MCAT Bio/Biochem Exam

What direction is DNA/RNA read and synthesized?

Read in the 3’-5’ direction and synthesized in the 5’-3’ direction

heterogeneous nuclear RNA (hnRNA)

The immediate product of transcription in eukaryotes before it is matured into mRNA

3’ poly-A tail

a string of approximately 250 adenine (A) nucleotides added to the 3' end of an hnRNA transcript to protect the eventual mRNA transcript against rapid degradation in the cytosol

Splicing 

the process in which noncoding sequences (introns) are removed and coding sequences (exons) are ligated together

Restriction enzyme I

a type of restriction enzyme where the cleavage site is far from the recognition site, often >1000 bp away

Requires ATP and S-Adenosylmethionine

Restriction enzyme II

a type of restriction enzyme in which the cleavage site is within or very close to the recognition site

Does not require ATP 

Restriction Enzyme III

a type of restriction enzyme in which the cleavage site is a short distance away from the recognition site (20-30 bp)

Requires ATP but does not hydrolyze it and magnesium

Restriction enzyme IV

a type of restriction enzyme in which the cleavage site targets modified DNA. 

Primarily requires magnesium 

azide 

imine

nitrile

enhancers 

DNA sequences that can be located further from the gene of interest, and work by binding transcription factors that twist DNA into a hairpin loop, bringing distant regions into close proximity for transcription to begin

Silencers

they are regions of DNA to which transcription factors known as repressors bind

effects of methylation on C and A residues

Methylation of C and A residues can reduce transcription by blocking the binding of transcription factors and creating a more compact, inaccessible chromatic structure

How does acetylation promote transcription?

attaching acetyl groups to lysine residues on histones, making them less positively-charged and causing a looser wrapping pattern that allows transcription factors to access the genome more easily

Role of MicroRNA in transcription and translation?

miRNAs can either repress transcription in some instances or activate transcription in others. To repress, miRNAs bind to the 3’ end of target mRNA, leading to its destruction or blocking ribosomes from translating.

To activate, miRNAs interact with gene promoters and recruit complexes that make the ribosomes more permissive

A, D, E, and K

what are the lipid-soluble vitamins

B and C

what are the water soluable vitamins

glycine (Gly, G)

alanine (Ala, A) 

valine (Val, V) 

methionine (Met, M)

leucine (Leu, L)

isoleucine (Ile, I)

proline (Pro, P)

phenylalanine (Phe, F) 

tryptophan (Trp, W)

serine (Ser, S)

threonine (Thr, T)

asparagine (Asn, N)

glutamine (Gln, Q)

cysteine (Cys, C)

tyrosine (Tyr, Y) 

aspartic acid (Asp, D)

glutamic acid (Glu, E)

histidine (His, H)

lysine (lys, k)

arginine (arg, R) 

positive sense RNA

a term for viruses synonymous to sense strand for DNA referring to the host mRNA that can be directly translated into proteins

negative sense RNA

a term for viruses synonymous to the antisense strand for DNA, referring to viral genome, or the complementary strand to the functional mRNA

RNA replicase

refers to an enzyme used by RNA viruses to copy their RNA genomes (negative-sense strands) to create the complementary RNA (positive sense strand) 

in vitro

in a test tube or petri dish

in vivo

in the living body

viral envelope

a lipid bilayer derived from the host cell membrane, which is embedded with glycoproteins 

cholesterol at high temperatures

stabilizes the phospholipid bilayers and reduces fluidity

cholesterol at low temperatures

prevents the fatty acid chains from getting too close to one another and freezing into a solid state

G1 phase

phase of the cell cycle in which the cell grows physically larger, copies organelles, and makes the molecule building blocks it will need in later steps

S phase 

The phase of the cell cycle in which the cell synthesizes a complete copy of the DNA in its nucleus 

