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What are proteins made of?
Proteins are polymers of amino acids; amino acids are often called residues. Oligopeptides are very small chains of amino acids, while polypeptides are longer chains.
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What is the alpha-carbon stereocenter in amino acids?
All human amino acids, except one, are chiral at the alpha carbon due to having four different substituents: an -R group, hydrogen, carboxylic acid, and amine.
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How are amino acids designated in terms of configuration?
Amino acids are designated as L- or D- based on the position of the amine group in a Fischer Projection. L means Left and D means Right. All native human amino acids are L-amino acids.
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Do L- and D- configurations correlate with R and S?
L- and D- do not correlate directly with R and S. Most L-amino acids are S, but some, like cysteine, are R.
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What determines the chemistry of amino acids?
The -R groups of amino acids largely determine their chemistry. The combination of -R groups in a protein determines its chemistry and folding pattern.
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How do -R groups affect substrate binding?
Substrate binding in an active site depends on complementary charges on the -R groups and their hydrophilicity or hydrophobicity.
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How do hydrophobic and hydrophilic -R groups affect protein folding?
Hydrophobic -R groups fold into the protein core, while hydrophilic -R groups are more common on the surface. Low hydrophobicity proteins may not fold into stable structures but can retain function.
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What determines reaction mechanisms in enzyme pockets?
Reaction mechanisms in enzyme pockets are determined by the chemistry of the -R groups present in that pocket.
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What should you consider when thinking about proteins or enzymes?
Consider the amino acids present and the chemistry of their -R groups.
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What knowledge is required for the MCAT regarding amino acids?
You must know amino acid -R group structure, chemistry, hydrophilicity vs. hydrophobicity, charges, aromatic properties, names, three-letter and single-letter abbreviations.
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What is the importance of semantic processing in studying amino acids?
Engaging in semantic processing helps in understanding and remembering amino acids better by identifying their real-life functions and commonalities, rather than rote memorization.
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What is suggested for learning about amino acids effectively?
Learn one real-life function for each amino acid -R group to help remember its structure and properties more easily.
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What are the three-letter and one-letter abbreviations for amino acids?
Three-letter: Ala (A), Arg (R), Asn (N), Asp (D), Cys (C), Gln (Q), Glu (E), Gly (G), His (H), Ile (I), Leu (L), Lys (K), Met (M), Phe (F), Pro (P), Ser (S), Thr (T), Trp (W), Tyr (Y), Val (V). One-letter: A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V.
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What are logical stabilizing features for an enzyme pocket based on substrate charge?
a) Positively charged: acidic amino acids (Asp, Glu). b) Negatively charged: basic amino acids (Lys, Arg). c) Polar: polar amino acids (Ser, Thr, Asn, Gln). d) Non-polar: non-polar amino acids (Ala, Val, Leu, Ile, Met, Phe).
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What is the role of 5-HTT in the central nervous system?
5-HTT is a monoamine transport protein responsible for the reuptake of serotonin from synapses.
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Which amino acid does 5-HTT have a high affinity for?
Tryptophan (Trp).
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What amino acids have charged R groups?
Aspartic acid (Asp), Glutamic acid (Glu), Lysine (Lys), Arginine (Arg), Histidine (His).
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What is a zwitterion?
A zwitterion is a dipolar version of an amino acid where positively and negatively charged functional groups cancel each other out, resulting in a neutral ion.
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What is the order of deprotonation for amino acids?
1) α-COOH Group (pKa ~ 2), 2) -R Group, ACIDIC (pKa ~ 4), 3) -R Group, His (pKa ~ 6), 4) α-NH3+ Group (pKa ~ 9), 5) -R Group, BASIC (pKa ~ 11-12).
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What is the conceptual definition of isoelectric point?
The isoelectric point is the pH at which an amino acid or protein carries no net electrical charge, making it less soluble in solution.
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What is the acid-base functionality of amino acids?
Amino acids are weak acids with at least two acidic protons: -COOH and -NH3+. Some have acidic side chains, resulting in three acidic protons.
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What is the significance of pKa values in amino acids?
pKa values predict the order in which acidic functional groups of an amino acid will be deprotonated and indicate buffering capacity near pKa.
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What are essential amino acids?
Essential amino acids cannot be synthesized by the body and must be ingested through diet.
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What are non-essential amino acids?
Non-essential amino acids can be synthesized by the body and do not need to be ingested.
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What is the role of amino acids as buffers?
Amino acids act as buffers when the pH is near the pKa of one of the acidic protons.
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What is the isoelectric point (pI)?
The isoelectric point is the pH at which an amino acid has no net charge.
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To which titration term is the isoelectric point most similar?
The isoelectric point is most similar to the half-equivalence point.
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How to estimate the isoelectric point for neutral amino acids?
pIneutral = average of pKa-amine group and pKa-carboxyl group.
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How to estimate the isoelectric point for acidic amino acids?
pIacidic = average of pKa-acidic R group and pKa-carboxyl group.
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How to estimate the isoelectric point for basic amino acids?
pIbasic = average of pKa-amine group and pKa-basic R group.
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What is the reaction type for peptide bond formation?
Peptide bond formation involves dehydration synthesis and acyl substitution.
