U4 LEC: GENOMES AND VARIANTS Flashcards
1
Q
Bacterial Genome consists of?
A
- nucleoid
- bacterial genomes
- chromosomal domains
- bacterial chromosomes
2
Q
Compact bacterial chromosome
A
Nucleoid
3
Q
About a third of the volume of the cell, has many independent chromosomal domains
A
Bacterial genomes
4
Q
Supercoil loop of DNA, randomly distributed
A
Chromosomal domains
5
Q
Majority are circular, some are linear
A
Bacterial chromosomes
6
Q
Linear bacterial chromosomes
A
- multiple1-Mb chromosomes (Borrelia species)
- 8-Mb chromosomes (Streptomyces species)
7
Q
Circular bacterial chromosomes are mostly represented by?
A
plasmids
8
Q
1-Mb chromosomes
A
Borrelia species
9
Q
8-Mb chromosomes
A
Streptomyces species
10
Q
These proteins assist in the level of compaction in bacterial genome.
A
Nucleoid-Associated Proteins
11
Q
How do NAPs help in organization of chromosome?
A
bridging, wrapping or bending, causes level of compaction
12
Q
NAPs
A
- HU
- SMC complex
- FIS
- IHF
- H-NS
13
Q
NAPs
Small protein subunit that bridges interconnecting sites between genome
A
H-NS
14
Q
NAPs
H-NS causes ______ with linear DNA and fold with each other
A
bridging
15
Q
NAPs
Antiparallel coiled hinged domain, wraps around to linear DNA causing it to coil
A
SMC complex
16
Q
NAPs
Appearance of SMC complex
A
Safety pin appearance
17
Q
NAPs
Abundant NAP, causes interlinkage between successive joints or part of linear DNA and causes to coil
A
HU
18
Q
NAPs
Alters and facilitates the formation of loops
A
IHF
19
Q
NAPs
Causes compact and organization but separate molecule that causes bridging with linear DNA
A
FIS
20
Q
Capsid is made up of?
A
capsid proteins wrapped around RNA or DNA
21
Q
Capsid follows general symmetry which includes
A
- Icosahedral
- Helical
22
Q
Capsid follows what structure?
A
- symmetrical
- quasisymmetrical
23
Q
Most common capsid structure
A
helical structure
24
Q
Virus that attacks bacteria
A
Bacteriophage
25
Structures of the Bacteriophage
- head (where the genome is located)
- tail (attachment point)
26
Virus may possess a capsule made up of?
lipid
27
T/F: Larger organisms have a larger genome.
True
28
How many genes do we have
25,000
29
1 gene will contain how many base pairs?
less than 1000
30
Largest known human gene, facilitates muscle injury repair and found in the X chromosome
Dystrophin (2.4M bases)
31
T/F: 99.9% of nucleotide bases are exactly the same in all people.
True
32
The Human Genome Project only took blood from?
5 people
33
More than _____ genes have an unknown function
12,000
34
Histone protein that has the most modification, most diverse and most variable
H2
35
This refers to when histone is removed, the gene is turned off
Knockout
36
Core histone protein, knockout phenotype
H2A
37
For DNA repair, sperm defect in meiosis
H2A.X
38
Gene activation and silencing, embryonic infertlity
H2A.Z
39
Unique Animal Chromosomes
- Lampbrush Chromosome
- Polyetylene chromosomes
40
These chromosomes are found in some amphibians
Lampbrush Chromosomes
41
Lampbrush Chromosomes
Found specifically in what amphibians?
Pleurodele amphibians
42
Lampbrush Chromosomes
Similar appearance to?
test tube brush
43
Lateral loops that extrude from the chromomeres at certain prositions
Lampbrush Chromosomes
44
Lampbrush Chromosomes
Appear at meiosis stage in which chromosomes resemble a?
series of beads on a string
45
Lampbrush Chromosomes
The loop is an _______ DNA segment that is actively _______.
extruded, transcribed
46
Lampbrush Chromosomes
Present in urodele amphibians
Oocytes (Diplotene prophase chromosomes)
47
These chromosomes are found in insects such as common house flies in their larvae
Polytene chromosomes
48
Polytene Chromosomes
Appearance
different protruding chromosomes with different synapsis, many arms
49
Polytene Chromosomes
Usually found at?
interphase nuclei
50
Polytene Chromosomes
Useful for?
analysis of many facets of eukaryotic interphase chromosome organization and the genome as a whole
51
Polytene Chromosomes
Develop from chromosomes of?
diploid nuclei by successive duplication of each chromosomal element
52
Gene Size of Rickettsia prowazekil
1.11Mb, 834 genes
53
Gene Size of Homo sapiens
3,300 Mb, 25,000 genes
54
Unique sequence, only 1 copy per haploid
Nonrepetitive
55
Nonrepetitive represents what regions?
coding (exons)
56
Introns contain?
repetitive DNA
57
T/F: The length of the nonrepetitive DNA increase with overall genome size.
True
58
Increase genome size in higher eukaryotes reflects?
increase amount and proportion of repetitive DNA
59
T/F: Genome size and gene number is weaker in prokaryotic genomes than in eukaryotic genomes.
