Kandpal 1 Flashcards
(122 cards)
1
Q
DNA sequence is important for…
A
- designing treatment options
- rational basis for treatment outcomes
- understanding disease mechanisms
2
Q
___ and ___ genomes have been sequenced completely
A
human and chimpanzee
3
Q
differences in human and chimp genomes
A
35 million single nucleotide changles
5 million insertion/deletion changes
various rearrangements
4
Q
___% difference between human and chimp DNA sequence
A
4%
5
Q
Differential susceptibilities to ___between human and chimps
A
malaria
6
Q
Cytochrome P450 (CYP)
A
enzymes carry out several reactions including hydroxylation (activation/inactivation) of drugs.
7
Q
___ may alter the activity of CYP enzymes
A
Polymorphisms
Drug dose needs to be adjusted based on genotype
Warfarin, a blood thinner, dose is dependent on the genotype (isoforms of CYP enzymes) of patients
8
Q
CRISPR/Cas technology
A
Clustered Regularly Interspaced Short Palindromic Repeats
(Specific mutations in DNA sequence can be corrected by using genome editing tools)
CRISPR exist in bacteria along with helicase and nuclease
9
Q
DNA bases
A
adenine guanine cytosine thymine (RNA has uracil instead of thymine)
10
Q
5 carbon sugar in DNA/RNA
A
deoxyribose in DNA
ribose in RNA
11
Q
nucleotides are joined by ___ ___
A
phosphodiester bonds.
5’ phosphate bonds to 3’ OH of next nucleotide
12
Q
sugar-phosphate forms the
A
DNA backbone
13
Q
2 strands of DNA of held by
A
H-bonds
14
Q
purines
A
adenine and guanine
15
Q
pyrimidines
A
cytosine, thymine,uracil
16
Q
adenine deamination –>
A
hypoxanthine
17
Q
guanine deamination –>
A
xanthine
18
Q
uracil methylated –>
A
thymine
19
Q
nucleoside
A
base + sugar
end in -ine
20
Q
nucleotide
A
nucleoside (base + sugar) + phosphate
mono- di- or tri- phosphate.
end in -ylate
21
Q
Nucleotide functions
A
part of DNA/RNA
cofactors
energy (ATP)
cell signaling (GTP in G protein coupled receptor)
22
Q
FAD, NAD use
A
electron carriers
23
Q
cyclic AMP and cGMP use
A
secondary messengers
24
Q
coenzyme A (CoA) use
A
carbon carrier in fatty acid metabolism
25
Gregor mendel history
1866
| unit factors/genetic determinants (genes)
26
debate on genetic material
DNA or proteins?
27
Griffith's experiment.
| used?
1928
DNA is genetic material
used Streptococcus pneumoniae
Virulent strain- S (smooth polysaccharide coat)
Avirulent strain- R (rough)
28
_________ purified the infection causing chemical as DNA.
Avery, McCarty and MacLeod
29
Hershey and Chase experiment
Which component of a bacteriophage enters the bacteria during infection?
30
Chargaff's rule
The abundance of A equals T, and C equals G in double stranded DNA (not in a single stranded DNA)
A=T and C=G does not hold good for single stranded DNA
31
Watson and Crick model
double helix structure held together by H bonds.
Biophysical data from X-ray diffraction /Crystal structure
32
Double Helix explained ___ synthesis of DNA
templated
33
H-bonded base-pairs in DNA can be ___and ___
denatured and renatured
34
denaturation follows
zero order kinetics
at specific temp, does not depend on concentration of DnA
35
renaturation follows
second order kinetics
dependent on concentration of both strands
36
A DNA
right handed, 11 bases/turn
37
B DNA
right handed, 10 bases/turn
38
Z DNA
left handed, 12 bases/turn
39
we primarily see ___ DNA in living cells
B DNA
40
hyperchromicity curves
Double stranded: absorbance doubles when 2 strands fall apart. almost 100% increase.
Single stranded: increases b/c strand gets straighter as H bonds are denatured within strand. only 10-15% increase.