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What is the nucleophile in peptide bond formation?
The nucleophile is the amine group nitrogen from the new amino acid.
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What is the electrophile in peptide bond formation?
The electrophile is the carbonyl carbon on the C-terminus of the growing peptide chain.
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How are peptides synthesized?
Peptides are synthesized from N-terminus to C-terminus.
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What is the resonance structure of a peptide bond?
Peptide bonds have resonance between the C=O bond and the nitrogen lone pair, giving double bond character.
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What is the significance of double bond character in peptide bonds?
Double bond character results in a rigid peptide bond with limited rotation.
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What do trypsin and chymotrypsin cleave?
Trypsin cleaves at arginine and lysine; chymotrypsin cleaves at phenylalanine, tryptophan, and tyrosine.
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What happens to isoleucine at pH below its pKa for the α-carboxylic acid?
Isoleucine will be neutral (–COOH) with no charge, and the amino group will be fully protonated (–NH3+), giving a net charge of 1+.
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What is the charge on isoleucine when pH is below the pKa of its α-carboxylic acid?
The charge on isoleucine will be 1+.
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What is the primary structure of proteins?
The primary structure is the amino acid sequence of the protein.
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What is the secondary structure of proteins?
The secondary structure refers to the local three-dimensional configuration of the peptide chain, such as alpha helices.
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What is the primary structure of a protein?
The amino acid sequence of the protein.
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What is the secondary structure of a protein?
The local three-dimensional configuration of the peptide chain.
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What defines alpha helices in protein secondary structure?
Hydrogen bonding between carbonyl oxygens and amide hydrogens that are four residues apart.
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How do R groups orient in alpha helices?
R groups are directed away from the alpha helix cylinder, perpendicular to a tangent plane.
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What defines beta sheets in protein secondary structure?
Hydrogen bonding between carbonyl oxygens in one row and amide hydrogens in the adjacent row.
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How do R groups orient in beta sheets?
R groups are directed perpendicular to the plane of the beta sheet, on both sides.
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What conformation do beta sheets assume?
Beta sheets assume a pleated conformation necessary for hydrogen bonding.
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What is the role of proline in alpha helices?
Proline is usually the first residue at the end of an alpha helix but rarely found inside due to introducing a kink.
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What is a common application of alpha helices?
Keratin, found in hair and nails, is made of alpha helices.
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What is a common application of beta sheets?
Fibroin, the molecule that makes up silk, consists of beta sheets.
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What defines tertiary structure in proteins?
The geometric, three-dimensional folding of alpha helices, beta sheets, and other moieties.
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What is quaternary structure in proteins?
The association of multiple folded proteins into a multi-subunit complex.
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What is a classic example of quaternary structure?
Hemoglobin, consisting of four protein chains (two alpha and two beta subunits).
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What is the function of heme in hemoglobin?
Each subunit contains one heme capable of binding one O2 molecule.
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What is positive cooperativity in hemoglobin?
Ligand affinity increases with each subsequent ligand binding, enhancing oxygen affinity.
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Where are charged side chains typically found in globular proteins?
On the surface if not paired with a complementary molecule; can be inside if paired with opposite charge.
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What is the hydrophobic core of a globular protein?
Hydrophobic R groups fold into the interior to escape water, stabilizing the protein.
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What states can proteins be referred to during folding?
Globule (fully folded), molten globule (partially folded), or molten (fully unfolded).
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What drives protein folding?
Interactions between various molecular forces and the hydrophobic effect.
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What do groups in a globular protein do to escape water?
They fold into the interior of the protein.
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What types of –R groups are found on the surface of a globular protein?
They are either polar or charged.
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What role do electrostatic interactions play in protein folding?
They encourage folding and stabilize the protein in its folded state.
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How do hydrogen bonds contribute to protein folding?
They encourage folding and stabilize the folded protein.
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What forms a disulfide bond in proteins?
Two oxidized cysteine residues form a disulfide (R-S-S-R) bond.
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What is the significance of disulfide bonds in keratin?
They determine how curly hair can be.
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What are salt bridges in proteins?
They are formed when acidic and basic –R groups undergo a neutralization reaction, resulting in a salt.
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What is the role of proline in protein structure?
Proline can disrupt 2° structure or contribute to 3° structure; it is often found at the beginning of α-helices and in turns of β-sheets.
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What is a solvation layer?
It is a layer of water that surrounds a dissolved protein, interacting closely with the protein's surface.
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How does entropy relate to protein folding?
Transitioning from solvation of non-polar regions to a polar protein surface increases entropy, contributing to protein stability.
As proteins fold, entropy decreases.
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What agents can cause protein denaturation?
Acid, heat, urea, and mercaptoethanol.
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What techniques are used for protein separation?
Isoelectric point and electrophoresis.
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What is the central dogma's relationship to protein functions?
The central dogma is important, but proteins also have other significant functions that are often tested on the MCAT.
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Where is calmodulin synthesized in the cell?
In the cytoplasm, as calmodulin is a protein coded by DNA.
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What must all proteins in the cell have been coded for?
DNA.
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List examples of binding proteins.
Hemoglobin, calmodulin, troponin, tropomyosin, histones, transcription factors, cell adhesion molecules.
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What are the components of the immune system?
