Chapter 6 Flashcards
1
Q
DNA
A
deoxyribonucleic acid; the molecule of heredity that encodes genetic information.
2
Q
Chemical studies locate DNA in []
A
chromosomes
3
Q
Nucleotide
A
a subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate group, and a sugar (deoxyribose in DNA; ribose in RNA).
4
Q
Transformation
A
a mechanism by which bacteria transfer genes from one strain to another; occurs when DNA from a donor is added to the bacterial growth medium and is then taken up from the medium by the recipient. The recipient cell is known as a transformant.
- The ability of a substance to change the genetic characteristics of an organism
5
Q
[] is the active agent of transformation
A
DNA
6
Q
DNA is a polymer of [] joined by [] . [] Nucleotides are made of [] , [] , and [] .
A
nucleotides; phosphodiester bonds; deoxyribose; phosphate one of four nitrogenous basis
7
Q
Where is DNA localized
A
DNA is localized almost exclusively in the chromosomes within the nucleus of a cell.
8
Q
What did Avery and his colleagues show
A
Avery and his colleagues showed purified DNA from virulent bacteria could transfer non-virulent bacteria into virulent bacteria, showing strong evidence for DNA as the genetic material.
9
Q
What did Hershey and Chase do?
A
Hershey and Chase grew T2 bacteria in the presence of either label proteins or label DNA. They found the radioactively tagged viral DNA contained genetic instructions to produce more virus particles.
10
Q
[] are the building blocks of DNA.
A
Nucleotides
11
Q
Polarity (definition and polarity of DNA)
A
the property of having distinct ends.
3 to 5
12
Q
5’ end:
A
the first nucleotide of an RNA or DNA molecule
13
Q
3’ end
A
the final nucleotide of an RNA or DNA molecule.
14
Q
The DNA helix consists of []
A
two antiparallel chains
15
Q
full structure of DNA
A
The DNA molecule consists of two strands that wind around one another to form a shape known as a double helix. Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate groups. Attached to each sugar is one of four bases–adenine (A), cytosine (C), guanine (G), and thymine (T).
16
Q
DNA is a type of []
A
nucleic acid
17
Q
double helix
A
two single DNA strands
18
Q
Each DNA strand is composed []
A
deoxyribose nucleotides with each strand being a polynucleotide.
19
Q
Each nucleotide has a…
A
phosphate group, nitrogenous base, and a 5 carbon sugar
20
Q
The backbone is []
A
an alternative of phosphate and sugars
21
Q
Each strand has a [] and [] on the ends of the strand. The double helix is [] meaning if there is a [] on one end the same end on the other strand will be a [] . The 3 and the 5 are related to the number of [].
A
5; 3; antiparallel ; 5; 3; carbons
22
Q
Each of the bases is attached to the []
A
DNA sugar
23
Q
The nucleotide are [] in a specific way and this encodes []
A
ordered; genetic information
24
Q
Pyrimidines:
A
Cytosine and Thymine
25
Purines:
Adenine and Guanine
26
Each of the nucleotides bind to another through []
hydrogen bonds
27
hydrogen bonds:
weak electrostatic bonds that result in a partial sharing of hydrogen atoms between reacting groups.
28
complementary base pairing:
during DNA replication, base pairing in which a complementary strand aligns opposite the exposed bases on the parent strand to create the nucleotide sequence of the new strand of DNA; hydrogen bonding between A:T and G⋮C that holds the two antiparallel strands of the DNA double helix together; can also enable formation of RNA–DNA or RNA–RNA double strands. (A pairs with U in RNA.)
29
The spatial requirements of the double helix...
demand each base pair must consist of one pyrimidine and one putrine.
30
The sum of the connections between the base pairs ...
is the key to the molecules stability
| DNA structure is the foundation of genetic function
31
The DNA molecule is a double helix ...
composed of two strands with nucleotides joined with phosphodiester bonds
32
Phosphodiester bond:
two hydroxyl groups in phosphoric acid react with a hydroxyl group on another to form two ester bonds.
33
The two strands are antiparallel meaning...
one strand is oriented in the 5 to 3 direction while the other complementary strand is 3-5.
34
Hydrogen bonding between...
he complementary bases A with T and G with C holds the two strands together
35
Most eukaryotes have a double stranded linear DNA but prokaryotes, chloroplasts, and mitochondria and some viruses...
have double stranded circular DNA. Other viruses contain a single stranded DNA linear or circular.
36
Most genetic information is read from...
unwound DNA chains
37
The unwinding of the DNA molecule...
exposes a single sequence of bases on each other the two strands
38
Transcription:
a sequence of RNA matching the DNA is synthesized
39
Replication:
A complementary sequence of DNA is synthesized.
40
True or False: Some genetic information is accessible without unwinding DNA
True
41
In some viruses, ...
RNA contain the genetic information
42
Retroviruses:
use RNA as their genetic material
43
RNA:
ribonucleic acid; a polymer of ribonucleotides. Different RNAs play important roles in protein synthesis and regulation of gene expression.
