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BIO 2600 > Chap 5/6 > Flashcards

Chap 5/6 Flashcards

(71 cards)

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1
Q

central dogma (and exception)

A

DNA -> RNA -> protein
Retroviruses use RNA to make DNA (reverse trasncription)

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2
Q

which nitrogenous bases match to each other

A

A-T
C-G

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3
Q

molecular structure of nucleotides

A

ribose sugar with a nitrogenous base attached to 1’ carbon and and phosphate group attached to 5’ carbon

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4
Q

nucleoside structure

A

ribose sugar with nitrogenous base attached to 1’ carbon

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5
Q

which nitrogenous bases are purines

A

adenine and guanine

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6
Q

which nitrogenous bases are pyrimidines

A

thymine, cytosine, and uracil

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7
Q

phosphodiester bond

A

forms between the 3’ hydroxyl group of one sugar and the 5’ phosphate of the next

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8
Q

hydrogen bonds in DNA

A

hold the two nitrogenous bases together; keep the DNA double-stranded structure together

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9
Q

number of hydrogen bonds between A-T and C-G

A

A-T: 2
C-G: 3

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10
Q

DNA synthesis direction

A

5’ to 3” direction
phosphodiester bond formed at the 3’ hydroxyl end of the growing DNa chain with the incoming 5’ phosphate group

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11
Q

handedness of the DNA double helix

A

right-handed

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12
Q

the lowest level of chromosome organization (2 parts):

A

nucleosome (core particle and linker DNA)

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13
Q

nucleosome core particle

A

consists of 8 histones and DNA wrapped around them

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14
Q

linker DNA

A

connects nucleosome cores

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15
Q

how can the nucleosome core particle be released from chromatin in test tube solution

A

nuclease digests the linker DNA but cannot attack the DNA wrapped around the nucleosome core

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16
Q

how can the DNA be releases from the histone octamer (nucleosome core particle dissociation)

A

high salt breaks ionic bonds

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17
Q

levels of chromosome packing

A

DNA double helix -> beads on a string chromatin -> chromatin fiber of packed nucleosomes -> chromatin fiber folded into loops -> assembles into mitotic chromosome

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18
Q

how does the beads on a string chromatin fold to become packed nucleosomes (fiber)

A

linker histone (H1) associates with linker DNA and pulls nucleosomes together into fiber

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19
Q

other involved proteins in chromosome packing

A

loop forming clamps, cohesins, condensins

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20
Q

chromatin remodeling complexes

A

use ATP to change the position of DNA wrapped around histones by loosening nucleosomal DNA and pushing it along histone core to expose DNA to other proteins
de-condense chromatin

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21
Q

euchromatin

A

regions of relaxed (less condensed) chromatin
more accessible for gene expression

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22
Q

heterochromatin

A

regions that contain more histones and are more condensed and less accessible
silent genes are more condensed
includes centromere and telomeres

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23
Q

epigenetic regulations of histones

A

chemical modifications on specific locations (amino acids) at the N-terminal of histones affect gene expression
ex: acetylation, methylation, phosphorylation