Antigens and antibodies.
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Give examples of structural proteins.
Actin, tubulin, keratin, elastin.
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What is the role of myosin in cells?
Power stroke and cellular transport.
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What do kinesins transport?
They move along microtubules from the (—) to (+) end.
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What direction do dyneins move along microtubules?
From the (+) to (—) end.
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What are enzymes?
Biological catalysts that increase reaction rates and lower activation energy.
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How do enzymes affect thermodynamic properties of reactions?
They do not alter thermodynamic properties.
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What is the relationship between enzymes and proteins?
All enzymes are proteins, unless stated otherwise.
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What is the role of cofactors in enzyme activity?
They are required by enzymes to function.
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What are coenzymes?
Non-protein species required by enzymes, not permanently attached.
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What do ligases do?
They add or synthesize large molecules, usually ATP-dependent.
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What are oxidoreductases involved in?
REDOX reactions.
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What do hydrolases catalyze?
Hydrolysis reactions.
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What is the mnemonic for remembering enzyme function?
Enzymes help reactions Over The HILL (Energy of Activation).
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What are the two theories of enzyme specificity?
Lock and Key model and Induced Fit model; Lock and Key has been largely dismissed.
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What factors affect enzyme activity?
pH, temperature, substrate concentration, and enzyme concentration.
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What are coenzymes?
Non-protein species NOT permanently attached to the enzyme but required by the enzyme to function.
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What are prosthetic groups?
Non-protein species that ARE permanently attached to the enzyme and are required by the enzyme to function.
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What is a simple protein?
A protein that contains only amino acids and no non-protein cofactors or prosthetic groups. If an enzyme, it is called an apoenzyme.
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What is a conjugated protein?
A protein associated with its cofactors, either covalently or via intermolecular attractions. Hemoglobin is an example.
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What is a holoenzyme?
A conjugated protein that, together with its cofactors, functions as an enzyme.
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What are fat-soluble vitamins?
Vitamins A, D, E, and K.
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What are water-soluble vitamins?
All vitamins that are not fat-soluble.
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Why can a person more easily overdose on fat-soluble vitamins?
Fat-soluble vitamins are stored in body fat and can accumulate to toxic levels, unlike water-soluble vitamins which are excreted more easily.
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What are the differences between vitamins and minerals?
Vitamins are organic compounds required in small amounts, while minerals are inorganic elements essential for various biological functions.
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What is the Michaelis-Menten (M-M) saturation curve?
A graph of reaction velocity vs. substrate concentration [S] that reveals the relationship between ½vmax and Km, illustrating saturation kinetics.
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What does Vmax represent in enzyme kinetics?
The maximum reaction velocity achieved by the enzyme when the substrate concentration is saturated.
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What does Km represent in enzyme kinetics?
The substrate concentration at which the reaction velocity is half of Vmax; it is a measure of the enzyme's affinity for its substrate.
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What is the Michaelis-Menten equation?
The relationship between reaction velocity, Km, and substrate concentration: V = Vmax[S]/(Km + [S]).
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What is the significance of Km being equal to [S] at ½Vmax?
It indicates that at half the maximum velocity, the substrate concentration is equal to the Michaelis constant, reflecting enzyme affinity.
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What are Lineweaver-Burk plots used for?
They are used to calculate Vmax and Km experimentally and to identify enzyme inhibition by analyzing changes in these parameters.
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What is reversible inhibition?
Inhibitor is not permanently bound; the enzyme is not completely disabled, allowing for potential recovery of function.
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What happens in competitive inhibition?
The inhibitor binds at the active site, resembling the substrate. Vmax remains unchanged, while Km increases.
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What happens in uncompetitive inhibition?
The inhibitor binds only to the enzyme-substrate complex, decreasing both Vmax and Km.
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What happens in non-competitive inhibition?
The inhibitor binds away from the active site, altering enzyme shape. Vmax decreases while Km remains unchanged.
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What happens to Vmax and Km in competitive inhibition?
Vmax = DECREASES; Km = NO CHANGE
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What happens to Vmax and Km in mixed inhibition?
Vmax = DECREASES; Km = DECREASES if inhibitor favors E-S; Km = INCREASES if inhibitor favors E.
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What is irreversible inhibition?
Inhibitor binds covalently to enzyme, disabling it for a prolonged period or permanently.
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What is feedback inhibition?
A type of non-competitive or allosteric inhibition where a product inhibits an earlier enzyme in a multi-step reaction.
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What is positive feedback? Provide a human body example.
A process where the output enhances the original stimulus. Example: oxytocin during childbirth.
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What are zymogens? Provide a human body example.
Inactive enzyme precursors activated by cleavage. Example: pepsinogen to pepsin.
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What are allosteric enzymes? Provide a human body example.
Enzymes that change shape upon binding of an effector, affecting activity. Example: phosphofructokinase.
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What is the empirical formula of monosaccharides?
(CH2O)n
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What prefix indicates a deoxysugar?
'deoxy-' indicates replacement of an -OH group with hydrogen.
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What distinguishes aldose from ketose?
Aldose contains an aldehyde group while ketose contains a ketone group.
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What are common monosaccharides for the MCAT?