41
heat
disrupts H bond
42
increase in [Na+] [K+]
stabilizes helix
43
increase in GC/AT ratio
stabilizes helix
GC is 3 bonds
AT is 2 bonds
44
urea and formamide
destabilize DNA helix
45
hybridization
annealing of complementary DNA strands
46
PCR
polymerase chain reaction
primer-template annealing
47
southern hybridization
hybridization of a probe fragment to DNA target
48
northern hybridization
hybridization of a probe fragment to RNA target
49
microarrays
- global profiling of gene expression
| - nucleotide polymorphisms
50
medically important applications of hybridization
- Disease diagnosis, Prenatal diagnosis, bacterial infections, virus infection and viral load
- Forensic medicine (Paternity test; Guilty vs Innocent verdict)
- -genotypic variations among individuals
51
___ are different in prokaryotic and eukaryotic DNA replication
Identities of proteins involved are different
52
Medical applications of molecular differences in prokaryotic and eukaryotic DNA replication
Differences in molecular machinery has allowed development of therapeutics (antibiotics)
53
cell doctrine
Every cell in the body arises from an existing cell.
54
cell cycle
orderly sequence of DNA duplication and cell division
55
DNA Replication is ___
Semiconservative
new DNA molecule has one parent strand and one new strand.
56
DNA Polymer Extends in ___ Direction
5’ to 3’
requires a primer in antiparallel orientation.
57
E. coli polymerase types
DNA Polymerase I
- Low processivity (DNA repair)
DNA Polymerase II
- Somewhat higher processivity (DNA repair)
DNA Polymerase III (DNA Replicase)
-Highest processivity (DNA replication)
58
DNA replicase
DNA polymerase III
59
Pol I activity
5’-3’ polymerization
5’-3’ exonuclease
3’-5’ exonuclease
60
Pol II activity
5’-3’ polymerization
| 3’-5’ exonuclease
61
Pol II (replicase) activity
5’-3’ polymerization
| 3’-5’ exonuclease
62
The primer attaches to the ___ end of the template strand.
3'
63
proofreading activity is ...
3 'to 5' exonuclease activity.
Pol III
64
adult humans have how many cells
10^14
65
% of human DNA is coding DNA
1%
66
E. coli error frequency after proofreading.
10^-9
67
human genome error rate
3/cell/replication
68
genome type E. coli
double stranded circular genome
69
replication beings at
origin of replication
70
__ binds to the origin or replication and denatures ___ base pairs
```
initiator protein (dnaA)
A-T
```
71
double stranded DNA is unwound by
helicase (dnaB)
| in an ATP dependent manner
72
strand unwound by helicase is stabilized by...
single-strand binding protein
73
Unwinding of one part of DNA leads to ___of other parts of DNA
overwinding
74
___ relieves overwinding
Type II topoisomerase (gyrase in E. coli)
makes a cut in DNA
75
___ synthesizes ___ nt long ___ primers
primase (dnaG)
15 nt long
RNA
76
___ are absolute requirements for replication
primers
77
DNA polymerase requires a ___ and a ___ with ___ group for the synthesis of a polynucleotide strand
template
primer with free 3'-OH group
78
___ adds new nucleotides to the 3’-OH end of the growing chain by copying the template sequence
DNA polymerase III (replicase, dnaE)
79
___ removes RNA primers
DNA polymerase I ( 5 to 3 exonuclease activity)
80
RNA primers are replaced by
extending DNA syntehesis
81
___ seals the gap in ____ ___ manner
DNA ligase
in ATP dependent manner
82
Polymer II is a ___
holoenzyme
83
holoenzyme subunits
- Catalytic core of three subunits a-e-q,
- Clamp subunits (b, b) for processivity
- Clamp loader (g complex)
- Assembly subunit (t, t)
84
Differences in mammalian and bacterial proteins can be exploited for ___
therapeutics:
| Selective targeting of infectious agents by antibiotics
85
targets for bacteria elimination
Enzymes of DNA replication, transcription, translation, cell wall synthesis
86
Microbes use ___ for killing neighboring microbes
natural products (metabolites)
87
Novobiocin is ___ inhibitor
replication
88
fluoroquinolones
inhibitors of?
