Lecture 5 - DNA and Chromosomes Flashcards
(100 cards)
1
Q
how is RNA different from DNA ?
A
RNA is a temporary copy of the genetic information from DNA, and consists of uracil instead of thymine
2
Q
what is the principle structure of nucleotides?
A
sugar phosphate + base (G, C, T, A), nucleotide
3
Q
what are DNA and RNA molecules considered?
A
heteropolymers
4
Q
what is cyclic ribose molecule, and what is it important for?
A
a key element in nucleotide structure that connects all other parts of nucleotide and is crucial for polymerization of nucleic acids
5
Q
what does a nucleotide consist of?
A
a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups
6
Q
what base does RNA have instead?
A
uracil instead of thymine
7
Q
what are the substrates for DNA synthesis?
A
dATP, dGTP, dCTP, dTTP
8
Q
what are the substrates for RNA synthesis?
A
ATP, GTP, CTP, UTP
9
Q
how are nucleic acids connected?
A
thru phosphodiester bond through ONE phosphate
10
Q
what gives rise to the polarity of the resulting DNA strand?
A
the chemical differences in the ester linkages
11
Q
what kind of bonds form between A and T, and how many?
A
2 hydrogen bonds
12
Q
what kind of bonds form between G and C, and how many?
A
3 hydrogen bonds
13
Q
what is the only way for the bases to pair?
A
if the 2 polynucleotide chains that contain them are antiparallel (oriented in opposite directions)
14
Q
how are the nucleotides linked together?
A
covalently by phosphodiester bonds that connect the 3’-hydroxyl (-OH) group of one sugar and the 5’ phosphate (-PO3) attached to the next
15
Q
what would be the reverse complementary sequence of: 5’ - GCTTAGC - 3’ ?
A
GCTAAGC
16
Q
what are the major and minor grooves?
A
spatial orientation of nucleoside monophosphate residues along the helix
17
Q
describe the major groove
A
wider and provides access to the bases
18
Q
what typically interacts with the major groove?
A
many proteins that bind to specific nucleotide sequences
19
Q
describe the minor groove
A
formed by phosphate, that further forms a phosphate backbone (a negatively charged ridge on the helix)
20
Q
what is the phosphate backbone responsible for?
A
for the binding of positively-charged moieties
21
Q
what did Walther Flemming use to discover chromatin?
A
aniline dyes
22
Q
what are the 2 forms of the bacterium Streptococcus pneumoniae?
A
- R strain (nonlethal)
2. S strain (lethal)
23
Q
what are some characteristics of the R strain of S. pneumoniae?
A
lacks the protective coat; its colonies appear flat and rough (hence R form)
24
Q
what are some characteristics of the S strain of S. pneumoniae?
A
forms colonies that look dome-shaped and smooth (hence S form)
25
what did Frederick Griffith discover about DNA being a chemical substance?
in an experiment w/ S. pneumoniae, Griffith discovered that heat-inactivated, infectious bacteria cannot infect anything that can actually pass the pathogenic factor to the harmless bacteria
- basically S form could permanently change/transform the nonlethal R strain into the deadly S strain
26
___ is right handed helix
dsDNA
27
how many base pairs compose 1 turn of double helix in DNA?
about 10
28
the paper by Oswald Avery titled "Purification and Physical Characterization of the Active Transforming Principle" offers evidence for what?
the papers offers rigorous proof for the first time that purified DNA extracted from pathogenic strain can act as genetic material
29
what is Chargaff's rule?
the relative content of A always equals the content of T, and the content of G always equals the content of C (A%=T% and G%=C%)
30
what else did Chargaff suggest?
that guanine and thymine bases should predominantly exist in keto forms, which favors the formation of hydrogen bonds between A-T and G-C pairs that are equal in distance
31
Watson and Crick's model of DNA suggested what?
that DNA bases most likely form hydrogen bonds between each other rather than with the molecules of water
32
how does guanine always interact with cytosine?
by forming 3 hydrogen bonds
33
how does adenine always interact with thymine?
by forming 2 hydrogen bonds
34
how do the "Watson-Crick pairs" line up on the helix?
lays in a plane that is parallel to the plane where the nearby base pairs form
- each pair has a rotational angle of about 32 degrees so that the helix makes a complete turn over about 10 base pairs
35
how are pi-stacking interactions formed?
formed when the parallel orientation of the base pair planes allow pi orbitals from the top and bottom heterocycles to overlap along the helical axis
36
what are pi-stacking interactions?
noncovalent, weak interactions that shared pi-orbitals of aromatic rings and other heterocycles form with each other
37
how are pi-stacking interactions different than van der Waals interactions?
