DNA Flashcards
1
Q
What is the difference between a nucleoside and a nucleotide
A
Nucleoside - contain a five carbon sugar and nitrogenous base
Nucleotide is a nucleoside + one to three phosphate groups
2
Q
What is the base-pairing rules according to Watson-Crick
A
A-T or A-U 2 H bonds
C-G 3 H bonds
3
Q
What are the three major structural differences between DNA and RNA
A
- T instead of U
- double stranded and single stranded
- sugar backbone is difference, deoxyribose and ribose
4
Q
How does the aromaticity of purines and pyrimidines underscore their genetic function
A
- the aromatciity makes the structure very stable and unreactive
- stability is important for storing genetic information and avoiding spontaneous mutations
5
Q
If a strand of RNA contained 15% C, 15% A, 35% G and 35% U, would this violate Chargaff’s rules. Why or why not
A
No, because RNA is single stranded, so the complementary strand rule for DNA does not hold true
6
Q
Where is DNA found
A
- bulk is found in chromosomes in the nucleus of eukaryotic cells
- some DNA is found in mitochondria and chloroplasts
7
Q
What is the structural difference between deoxyribose and ribose
A
both are five carbon sugars
- the C2 position in deoxyribose is a H
- the C2 position in ribose is a OH
8
Q
What is the backbone of DNA composed of
A
- alternating sugar and phosphate
- nucleotides are joined by 3’ to 5’ phosphodiester bonds
9
Q
What is the charge of DNA and why
A
- negative charge because phosphates carry a negative charge
10
Q
The 5’ end of DNA will contain a ___ group and the 3’ end of DNA will contain a ___ group
A
5’ end has OH or phosphate group bonded to C5
3’ end has free OH on C3
11
Q
DNA goes in which direction
A
5’ to 3’
12
Q
What does CUT the PY stand for, how many rings
A
Cytosine, Uracil, and Thymine are all pyrimidines
one ring
13
Q
What does PUR As Gold stand for, how many rings
A
Adenine and Guanine are all purines
two rings
14
Q
What are the four rules for aromatic compounds
A
- cyclic
- planar
- conjugated - alternating single and double bonds or lone pairs
- 4n+2 - Hückel’s Rule
15
Q
DNA strands are ____ to one another
A
antiparallel
16
Q
The sugar phosphate backbone is on the _____ of the double helix and the nitrogenous bases are on the ____ of the double helix
A
outside
inside
17
Q
What is Chargaffs rule
A
the amount of A = T
the amount of C = G
the total amount = 100
Total purines = Total pyrimidines
This does not apply to RNA, because it is single stranded
18
Q
What is the complementary strand for 5’ ATCG 3’
A
5’ CGAT 3’
must be complementary and antiparallel
19
Q
How many H bonds are between A and T, C and G
A
2 H bonds
3 H bonds
- this is why a molecule with more C and G will have a higher melting point - because it takes more heat to break all the bonds compared to A T bonds
20
Q
What is B and Z DNA
A
B DNA is a right handed helix - most common and stable
Z DNA is a left handed helix - less common, less stable
21
Q
The major and minor groves in DNA provide _____
A
binding sites for regulatory proteins
22
Q
Where do regularly proteins bind to DNA
A
on the major and minor groves of the double helix
23
Q
What bases are pyrimidines and what bases are purines
A
pyrimidines are CUT - one ring
purines are AG - two rings
24
Q
How does DNA become denatured
What are commonly used methods to denature DNA
A
by being placed in conditions that disrupt hydrogen bonding and base - pairing
heat, alkaline pH, chemicals (formaldehyde, urea)
25
What is reannelaing of DNA
brining the DNA strands back together usually accomplished if the denaturing agent is slowly removed
26
Compare Heterochromatin and Euchromatin
- Where located
- Density
- Color under light microscopy
- Expression
- During which cell stage
Heterochromatin - nucleus, dense, dark, unexpressed, interphase
Euchromatin - nucleus, uncondensed, light, expressed, interphase
27
What prevents DNA replication from extending to the end of a chromosome and losing sequence
telomeres
28
Telomeres are
- located
- prevent DNA unraveling by
- during replication
- can be reversed by (partially)
- type of DNA sequences
- at the end of chromosomes - in the nucleus 5' end
- high GC content prevent the DNA from unraveling
- shorten during replication
- can partially be reversed by enzyme telomerase
- contain repetitive sequences of noncoding DNA
29
Centromeres are
- located
- separated
- contain strong bonds because of
- in the middle of chromosomes, holding sister chromatids together
- separated during anaphase of mitosis
- high GC content to maintain strong bond between chromatids
30
How many chromosomes do human cells have
46
31
What forms a nucleosome
- when DNA is wrapped around histone proteins (H2A, H2B, H3, H4) and stabilized by H1
32
As a whole DNA and its associated histones make up ____ in the nucleus
chromatin
33