examples
synthetic antibiotics
inhibitors of replication
levofloxacin, ciprofloxacin (FDA approved for anthrax infection)
89
Streptomyces niveus produce an ___class of antibiotics such as ___(replication inhibitor
aminocoumarin
Novobiocin
90
___make transient cuts on DNA and change linking number (Total # of basepairs/10.4)
Topoisomerases
91
type I topoisomerases
make a nick in only one strand of DNA and binds to 3' end of phosphodiester back bone
92
type II topoisomerases
eg. bacterial DNA gyrase
make two cuts, one in each strand.
93
___ and ___ are target enzymes for quinolones/fluoroquinolones
Bacterial DNA gyrase (Topoisomerase type II) and topoisomerase IV
94
gyrase is ___ (A2B2)
heterotetramer
- To make the cut Tyr122 on GyrA forms covalent linkage with the 5’P of DNA. The DNA is subsequently religated.
- GyrB carries out ATP hydrolysis.
95
topoisomerase IV is ...
heterotetramer (C2E2)
96
fluoroquinolones prevent ....
the reversible ligation step carried out by GyrA
97
Novobiocin competes with ___ for binding to ___
ATP
| GyrB
98
___ is the target enzyme for anticancer drugs
mammalian topo I
99
Topotecan (Hycamtin) is FDA approved for ___
ovarian cancer and small cell lung cancer.
Topotecan stabilizes Topo I-DNA complex and prevents the religation step (inhibition of replication)
100
logic for antibiotic resistance
- Bacterial genomes are small
- Replication and doubling times are shorter
- Errors in replication are likely to occur
- These errors lead to mutations and produce mutant bacteria
101
resistance to quinolone, point mutations
N-terminal end of GyrA (most mutations).
C-terminal end of GyrB (few mutations).
102
more proteins in ___ replication system
eucaryotic
103
genome size E. coli vs mammalian
E. coli - 4.64 million basepairs, circular DNA
mammalian - 23 pairs of linear chromosomes, 3.2 billion basepaires
104
___ have single origin of replication
E. coli
105
Mammalian uses ___ origins or replication
multiple (about 1000)
| sequence not well defined
106
E. coli uses the ___ polymerase for leading and lagging strand synthesis
same
107
mammalian uses ____
polymerases for leading and lagging strand synthesis
108
Mammalian RNA primer is degraded by
RNaseH
RNaseH degrades RNA part of an RNA-DNA hybrid
109
Mammalian Okazaki fragments-
0.1- 0.2 Kb
110
E. coli Okazaki fragments-
1.0- 2.0 Kb
111
Polymerase alpha
primase
112
Polymerase beta
repair
113
Polymerase gamma
mitochondrial replication
114
Polymerase delta
nuclear replication
115
Polymerase epsilon
nuclear replication
116
end replication problem
In linear mammalian chromosomes, when replication fork reaches the end, RNA primer can’t be placed for the last Okazaki fragment
- Once the RNA primer is removed from the 5’ end, it can not be filled up.
- No polymerase available with 3’-5’ activity
- 5’ ends will shorten after each replication cycle
117
telomeres
maintain integrity of chromosome
seal end of chromosome
- Prevent undesirable fusion
- Prevent aberrant recombination
- Telomeres attach chromosomes to nuclear envelope
- Telomeres facilitate replication
118
telomeres have ___ repeats
hexameric
TTAGGG in human cells (up to 15 Kb)
TTGGGG in Tetrahymena
119
telomerase
Ribonucleoprotein (RNP)
Protein + RNA
synthesize telomeric repeats
reverse transcriptase (RNA dependent DNA polymerase)
120
telomerase activity
Somatic cells (differentiated cells) have no detectable activity
Germ cells, stem cells have detectable activity
121
telomerase and human cancer
normal tissue - no telomerase
tumor - activity
germ cells - activity
122
cancer, targets for intervention
-Telomerase activity
Inhibition would prevent tumor growth
-Telomere structure
Interference may prevent telomere extension
