MCAT

The Bio/Biochem section tests how living systems work at every level, from the chemistry of amino acids and enzymes to the integrated function of organ systems. Expect passages built on experiments and data: you will need to recall core facts quickly and apply them to unfamiliar scenarios.

Amino Acids and Proteins

Amino acids are the building blocks of proteins. Each contains an amino group, a carboxyl group, a hydrogen atom, and a distinctive R group (side chain) attached to a central alpha carbon. The R group determines the chemical properties of each amino acid. Twenty standard amino acids are encoded by the genetic code, classified by their R groups:

The20Standardaminoacidsbyside-Chainclass

Class	AminoAcids
Nonpolaraliphatic	Glycine alanine valine leucine isoleucine methionine proline , , , , , ,
Aromatic	Phenylalanine tyrosine tryptophan , ,
Polaruncharged	Serine threonine cysteine asparagine glutamine , , , ,
Positivelycharged(basic)	Lysine arginine histidine , ,
Negativelycharged(acidic)	Aspartate glutamate ,

At physiological pH, amino acids exist as zwitterions, carrying both positive and negative charges. The isoelectric point (pI) is the pH at which an amino acid has no net charge.

NeutralAminoAcids					AcidicAminoAcids					BasicAminoAcids
pI = average of pK a1 and pK a2					pI = average of pK a1 and pK aR					pI = average of pK a2 and pK aR

Peptide bonds form between the carboxyl group of one amino acid and the amino group of another through a dehydration reaction. Resonance gives the peptide bond partial double-bond character, making it planar and rigid; it is typically in the trans configuration.

Level	Description	StabilizedBy
Primary	Linearsequenceofaminoacids	Peptide(covalent)bonds
Secondary	Localfolding:alphahelicesandbetasheets	Hydrogenbondsbetweenbackboneatoms Inanalphahelix .
		(right-handed coil) the carbonyl oxygen of residue n bonds the ,
		amidehydrogenofresiduen+4;betasheetsareextended
Tertiary Quaternary	Overall3-Dshapeofonepolypeptide Arrangementofmultiplepolypeptide subunits	strandsinparallelorantiparallelorientation 1 Hydrophobicinteractions hydrogenbonds ionicbonds , , , disulfidebridges andvanderWaalsforces , Thesamenoncovalentforcesanddisulfidebondsbetween subunits

Protein folding is driven primarily by the hydrophobic effect, which buries nonpolar residues in the protein interior. Chaperone proteins assist proper folding and prevent aggregation; misfolded proteins can form aggregates associated with diseases such as Alzheimer's and prion diseases. Denaturation is the loss of secondary, tertiary, and quaternary structure while primary structure remains intact. Denaturing agents include heat, extreme pH, organic solvents, detergents, and heavy metals, and denaturation may be reversible or irreversible depending on conditions.

Enzymes

Enzymes are biological catalysts that accelerate reactions without being consumed. Most are proteins, though some RNA molecules (ribozymes) are catalytic. Enzymes lower activation energy by stabilizing the transition state; they do not change ΔG or the equilibrium position. Substrate binding and catalysis occur at the active site. The lock-and-key model proposes rigid complementarity between enzyme and substrate, while the induced-fit model proposes that binding induces conformational changes that optimize the interaction.

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

Vmax is the maximum velocity when the enzyme is saturated. Km is the substrate concentration at half-maximal velocity and reflects affinity: a lower Km means higher affinity.

1/v = (Km/Vmax)(1/[S]) + 1/Vmax

y-intercept = 1/Vmax · x-intercept = −1/Km · slope = Km/Vmax

Inhibitor	Binds	K m	V max	Lineweaver-Burk Signature
Competitive	Activesite;competeswithsubstrate	Increases	Unchanged	Lines cross on the y-
				axis
Noncompetitive	Allostericsite regardlessofsubstrate ,	Unchanged	Decreases	Lines cross on the x-
	binding			axis
Uncompetitive	Only the enzyme-substrate complex	Decreases	Decreases	Parallellines
Mixed	FreeenzymeandEScomplex with ,	Increasesor	Decreases	Linescrossoffboth
	differentaffinities	decreases		axes

Carbohydrates

Carbohydrates are polyhydroxy aldehydes (aldoses) or ketones (ketoses), classified by carbon number: trioses (3C), tetroses (4C), pentoses (5C), hexoses (6C), and heptoses (7C). D and L designations refer to the configuration at the highest-numbered chiral carbon, and most biological sugars are D-isomers. Epimers differ at only one chiral center; anomers differ at the hemiacetal or hemiketal carbon (the anomeric carbon).