As a whole DNA and its associated histones make up ____ in the nucleus
chromatin
34
What does telomerase do
- an enzyme that partially reverses the action of telomeres
35
What is a similarity between telomeres and centromeres
both contain a high GC content
in telomeres this prevents DNA unwinding
in centromeres helps with strong bond between chromatids
36
What is the function of helicase
- unwinds the DNA
- in eukaryotes and prokaryotes
- during replication
37
What enzymes main role is to unwind the DNA
- Helicase
| - in eukaryotes and prokaryotes
38
What is the function of single-stranded DNA- binding protein
- prevents reannelaing of DNA double helix during replication
- in eukaryotes and prokaryotes
39
What is the function of DNA topoisomerases
- knick the DNA strand to reduce torsional strain and then reseals
- reduces torsional strain from positive supercoils by introducing nicks in the DNA strand
- in eukaryotes and prokaryotes
40
What is the function of primase
- places an RNA primer on DNA to to begin replication
| - in eukaryotes and prokaryotes
41
What is the function of DNA polymerase III and DNA polymerase alpha
- adds nucleotides to growing daughter strand
- in prokaryotes (III)
- in eukaryotes (alpha)
42
What is the function of DNA polymerase I
- fills in gaps left behind after RNA primer is remvoed
| - in prokaryotes
43
What is the function of RNase H
- removes RNA primer
| - in eukaryotes
44
What is the function of DNA ligase
- joins DNA strands - specifically between Okazaki fragments
- in eukaryotes and prokaryotes
45
What enzyme unwinds the DNA in eukaryotes and prokaryotes
helicase
| - both
46
What enzyme prevents the reannealing of DNA in the double helix during replication in eukaryotes and prokaryotes
single stranded DNA-bining protein
| - both
47
What enzyme places the RNA primer in eukaryotes and prokaryotes
primase
| - both
48
What enzyme adds nucleotides to the growing daughter strand in eukaryotes and prokaryotes
Pro - DNA polymerase III
| Eukaryote - DNA polymerase alpha
49
What enzyme fills in the gaps left behind after RNA primer is removed in eukaryotes and prokaryotes
DNA polymerase I
| - prokaryotes
50
What enzyme removes the RNA primer in eukaryotes and prokaryotes
RNase H
| - eukaryote
51
What enzyme joins DNA strands in eukaryotes and prokaryotes
DNA ligase
| - both
52
What enzyme reduces torsional strain from possible supercoils by introducing nicks in the DNA strand in eukaryotes and prokaryotes
DNA topoisomerases
| - both
53
Is the leading or lagging strand more prone to mutations, why
lagging strand,
- more chances of mutation because of the stop and go process of DNA replication
- contains more RNA primers, so there will be more fill ins increasing the change of mutations
leading strand is a continuous process
54
What is the replisome
aka replication complex
| set of specialized proteins that assist the DNA polymerases during the process of DNA replication
55
What is the origin of replication
- DNA unwinds to this point and replication begins
56
The direction of new DNA is in which direction and what does this cause
- both directions
| - causing a replication fork - with a leading and lagging strand
57
Compare and contrast the leading and lagging strands
leading strand
- continuous
- needs one RNA primer in theory
lagging strand
- stop and go process
- needs multiple RNA primers
58
Write out the DNA replication process in eukaryotes (prokaryotes)
1. Helicase unwinds DNA into two strands -- There is supercoiling while the NDA is unwinding so DNA topoisomerases add negative supercoils ahead of helicase and nick the strand to reduce this torsional strain
2. Single strand DNA-binding proteins prevent the DNA strands from coming back together and prevents degradation by nucleases
3. Primase adds an RNA primer to allow replication to begin on the strands
5. DNA polymerase alpha (DNA polymerase III) reads the parent strand and starts to add nucleotides to synthesize the daughter strand - can only synthesis 5' to 3'
6. Leading and lagging strands
Leading strand is continuously copied, read from 3' to 5' and synthesized from 5' to 3', in theory only one RNA primer is needed
Lagging strand is not oriented in the correct direction, Okazaki fragments are produced, DNA polymerase completes one Okazaki fragment and then moves to the next, needs multiple RNA primers (one is needed to synthesize each Okazaki fragment) - DNA ligases helps to join Okazaki fragments
7. RNA primer is removed by RNase (Polymerase I) - exonuclease
8. DNA polymerase delta (DNA polymerase I) adds DNA nucleotides where the RNA primer was
9. DNA ligases seals the end of DNA molecules making one continuous strand - joins DNA strands
59
Is DNA replication faster in eukaryotes or prokaryotes
- Slower in eukaryotes and faster in prokaryotes
60
Compare contrast between prokaryotes and eukaryotes