1. pi-clouds are capable of interacting with each other at large than the distance the van der Waals interactions permit
2. the orientation between pi-clouds does not necessarily reflects the adequate proximity of the electrons to the nuclei, which is pivotal for van der Waals interactions
38
how can hydrogen bonds be broken down?
by increasing temperature
39
what is the effect of cooperativity?
the formation of Watson-crick interactions in one area facilitates the formation of base pairs in another area
40
what kind of curve appears on a DNA melting profile?
sigmoidal curve
41
characteristic melting point is ___
GC-dependent
42
DNA may be detected by what?
UV absorption and intercalating dyes
43
DNA bases absorb UV at ___ nm
about 260 nm
44
what is a type of intercalating dyes and what would it appear as?
Ethidium bromide; would exhibit very strong orange fluorescence in complex with DNA
45
what are the steps to gel electrophoresis?
1. DNA samples loaded into agarose gel
2. Gel electrophoresis used to separate DNA based on size
3. stained w/ Ethidium Bromide and visualize under UV light
46
DNA replication is semi-___
conservative
47
each DNA strand serves as what? and what is it based on?
as a template for the synthesis of the daughter strand;
| based on nucleotide complementation
48
what does semi-conservative mean in DNA replication?
that each copy of DNA consists of an original strand and a synthesized strand
49
what is the semi-conservative mechanism?
each newly formed double helix has an old strand from the parental helix and a new strand
50
how do unicellular organisms pass on DNA?
thru the germline cells from generation to generation in multicellular species
51
what were the 3 models of DNA replication that were originally proposed?
1. semi-conservative
2. dispersive
3. conservative
52
what did the dispersive model propose?
each generation of replicated DNA molecules will be a mosaic of DNA from the parents strands and the newly synthesized DNA
53
what did the conservative model propose?
the parent molecule remains intact after being copied
| - the first round of replication would yield the original parent double helix and an entirely new double helix
54
what was the Meselson-Stahl experiment?
they used heavy nitrogen isotope to differentiate DNA species after the round of replication thru the different density and thus floatation in the cesium chloride density gradient
55
how did the Meselson-Stahl experiment work?
- bacteria grown over several generations in a medium containing either 15N (heavy isotope) or 14N (light isotope) to label their DNA
- cells are broken open
- DNA loaded into ultracentrifuge tube containing a cesium chloride salt solution (yellow)
- tubes centrifuged at high speeds for 2 days to allow the cesium chloride to form a gradient with low density at the top, and high density at bottom
- when gradient forms, DNA will migrate to region where its density matches that of the salt surrounding it
- heavy and light DNA molecules will collect in different positions in tube
56
where is the origin of replication?
at the specialized AT-rich areas
57
what does the propagation of Y-shaped two replication forks allow?
separation and synthesis of DNA at each replication origin continue in 2 directions
58
what are some characteristics of bacterial chromosomes?
- circular
- relatively short
- have ONE (1) origin of replication
59
what bond does the 3' hydroxyl group at the newly synthesized strand form?
a phosphodiester bond with the incoming nucleotide
60
what direction does the growth occur during DNA synthesis?
5' to 3' direction
61
what are the substrates for deoxyribonucleic acid polymerization?
deoxyribonucleoside triphosphates
62
what are the products of nucleic acid polymerization?
nucleic acid strand and pyrophosphates
63
where is the energy for polymerization of nucleic acids derived from?
the hydrolysis of high energy phosphoanhydride bonds
64
what is the enzyme called that carries out polymerization of nucleic acids?
polymerases
65
where does DNA polymerase adds a deoxyribonucleotide?
to the 3' end of a growing DNA strand
66
what is the DNA polymerase capable of?
proofreading the DNA synthesis by stopping, backtracking, and excising misincorporated nucleotide
67
for proofreading to take place, which direction should DNA polymerization proceed?
