Molecular Bio (Chp 4) Flashcards
(82 cards)
1
Q
Purine bases
A
A and G
two rings
(mnemonic: silver (AG) is pure)
2
Q
Pyrimidine bases
A
C, U, and T
single ring
(mnemonic: pyramids are sharp and CUT you)
3
Q
phosphodiester bond
A
covalently links nucleotides in DNA chain
4
Q
H bonds in DNA
A
(Purine-pyrimidine)
A-T (2 H bonds)
G-C (3 H bonds)
5
Q
DNA structure characteristics
A
- double stranded
- antiparallel (5’ on one end paired with 3’ of other)
- coiled
6
Q
of chromosomes in humans
A
46 (23 inherited from each parent)
7
Q
prokaryote (bacterial) genome
A
single circular chromosome
8
Q
viral genome
A
linear or circular DNA or RNA
9
Q
DNA gyrase
A
(prokaryote)
uses ATP E to twist DNA
10
Q
Packing/condensing of human DNA
A
- wrapped around histones
- nucleosomes (resemble ball on a string) = wrapped around 8 histones
- chromatin - wrapped nucleosomes
11
Q
centromere
A
region of chromosome where spindle fibers attach during cell division (attach via kinetochores)
12
Q
transcription
A
DNA (T) > RNA (U)
13
Q
translation
A
RNA > proteins
accomplished by the ribosome
14
Q
Central Dogma
A
DNA > RNA > protein
information DNA is used to create actual products (proteins - ex: enzymes, structural proteins, etc.)
15
Q
codon
A
nucleic acid word (3 nucleotide letters)
16
Q
stop codons
A
also called nonsense codon
UAA - your are annoying
UGA - you go away
UAG - you are gone
17
Q
DNA code
no ambiguity vs degenerate
A
no ambiguity - DNA code can only be read one way
degenerate - two or more codons coding for the same amino acid
18
Q
replication
A
duplication of DNA - occurs during synthesis phase of cell cycle
- semiconservative
19
Q
helicase
A
enzyme that unwinds and separates double helix at origin of replication
20
Q
topoisomerase
A
enzymes that cut one or both strands and unwrap DNA helix > releases excess tension caused by helicase
21
Q
single strand binding protein (SSBPs)
A
protects DNA that has been unpackaged in prep for replication and keeps separated
22
Q
DNA polymerase
A
catalyzes elongation of daughter strand using parental template
- checks each new nucleotide to make sure it forms correct base pair
- polymerization occurs in 5’ to 3’ ALWAYS
- requires a template and primer
23
Q
okazaki fragments
A
small chunks of DNA comprising lagging strand
24
Q
DNA pol III
A
v fast, v accurate elongation of leading strand
25
DNA pol I
adds nucleotides at the RNA primer but more slowly than DNA pol III
- important for excision repair
26
germline mutations
mutations that can be passed onto offspring
27
somatic mutations
mutations in nongametic cells > not passed on to offspring
28
point mutation
single base pair substitutions (ex A in place of G)
can be:
-transitions - sub pyrimidine for another pyrimidine
-transversions - sub pyrimidine for purine
types:
- missence, nonsense, and silent
29
missence mutation
a point mutation that causes one amino acid to be replaced with a different amino acid
30
nonsense mutation
a point mutation that causes a regular codon to be replaced by a stop codon
> prematurely shortens the protein
31
silent mutation
a point mutation where a codon is changed into a new codon that codes for the same amino acid
> no change in amino acid sequence
32
Insertion mutation
addition of one or more extra nucleotides into the DNA sequence
33
Deletion mutation
removal of nucleotides from DNA sequence
34
frameshift mutation
mutations that change the reading frame
35
inversion mutation
section of DNA sequence is flipped (inversed) from end to end
36
amplification mutation
segment of chromosome is duplicated
37
translocation
recombination occurs between nonhomologous chromosomes
38
Types of DNA repair
direct reversal
homology dependent repair - excision repair
post-replication reapir
double strand break repair - homologous recombination, nonhomologous end joining
39
Direct reversal
direct reversal of DNA damage (example: repair of UV induced pyrimidine photodimers using visible light)
40
homology dependent reapir
because DNA is double stranded, mutations on one strand can be fixed using undamaged, complimentary info on the other
41
excision repair
removing defective bases or nucleotides and replacing them
42
post replication repair
mismatch repair pathway targets mismatched watson-crick base pairs that weren't repaired by DNA pol proofreading during replication
43
double strand break repair
(double strand breaks can be caused by: reactive oxygen species, ionizing radiation, UV light or chemical agents)
(2) pathways to help fix
1. homologous recombination - one sister chromatid can help repair a DSB in the other
2. nonhomologous end joining - nonspecific end joining
44
How is RNA distinct from DNA
(3) ways:
1. single stranded (except in some viruses)
2. contains uracil instead of thyamine
3. pentose ring in RNA is ribose rather than 2' deoxyribose
4. several types: (are empty - R M T)
- rRNA - ribosomal
- mRNA - messenger
- tRNA - transfer
45
mRNA
carries genetic info to the ribosome where it can be translated into a protein
46
tRNA
responsible for translating the genetic code - carries amino acids from cytoplasm to the ribosome to be added to growing polypeptide
47
rRNA
serve as components of the ribosome
48
transcription
synthesis of RNA using DNA as the template
| -proceeds 5' to 3'
49
introns vs extrons
