MCAT Bio/Biochem 2022

What happens during non competitive binding?

binds at allosteric site

How are peptide bonds formed? Broken?

dehydration synthesis

hydrolysis

What is the tertiary structure of a protein?

3D structure including bending from hydrophilic/hydrophobic interactions R groups

What is the quaternary structure of a protein?

interactions between different polypeptide chains in proteins composed of more than one polypeptide (subunit interaction)

How are carbohydrates broken down into CO2?

oxidation through combustion

How are carbohydrates linked?

glycosidic linkages through a dehydration reaction

What is sucrose?

glucose + fructose

What is lactose?

glucose + galactose

What is maltose?

glucose + glucose

What is cellulose?

glucose + glucose

What is starch?

storage form of glucose in plants

glycogen

What do alpha linkages look like? Beta?

alpha: H points up, straight bond with O

Beta: H points down, zigzag bond with O

What are triglycerides?

lipids(fat)

stores for fatty acid

3 fatty acids esterified to a glycerol

energy stores

What is another name for lipophilic?

hydrophobic

What is Z? E?

Z: cis

E: trans

What are fatty acid stored as?

fat

What do lipase do?

break down fats into fatty acids and glycerol

Why are fats more efficient energy storage molecules than carbohydrates?

packging: hydrophobicity allows fats to pack together more closely

energy content: more than carbohydrates

Does decreasing lipid tail increase or decrease fluidity?

increase

What doe steroids look like? How are they made?

cholesterol

What is an anhydride linkage?

two phosphates bond together to form pyrophosphate

What is the first law of thermodynamics?

Energy can be transferred and transformed, but it cannot be created or destroyed.

What is the second law of thermodynamics?

Every energy transfer or transformation increases the entropy of the universe.

What is the enthalpy equation?

H = E + PV

Is a negative G endergonic or exergonic?

exergonic

What is the Gib's free energy equations?

What does a catalyst or enzyme do? Is a catalyst or enzyme used up in a reaction?

lowers activation ennergy, does not change delta G

no its always there

How do we produce glucose?

oxidative catabolism

What is a nucleoside?

base + sugar (no phosphate)

Do purines have one or two rings?

two

Do pyrimidines have one or two rings?

one

How are nucleotides linked?

3'OH-5'P phosphodiester bond

How is the double helix held together?

Weak hydrogen bonds between the pairs of bases

Vaan der Waals

What does DNA gyrase do?

unwinds DNA using ATP

What are kinetochores?

The point on a chromosome by which it is attached to a spindle fiber during division.

What are telomeres?

DNA at the tips of chromosomes

6-8 bp long and guanine rich

What are copy number variants?

genomic loci that are present in some cells or individuals with extra or fewer copies

What are tandem repeats?

repetitive segments of DNA that do not code for proteins

unstable

Where does translation happen?

ribosome

What are the stop codons?

UAA, UAG, UGA

What are the start codons?

AUG (methionine)

What phase does DNA replicate?

S phase of interphase

What is helicase?

Unzips DNA at point of origin

What is topoisomerase?

corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands

What are single strand binding proteins?

bind to and stabilize single-stranded DNA

What does DNA polymerase require?

template and primer

How are Okazaki fragments joined together?

DNA ligase

What does DNA polymerase I do? II? III? IV? V?

I: removes the RNA primer and replaces it with DNA

II: DNA repair

III:It builds a strand of DNA.

IV & V: Error prone; used to stall other polymerases when DNA repair pathways have been activated.

What is the Hayflick limit?

Cells divide only a certain number of times and then die

What are the types of mutations?

silent: same amino acid

missense: different amino acid

nonsense: stop

frameshift

What are transposons? IS element? Complex? Composite?

segments of DNA that can move from one region of DNA to another

IS: only transposon

Complex transposon: transposon + genes

Composite transposon: transposon + central region + transposon

What do inverted repeats do for transposons?

allow for movement

What is excision repair?

Removal of damaged DNA segments followed by repair synthesis with the correct nucleotide sequence

before replication

What is homologous recombination?

The swapping of chromosome parts between homologous pairs

What is nonhomologous end joining?

brings together 2 ends of DNA fragments to repair double-stranded breaks. no requirement for homology

Are eukaryotes monocistronic or polycistronnic? Prokaryotes?