44
Differences between DNA and RNA:
1. RNA has ribose instead of deoxyribose as its sugar
2. RNA has the base uracil instead of thymine, however U like T pairs with A
3. Most RNA molecules are single stranded containing fewer nucleotides than DNA molecules.
4. RNA has a complicated structure of short double stranded segments interspersed with single stranded loops.
This is because RNA can fold bringing together two oppositely oriented regions carrying complementary nucleotide sequences to for smaller segments within the molecule.
5. RNA also runs 5 to 3
6. RNA is much less stable than DNA.
7. RNA plays in the production of proteins and plays a significant role in DNA replication.
8. DNA carries the genetic information in the sequence of its four bases
9. The base sequence of DNA can be read from a single unwound strand during replication or transcription. In addition, specialized proteins can recognize and bind to short base sequences accessible in the grooves of double stranded DNA.
10. RNA contains ribose rather than deoxyribose and uracil instead of thymine, RNA is generally single stranded instead of double.
45
DNA replication
Watson and Crick said in their paper “it has not escaped our notice that the specific pairing we have postulated immediately suggest a possible copying mechanism for genetic material”
Watson and Crick postulated the double helix unwinds to expose the bases in each strand of DNA with each strand acting as a template for the second strand.
The A on one strand becomes a T on a new strand and C a G and so on.
One the complementary base pairings and hydrogen bonds are formed, enzymes join the bases and nucleotides.
46
How many types of replication?
3
47
Semiconservative:
a mechanism of DNA replication in which each single strand of the parent double helix serves as template for synthesis of its complement. The result is two daughter double helixes that each contain one of the original DNA strands intact (conserved) and one completely new strand. In g2 have a mixture of new dna and the mixed strands
48
Conservative:
Resulting daughter DNA strands are either double helixes of new strands or the original in gen 1, and mostly new strands with some only in G2.
49
Dispersive:
Patches of the new DNA are the new and the old in both generations
50
Matthew Meselson and Franklin Stahl Experiment
- They wanted to distinguish parental DNA from daughter DNA
- Grew ecoli in N14 medium serving as a control
- Grew ecoli in a N15 medium, resulting cells with N15 atom DNA
- Took the N15 DNA and put them into a N14 solution and let it replicate
- 30 minute replication: strands with half N15 and N14
- Long replication: All cells with N14
Mixed the N14 cells, N14 and N15, and N15 cells and mixed them in a solution and centrifuged them
- When the DNA from each sample was centrifuged (density gradient centrifugation) in a cesium chloride gradient, found cells with N14 dna were at the top, N14 and N15 were in the middle, and N15 was at the bottom.
- Results showed DNA replication was semiconservative since generation 1, 30 minutes of N15 and N14 had strands with one N15 and one N14, and longer generation had the mixed strands and the strands with only N15. This matched a semiconservative view.
51
DNA polymerase:
a complex enzyme that forms a new DNA strand during replication by adding nucleotides reverse complementary to a template, one by one, to the 3' end of a growing strand. It has strict operating requirements.
52
DNA polymerase 1
an enzyme found in prokaryotes which help in bacterial DNA replication. It is the first type of DNA polymerase discovered by Arthur Kornberg in 1956. This enzyme is present in all prokaryotic organisms. Pol 1 is encoded by the gene polA and is composed of 928 amino acids. It has a 5’ to 3’ exonuclease activity; thus, it is popular as a DNA repairing enzyme rather than a DNA replicating enzyme. It also has the ability to catalyze multiple polymerizations prior to releasing the template DNA, and connecting Okazaki fragments together by filling new DNA, and removing RNA primers.Pol 1 isolated from E Coli was extensively used in molecular applications.
53
DNA polymerase 2
DNA polymerase 2 (Pol 2) is a prokaryotic enzyme which catalyzes the DNA replication. It belongs to the polymerase B family and is encoded by the gen polB. It was first discovered from E Coli by Thomas Kornberg in 1970. Pol 2 is a globular protein composed of 783 amino acids. It has both 3’ to 5’ exonuclease activity and 5’ to 3’ polymerase activity. It interacts with DNA polymerase 3 enzymes to maintain the fidelity and processivity of DNA replication. Pol 2 also has the ability to proofread the newly synthesized DNA for accuracy.
54
DNA polymerase 3
DNA polymerase 3 (Pol 3) is the main enzyme which catalyzes the DNA replication in prokaryotes. It belongs to the family C polymerase and is encoded by the gene polC. It was discovered by Thomas Kornberg in 1970. Pol 3 is a component of replication fork and can add 1000 nucleotides per second to the newly polymerizing DNA strand.
Pol 3 is a holoenzyme composed of ten distinct proteins and has three functional molecules namely α, ε and θ. Three functional molecules of Pol 3 are separately responsible for three actions of the enzyme. The α subunit manages the polymerization of DNA while the ε manages the exonuclease proofreading activity of the pol 3 enzyme. The θ subunit helps the ε subunit for proofreading.