Cyclization forms hemiacetals (from aldoses) or hemiketals (from ketoses). Six-membered rings are pyranoses and five- membered rings are furanoses. In glucose, the anomeric hydroxyl is axial in the alpha anomer and equatorial in the beta anomer.

Sugar	Composition	Notes
Glucose	Aldohexose	Primarycellularfuel
Fructose	Ketohexose	Abundantinfruits
Galactose	Aldohexose	C4epimerofglucose
Mannose	Aldohexose	C2epimerofglucose
Ribose Maltose Lactose	Aldopentose Glucose+glucose Galactose+glucose	SugarcomponentofRNA α-1 ,4 linkage; reducing sugar β-1 ,4 linkage; reducing sugar	1

Keysugarsandglycosidiclinkages(Continued)

Sugar	Composition	Notes
Sucrose	Glucose+fructose	α-1 ,β-2 linkage; not reducing because both anomeric carbons are in ,
		theglycosidicbond
Starch	Amyloseandamylopectin	Plantstoragepolysaccharide
Glycogen	Glucosepolymer	Animal storage; highly branched α-1 ,4 linkages with α-1 ,6 branch ,
		points
Cellulose	Glucosepolymer	Plant cell walls; β-1 ,4 linkages that humans cannot digest

Reducing sugars have a free anomeric carbon that can open to the aldehyde or ketone form and reduce oxidizing agents. Glucose, fructose, maltose, and lactose are reducing sugars.

Lipids

Lipids are hydrophobic or amphipathic molecules that include fats, phospholipids, steroids, and fat-soluble vitamins. Fatty acids are carboxylic acids with long hydrocarbon chains. Saturated fatty acids have no double bonds and pack tightly; unsaturated fatty acids have one or more double bonds, usually cis, creating kinks that reduce packing. The essential fatty acids (linoleic and linolenic acid) must be obtained from the diet.

Glycerol esterified to three fatty acids. They store energy and

Amphipathic: polar head, nonpolar tails. Glycerophospholipids

provide more energy per gram than carbohydrates because

(head groups choline, serine, ethanolamine, inositol) have a

they are more reduced.

glycerol backbone; sphingolipids have a sphingosine backbone.

Lipoprotein	Function
Chylomicrons	Transportdietarylipidsfromtheintestine
VLDL	Transportstriglyceridesfromtheliver
LDL	Deliverscholesteroltotissues
HDL	Removesexcesscholesterolfromtissuesforexcretion

Nucleic Acids

Nucleotides consist of a nitrogenous base, a pentose sugar, and one to three phosphate groups; nucleosides lack phosphate. Bases are purines (adenine, guanine) or pyrimidines (cytosine, thymine, uracil). DNA contains deoxyribose and A, G, C, and T; RNA contains ribose and A, G, C, and U. The 2′-hydroxyl group of ribose makes RNA more susceptible to hydrolysis than DNA.

DNA consists of two antiparallel strands wound in a right-handed double helix, joined by hydrogen bonds between complementary bases: A–T (two hydrogen bonds) and G–C (three hydrogen bonds). The major and minor grooves allow protein binding.

DNA replication is semiconservative: each daughter molecule has one parental and one new strand. Replication begins at origins and proceeds bidirectionally. DNA polymerase synthesizes only in the 5′ to 3′ direction and requires a primer, so the leading strand is made continuously and the lagging strand is made as Okazaki fragments.

Enzyme	Role
Helicase	Unwindsthedoublehelix
Single-strand binding proteins	Preventtheseparatedstrandsfromreannealing
Topoisomerase	Relievessupercoilingaheadofthefork
Primase	SynthesizesRNAprimers
DNApolymeraseIII	Mainreplicativeenzymeinprokaryotes
DNApolymeraseI	Removesprimersandfillsthegaps
DNAligase	JoinsOkazakifragments

Mechanism	Corrects
Mismatchrepair	Replicationerrors
Baseexcisionrepair	Damagedbases
Nucleotideexcisionrepair	Bulkylesionssuchasthyminedimers
Double-strand break repair	Brokenchromosomes byhomologousrecombinationornonhomologousendjoining ,