Midterm 1 Flashcards
(88 cards)
1
Q
Chromosomes
A
Long double-stranded DNA molecules
2
Q
What is the purpose of DNA packaging?
A
Increases organization, thus no messes
3
Q
What is the structure of bacteria chromosomes?
A
Single, circular DNA
4
Q
Chromatin
A
DNA and protein
5
Q
Homologous chromosomes
A
The maternal and paternal chromosomes of a pair
6
Q
What technique does chromosome painting use?
A
DNA hybridization
7
Q
How does chromosome painting work?
A
Different colours of fluorescent dye are applied to the chromosome which can form base pairs (hybridize) to certain ones
8
Q
What is the traditional way of staining?
A
Dyes that bind to certain DNA sequences, such as those with A-T vs G-C, producing different bands
9
Q
Karyotype
A
A display of the full set of 46 chromosomes with homologous one numbered and arranged in pair
10
Q
Gene
A
Segment of DNA that contains instructions to make a functional protein or RNA molecule
11
Q
What do the RNA molecules produce?
A
A protein or can be the final product itself
12
Q
Genome
A
The total genetic information carried by all the chromosomes in a cell or organism
13
Q
What genomes are very compact?
A
Bacteria
14
Q
What additional DNA do eukaryotes have?
A
Junk DNA that doesn’t code (intron)
15
Q
What is the purpose of junk DNA?
A
Evolution of species or for activity of the genes
16
Q
Does junk DNA differ between organisms?
A
No, it’s highly conserved
17
Q
What is the relationship between gene number and total genome size?
A
There isn’t a relationship just that it’s roughly correlated with species complexity
18
Q
What makes up the cell cycle?
A
Interphase and mitosis
19
Q
Interphase
A
Where chromosomes are duplicated and the cell grows
20
Q
Mitosis
A
The chromosomes are distributed to two daughter nuclei
21
Q
How do the chromosomes appear during interphase?
A
Long, thin threads that can’t be seen under a microscope
22
Q
Replication origin
A
Where DNA replication begins based on a sequence
23
Q
How many replication origins are in a eukaryote?
A
Multiple that occur bidirectionally
24
Q
What is the structure of a telomere?
A
Repeated nucleotide sequences
25
What is the purpose of a telomere?
Prevent DNA from being broken during cellular division (at the ends) and aids in replication of chromosome ends
26
How do chromosomes appear in mitosis?
Condensed and can be viewed under a microscope
27
What are the basic points in mitosis?
1. Chromosomes condense
2. Nuclear envelope breaks down
3. Mitotic spindles attach to sister chromatids
4. They pull apart to opposite sides
5. Nuclear envelope reforms and two separate cells are formed (split)
28
What three DNA sequence elements are important?
1. Telomere
2. Replication origin
3. Centromere
29
What is the purpose of a centromere?
Attaches the duplicated chromosomes to a mitotic spindle, thus allowing segregation of the two and holds the chromosomes compact
30
How do chromosomes exist within the interphase nucleus?
Occupy a particular region either on the nuclear envelope or in the nuclear lamina
31
What is the purpose of the nuclear lamina?
The protein meshwork that supports the envelope
32
What exists within the nucleolus?
Parts of the different chromosomes that carry genes to encode for ribosomal RNA
33
What is the purpose of heterochromatin?
Contain noncoding DNA and few genes where dense chromosomes exist
34
What is the purpose of histones?
Packing chromatins
35
What is the structure of a nucleosome?
Core particle with wrapped DNA, linker DNA, and H1
36
How is the core particle revealed?
Nuclease which cut down the phosphodiester bond between nucleotides
37
What histones form a core particle?
The histone octamer has two molecules of each: H2A, H2B, H3, and H4
38
What does the formation of multiple nucleosomes lead to?
Chromatin thread
39
What is the structure of each histone in the octamer?
Long, unstructured N-terminal amino acid tail
40
How do the histone octamer differ between species?
Don't as they are highly conserved due to their vital role in controlling eukaryotic chromosome structure
41
What does the packaging of multiple nucleosomes depend on?
H1, as it pulls the adjacents ones into a repeating array (condensed)
42
What is the structure of histone 1?
Globular region with a pair of long tails are its C-terminal and N-terminal ends
43
What is the purpose of the long C-terminal tail?
Required for H1 to bind to chromatin
44
How are chromatin fibers folded?
Into a series of loops
45
DNA repair
Correct temporary DNA damage
46
What happens if there is a malfunction in a repair protein?
Malfunctions in some repair proteins result in an infective inherited gene that can't repair damaged DNA
ex. one of UV radiation
47
How do depurination and deamination take place?
Both spontaneous loss reactions
48
What is not broken in depurination and deamination?
Phosphodiester backbone
49
What is depurination?
The loss of a purine base (A and G) by removing a purine base from the nucelotide
50
What does depurination result in?
Lesions to the DNA (similar to missing teeth)
51
What is deamination?
The loss of an amino group from a cytosine in DNA to produce the base uracil
52
How can chemical changes in DNA occur?
1. Depurination
2. Deamination
3. Chemically reactive by-products of cell metabolism that react with bases to alter their properties
53
Thymine dimer
The covalent linkage between two adjacent pyrimidine bases caused by UV radiation
54
What happens if deamination is left uncorrected?
