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MCAT - Bio > Molecular Biology (C3) > Flashcards

Molecular Biology (C3) Flashcards

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1
Q

Nucleotide

A

1) sugar - ribose (2’OH) or deoxyribose
2) base - adds to 1’C
3) phosphate - adds to 5’C

1+2 = nucleoside = sugar + base

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2
Q

Topoisomerases

A

enzymes that cut one or both of the strands and unwrap helix, releasing excess tension created by helicases

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3
Q

Single-stranded binding proteins - SSBPs

A

protect DNA that has been unpackages in preparation for the replication and help keep the strands unseparated

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4
Q

DNA Polymerase

A

catalyzes the elongation of the daughter strand using the parental template, and elongates the primer by adding dNTPs to its 3’ end

3’ OH group acts as nucleophile in the polymerization rxn to displace 5’ pyrophosphate from the dNTP to be added

polymerization occurs in 5’ - 3’ direction

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5
Q

Nucleic acid polymerization

A

5’-3’ synthesis and base sequence
antiparallel and complementary
phosphodiester bond

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6
Q

Prokaryotic Replication

A

theta replication - 1 chromosome –> 1 Origin of Replication
single circular DNA in cytosol

5 DNA pol:

1) DNA pol III - super-fast, accurate elongation 5’-3’, also 3’-5’ exonuclease activity (proofreading)
2) DNA pol I - adds nuc at RNA primer, 5’-3’, then DNA pol III takes over

3) DNA pol II - 5’-3’ polymerase activity, 3’-5’ exonuclease proofreading function, backup for DNA pol III
4) /5) DNA pol IV and DNA pol V - error prone in 5’-3’ polymerase activity, part of prok checkpoint pathway

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7
Q

Prok - DNA packaging

A

genome = all the DNA in an organism

1) methylation: add CH3 groups to their DNA to protect from being degraded by enzymes (restriction enzymes chop up DNA, restrict growth of viruses, whose DNA is not methylated)
2) supercoiling: DNA gyrase –> topoisomerase

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8
Q

Euk - DNA packaging

A

several linear chromosomes
DNA - nucleosomes - chromatin - chromosomes

euchromatin: unwound, stains lightly
heterochromatin: tightly wound, stains darker

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9
Q

nucleosome

A

DNA wrapped around histones

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10
Q

Euchromatin

A

unwound

stains lightly

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11
Q

Heterochromatin

A

tightly wound

stains darker

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12
Q

Centromere

A

region of chromosome where:

1) sister chromatids are held together
2) mitotic spindle attaches

short arm = p
long arm = q

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13
Q

Telomeres

A

ends of euk linear chromosomes
short seq repeats: TTAGGG
stabilize ends of chromosomes, protect from degradation

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14
Q

Telomerase

A

enzyme that adds repetitive nucleotide sequences to the ends of chromosomes and therefore lengthens telomeres
ribonucleoprotein complex: RNA primer + RT enzyme
DNA repeat = 5’-TTAGGG-3’

“immortal cells”, germ-line cells, embryonic stem cells, some WBCs

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15
Q

Hayflick limit

A

of times a normal human cell type can divide until telomere length stops cell division

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16
Q

Physical Mutagens

A

Ionizing radiation - X-rays, alpha particles, gamma rays:

  • DNA breaks
  • if only on 1 strand, can be easily patched up b/c helix still in 1 piece
  • if double-stranded break, difficult to put back together
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17
Q

UV light

A

causes photochemical damage to DNA

ex: if 2 pyrimidines (2 Cs or 2 Ts) are beside each other on a DNA backbone, UV light can cause them to become covalently linked, they distort the backbone and can cause mutations in DNA replication if not repaired

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18
Q

Mutagen

A

any compound that can cause mutations

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19
Q

Biological agents

A

can cause mutations

ex: DNA pol - can make a mistake
ex: viruses
ex: transposons - can induce mutations

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20
Q

Central Dogma

A

(replication)DNA - RNA - Protein

DNA-RNA: transcription
RNA-Protein: translation

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21
Q

Codons to know

A

START = AUG (met)

STOP = UAA, UGA, UAG
u are away, u go away, u are gone

Trp = UGG (only 1 codon, only 1 tRNA to translate it)

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22
Q

Types of Mutations - 7

A

1) point
2) insertions
3) deletions
4) inversions
5) amplifications
6) translocations and rearrangements
7) loss of heterozygosity

2,3,4 - can be caused by transposons

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23
Q

Point Mutations

A

single bp substitutions
can be transitions (pyr for pyr, pur for pur) or transversions (pyr for pur, pur for pyr)
3 types: missense, nonsense, silent

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24
Q

Missense Mutation

type of point mutation

A

1 AA replaced with different AA

may not be serious if AAs are similar ex: substituting valine for leucine

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25
Q

Nonsense Mutation

type of point mutation

A

stop codon replaces a regular codon and prematurely shortens the protein

26
Q

Silent Mutation

type of point mutation

A

codon changed to new codon for same AA, no change in protein’s AA sequence

27
Q

Insertions

A

addition of 1 or more nucleotides to DNA sequence

28
Q

Deletions

A

removal of nucleotides from DNA sequence

29
Q

Frameshift Mutations

A

mutations that cause a change in the reading frame
very serious
can lead to premature termination of translation

not all insertions/deletions are frameshift mutations, if insert/delete 1 whole codon or several whole codons, you add/remove AAs from polypeptide w/o changing reading frame