- origin of replication
- unwinding of DNA
- stabilization of unwound template strands
- synthesis of RNA primers
- synthesis of DNA
- removal of RNA primers
- replacement of RNA primer location with DNA
- joining of Okazaki fragments
- removal of positive supercoils ahead of advancing replication forks
- synthesis of telomeres
- one vs multiple per chromosome
- helicase
- single strand DNA binding proteins
- primase
- DNA polymerase III and DNA polymerase alpha
- DNA polymerase I and RNase H
- DNA polymerase I and DNA polymerase delta
- DNA ligase
- DNA topoisomerases
- do not have, telomerase
61
What are oncogenes
- develop from mutations of porto-oncogenes and promote rapid cell cycling
62
What is cancer
- unchecked cell proliferation with the ability to spread by local invasion or metastasize (migrate to other parts of the body via lymphatic or circulatory system)
63
What are tumor suppressor genes
- code for proteins that reduce cell cycling or DNA repair
64
What can happen if there is a mutation in the tumor suppressor genes
- can cause cancer, because the gene is no longer producing proteins that reduce cell cycling or repair DNA
65
What enzyme proofreads the DNA
- DNA polymerase - proofreads its work and excesses incorrectly matched bases
- daughter strand is identified by its lack of methylation and corrected accordingly
66
Durning proofreading how does DNA polymerase tell the difference between the parent and daughter strand
- the parent strand is more methylated
| - the daughter strand lacks methylation
67
Compare the four DNA repair mechanisms
- Proofreading by DNA polymerase
- Mismatch Repair
- Nucleotide Excision Repair
- Base Excision Repair
- Phase of the cell cycle it occurs
- key enzymes or genes
Proofreading by DNA polymerase
- S
- DNA polymerase
Mismatch Repair
- G2
- MSH2 and MLH1 (eukaryote) MutS and MutL(prokaryotes)
Nucleotide Excision Repair
- G1/G2
- excision endonuclease
Base Excision Repair
- G1/G2
- glycosylase, AP endonuclease
68
What are key structural differences between the types of lesions corrected by nucleotide excision repair and those corrected by base excision repair
Nucleotide excision repair corrects lesions large enough to distort the double helix and base excision repairs small lesions that do not distort the double helix shape
69
Explain DNA repair by proofreading
- occurs during S phase
- DNA polymerase
- proofreads its work and excesses incorrectly matched bases
- parent strand is more methylated
70
Explain DNA repair by Mismatch repair
- occurs during G2
- MSH2 and MLH1 (eukaryote) and MutL and MutS (prokaryotes)
- enzymes above detect the errors that happened during the S phase and removes them
71
Explain DNA repair by Nucleotide Excision Repair
- occurs during G1 and G2
- excision endonuclease
- Thymine dimers (as result of UV light) form in the double helix of the DNA, distorting the shape, this repair mechanism via excision endonucleases remove the dimer and then DNA polymerase can fill in the gap the dimer causes using the undamaged strand as the template and then DNA ligase seals the strand
72
Explain DNA repair by base excision repair
- occurs during G1 and G2
- glycosylase and AP endonuclease
- wrong base is detected and the base is recognized by glycoslyase enzyme and removed, this leaves an AP site (Apurinic/Apyrimidinic), the AP endonuclease recognizes this site and removes the damaged sequences, then DNA polymerase can fill in the gaps and DNA ligase can seal the strand
73
When creating a DNA library, what are some of the advantages of genome libraries? What about cDNA libraries?
Genomic DNA libraries include all of the DNA of an organism's genome, including non coding regions, this is useful for studying DNA introns, centromeres, or telomeres
cDNA libraries only include expressed genes from a given tissue, used to express recombinant proteins or to perform gene therapy
74
What does PCR accomplish for the researchers? What does Southern Blotting accomplish?
PCR increases the number of copies of a given DNA sequence and can be used for a sample containing few copies of a given DNA sequence
Southern Blotting is useful when searching for a particular DNA sequence because it separates DNA fragments by length and then probes for a sequence of interest
75
During DNA sequencing, why does the DNA polymer stop growing once a dideoxyribonucleotide is added?
Dideoxyribonucleotide lacks the 3' OH group that is required for DNA strands to elongate. When this is added to a growing stand, no more molecules can attach, they can't form a bond
76
What is the difference between a transgenic and a knockout mouse?
Transgenic mice have a gene introduced into their germ line or embryonic stem cells to look at the effects of that gene, best suited to study dominate genes
Knockout mice are those in which a gene of interest has been removed.