G2 phase

the phase of the cell cycle in which the cell grows more, makes proteins and organelles, and begins to reorganize its contents in preparation for mitosis

interphase

the collective name for G1, S, and G2

M phase 

The phase of the cell cycle in which the cell divides its copied DNA and cytoplasm to make two new cells 

G0 phase

The phase of the cell cycle in which the cell is resting and not actively preparing to divide

30s subunit

the smaller component of the prokaryotic ribosome responsible for binding to messenger RNA and decoding the genetic message

50s subunit 

the larger component of the prokaryotic ribosome that catalyzes peptide bond formation 

60s subunit

the larger subunit of the eukaryotic ribosome

40s subunit

the smaller subunit of the eukaryotic ribosome

peptidoglycan 

an important component of many bacterial cell walls and is not found in animal cells 

gram-positive bacteria

a type of bacteria that contains a thick peptidoglycan cell wall outside its cell membrane. Crystal violet stain adheres to the cross-links within the peptidoglycan structure, causing the bacterium to appear purple when visualized

gram negative bacteria

a type of bacteria that contains both an outer and an inner plasma membrane and a thin peptidoglycan wall causing it to appear stained pink when visualized

does anabolism or catabolism produce energy?

catablolism

what happens to reduced cofactors when they are used for anabolic processes? 

they become oxidized 

ratio of cofactors that drives catabolism?

high NAD+/NADH ratio or low NADH/NAD+ ratio

More of the oxidized form encourages catabolism and the release of energy

AUG codon

start codon - codes for methionine

UGA, UAG, and UAA codons

stop codons 

degree of burial

refers to the extent to which a specific amino acid residue or a functional group within a protein is shielded from the surrounding solvent; in other words, it measures it’s degree of hydrophobicity

adanine

guanine

cytosine

thymine

uracil 

common labeling agents in an assay?

fluorophores, enzymes, or radioisotopes

is insulin a peptide hormone or a steroid hormone?

peptide

what are the common steroid hormones?

cortisol, aldosterone, testosterone, estradiol, and progesterone

What are the common peptide hormones? (water soluable) 

insulin, glucagon, parathyroid hormone, calcitonin, growth hormone, prolactin, oxytocin, antidiuretic hormone, Adrenocorticotropic Hormone, Luteinizing Hormone, and follicle-stimulating hormone 

PCR

a lab technique that creates millions of copies of a specific DNA segment rapidly. The process consists of repeating three core steps:

1. denaturation

2. annealing

3. Extension

dNTPs

the standard building blocks of natural DNA and are used for replication and PCR

ddNTPs

modified nucleotides that are lacking a hydroxyl group, preventing the addition of the next nucleotide. Used in Sanger Sequencing to determine the DNA sequence

divalent ions 

ions that carry an electrical charge of +2 or -2 

nondisjunction

when a cell can receive too many or two chromosomes during anaphase 

prophase I

Homologous chromosomes (1 chromosome (2 chromatids) from the mother and 1 chromosome (2 chromatids) from the father) pair up to form structures called tetrads. Crossing over occurs, leading to the genetic exhcange of information between non-sister chromatids 

chiasmata

points on the non-sister chromatids where crossing over occurs

metaphase I

the paired homologous chromosomes align randomly along the metaphase plate

independent assortment

the orientation of each pair of homologous chromosomes is random

anaphase I

Homologous chromosomes separate and move toward opposite poles while sister chromatids remain attached at the centromere and move together as a single unit

telophase I

chromosomes arrive at the poles. The nuclear envelope reforms around the haploid sets

prophase II 

The nuclear envelope breaks down and the spidle apparatus reforms 

metaphase II

the chromosomes (each still composed of two sister chromatids) aling individually along the metaphase plate

anaphase II

sister chromatids finally separate at the centromere and move as individual chromosomes toward opposite poles

telophase II

chromosomes arrive at the poles and the nuclear envelope reforms 

kinase 

an enzyme that produces phosphorylation 

Henderson Hasselbalch equation

the primary use for this equation is to describe and design buffer solutions with a desired pH