30
Q

Inversions

A

when a segment of a chromosome is reversed end to end

chromosome undergoes breakage and rearrangement within itself

31
Q

Chromosome amplification

A

when a segment of a chromosome is duplicated

32
Q

Translocations

A

result when recombination occurs b/w nonhomologous chromosomes
can create gene fusion, where new gene product is made from parts of 2 genes that were not previously connected - common occurrence in many types of cancer
can be balanced (no genetic info lost), or unbalanced (genetic info lost/gained)

33
Q

Transposons

A

mobile genetic elements within their genomes
jumping genes
all contain a gene that codes for a protein called a transposase (cut and paste activity), where it catalyzes that mobilization of the transposon (excision from donor site) and intergration into new genetic location (acceptor site)
3 types:
1) IS element
2) complex transposon
3) composite transposon
can cause mutations if jump to important part of genome
can affect gene expression or cause mutations
can cause structural changes to chromosomes when they work in pairs (if chromosome has 2 transpoonson with same direction, transposons can line up beside each other so they are parallel, this causes chromosomal segment b/w them to loop around, recombination occurs b/w the transposon and this causes deletion of the DNA b/w the transposons, original chromosome completely loses the DNA segment b/w the transposons. segment of DNA that’s lost takes 1 transposon w/ it and can jump back into genome somewhere else, causing chr rearrangement)

34
Q

Loss of heterozygosity

A

if a deletion removes the normal copy of the gene, the only remaining copy is the mutated version
makes the locus hemizygous: only 1 gene copy in the diploid organism

*diploid organisms have 2 copies of each gene, and generally a mutation in 1 copy is tolerated as long as the other copy of the gene is normal

35
Q

Haploinsufficiency

A

a diploid organism has only a single functional copy of a gene, and this single copy is not enough to support a normal state

36
Q

Inborn errors of metabolism

A

huge group of genetic diseases that involve disorders of metabolism
most due to single mutation in single gene that codes for some sort of metabolic enzyme

37
Q

Cancer

A

driven by mutation accumulation

inherited or carcinogen exposure

38
Q

Mutation Repair

A

Bad Bases (mismatched, oxidized, crosslinked, etc.):

1) mismatch repair pathway
2) nucleotide excision repair

Brokem Chromosomes (physical damage, X rays):

3) homology-directed repair
4) non-homologous end-joining

DNA Rearrangement (transposons):
5) generally don't lead to repair mechanisms
39
Q

Mismatch Repair

A

during, or shortly after replication

parent strand is methylated, while daughter strand is not, can identify daughter/parent

40
Q

Base/Nucleotide Excision Repair

A

can happen at any time in cell cycle (ideally before replication)
remove bad base, replace with good base

41
Q

Homology-Directed Repair (H-D R)

A

must happen after replication (when the sister chromatid is present)
use (identical) sister chromatid as template to fix broken chromosome

42
Q

Non-Homologous End-Joining

A

can happen at any time in cell cycle
ligate broken ends together
mutagenic b/c usually lose some bases
can also result in translocations

even poorly repaired chromosomes are better than a broken chromosome
not as good as H-D R

43
Q

Types of RNA

A

rRNA: ribosomal
mRNA: messenger
tRNA: transfer
hnRNA: heterogenous nuclear (preprocessed mRNA - initial transcript)
miRNA & siRNA: micro, small interfering (complementary to RNA, binds to mRNA and prevents translation)

44
Q

Replication vs Transcription

A 
Similarities:
- START site
- 5'-3' direction
- DNA template
Differences:
- STOP site
- no primer
- no editing
a. transient, b. but not passed to offspring, c. more tolerant of mutations
45
Q

Transcription

A

transcription is the primary point of regulation for translation
regulation:
1) promoter:
- strong: high affinity for RNA pol - lot of RNA transcribed
- weak: low affinity for RNA pol - less RNA transcribed
2) DNA binding proteins:
- repressors
- enhancers

46
Q

Prokarotic Transcription

A

transcription and translation at same time in same place
no mRNA processing
polycistronic = many diff proteins from single mRNA
1 RNA pol

47
Q

Eukaryotic Transcription

A 
transcription and translation at diff times, in diff places
mRNA processing: 
- a. 5' G-cap
- b. 3' poly-A tail
- c. splicing
monocistronic = one mRNA, one protein
3 RNA pol:
1) RNA pol I - rRNA
2) RNA pol II - mRNA
3) RNA pol III - tRNA
^R,M,T
48
Q

tRNA

A

at least 20 tRNA amd at most 61
aminoacyl tRNA synthetase
2 ATP to load AAs
example of tRNA actually carrying met (AA): met-tRNA^met