Glyceraldehyde, dihydroxyacetone, ribose, deoxyribose, glucose, fructose, galactose, mannose.
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What are common disaccharides?
Lactose (galactose + glucose), maltose (glucose + glucose), sucrose (glucose + fructose).
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What is the difference between pyranose and furanose?
Pyranose is a 6-membered ring; furanose is a 5-membered ring.
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What are hemiacetals and hemiketals?
Hemiacetals are cyclical aldehydes; hemiketals are cyclical ketones.
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What happens to Vmax and Km with noncompetitive inhibitors?
Vmax = DECREASES; Km = NO CHANGE.
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What is the effect of irreversible inhibitors on enzymes?
They bind covalently, permanently disabling the enzyme.
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What is the outcome of a Lineweaver-Burk plot for a noncompetitive inhibitor?
The new curve is below existing curves with a lower Vmax.
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What is the outcome of a Reaction Rate vs. Substrate Concentration graph with an irreversible inhibitor?
The graph shows decreased reaction rate compared to no inhibitor, affecting Vmax.
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What are the two types of cyclic structures in hexoses?
Pyranose (6-member ring) and Furanose (5-member ring).
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What is the difference between hemiacetals and hemiketals?
Hemiacetals are cyclical aldehydes, while hemiketals are cyclical ketones.
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What is the difference between R/S and D-/L configurations?
R and S are not the same as D- and L; D-sugars are found in humans, L-sugars are not.
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What are D-sugars?
D-sugars are all sugars found in the human body.
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What distinguishes D-glucose from L-glucose?
D-glucose has the furthest -OH group from the carbonyl on the RIGHT; L-glucose has it on the LEFT in Fischer projection.
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What are anomers?
Anomers are the same molecule with different stereochemistry at the anomeric carbon, e.g., α-glucose vs. β-glucose.
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What are epimers?
Epimers are different molecules that are a type of diastereomers, e.g., glucose vs. galactose.
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What is the process of ring-closing in carbohydrates?
Intramolecular nucleophilic substitution occurs when the -OH group on the chiral carbon attacks the carbonyl carbon.
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What is the hydrolysis of the glycoside linkage?
Polymer(n) + H2O → Polymer(n-1) + monomer.
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What is keto-enol tautomerism in monosaccharides?
Sugars can alternate between keto and enol forms, similar to other ketones and aldehydes.
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How do monosaccharides polymerize?
Monosaccharides combine to form disaccharides and then polysaccharides.
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What is the difference between α-linkage and β-linkage in polysaccharides?
α-linkage is trans (opposite side of CH2OH), while β-linkage is cis (same side as CH2OH).
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What is glycogen?
Glycogen is a branched, α-linked glucose polymer used for energy storage in animals.
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What is starch?
Starch is a branched, α-linked glucose polymer used for energy storage in plants.
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What is cellulose?
Cellulose is a β-linked glucose polymer used for energy storage in plants, indigestible to animals without symbiotic bacteria.
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What defines lipids?
Lipids are biomolecules that are hydrophobic and include fats, oils, waxes, and more.
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What are the two major characteristics of lipids?
1) Lipids are biomolecules; 2) Lipids are hydrophobic.
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What are fatty acids?
Fatty acids are carboxylic acids with long hydrocarbon chains, important components of lipids.
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What are triacylglycerols?
Triacylglycerols (triglycerides) consist of a glycerol backbone with three fatty acids attached via ester linkages.
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What is the difference between saturated and unsaturated fats?
Saturated fats have no double bonds; unsaturated fats have one or more double bonds, generally healthier.
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What are phospholipids?
Phospholipids are lipids with two fatty acid moieties and a phosphate group attached to a glycerol backbone.
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What is the structure of the most basic phospholipid?
The most basic phospholipid, phosphatid, has two fatty acids and a phosphate group attached to glycerol.
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What is the most basic phospholipid?
Phosphatid, with two fatty acid moieties and a phosphate group attached to the glycerol backbone.
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What is saponification?
The hydrolysis of an ester, such as triglycerides or phospholipids.
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What are triacylglycerols and phospholipids classified as?
Both are classified as esters.
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What is the structure of all steroids?
All steroids are 4-member ring structures.
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What are prostaglandins?
Lipid mediators with autocrine and paracrine functions throughout the body.
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How do prostaglandins differ from endocrine hormones?
Prostaglandins are produced and released throughout the body and act locally, unlike endocrine hormones.
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Which lipids are amphipathic?
Fatty acids, phospholipids, and glycolipids are amphipathic lipids.
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How many unique proteins can be formed from four amino acids without repetition?
24 unique proteins can be formed, using n!, or 432*1
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What is the factorial method for calculating unique protein formations?
The factorial method is n! where n is the number of unique items.
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What is the significance of the N-terminus and C-terminus in proteins?
Peptide order matters; A-B-C is not the same as C-B-A due to N-terminus and C-terminus distinction.
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What is the 21st amino acid in the common amino acid chart?
Selenocysteine is the 21st amino acid.
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What is the total number of common amino acids?
20 common amino acids plus Selenocysteine as the 21st.
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What is unique about Selenocysteine?
It is proteinogenic but not coded for by DNA.
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How is Selenocysteine incorporated during protein synthesis?
