promote DNA repair; mutations are described as 'cutting the brakes.'

Nucleoside

A 5-carbon sugar and a nitrogenous base but no phosphate groups.

Chargaff’s Rules

States that the number of purines equals the number of pyrimidines ($A=T$; $C=G$).

Heterochromatin

Dark, dense, and transcriptionally silent DNA in the nucleus.

Euchromatin

Light, uncondensed, and transcriptionally expressed DNA in the nucleus.

Telomeres

The ends of chromosomes containing high GC-content to prevent DNA unraveling.

Wobble

The 3rd base in a codon that allows mutations to occur without affecting the protein sequence.

Nonsense Mutation

A point mutation that produces a premature STOP codon.

Shine-Dalgarno Sequence

The site where the 30S ribosome attaches in prokaryotes during translation initiation.

Chaperones

Proteins that assist in the folding of newly synthesized proteins.

Operons

Inducible or repressible clusters of genes transcribed as a single mRNA.

Introns

Portions of hnRNA that are spliced out and stay in the nucleus; enable alternative splicing.

Exons

The portions of RNA that exit the nucleus to form mature mRNA.

Osmotic Pressure

A colligative property conceptualized as 'sucking' pressure. Formula: $\pi = iMR T$.

Simple Diffusion

Passive transport of small, nonpolar molecules from high to low concentration until equilibrium.

Symport

Secondary active transport where both particles flow in the same direction.

GLUT-4

A glucose transporter found in adipose tissue and muscle that is stimulated by insulin and has a low $K_m$.

PFK-1 (Phosphofructokinase-1)

The rate-limiting enzyme of glycolysis that converts fructose 6-phosphate to fructose 1,6-bisphosphate.

Pyruvate Carboxylase

A gluconeogenesis enzyme that converts pyruvate to oxaloacetate, bypassing pyruvate kinase.

Glucose-6-phosphate dehydrogenase (G6PD)

The rate-limiting enzyme of the Pentose Phosphate Pathway, activated by $NADP^+$ and insulin.

Isocitrate Dehydrogenase

The rate-limiting step of the citric acid cycle; inhibited by ATP and NADH, activated by ADP and $NAD^+$.

Complex I (ETC)

NADH-CoQ Oxidoreductase; transfers electrons from NADH to FMN and then to CoQ, translocating 4 $H^+$ ions.

ATP Synthase F0 Portion

An ion channel in the inner mitochondrial membrane that allows $H^+$ to flow down its gradient.

HMG-CoA Reductase

The rate-limiting enzyme of cholesterol synthesis, responsible for synthesizing mevalonate.

Ketogenic Amino Acids

Amino acids that can be converted into acetyl-CoA and ketone bodies; leucine and lysine are solely ketogenic.

Respiratory Quotient (RQ)

Estimates fuel composition consumed by the body. Formula: $RQ = \frac{CO_2 \text{ produced}}{O_2 \text{ consumed}}$.

Amino Acid Structure

Consist of an amino group (NH2), a carboxyl group (COOH), a hydrogen atom, and a unique side chain (R group) all attached to a central carbon atom.

Essential Amino Acids

Amino acids that cannot be synthesized by the body and must be obtained from the diet; they include histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

Non-Essential Amino Acids

Amino acids that can be synthesized by the body; they include alanine, aspartic acid, glutamic acid, and serine.

Amino Acid Classification

Aliphatic, aromatic, sulfur-containing, acidic, basic, and amine derivatives based on their side chains.

Zwitterion Form

The dipolar form of an amino acid at its isoelectric point, where the amino group is protonated (NH3+) and the carboxyl group is deprotonated (COO-).