Substitution of one base and therefore the replicate machinery will insert an adenine (uracil)
55
What happens if depurination is left uncorrected?
Loss of a nucleotide pair and therefore the replication machinery skips it, resulting in a daughter DNA molecule having a deletion.
56
What do thymine dimers cause to replication machinery?
Stall it at the site of damage
57
What do repair mechanisms depend on?
The double-helical DNA, specifically at least one strand that is not altered
58
Explain the steps of repair mechanisms.
1. Damaged DNA recognized by enzymes and nuclease cleave the covalent bonds around the damaged section to leave a gap (unique)
2. A repair DNA polymerase binds to the 3' hydroxyl end of the cut DNA strand and fills in the gap with a complementary sequence to the undamaged strand
3. The nick in the backbone is sealed by DNA ligase
59
What is a mismatch repair?
Fixes the copying errors of a replication machinery where there is a mispaired nucleotide.
60
How inaccurate in the replication machine (DNA replication with proofreading)?
Makes one mistake in 10^7 nucleotides copied
61
How does the mismatch repair system work?
1. Proteins recognize the mismatch
2. Remove a portion of the strand with the error (nucleases)
3. Resynthesize the missing DNA
62
What happens if a mismatch is left uncorrected by the replication machinery?
Permanent mutation in the next round of DNA replication
63
How does the mismatch system decided which strand to remove the portion from?
In bacteria the newly synthesized DNA is less methylated, plus other strategies
64
What does mismatch repair play a huge role in?
Preventing cancer
65
How does mismatch nucleotides result in cancer?
Predisposition is caused by inherited mutations in genes that encode mismatch repair gene (both copies damaged = more likely to develop mutations and become cancerous).
66
What are double stranded breaks caused by?
Radiation or mishaps at the replication fork
67
Why are double stranded breaks dangerous?
Fragmentation of chromosomes and loss of genes
68
Why are double stranded breaks difficult to repair?
The broken pieces separate so there is no copy to reconstruct missing information
69
Nonhomologous end joining
Where the broken ends are rapidly glued back together before the DNA fragments and drifts apart
70
Explain the steps of nonhomologous end joining
1. Break cleaned by nuclease that chews back broken ends to produce flushed ones
2. Flushed ends stitched together by DNA ligase
71
What is the problem with nonhomologous end joining?
Nucleotides are lost at the site of repair, thus disrupting the activity of the gene
72
Why use homologous recombination?
Restore the original DNA sequence at the site of the break; no loss of genetic information.
73
When does homologous recombination occur?
When there is a double stranded break in a daughter DNA strand, but before the daughter DNA strands are separated, so that the undamaged strand can be used as the template. MUST have identical sequences around the damage.
74
Explain the steps of homologous recombination.
1. Nuclease chews the 5' ends of the two broken strands at the break
2. Enzymes enter the 3' ends of the unbroken DNA and search for a complementary sequence through base pairing
3. Invading strand elongated by repair DNA polymerase
4. Additional DNA synthesis at the 3' ends of the strands of the broken double helix
5. DNA ligation
75
What is homologous recombination used in?
Exchange of genetic information during the formation of the germ cells; meiosis.
76
How can mutations be deadly? Give example.
A single nucleotide change in a vital position can alter protein function to poor or none at all
ex. single nucleotide in hemoglobin gene = sickle cell anemia which produces sickle red blood cells leading to blocking small vessels, thus organ failure
77
Why must reproductive cells be protected against mutation?
A mutation in a germ cell will be passed onto all the cells in the body that develop from it and those germ cells responsible for the next generation as well.
78
Why must somatic cells be protected from mutation?
Mutations in somatic cells lead to variations where some can grow uncontrabbly = cnacer
79
Explain cancer in terms of mutations.
The gradual accumulation of random mutations in a somatic cell.
80
Give an example of DNA mutations were preserved.
Those that have no effect on the fitness of the organism. For instance, humans and chimps have DNA sequences that are at least 98% identical.
81
Mutation
The permanent change to a DNA nucleotide sequence
82
Replisome
The complex replication machine that contains different proteins with specific functions for DNA replication
83
How inaccurate is DNA replication with mismatch repair?
1 in 10^9 nucleotides
84
How inaccurate is DNA replication (without proofreading or the mismatch repair)?
1 in 10^5 nucleotides
85
What can the inaccuracy of the mismatch repair lead to (in terms of biological disorders)?
Mutations can lead to heritable changes which make someone more susceptible to a gene
ex. BRCA1/2
- therefore if already have one functional copy = more likely to get disorder (loss of heterozygosity)
86
When does nonhomologous end joining occur? Why?
G1 since the chromosomes are farther apart from one another, thus there would be more differences in their sequences
87
When does homologous recombination occur? Why?
S and G2 because chromosomes are closer to each other/duplicated, so similar sequences (templates).
88
What is the difference between endonuclease and exonuclease?
Endonuclease can cleave bonds internal in a phosphodiester bond (thus removing multiple) while exonuclease cleave at the end of bonds, to remove singular nucleotides