The DNA codes for a translation factor that causes the ribosome to insert Selenocysteine for a STOP codon.
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Why might MCAT authors highlight Selenocysteine?
Due to its unique incorporation mechanism as a proteinogenic amino acid.
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What are proteins made of?
Proteins are polymers of amino acids; amino acids are often called residues. Oligopeptides are very small chains of amino acids, while polypeptides are longer chains.
What is the alpha-carbon stereocenter in amino acids?
All human amino acids, except one, are chiral at the alpha carbon due to having four different substituents: an -R group, hydrogen, carboxylic acid, and amine.
How are amino acids designated in terms of configuration?
Amino acids are designated as L- or D- based on the position of the amine group in a Fischer Projection. L means Left and D means Right. All native human amino acids are L-amino acids.
Do L- and D- configurations correlate with R and S?
L- and D- do not correlate directly with R and S. Most L-amino acids are S, but some, like cysteine, are R.
What determines the chemistry of amino acids?
The -R groups of amino acids largely determine their chemistry. The combination of -R groups in a protein determines its chemistry and folding pattern.
How do -R groups affect substrate binding?
Substrate binding in an active site depends on complementary charges on the -R groups and their hydrophilicity or hydrophobicity.
How do hydrophobic and hydrophilic -R groups affect protein folding?
Hydrophobic -R groups fold into the protein core, while hydrophilic -R groups are more common on the surface. Low hydrophobicity proteins may not fold into stable structures but can retain function.
What determines reaction mechanisms in enzyme pockets?
Reaction mechanisms in enzyme pockets are determined by the chemistry of the -R groups present in that pocket.
What should you consider when thinking about proteins or enzymes?
Consider the amino acids present and the chemistry of their -R groups.
What knowledge is required for the MCAT regarding amino acids?
You must know amino acid -R group structure, chemistry, hydrophilicity vs. hydrophobicity, charges, aromatic properties, names, three-letter and single-letter abbreviations.
What is the importance of semantic processing in studying amino acids?
Engaging in semantic processing helps in understanding and remembering amino acids better by identifying their real-life functions and commonalities, rather than rote memorization.
What is suggested for learning about amino acids effectively?
Learn one real-life function for each amino acid -R group to help remember its structure and properties more easily.
What are the three-letter and one-letter abbreviations for amino acids?
Three-letter: Ala (A), Arg (R), Asn (N), Asp (D), Cys (C), Gln (Q), Glu (E), Gly (G), His (H), Ile (I), Leu (L), Lys (K), Met (M), Phe (F), Pro (P), Ser (S), Thr (T), Trp (W), Tyr (Y), Val (V). One-letter: A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V.
What are logical stabilizing features for an enzyme pocket based on substrate charge?
a) Positively charged: acidic amino acids (Asp, Glu). b) Negatively charged: basic amino acids (Lys, Arg). c) Polar: polar amino acids (Ser, Thr, Asn, Gln). d) Non-polar: non-polar amino acids (Ala, Val, Leu, Ile, Met, Phe).
What is the role of 5-HTT in the central nervous system?
5-HTT is a monoamine transport protein responsible for the reuptake of serotonin from synapses.
Which amino acid does 5-HTT have a high affinity for?
Tryptophan (Trp).
What amino acids have charged R groups?
Aspartic acid (Asp), Glutamic acid (Glu), Lysine (Lys), Arginine (Arg), Histidine (His).
What is a zwitterion?
A zwitterion is a dipolar version of an amino acid where positively and negatively charged functional groups cancel each other out, resulting in a neutral ion.
What is the order of deprotonation for amino acids?
1) α-COOH Group (pKa ~ 2), 2) -R Group, ACIDIC (pKa ~ 4), 3) -R Group, His (pKa ~ 6), 4) α-NH3+ Group (pKa ~ 9), 5) -R Group, BASIC (pKa ~ 11-12).
What is the conceptual definition of isoelectric point?
The isoelectric point is the pH at which an amino acid or protein carries no net electrical charge, making it less soluble in solution.
What is the acid-base functionality of amino acids?
Amino acids are weak acids with at least two acidic protons: -COOH and -NH3+. Some have acidic side chains, resulting in three acidic protons.
What is the significance of pKa values in amino acids?
pKa values predict the order in which acidic functional groups of an amino acid will be deprotonated and indicate buffering capacity near pKa.
What are essential amino acids?
Essential amino acids cannot be synthesized by the body and must be ingested through diet.
What are non-essential amino acids?
Non-essential amino acids can be synthesized by the body and do not need to be ingested.
What is the role of amino acids as buffers?
Amino acids act as buffers when the pH is near the pKa of one of the acidic protons.
What is the isoelectric point (pI)?
The isoelectric point is the pH at which an amino acid has no net charge.
To which titration term is the isoelectric point most similar?
The isoelectric point is most similar to the half-equivalence point.
How to estimate the isoelectric point for neutral amino acids?
pIneutral = average of pKa-amine group and pKa-carboxyl group.
How to estimate the isoelectric point for acidic amino acids?
pIacidic = average of pKa-acidic R group and pKa-carboxyl group.
How to estimate the isoelectric point for basic amino acids?
pIbasic = average of pKa-amine group and pKa-basic R group.