E: mono

P: poly

What is heterogeneous nuclear RNA?

RNA before processing events (cap and tail or splicing)

What is small nuclear RNA (snRNA)? MicroRNA (miRNA)? PIWI-innteracting RNA (piRNA)? long ncRNA?

snRNA: RNA that deals with splicing in RNA processing

miRNA: act as regulators

piRNA: single stranded, short RNA that prevents transposons from mobilizing

long ncRNA: long RNA that controls transcription by regulating promoter and control splicing and translation. Function in imprinting and X-chromosome inactivation

What is the core enzyme?

Helps to initiate and synthesize RNA. 4 main polypeptides (2 alpha, 1 beta, 1 beta prime) 1 sigma bound only at initiation in prokaryotes

CANNOT ALONE CARRY OUT TRANSCRIPTION

What is a sigma factor or haloenzyme?

a protein needed only for initiation of RNA synthesis that helps find the promoter and increase specific affinity

What is the Pribnow box?

promoter sequence that forms a closed complex when initiated

Do prokaryotes have introns?

nope

What does RNA polymerase I do in prokaryotes? II? III?

I: transcribes rRNA

II: transcribes mRNA

III: transcribes tRNA

Where is the amino acid attached on the tRNA?

3' end

What is the Wobble Hypothesis?

There are fewer tRNAs than codons. It was proposed that the 3' end of the codon allows for a more relaxed bonding with the 5' base of the anticodon. The potential for non-Watson-Crick base pairing at this position allows a single tRNA to pair with several different codons.

What is amino acid activation?

When tRNA attaches to amino acid in cytoplasm (requires ATP)

How big are the prokaryotes ribosome? Eukaryotes?

P: 70S

E: 80S

What are the binding sites of ribosomes?

-A site holds tRNA that carries the next amino acid

-P site holds tRNA that carries the growing polypeptide chain

-E site is the exit site where tRNAs leave the ribosome

what is the Shinne-Dalgarno sequence?

prokaryote ribosome binding site that starts transcription

How does initiation start in prokaryotes?

binding IF1 and IF3 to mRNA and then IF2 joins in

What is the lac operon?

inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose

What is the trp operon?

repressible operon

What makes the amino acids acidic?

Negative side chains due to presence of carboxyl group

What makes the amino acids basic?

Positive side chains due to amino groups

What is unique about histidine?

it exists in both a protonated and deprotonated state

What makes the amino acid non polar?

alkyl or aromatic side chain

Which amino acids can be phosphorylated?

serine, threonine, tyrosine

Which amino acids contain sulfur?

cysteine and methionine

What happens when pH is less than the pKa? pH more than?

Less: protonation

More: deprotonation

What happens in tertiary structures?

hydrophobic/hydrophilic interactions

What is the hydrophobic effect?

hydrophobic regions of the protein in its tertiary structure are moved inward and the hydrophilic regions outward

Do enzymes have a thermodynamic or kinetic role?

kinetic only (influencing rate - kinetic - not favorability -thermodynamic)

What does isomerase do?

rearrangement of atoms

What does lyase do?

Cuts C-C bonds w/ ATP

What does oxidoreductase do?

oxidation-reduction reactions

What does polymerase do?

extends DNA chain

What is covalent modification?

phosphorylation by kinases can alter function of proteins

Are allosteric sites covalent or non covalent? Reversible or irreversible?

non covalent

Reversible

What is Vmax?

the maximum rate of reaction -- when the enzyme is saturated with substrate

What is Km?

Substrate concentration at 1/2 Vmax

What is a low Km?

enzyme has high affinity for substrate

What does is non competitive inhibition [S] vs. [V]?

Lowe Vmax

no change Km

What does is competitive inhibition [S] vs. [V]?

No change Vmax

raise Km

What happens during uncompetitive binding?

binds at enzyme-substrate complex

What does is uncompetitive inhibition [S] vs. [V]?

lower Km and Vmax

What happens during mixed type inhibition binding?

lower Vmax

Km varies

In a line weaver burk plot, what is the slope? Y intercept? X intercept?

What is a competitive line weaver burk plot?

What is a noncompetitive line weaver burk plot?

What is a uncompetitive line weaver burk plot?