introns - INtervening sequences of RNA
| extrons - RNA that gets EXpressed
50
spliceosome
mediates splicing (removing introns from RNA seq)
51
modification of hnRNA before translation
| mRNA processing
1. 5' cap added to end of molecule
2. 3' poly A tail
3. splicing - remove introns
mnemonic: introns in nucleus, exons exit nucleus
52
RNA pol products for:
RNA pol I
RNA pol II
RNA pol III
RNA pol I = most rRNA
RNA pol II = hnRNA (ultimately mRNA)
RNA pol III = tRNA
Are empty (R M T)
53
translation
synthesis of polypeptides according to aa sequence dictated by sequence of codons in mRNA
54
tRNA (transfer RNA)
stem and loop structure stabilized by H bonds
each tRNA is specific to one amino acid (while each amino acid can have several tRNAs)
regions:
-anticodon region recognizes mRNA codon to be translated
-amino acid acceptor site - where amino acid attaches to tRNA
55
wobble hypothesis
first 2 anticodon-codon pairs in tRNA follow normal base pairing rules BUT the third position is more flexible
> allows for less tRNAs than would be predicted
56
ribosome
```
prokaryote = 70s ribosome
eukaryote = 80s ribosome
```
float around in cytoplasm, each has a small and large subunit
binding sites:
- A site - where tRNA delivers aa
- P site - where growing peptide chain is and aa is added
-E site - where now empty tRNA exits ribosom
57
prokaryotic translation occurs ___
while mRNA is being made ribosome attaches and begins translating it
58
translation stages
(3)
1. initiation - small ribosomal unit binds 2 initiation proteins (IF1 and IF3), then binds the mRNA transcript, then tRNA along with IF3, then 50S subunit completes complex
2. elongation - A > P > E
3. termination - a stop codon appears in A site (UAA, UAG, and UAA)
total E required to make = # amino acids * 4
59
diff btw prokaryotic translation and eukaryotic translation
- eukaryote = larger ribosome (80S > 70S)
- eukaryote mRNA must be processed before translated (spliced, poly A tail, 5' cap)
- N- terminal amino acid is diff (Met instead of fMET)
- eukaryote mRNA must be transported from nucleus to cytoplasm (>transcription and translation can't occur at the same time in eukaryotic)
60
Controlling gene expression at DNA level
- DNA methylation and chromatin remodeling
- Gene dose
- Gene imprinting
- X chromosome inactivation
61
Controlling gene expression at DNA level
| - DNA methylation and chromatin remodeling
DNA methylation turns off eukaryotic gene exp by:
1. blocks the gene from transcriptional proteins
2. certain proteins bind methylated CpG groups and recruit chromatin remodeling proteins that change winding of DNA around histones
62
Controlling gene expression at DNA level - Gene Dose
increase copy number > increase quantities of corresponding protein
gene deletion > decrease in gene expression
63
Lac Operon
components
P region - promoter site on DNA
O region - operator site to which Lac represser binds
Z gene - codes for enzyme beta-galactosidase, cleaves lactose into glucose and galactose
Y gene - codes for permease, protein that transports lactose into the cell
A gene - codes for trancetylase - transfer an acetyl group from AcetylCoA to beta-galactosidase
regulatory sequences
crp - located at distant site, codes for catobolite activator protein
I gene - located at distant site, codes for Lac repressor protein
64
nucleoside characteristics
sugar
base (1')
no phosphates
65
nucleotide characteristics
sugar
base (1')
phosphates (5')
66
deoxyribose
used in DNA
| no O on 2'
67
ribose
used in RNA
68
DNA synthesis direction
5' > 3'
69
DNA packing in prokaryotes
1. methylation - protection from restriction enzymes
| 2. supercoiling - via DNA gyrase
70
telomere
short sequence repeats at end of chromosome - stabilizes end of chromosome
71
start codone
AUG - methionine
72
polymerase errors
1. point mutations
2. small repeats
3. insertion/deletion
repaired by:
mismatch repair pathway - only during or shortly after replication
nucleotide excision repair
73
endogenous damage
1. oxidized DNA
2. cross-linked bases
3. double or single strand breaks
fixed by:
homology directed repair
non-homology directed repair (often results in mutations)
74
exogenous damage
1. UV radiation > pyrimidine dimers - forms base pairs on same strand
- repaired by: direct reversal with white light (doesnt work for humans though)
2. X rays > double stranded breaks
3. chemicals > physical damage, intercalation
75
DNA replication
| (4) general rules
1. semiconservative - retains 1 parent strande
2. 5' -> 3' synthesis
3. requires a primer (RNA dimer)
4. requires a template
76
primase
synthisizes RNA primer at origin of replication
77
ligase
connects okazaki fragments (lagging strands)
78
Prokaryotic DNA replication
theta replication
- 1 origin of replication
- (5) DNA pol - only need to know III and I
III - high processivity, fast, add at 400 bp, no known function of DNA repair
I - low processivity, slow, DNA excision repair
79
eukaryotic replication
replication bubbles
- multiple origins of replication
- multiple RNA pol (not asked about)
80
Prokaryotic mRNA is polycistonic or monocistonic
polycistonic - many different proteins from single mRNA
81
eukaryotic mRNA is polycistonic or monocistonic
monocistonic - one mRNA = 1 protein
82
Translation E requirement
| ribosome
formula = # amino acids * 4