49
Q

Wobble Hypothesis

A

first 2 codon-anticodon pairs bind normally (normal Watson-Crick pairing)
3rd anticodon more flexible
also, an A on tRNA can get converted to inosine allowing for even more flexibility

wobble base pairing happens where there is G, U, I at the 5’ end of the anticodon
can use same tRNA to translate different codons - fewer tRNAs are necessary

50
Q

Ribosomes

A

Prok:
large = 50S
small = 30S
total = 70S

Eukaryote:
large = 60S
small = 40S
total = 80S

prok are odd, euk are even
ribozymic activity of the ribosome found in large subunit of both prok and euk ribosomes

51
Q

Translation

A

P site = growing Protein held here
A site = new AA added here
E site = Exit site
- shift mRNA down 1 codon - translocation

2 ATP to attach AA to free-floating tRNA
2 ATP for peptide bond to form

52
Q

STOP codon in A site

A

a. no tRNA that recognizes a STOP codon
b. instead, bind a “release factor”
c. release factor breaks the bond b/w the final tRNA and the final AA (i.e., “releases” the completed protein)

53
Q

Translation - Energy Requirements

A

AA x4 = # ATP needed

tRNA loading - 2 ATP per tRNA
Initiation - 1 ATP
A site binding - 1 ATP per tRNA
Translocation - 1 ATP each time
Termination - 1 ATP
54
Q

AA Activation/tRNA loading/Peptide bond formation

A

1) AA attached to AMP to form aminoacyl AMP
- nucleophile = acidic oxygen of the AA
- leaving group (LG) = PPi
2) pyrophosphate LG is hydrolyzed to 2 orthophosphates (provides energy to attach AA to its tRNA molecule)
- rxn highly favourable
3) tRNA loading (unfavourable rxn) driven forward by destruction of high-energy aminoacyl-AMP bond created in step 1

requires 2 ATP equivalents b/c uses 2 high-energy bonds
ATP equivalent = single high-energy P bond
2 ATP equivalents = hydrolyzing 2 ATP to 2 ADP+2Pi OR ATP to AMP+2Pi

2 functions:

1) specific + accurate AA delivery
2) thermodynamic activation of the AA

55
Q

Aminoacyl-tRNA Synthetases

A

specific to each AA

at least 1 aminoacyl-tRNA synthetase for each AA

56
Q

Post-Translational Modification

A

1) Protein folding:
- aided by chaperonins
2) Covalent modification:
- disulphide bonds, glycosylation, phosphorylation, etc.
3) Processing:
- cleavage to form active protein (e.g., zygomens)

57
Q

Prokaryotic Translation

A

no promoter, has ribosome-binding site –> Shine-Dalgarno sequence (-10)
3 distinct stages:
1) initiation: initiator tRNA (tMet-tRNAfMet)
- initiator tRNA sites in P site of 70S ribosome, H-bonded to start codon (AUG)
- only initiates translation when preceded by Shine-Dal. seq.
2) elongation:
- 3 step cycle:
1. aminoacyl-tRNA enters A site and H-bonds with 2nd codon
2. peptidyl transferase activity of the large subunit catalyzes formation of peptide bond b/w fMet and 2nd AA (amino group of AA#2 acts as nucleophile and tRNAfMet is LG; it dissociates from the ribosome)
3. translocation: tRNA#1 moves to E site, tRNA#2 (holding growing polypeptide) moves into P site, and next codon to be translated moves to A site
direction of synthesis: N–>C (since N of AA#2 binds to C of AA#1)
as polypeptide elongates, its N terminus will come snaking out of the ribosome
3) termination:
- stop codon appears at A site
- release factor enters A site (causes peptidyl transferase to hydrolyze the bond b/w the last tRNA and the completed polypeptide)

58
Q

Eukaryotic Translation Differences from Prok

A

ribosome larger than prokaryote (80S)
mRNA must be processed before translation - spliced, with cap and tail
Met not fMet
mRNA transported from nucleus to cytoplasm

59
Q

Eukaryotic Translation

A

Initiation:
5’UTR seqs. (Kozak seq) - starts at 5’ end of mRNA
initiation complex: 40S small subunit, Met-tRNAMet, euk. initiation factors (eIFs)
- scans mRNA from 5’ end, looking for start codon, once found, 60S subunit recruited and translation begins
- eIFs: number of proteins closely controlled, affects amount of translation occurring, levels = rate-limiting step for translation
- newly formed polypeptide chains emerging from polyribosome in euk are all same (b/c monocistronic)

60
Q

Processes that can occur simultaneously in Eukaryotes

  • on same RNA molecule
  • need to occur in same compartment
A

transcription & splicing - both occur in nucleus

61
Q

Cap-Independent Translation

A

thought that all euk translation started at 5’ end of mRNA (assumed euk transcripts to be monocistronic and codedn for 1 polypeptide chain, b/c of important role of 5’mRNA recognition, its called cap-independent translation)
- euk sometimes capable of starting translation in middle of mRNA molecule (b/c beginnign of translation doesn’t require 5’cap of mRNA)
^transcript must have an interrnal ribosome entry site (IRES)

62
Q

Controlling Gene Expression

A

DNA level

RNA level

MCAT - Bio (13 decks)

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