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Genetics 431: Molecular Genetics > ch 1-5, 11 > Flashcards

ch 1-5, 11 Flashcards

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1
Q

forward vs reverse genetics

A

forward: phenotype –> genotype
reverse: genotype –> phenotype

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2
Q

why use DNA for long term storage of genetic info?

A

2’ OH RNA is rapidly hydrolyzed under basic conditions, DNA is not

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3
Q

why is 5’ methyl cytosine often a hot spot for mutation?

A

5’ methyl C deaminates to T

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4
Q

why does DNA have T and not U?

A

C deaminates to U
uracil is removed from DNA by uracil-DNA glycosylase

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5
Q

DNA binding proteins ……………. bind AT or CG

A

do not directly
instead, they bind the edges of the bp

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6
Q

recognition element

A

protein a-helix can easily bind to major groove if it has the correct pattern of H bonding

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7
Q

how many possible HB patterns in major groove?

A

3bp = 64

4^N

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8
Q

how are polynucleotide chains flexible?

A

rotation around glycosidic bond

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9
Q

sugar pucker

A

pentose pops up
C2’endo in DNA
C3’endo in RNA

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10
Q

what does methylation of C5 of G do?

A

shifts equilibrium to favor Z-DNA by binding a hydrophobic patch

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11
Q

Hoogsteen pairing

A

triplexes- 3-stranded proteins
rare but occurs in nature

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12
Q

how can thermodynamics predict RNA structure?

A

the one with the most negative delta G is predicted to occur

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13
Q

Pseudoknots

A

an RNA structure that allows you to stop/pause to do frame shifting

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14
Q

what allows G=U?

A

wobble base pairs due to greater structural flexibility of RN
unique recognition sites for aminoacyl-tRNA synthetases, ribosomes, ad other RNAs

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15
Q

hyperchromic effect

A

increased UV absorption when it undergoes a structural change, like denaturation

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16
Q

when can DNA supercoil?

A

when ends are fixed (like circular bacterial chromosome) or the loop domains of eurkaryotic chromosomes

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17
Q

what type of winding happens predominantly in natural DNA?

A

underwining (negative supercoiling)

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18
Q

what type of DNA favor strand separation?

A

underwound DNA, negative supercoils

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19
Q

type 2 topoisomerase

A

cant introduce - supercoils but can relax - and + by untangling DNA

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20
Q

how do topoisomerases change underwinding?

A

by changing LK

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21
Q

small proteins in a 1% gel electrophoresis

A

stack at the bottom
if small, go right through

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22
Q

pulse-field electrophoresis

A

Separates DNA based on time required to reorient after the direction of the electric field changes
small DNA reorients more quickly and thus moves faster

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23
Q

how id DNA visualized with UV light?

A

EtBr: dna intercalator, inserting itself between base pairs
GelRed: less toxic because cant cross all membranes

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24
Q

what is used as controls on Northern blots?