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24
Q

acetylation of lysine (k) effects

A

loosens chromatin structure - increases accessibility

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25
carbon on the deoxyribose sugar where new where new deoxyribonucleotide will attach
3'
26
carbon that differs on ribose sugar in RNA and DNA
carbon 2' has H attached in DNA has OH group in RNA
27
semiconservative model
every daughter helix is comprised of one conserved parent strand (template) and one newly synthesized strand
28
where are DNA bases added to deoxyribose sugar
where OH group is on 1' carbon
29
what provides the energy for DNA polymerase to form phosphodiester bond along growing DNA chain
hydrolysis of nucleoside triphosphate into nucleoside monophosphate (releases pyrophosphate)
30
how does DNA polymerase proofread and correct errors
contains two catalytic domains: P and E P: polymerization E: Editing
31
why does DNA polymerase have to move in the 5' to 3' direction
if it moved 3' to 5' it could not proofread and still continue forward because it wouldn't have the energy provided to form phosphodiester bond
32
DNA helicase
unwinds the DNA double helix by breaking H bonds
33
replication initiator proteins
recognize and bind to origin of replication
34
why are many origins of replication A-T rich regions
A-T bases connected by 2 H bonds (not 3 like C-G)
35
number of replication origins in bacteria and humans
bacteria have 1 humans have many per chromosome
36
Replication forks
2 y-shaped junctions that extend both direction from origin of replication place where DNA synthesis occurs
37
where does the replication machinery assemble and start its movement
replication forks (2- one for each direction)
38
Okazaki fragments
the successive separate small fragments of DNA that is made on the lagging strand
39
what does DNA polymerase require to bind and start synthesizing DNA
a base paired (double stranded) end
40
Primase function
RNA polymerase that makes RNA primer for DNA polymerase to bind to (using DNA single strand template ) - 5' to 3' direction
41
What base does RNA polymerase use that's different from DNA polymerase
U instead of T, U base pairs with A
42
primers required on leading and lagging strands
leading strand: 1 lagging strand: multiple
43
Nucleases function in DNA synthesis
removes RNA primers
44
Repair polymerase function in DNA synthesis
synthesizes DNA where primers have been removed, uses ends of Okazaki fragments to bind to
45
DNA ligase function in DNA synthesis
joins 5' phosphate and 3' hydroxyl of fragments by catalyzing formation of phosphodiester bond to create continuous strand
46
which DNA synthesis enzymes use ATP
DNA ligase, helicase, clamp loader, and primase
47
why do chromosomes become shorter when DNA is replicated
the leading strand is synthesized to the end, but when the primer on the end of the lagging strand is removed, repair DNA polymerase cannot attach and replace RNA at the end of the strand
48
telomeres
long repetitive nucleotide sequences that are added to the end of every chromosome which allow the lagging strand to be completed by DNA polymerase
49
telomerase
adds additional telomere repeats to the template strand and keeps telomeres long enough carries short RNA template whose sequence is complementary to the DNA telomere sequence
50
single strand DNA binding proteins
binds to the single stranded DNA to prevent it from reforming base pairs
51
sliding protein clamps
hold the DNA polymerase on the leading and lagging strands facilitating its sliding
52
DNA topoisomerase
relives the tension that builds up in front of replication fork by temporary nicks (single or double stranded)
53
ways that DNA tension is relived when unwinding
DNA
54
how does UV radiation damage DNA
two adjacent thymine bases become covalently attached forming a thymine dimer
55
how are thymine dimers removed and corrected, and how does it affect replication
nucleotide excision pair stalls replication machinery
56
spontaneous DNA damage (2)
depurination and deamination
57
depurination
loss of purine base (A or G) from DNA will cause deletion (and frame shift mutation) if left unrepaired
58
deamination
loss of amino group from cytosine to form uracil will cause base pair change (point mutation) if left unrepaired
59
if replication errors are unrepaired how does this effect further replication
error strand produces double strand with permanent mutation which can cause diseases
60
what is DNA redundancy
more than one codon codes for the same amino acid (silent mutation)
61
sickle cell anemia point mutation
single nucleotide change of beta globin gene > abnormal hemoglobin
62
what must a person inherit to develop sickle cell anemia
two copies of mutant beta globin gene
63
deamination and depurination are repaired by what mechanism
base excision repair mechanism
64
base excision repair mechanism steps
1. identification of the damaged base 2. excision of the nucleotide 3. resynthesis by DNA polymerase 4. ligation by DNA ligase
65
excision in DNA repair
damage is cut out by nuclease specific for type of DNA damage
66
which enzyme restores original sequence in gap after excision cuts it out in base excision repair
repair DNA polymerase
67
DNA ligase function in DNA repair
seals the nick left in the backbone of repaired strand
68
nonhomologous end joining
mechanism to repair double strand breaks two broken ends are brought together by enzymes and rejoined rejoined by ligation results in short deletions, quick but could cause gene disfunction
69
homologous recombination repair
mechanism that repairs double strand breaks with no loss of genetic information uses other newly replicated double strand as template-must happen while two copies are near each other
70
steps in homologous recombination
1. d.s. break in one newly replicated DNA 2. nucleases digests more DNA in 5' direction on each strand (opposite directions) 3. damaged DNA crosses over and DNA is synthesized using undamaged DNA as the template 4. invading strand released and DNA synthesis continues using complementary strands as template + ligation
71
is what other situation is homologous recombination used
meiosis- paired chromosomes from parents align and cross over to cause genetic variation

BIO 2600 (15 decks)

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