What is the reaction type for peptide bond formation?
Peptide bond formation involves dehydration synthesis and acyl substitution.
What is the nucleophile in peptide bond formation?
The nucleophile is the amine group nitrogen from the new amino acid.
What is the electrophile in peptide bond formation?
The electrophile is the carbonyl carbon on the C-terminus of the growing peptide chain.
How are peptides synthesized?
Peptides are synthesized from N-terminus to C-terminus.
What is the resonance structure of a peptide bond?
Peptide bonds have resonance between the C=O bond and the nitrogen lone pair, giving double bond character.
What is the significance of double bond character in peptide bonds?
Double bond character results in a rigid peptide bond with limited rotation.
What do trypsin and chymotrypsin cleave?
Trypsin cleaves at arginine and lysine; chymotrypsin cleaves at phenylalanine, tryptophan, and tyrosine.
What happens to isoleucine at pH below its pKa for the α-carboxylic acid?
Isoleucine will be neutral (–COOH) with no charge, and the amino group will be fully protonated (–NH3+), giving a net charge of 1+.
What is the charge on isoleucine when pH is below the pKa of its α-carboxylic acid?
The charge on isoleucine will be 1+.
What is the primary structure of proteins?
The primary structure is the amino acid sequence of the protein.
What is the secondary structure of proteins?
The secondary structure refers to the local three-dimensional configuration of the peptide chain, such as alpha helices.
What is the primary structure of a protein?
The amino acid sequence of the protein.
What is the secondary structure of a protein?
The local three-dimensional configuration of the peptide chain.
What defines alpha helices in protein secondary structure?
Hydrogen bonding between carbonyl oxygens and amide hydrogens that are four residues apart.
How do R groups orient in alpha helices?
R groups are directed away from the alpha helix cylinder, perpendicular to a tangent plane.
What defines beta sheets in protein secondary structure?
Hydrogen bonding between carbonyl oxygens in one row and amide hydrogens in the adjacent row.
How do R groups orient in beta sheets?
R groups are directed perpendicular to the plane of the beta sheet, on both sides.
What conformation do beta sheets assume?
Beta sheets assume a pleated conformation necessary for hydrogen bonding.
What is the role of proline in alpha helices?
Proline is usually the first residue at the end of an alpha helix but rarely found inside due to introducing a kink.
What is a common application of alpha helices?
Keratin, found in hair and nails, is made of alpha helices.
What is a common application of beta sheets?
Fibroin, the molecule that makes up silk, consists of beta sheets.
What defines tertiary structure in proteins?
The geometric, three-dimensional folding of alpha helices, beta sheets, and other moieties.
What is quaternary structure in proteins?
The association of multiple folded proteins into a multi-subunit complex.
What is a classic example of quaternary structure?
Hemoglobin, consisting of four protein chains (two alpha and two beta subunits).
What is the function of heme in hemoglobin?
Each subunit contains one heme capable of binding one O2 molecule.
What is positive cooperativity in hemoglobin?
Ligand affinity increases with each subsequent ligand binding, enhancing oxygen affinity.
Where are charged side chains typically found in globular proteins?
On the surface if not paired with a complementary molecule; can be inside if paired with opposite charge.
What is the hydrophobic core of a globular protein?
Hydrophobic R groups fold into the interior to escape water, stabilizing the protein.
What states can proteins be referred to during folding?
Globule (fully folded), molten globule (partially folded), or molten (fully unfolded).
What drives protein folding?
Interactions between various molecular forces and the hydrophobic effect.
What do groups in a globular protein do to escape water?
They fold into the interior of the protein.
What types of –R groups are found on the surface of a globular protein?
They are either polar or charged.
What role do electrostatic interactions play in protein folding?
They encourage folding and stabilize the protein in its folded state.
How do hydrogen bonds contribute to protein folding?
They encourage folding and stabilize the folded protein.
What forms a disulfide bond in proteins?
Two oxidized cysteine residues form a disulfide (R-S-S-R) bond.
What is the significance of disulfide bonds in keratin?
They determine how curly hair can be.
What are salt bridges in proteins?
They are formed when acidic and basic –R groups undergo a neutralization reaction, resulting in a salt.
What is the role of proline in protein structure?
Proline can disrupt 2° structure or contribute to 3° structure; it is often found at the beginning of α-helices and in turns of β-sheets.
What is a solvation layer?
It is a layer of water that surrounds a dissolved protein, interacting closely with the protein's surface.
How does entropy relate to protein folding?
Transitioning from solvation of non-polar regions to a polar protein surface increases entropy, contributing to protein stability.
As proteins fold, entropy decreases.
What agents can cause protein denaturation?
Acid, heat, urea, and mercaptoethanol.
What techniques are used for protein separation?
Isoelectric point and electrophoresis.
What is the central dogma's relationship to protein functions?
The central dogma is important, but proteins also have other significant functions that are often tested on the MCAT.
Where is calmodulin synthesized in the cell?
In the cytoplasm, as calmodulin is a protein coded by DNA.
What must all proteins in the cell have been coded for?
DNA.
List examples of binding proteins.
Hemoglobin, calmodulin, troponin, tropomyosin, histones, transcription factors, cell adhesion molecules.