False
weaker sa eukaryotic
60
Moderately Repetitive Sequences
- Interspersed Elements (Repetitive Transposed Sequences)
- Tandem Repeated DNA (VNTRs and STRs)
61
under Moderately Repetitive Sequences
- Transposons
- SINEs
- LINEs
62
Most common moderately repetitive sequences
Transposons
63
selfish or junk DNA
Transposons
function on their own pero walang ambag aw
64
Short sequences of DNA, ability to move to new locations in the genome
Transposons
65
Opposite of transposons
Retrotransposons (difference in size)
66
Retrotransposons include?
- Short interspersed elements
- Long interspersed elements
67
<500 base pairs, present in 500 times or more
SINEs
68
200 to 300 base pairs long, dispersed uniformly throughout the genome, potential for transposition within the genome related to chromosome rearrangements during evolution
Alu family
69
6kb in length, may be present 850,000 times in human genome
LINEs
70
under Tandem Repeated DNA
- Short Tandem Repeats (STRs)
- Variable Number Tandem Repeats (VNTRs)
71
STRs are under microsatellites with ______ repeats and an array size on the order of _______ units
2- to 5- bp repeats, 10-100 units
72
Dispersed throughout the genome and vary among individuals in the number of repeats present at any site.
Short Tandem Repeats (STRs)
73
STRs are in the form of?
di-, tri-, tetra-, pentanucleotides
74
VNTRs are under microsatellites with ______ repeats and an array size of _______
10- to 100-bp (usually around 15-bp), 0.5-30 kb
75
VNTRs
How many base pairs long?
15 to 100bp
76
VNTRs
Found?
within and between genes
77
T/F: In VNTRs, number of tandem copies of each specific sequence at each location varies from one individual to the next.
True
78
VNTRs
Variation in size between individual humans is the basis for?
DNA fingerprinting
79
Highly repetitive sequences
Satellite DNA (satDNA)
80
Highly repetitive DNA, short sequences repeated a large number of times
satDNA
81
satDNA
Variable ______ repeat forms array up to ______
AT-rich, 100Mb
82
satDNA
Monomer length
150 to 400bp
83
satDNA
Located at?
heterochromatic regions
84
satDNA
Mostly in?
- centromeric
- subtelomeric
- also at intercalary positions
85
satDNA
Likely involved in?
sequence-specific interactions and subsequently in epigenetic processes
86
satDNA
Has a sequence-independent role in?
formation and maintenance of heterochromatin
87
satDNA
These produce siRNAs
Transcripts
88
satDNA
siRNAs are involved in the posttranscriptional gene regulation through?
action of RNA-induced silencing complex (RISC)
89
Noncoding RNAs have been found to play an important role in?
neuronal functions
90
Appear to turn over rapidly, but can be strongly influenced by positive selection.
MicroRNAs
91
These are dead genes, may evolve functions in regulating expression of related genes and may regulate parenteral genes.
Pseudogenes
92
Pseudogenes are DNA sequences representing?
evolutionary vestiges of duplicated copies of genes that have undergone significant mutational alteration
93
Genome will evolve because of?
errors it may encounter during central dogma
94
What dictates the pace of evolution of an organism?
- how often does the organism have a mutation
- how efficient is the organism to fix the mutation
95
In homo sapiens, rate of fixation is ______ and rate of mutation is _______
high, low
96
In bacteria, rate of fixation is ____ and rate of mutation is ______
low, high
97
Introduction of Mutation
- replication error or DNA damage
- protein-coding region
- substitution mutation
98
Second step, over successive generations, molecular change a feature of the entire phylogenetic unit such as population, species, or lineage
Fixation of Mutation
99
Fixation of Mutation is predictable by?
probability (selectively neutral or near-neutral)
100
Random changes in the frequency of a mutational variant in a population
Genetic Drift
101
Genetic Drift
A variant may be either?
lost or fixed
102
Genetic Drift
Usually in the form of?
nucleotide substitutions
103
This is a combination of the mutation rate and the rate of fixation
Evolutionary Rate
104
Substitution rate is _________ mutation rate
equal to
105
Overall influence that a life history trait has on sequence evolutionary rate is largely a result of?
magnitude and directions of its effects on mutation and fixation rates
106
Mechanisms of Genome Evolution
- Gene duplication
- De novo origination
- Horizontal gene transfer
- Gene Recombination
- New Gene Regulatory Systems
- Transposable Elements
- Molecular Evolution of Repetitive DNA Sequences
- Evolution Rate of Repetitive DNA Sequences
107
Evolution of Prokaryotic Genome
- The Streamlining Hypothesis
- The Muller Ratchet
108
First theory for genome evolution for prokaryotes
Streamlining Hypothesis
109
Streamlining Hypothesis
If an organism evolves, it will prefer a?
smaller genome, less use of energy
110
Streamlining Hypothesis
Natural selection will favor?
genome reduction and low GC content
111
Streamlining Hypothesis
Faster change in DNA if there is?
low GC content *has stronger bonds)
112
Streamlining Hypothesis
Most common explanation for genome reduction in?
free-living bacteria
113
Streamlining Hypothesis
Organisms do this selection by?
cellular economization
114
Streamlining Hypothesis
Mainly determined by?
intracellular environment
115
This theory states that the effect of mutation is cumulative.