5' to 3' direction
68
why can DNA synthesis be performed from 3' to 5'?
proofreading would remove high-energy phosphates and block the synthesis
69
what is the leading strand?
the strand at the replication fork that can be extended continuously as it provides 3' end that can be extended in the direction of the propagating fork
70
what are Okazaki fragments?
short fragments of DNA that are used for the lagging strand of DNA during replication
71
how is the lagging strand replicated and what happens with the Okazaki fragments?
DNA polymerase uses a backstitching mechanism by synthesizing the Okazaki fragments in the 5' to 3' direction, and then moves back along the template strand (towards the fork) before synthesizing the next fragment
- the Okazaki fragments are later ligated together once they are fully extended and cover the template strand completely
72
how does RNA synthesis work then?
there is a special DNA polymerase called primase that synthesizes a short RNA fragment (called the RNA primer) on the template strand that is further extended by DNA polymerase
73
what are the multiple enzymes that work together to synthesize the lagging DNA strand, and how?
- RNA primers are extended by a replicative DNA polymerase to produce Okazaki fragments
- primers are subsequently removed by nucleases that recognize RNA strand in an RNA-DNA hybrid and degrade it
- this leaves gaps that are filled in by a repair DNA polymerase that can proofread it as it fills in the gaps
- completed DNA fragments are finally joined together by an enzyme called DNA ligase (which catalyzed the formation of a phosphodiester bond between the 3'-hydroxyl of one fragment and 5' phosphate end of next, thus linking the sugar-phosphate backbones)
74
how is the copying of both DNA strands coordinated and carried out by?
by a complex replication machine called replisome
75
what resolves torsional stress during the unwinding of the double helix?
topoisomerase
76
what are powerful chemotherapeutic agents against cancer cells?
topoisomerase inhibitors
77
what is the ribozyme that extends the 3' end of DNA by extending telomere repeats?
telomerase
78
genes encode mostly for ___
proteins
79
what else would genes encode for?
special types of RNA that do not encode proteins
80
what are chromosomes?
long stretches of DNA that contain genes
81
what does a nucleotide sequence of DNA usually contain?
gene sequences and intergenic, non-coding regions
82
what is the average size of the human chromosome?
about 130 million base pairs (which is about 2 inches long)
83
during mitosis, chromosomes are ___
condensed and highly visible
84
what is a chromatid?
very long DNA molecules with its associated proteins
85
what is the centromere?
the non-coding region that is used as an attachment site for the microtubules to separate sister chromatids from each other
86
what is a karyotype?
condensed, mitotic chromosomes that have a distinct appearance and is specific among species
87
how are chromosomes usually numbered?
by length
88
does the length of the chromosome and their number always correlate with the complexity of the organism?
no, it does NOT always correlate
89
during interphase, are chromosomes randomly distributed in the nucleus?
no they are not randomly distributed
90
what is the nuclear lamins?
intermediate filaments that are a fine woven network of special cytoskeletal proteins
91
where is the nuclear lamins located?
they form the lining on the inner surface of nuclear membrane and provide structural and functional support and organizing chromosomes
92
what is heterochromatin, and where is it located?
it is especially dense regions of chromatin; located mainly around the periphery of the nucleus, immediately under the nuclear envelope
93
what does the heterochromatin contain?
contains the genes for ribosomal RNAs
94
what is euchromatin?
a more extended form of chromatin
95
while mitotic chromosomes are highly condensed, interphase chromatin is ___
more loose
96
what is the nucleosome?
a nucleoprotein structure, where 4 homodimers of histones form oligomeric complex
97
the formation of nucleosome is a ___ process, where histones bind ____
spontaneous; cooperatively
98
how is euchromatin structured?
by loop domains
99
how can chromatin decondensation be achieved without dissociation of histones from DNA?
the chromatin-remodeling complex by sliding DNA along the histone octamers, which cause the nucleosomes to end up being spread farther from each other by increasing the size of linker DNA
100
how does the position effect cause the silencing of the genes?
due to the close proximity of active euchromatin genes to heterochromatin region, this may lead to condensation of euchromatin
- this often occurs when there are chromosomal rearrangements of the parts, and the area that used to be pure euchromatin ends up next to heterochromatin which inactivates some genes