55
DNA replication is a [] regulate complex process
tightly
56
Initiation:
the first phase of DNA replication, transcription, or translation needed to set the stage for the addition of nucleotide or amino acid building blocks during elongation.
The first step in DNA replication is to ‘unzip’ the double helix structure of the DNA? molecule. This is carried out by an enzyme? called helicase which breaks the hydrogen bonds? holding the complementary? bases? of DNA together (A with T, C with G). The separation of the two single strands of DNA creates a ‘Y’ shape called a replication ‘fork’. The two separated strands will act as templates for making the new strands of DNA.
57
Elongation:
phase of DNA replication, transcription, or translation when nucleotides or amino acids are added successively to a growing macromolecule.
58
lagging strand
strand is oriented in the 3’ to 5’ direction (towards the replication fork),
59
leading strand
strand is oriented in the 5’ to 3’ direction (away from the replication fork)
60
True or False: As a result of the different orientations pf the lagging and leading strand, the two strands are replicated differently.
True
61
Leading strand replication:
A short piece of RNA ?called a primer? (produced by an enzyme called primase) comes along and binds to the end of the leading strand. The primer acts as the starting point for DNA synthesis. DNA polymerase? binds to the leading strand and then ‘walks’ along it, adding new complementary? nucleotide? bases (A, C, G and T) to the strand of DNA in the 5’ to 3’ direction. This sort of replication is called continuous.
62
Lagging strand replication:
Numerous RNA primers are made by the primase enzyme and bind at various points along the lagging strand. Chunks of DNA, called Okazaki fragments, are then added to the lagging strand also in the 5’ to 3’ direction. This type of replication is called discontinuous as the Okazaki fragments will need to be joined up later.
63
Once all of the bases are matched up
A with T, C with G), an enzyme called exonuclease strips away the primer(s). The gaps where the primer(s) were are then filled by yet more complementary nucleotides. The new strand is proofread to make sure there are no mistakes in the new DNA sequence. Finally, an enzyme called DNA ligase? seals up the sequence of DNA into two continuous double strands. The result of DNA replication is two DNA molecules consisting of one new and one old chain of nucleotides. This is why DNA replication is described as semi-conservative, half of the chain is part of the original DNA molecule, half is brand new. Following replication the new DNA automatically winds up into a double helix.
64
The DNA molecule is reproduced by...
semiconservative replication. The two DNA strands separate and each acts as a template for the synthesis of a new complementary strand
65
DNA polymerase synthesizes DNA in the []
5 to 3 direction by adding nucleotides successively onto the 3 end of a growing DNA chain
66
DNA polymerase requires a supply of
four deoxyribonucleotide triphosphates, a single stranded DNA template, a primer of either DNA of RNA with a free 3 hydroxy group.
67
At the DNA replication fork, DNA polymerase
synthesizes the leading strand continuously while the lagging strand is synthesized as multiple Okazaki fragments are then joined by DNA ligase.
68
The integrity of DNA is preserved by
redundancy in the two strands, the precision of the enzymes synthesizing DNA, and the enzymes repairing the damage.
69
Homologous recombination
1. Used to fix double strand breaks
2. Occurs in somatic cells
3. Can be the repair from inside sources such as enzymes or external like radiation
4. Restart replication at a stalled replication fork
5. Reinitiate collapsed replication fork
6. Restore maintenance in the absence of telomerase
70
Gene conversion is
changing from one allele to another
Gene conversion is a process whereby one allele in a heterozygote is physically changed into the other and provides evidence for heteroduplex formation during recombination events
71
Heteroduplex formation:
a region of double-stranded DNA in which the two strands have nonidentical (though similar) sequences. Heteroduplex regions are often formed as intermediates during crossing-over.
Start with two separate chromosomes and a crossing over event occurs close to one of the alleles
Ex: crossing over occurs changing a recessive allele to a dominant
Results in irregular segregation and irregular allele in the gametes
- Ex: 2 with dominant allele and 1 with recessive
72
Holiday model of homologous recombination
There is a cut in the chromosome
A strand exchanges with the other creating a x called the holiday junction. It is where strand is exchanged. This can occur because the genetic codes on the chromosomes are highly similar.
73
Holliday junctions:
interlocked regions of two nonsister chromatids in recombination intermediates.
74
Homologs [] , [] , and [] . The [] with phage lambda provided key evidence for this key aspect of recombination
physically break; exchange parts; rejoin; Meselson wiggle experiment
75
The region where exchange parts happened is called a []
holiday junction
76
The rejoined body is called a []
heteroduplex formation
77
Crossing over occurs between...
non sister chromatids after DNA replication
78
Breakage and repair generate ...
reciprocal products of recombination
79
precision of crossover over
Precision in the exchange with no gain or loss in the nucleotides prevents mutations from occurring. Geneticists originally deduced the precision of crossover over from observing the recombination does not cause mutations.
Results in gene conversion and gene diversity