Muller Ratchet
116
This refers to small mutations one point at a time, and gradually overtime will accumulate and lead to a full-blown evolution.
Muller Ratchet
117
In populations undergoing constant bottlenecks and no recombination, genome reduction occurs through?
accumulation of slightly deleterious mutations
118
Muller Ratchet
Typical characteristics of these genomes, such as their large _____ content reflect known mutational biases rather than adaptations evolved by selection.
A+T
119
Impact of Genome Reduction on Host-Associated Bacteria
Modifications of some genes coded in the ______ genome could allow the ______ to cope with loss of otherwise essential genes
reduced, endosymbiont
either the genome is already present sa host or sa bacteria
120
Impact of Genome Reduction on Host-Associated Bacteria
The presence of __________ in the genomes of cosymbionts (if any) may compensate for _______ in the endosymbiont
complementary genes, gene losses
endosymbiont retains genome, cosymbiont loses it
121
Impact of Genome Reduction on Host-Associated Bacteria
Genes coded in the genome of the ____ compensate for gene losses in the genome of the ______
host, endosymbiont
122
under Impact of Genome Reduction on Host-Associated Bacteria
- host origin
- from the endosymbiont and transferred to the host
- horizontally transferred from unrelated organisms not participating in the symbiosis to the host genome or its endosymbionts
123
The mitochondrial genome is particular to what lineage?
matrilineal
124
Mitochondrial genome
Base pairs and genes
17,000bp
32 genes
125
T/F: The mitochondrial gene is not used for studies because it is very small.
True
very small din impact sa health ng patient
126
If there is error with RNA splicing, there will be a problem with the?
protein
127
Incomplete splicing produces a?
truncated protein
128
Only half of the exon is spliced
Cryptic splicing
129
This leads to disease.
Mutation
130
This can alter the expression of the organism.
Polymorphism
131
Refers to the position or location of a gene in the genome
Locus
132
Genetic loci are defined by chromosomal location using?
- chromosome bands (G-band or R-band)
- molecular markers (microsatellites)
133
Separate pairs of genetic expression located on opposite sides of the chromosome, may be homozygous or heterozygous
Allele
134
These are related to alterations in the nucleotide sequence of a gene.
Allelic differences
135
Refers to one nucleotide change, can be a sequence polymorphism
Single Nucleotide Polymorphisms (SNPs)
136
T/F: Tandem repeats are used in the laboratory for crime scenes.
True
137
Used for paternity testing
VNTRs
138
Used for investigations
STR
139
T/F: Each individual has a different number of tandem repeats.
True
140
STR dinucleotide repeat is only about ___ the same
8%
141
Tetranucleotide repeat is only about ____ the same
0.3%
142
T/F: Twins have the same identical VNTR.
True
almost the same lang
143
T/F: You may also look at tandem repeats during DNA fingerprinting.
True
144
Mutation is present from the very start
Germline mutations
145
Acquired mutations
Somatic mutations
146
<1% of population, Carrier, Diseased
Mutation
147
>1% of population, not affected, >90% SNPs, not associated with a disease
Polymorphism
148
Refers to one nucleotide mutation
Point mutation
149
Same type of mutation
Transition (pur to pur, pyr to pyr)
150
Purine to pyrimidine
Transversion
151
T/F: Polymorphisms can make a person more susceptible.
True
152
Genetic Polymorphism
Structural
- gain/loss of chromosome segments
- translocations
- rearrangements
- gene amplifications
153
Genetic Polymorphism
Molecular
- deletions/insertions
- nucleotide repeats (di-, tri)
- point mutations (RFLPs, SNPs)
154
Most common type of mutation
Substitution
155
Refers to codon changes, affects gene transcript splicing
Point Mutations (Base Pair Substitution)
156
This is produced by deletions, insertions, or splicing errors.
Frame-shift mutations
157
Refers to change in codon to a different amino acid, transition or transversion substitutions
Missense mutation
158
Change in amino acid, but possess same properties
Conservative missense mutation
159
Change in amino acid, but the properties are not the same
Nonconservative missense mutation
160
This refers to substitution, change in codon but same amino acid and does not cause a change in protein.
Silent Mutations
161
This results into a truncated protein due to a change in codon to a stop codon.
Nonsense or Stop Mutations
162
Splice Site Mutations
- Exon skipping (incomplete splicing)
- Intron inclusion
- Cryptic splicing
163
under Deletion Mutation
- Cystic Fibrosis
- Duchenne muscular dystrophy
164
70% due to F508
Cystic Fibrosis
165
~60% cases due to large deletions, 8% small deletions
Duchenne muscular dystrophy
166
Insertion or deletion of nucleotides, reading frame is altered
Frameshift mutations
167
When these tandem repeats accumulate, it causes mutations
Dynamic mutation
168
Example of Dynamic Mutation
Trinucleotide Repeat Expansion
169
Tandem repeats and gene of Huntington disease
> 40 CAG, Huntingtin gene