What are the components of the immune system?
Antigens and antibodies.
Give examples of structural proteins.
Actin, tubulin, keratin, elastin.
What is the role of myosin in cells?
Power stroke and cellular transport.
What do kinesins transport?
They move along microtubules from the (—) to (+) end.
What direction do dyneins move along microtubules?
From the (+) to (—) end.
What are enzymes?
Biological catalysts that increase reaction rates and lower activation energy.
How do enzymes affect thermodynamic properties of reactions?
They do not alter thermodynamic properties.
What is the relationship between enzymes and proteins?
All enzymes are proteins, unless stated otherwise.
What is the role of cofactors in enzyme activity?
They are required by enzymes to function.
What are coenzymes?
Non-protein species required by enzymes, not permanently attached.
What do ligases do?
They add or synthesize large molecules, usually ATP-dependent.
What are oxidoreductases involved in?
REDOX reactions.
What do hydrolases catalyze?
Hydrolysis reactions.
What is the mnemonic for remembering enzyme function?
Enzymes help reactions Over The HILL (Energy of Activation).
What are the two theories of enzyme specificity?
Lock and Key model and Induced Fit model; Lock and Key has been largely dismissed.
What factors affect enzyme activity?
pH, temperature, substrate concentration, and enzyme concentration.
What are coenzymes?
Non-protein species NOT permanently attached to the enzyme but required by the enzyme to function.
What are prosthetic groups?
Non-protein species that ARE permanently attached to the enzyme and are required by the enzyme to function.
What is a simple protein?
A protein that contains only amino acids and no non-protein cofactors or prosthetic groups. If an enzyme, it is called an apoenzyme.
What is a conjugated protein?
A protein associated with its cofactors, either covalently or via intermolecular attractions. Hemoglobin is an example.
What is a holoenzyme?
A conjugated protein that, together with its cofactors, functions as an enzyme.
What are fat-soluble vitamins?
Vitamins A, D, E, and K.
What are water-soluble vitamins?
All vitamins that are not fat-soluble.
Why can a person more easily overdose on fat-soluble vitamins?
Fat-soluble vitamins are stored in body fat and can accumulate to toxic levels, unlike water-soluble vitamins which are excreted more easily.
What are the differences between vitamins and minerals?
Vitamins are organic compounds required in small amounts, while minerals are inorganic elements essential for various biological functions.
What is the Michaelis-Menten (M-M) saturation curve?
A graph of reaction velocity vs. substrate concentration [S] that reveals the relationship between ½vmax and Km, illustrating saturation kinetics.
What does Vmax represent in enzyme kinetics?
The maximum reaction velocity achieved by the enzyme when the substrate concentration is saturated.
What does Km represent in enzyme kinetics?
The substrate concentration at which the reaction velocity is half of Vmax; it is a measure of the enzyme's affinity for its substrate.
What is the Michaelis-Menten equation?
The relationship between reaction velocity, Km, and substrate concentration: V = Vmax[S]/(Km + [S]).
What is the significance of Km being equal to [S] at ½Vmax?
It indicates that at half the maximum velocity, the substrate concentration is equal to the Michaelis constant, reflecting enzyme affinity.
What are Lineweaver-Burk plots used for?
They are used to calculate Vmax and Km experimentally and to identify enzyme inhibition by analyzing changes in these parameters.
What is reversible inhibition?
Inhibitor is not permanently bound; the enzyme is not completely disabled, allowing for potential recovery of function.
What happens in competitive inhibition?
The inhibitor binds at the active site, resembling the substrate. Vmax remains unchanged, while Km increases.
What happens in uncompetitive inhibition?
The inhibitor binds only to the enzyme-substrate complex, decreasing both Vmax and Km.
What happens in non-competitive inhibition?
The inhibitor binds away from the active site, altering enzyme shape. Vmax decreases while Km remains unchanged.
What happens to Vmax and Km in competitive inhibition?
Vmax = DECREASES; Km = NO CHANGE
What happens to Vmax and Km in mixed inhibition?
Vmax = DECREASES; Km = DECREASES if inhibitor favors E-S; Km = INCREASES if inhibitor favors E.
What is irreversible inhibition?
Inhibitor binds covalently to enzyme, disabling it for a prolonged period or permanently.
What is feedback inhibition?
A type of non-competitive or allosteric inhibition where a product inhibits an earlier enzyme in a multi-step reaction.
What is positive feedback? Provide a human body example.
A process where the output enhances the original stimulus. Example: oxytocin during childbirth.
What are zymogens? Provide a human body example.
Inactive enzyme precursors activated by cleavage. Example: pepsinogen to pepsin.
What are allosteric enzymes? Provide a human body example.
Enzymes that change shape upon binding of an effector, affecting activity. Example: phosphofructokinase.
What is the empirical formula of monosaccharides?
(CH2O)n
What prefix indicates a deoxysugar?
'deoxy-' indicates replacement of an -OH group with hydrogen.
What distinguishes aldose from ketose?
Aldose contains an aldehyde group while ketose contains a ketone group.
What are common monosaccharides for the MCAT?
Glyceraldehyde, dihydroxyacetone, ribose, deoxyribose, glucose, fructose, galactose, mannose.
What are common disaccharides?