A

housekeeping genes

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25
what generates DNA with complementary ends?
palindromic sequence
26
cloning vectors key features
1. origin of replication 2. electable marker 3. insertion site for foreign DNA
27
Gibson assembly
-can join multiple segments of DNA without need for compatible (stickY) ends in a single isothermal reaction (one temperature)
28
Reverse transcriptase
-generates complementary DNA (cDNA) from an RNA template -comes from retroviruses
29
template switching RT
Problem: want to make full cDNA, how do we come back? RT add some Cs, old nucleotide has some Gs Use that to use something to go backwards
30
what is needed for PCR?
1. DNA template 2. primers complementary to ends of target 3. dNTP 4. thermostable DNA pol
31
Taq pol
heat-stable DNA pol does NOT have proofreading activity
32
what do PCR lengths depend on?
G+C content as well as temp and desired stringency of hybridization
33
what does BME do?
breaks disulfide bonds
34
SNPSs between any 2 individuals
3 million
35
contigs
long contiguous stretches of chromosome DNA
36
order of markers is the same on ............
genetic and physical maps
37
physical distance (bp) does not equal map distance in % recomb
-frequency of recombindation can differ 100-fold -in humans there are 30,000 recomb hot spots spaced every 50-100 kb
38
The nucleus of a typical diploid human cell in the G1 phase of the cell cycle contains about ____ different types of protein coding genes
20,000
39
DNA gyrase introduces negative supercoils into DNA. What will this do to relaxed, covalently closed DNA?
The DNA will become overwound and linking number will decrease
40
how long are PCR primers
20 ntds
41
purpose of high-resolution recombination mapping
landmarks for anchoring sequence info
42
haplotypes
DNA variants that are inherited together because they are close to each other on the same chromosome
43
c value paradox
lack of correlation between genome size (DNA value) and developmental, metabolic, or behavioral complexiity
44
what % of the genome is transcribed?
more than 80%
45
pseudogenes
inactive genes
46
how can humans and apes be related?
human chrom. 2 is the result of head-to-head fusion of telomeres of chromosomes homologous to chrom 12 and 13 of apes (Robertsonian translocation)
47
what are hominids
extinct members of the human lineage (not our ancestors, but cousins)
48
most current humans from Europe and Asia but not .......have .......
not Africa 1-3% Neanderthal DNA
48
Neanderthal genes that show evidence of positive selection
genes that affect keratin function in skin and hair neanderthal version of some genes involved in immune system function
49
what could contribute to disease in modern humans?
neanderthal genes
50
Tibetans
high altitude adaptation caused by introgression of Denisovan-like hypoxia gene, EPAS1
51
Denisovans
sequences make up 5% of DNA from modern Melanesians, Papuans, and Aboriginals
52
telomerase TER RNA TERT
**telomerase**: ribonucleoprotein enzyme (protein + essential RNA) **TER RNA**: template for the repeated addition of G-rich telomeric repeats to the chromosome 3' end **TERT**: reverse transcriptase that copies the TER template
53
how are the ends of chromosomes preserved during DNA replication?
telomerase has its own primer (uses DNA as the primer), uses RT because copies DNA telomeres promote T-loop structure, which protects DNA ends and blocks DNA damage response
54
chromosome disjunction
cohesins- ring-like proteins that prevent premature separation separase- cleaves cohesin at anaphase
55
what is anaphase driven by?
APC and activator Cdc20 --> triggers both activation of separase and also degrades cyclins less CDK activity --> exit from M phase
56
by how much do chromosomes compact?
7000 fold
57
what makes up nucleosome core?
H2A H2B H3 H4 made up of Lys and Arg core is highly conserved because highly specialized core has a well-ordered crystalline structure
58
who has the least neanderthal DNA?
humans from Africa
59
what does linker histone H1 do?
goes at the end and compacts nucleosomal arrays
60
what do N-terminal tails of histones do?
interact with adjacent nucleosomes compacting chromatin
61
what can both DNA pol 1 and DNA pol 3 do?
back up and removed mismatched bases using 3' --> 5' proofreading exonuclease activity
62
what defines helicase polarity?
the tracking strand, NOT complement
63
what removes 5' --> 3' exonuclease
subtilisn (useful in making blunt ends nd making DS DNA from SS)
64
Trombones
just know that we have problem that in DNA rep, 2 things going different directions As you go forward, also reaching around going backwards to get lagging strand, let go, start another okazaki fragment
65
Ter sites
where E. coli DNA rep ends asymmetric and have polarity
66
what does reverse transcriptase (RT) do?
generates complementary DNA (cDNA) from RNA template
67
Telomerase
has its own RNA template, combines the end and uses its own template Not expressed in normal somatic cell. Only germ cells
68
how to tell end of chromosome vs DS DNA break
telomeres
68
Huntington disease
autosomal dominant disease that causes progressive neurodegeneration (only expands in males) normal range: 11-35 threshold for disease: >35
69
fragile-X syndrome
1/1500 men most common cause of inherited mental retardation CGG repeat just upstream of FMR1 (protein involved in regulating translation) normal: 6-54 transmitting: 52-230 (full mutation to grandchildren) affected: 230-2300 copies (inactivates FMR1)
70
UV light mutagens
pyrimidine dimers 50-100/ cell/ sec/ in sunlight
71
after base selection and proofreading, mistakes occur every
10^6 or 10^8 incorporation events (every generation)
72
DNA lesions /day in E.Coli and Eukaryotes
E. Coli: 1K per day Eukaryotes: 100k per day
73
what does Dam methylase recognize?
GATC
74
what type of enzyme is MutH
nickase
75
XPV
PolH bypass UV lessions error free repair for thymidine dimers involved in Xeroderma
76
what induces SOS genes?
RecA
77
what does LexA do?
represses SOS genes
78
recombinations used to repair stalled/damaged DNA replication forks
1. translesion synthesis 2. repair initiated: run over it 3. fork stalls: backwards branch migration
79
what happens if DNA pol encounters a SS region?
fork collapses can repair by DS break repair (RecBCD, etc)
80
nonhomologous ends joining
1. Ku70-Ku80 bind to ends of ds break 2. DNA-PKcs and artemis add phosphate to each other 3. widening of ds break 4. annealing 5. XRCC5, XLF, DNA ligase 4 seal nicks (not very selective) 6. ligation

Genetics 431: Molecular Genetics (8 decks)

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