Lactose (galactose + glucose), maltose (glucose + glucose), sucrose (glucose + fructose).
What is the difference between pyranose and furanose?
Pyranose is a 6-membered ring; furanose is a 5-membered ring.
What are hemiacetals and hemiketals?
Hemiacetals are cyclical aldehydes; hemiketals are cyclical ketones.
What happens to Vmax and Km with noncompetitive inhibitors?
Vmax = DECREASES; Km = NO CHANGE.
What is the effect of irreversible inhibitors on enzymes?
They bind covalently, permanently disabling the enzyme.
What is the outcome of a Lineweaver-Burk plot for a noncompetitive inhibitor?
The new curve is below existing curves with a lower Vmax.
What is the outcome of a Reaction Rate vs. Substrate Concentration graph with an irreversible inhibitor?
The graph shows decreased reaction rate compared to no inhibitor, affecting Vmax.
What are the two types of cyclic structures in hexoses?
Pyranose (6-member ring) and Furanose (5-member ring).
What is the difference between hemiacetals and hemiketals?
Hemiacetals are cyclical aldehydes, while hemiketals are cyclical ketones.
What is the difference between R/S and D-/L configurations?
R and S are not the same as D- and L; D-sugars are found in humans, L-sugars are not.
What are D-sugars?
D-sugars are all sugars found in the human body.
What distinguishes D-glucose from L-glucose?
D-glucose has the furthest -OH group from the carbonyl on the RIGHT; L-glucose has it on the LEFT in Fischer projection.
What are anomers?
Anomers are the same molecule with different stereochemistry at the anomeric carbon, e.g., α-glucose vs. β-glucose.
What are epimers?
Epimers are different molecules that are a type of diastereomers, e.g., glucose vs. galactose.
What is the process of ring-closing in carbohydrates?
Intramolecular nucleophilic substitution occurs when the -OH group on the chiral carbon attacks the carbonyl carbon.
What is the hydrolysis of the glycoside linkage?
Polymer(n) + H2O → Polymer(n-1) + monomer.
What is keto-enol tautomerism in monosaccharides?
Sugars can alternate between keto and enol forms, similar to other ketones and aldehydes.
How do monosaccharides polymerize?
Monosaccharides combine to form disaccharides and then polysaccharides.
What is the difference between α-linkage and β-linkage in polysaccharides?
α-linkage is trans (opposite side of CH2OH), while β-linkage is cis (same side as CH2OH).
What is glycogen?
Glycogen is a branched, α-linked glucose polymer used for energy storage in animals.
What is starch?
Starch is a branched, α-linked glucose polymer used for energy storage in plants.
What is cellulose?
Cellulose is a β-linked glucose polymer used for energy storage in plants, indigestible to animals without symbiotic bacteria.
What defines lipids?
Lipids are biomolecules that are hydrophobic and include fats, oils, waxes, and more.
What are the two major characteristics of lipids?
1) Lipids are biomolecules; 2) Lipids are hydrophobic.
What are fatty acids?
Fatty acids are carboxylic acids with long hydrocarbon chains, important components of lipids.
What are triacylglycerols?
Triacylglycerols (triglycerides) consist of a glycerol backbone with three fatty acids attached via ester linkages.
What is the difference between saturated and unsaturated fats?
Saturated fats have no double bonds; unsaturated fats have one or more double bonds, generally healthier.
What are phospholipids?
Phospholipids are lipids with two fatty acid moieties and a phosphate group attached to a glycerol backbone.
What is the structure of the most basic phospholipid?
The most basic phospholipid, phosphatid, has two fatty acids and a phosphate group attached to glycerol.
What is the most basic phospholipid?
Phosphatid, with two fatty acid moieties and a phosphate group attached to the glycerol backbone.
What is saponification?
The hydrolysis of an ester, such as triglycerides or phospholipids.
What are triacylglycerols and phospholipids classified as?
Both are classified as esters.
What is the structure of all steroids?
All steroids are 4-member ring structures.
What are prostaglandins?
Lipid mediators with autocrine and paracrine functions throughout the body.
How do prostaglandins differ from endocrine hormones?
Prostaglandins are produced and released throughout the body and act locally, unlike endocrine hormones.
Which lipids are amphipathic?
Fatty acids, phospholipids, and glycolipids are amphipathic lipids.
How many unique proteins can be formed from four amino acids without repetition?
24 unique proteins can be formed, using n!, or 432*1
What is the factorial method for calculating unique protein formations?
The factorial method is n! where n is the number of unique items.
What is the significance of the N-terminus and C-terminus in proteins?
Peptide order matters; A-B-C is not the same as C-B-A due to N-terminus and C-terminus distinction.
What is the 21st amino acid in the common amino acid chart?
Selenocysteine is the 21st amino acid.
What is the total number of common amino acids?
20 common amino acids plus Selenocysteine as the 21st.
What is unique about Selenocysteine?
It is proteinogenic but not coded for by DNA.
How is Selenocysteine incorporated during protein synthesis?
The DNA codes for a translation factor that causes the ribosome to insert Selenocysteine for a STOP codon.
Why might MCAT authors highlight Selenocysteine?
Due to its unique incorporation mechanism as a proteinogenic amino acid.
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