Exam 3 - Genetics Flashcards
(122 cards)
1
Q
The genome comprises ___ the genetic material that an organism possesses
A
all
In bacteria, it is typically a single circular chromosome
In eukaryotes, it refers to one haploid set of nuclear chromosomes and the mitochondrial genome (and if a plant the chloroplast genome)
2
Q
The main function of the genetic material is to:
A
store the information required to produce an organism
The DNA molecules does that through its base sequence
3
Q
Where is the bacterial chromosome found, what is its shape, and how long is it?
A
The bacterial chromosome is found in a region of the cell called the nuceloid
The nucleoid is not membrane bound, so the DNA is in direct contact with the cytoplasm
Bacterial chromosomal DNA is usually circular and only a few million nucleotides in length
4
Q
Do prokaryotes have introns?
A
No
Gene sequences that encode for proteins (and thus are transcribed) account for the majority of bacterial DNA
The nontranscribed DNA between adjacent genes are termed intergenic regions
5
Q
To fit within the bacterial cell, the chromosomal DNA must be compacted about a ____-fold
A
1000
This involves the formation of loop domains (microdomains) which are typically ~10,000 bp
The number of loop domains varies depending on size of the bacterial chromosome and the species
Adjacent microdomains are further organized into macrodomains (80-100 microdomains)
6
Q
What are nucleoid associated proteins (NAPs) and what is their function?
A
Bacteria use DNA binding proteins called nucleoid associated proteins (NAPs) to form microdomains and macrodomains
Facilitate compaction and organization
Bend DNA or facilitate DNA-DNA interactions
Facilitate segregation
Help with gene regulation
7
Q
The chromosomal DNA is _______ supercoiled
A
negatively
8
Q
What are the two major effects of negative supercoiling?
A
- Helps in the compaction of the chromosome
- Creates tension that may be released by DNA strand separation
9
Q
The control of supercoiling in bacteria is accomplished by two main enzymes:
A
DNA gyrase and DNA topoisomerase
The competing action of these two enzymes governs the overall supercoiling of bacterial DNA
10
Q
What does DNA gyrase (aka DNA topoisomerase II) do?
A
Introduces negative supercoils using energy from ATP
It can also relax positive supercoils when they occur
Can untangle intertwined DNA molecules
11
Q
What does DNA topoisomerase I do?
A
Relaxes negative supercoils
12
Q
Where are eukaryotic chromosomes found, what do they look like, and how long are they?
A
Eukaryotic species contain one or more sets of chromosomes
Each set is composed of several different linear chromosomes
The total amount of DNA in eukaryotic species is typically much greater than in bacterial cells
Chromosomes in eukaryotes are located in the nucleus
13
Q
The DNA-protein complex found in eukaryotic chromosomes is termed
A
chromatin
14
Q
Three types of DNA sequences are used for chromosomal replication and segregation:
A
Origins of replication
Centromeres (the kinetochore is the protein complex that interacts with the centromeric region)
Telomeres (located at DNA ends - maintain chromosome integrity)
15
Q
Eukaryotic genomes vary substantially in size, is this variation related to the complexity of the species?
A
In many cases no
For example, there is a two-fold difference in the size of the genome in two closely related salamander species
The difference in the size of the genome is not because of extra genes, rather, the accumulation of repetitive DNA sequences
These do not encode proteins
16
Q
Genes are located between the ____ and ______ regions along the entire chromosome
A
centromeric, telomeric
A single chromosome usually has a few hundred to several thousand genes
17
Q
Genes are relatively small in _____ eukaryotes
A
lower (such as yeast)
They primarily contain the sequences that encode the amino acid sequences within proteins
I.e. very few, short introns are present
18
Q
Genes are long in ______ eukaryotes
A
higher (such as mammals)
Tend to have many introns (non coding intervening sequences)
Intron lengths from less than 100 to more than 10,0000 bp
19
Q
Unique or non-repetitive sequences
A
Found once or a few times in the genome
Includes structural genes as well as intergenic areas
In humans, make up roughly 41% of the genome
20
Q
Moderately repetitive sequences
A
Found a few hundred to several thousand times
Genes that you need a lot of
Includes:
Genes for rRNA and histones
Origins of replication (OriR)
Sequences that regulate gene expression and translation (basal promoters, transcription factor binding elements)
Transposable elements
21
Q
Highly repetitive sequences
A
Found tens of thousands to millions (>50% of genome)
Each copy is relatively short (a few nucleotides to several hundred in length)
Some sequences are interspersed throughout the genome (Alu family in humans)
Other sequences are clustered together in tandem arrays
(These are commonly found in the centromeric and in the telomeric regions)
22
Q
The compaction of linear DNA in eukaryotic chromosomes involves interactions between ____ and ________
A
DNA and many different proteins
Proteins bound to DNA are subject to change during the life of the cell
These changes affect the degree of chromatin compaction
CHROMATIN= chromosomal DNA and proteins that bind it
23
Q
Nucleosomes
A
The repeating structural unit within eukaryotic chromatin is the nucleosome
Composed of a double-stranded segment of DNA wrapped around an octamer of histone proteins
24
Q
Histone octamer
A
2 copies of each of 4 different histones (8 histones total)
25
146 bp of DNA make _____ negative superhelical turns around the octamer
1.65
26
Nucleosomes form a ___ nm fiber
30 nm
Overall structure of connected nucleosomes resembles “beads on a string”
This structure shortens the DNA length about seven-fold
27
Histone proteins contain many ____-charged amino acids
positively (lysine and arginine)
28
Histones bind to the _____ along the DNA backbone
phosphates
Histone proteins have globular domain and flexible, charged amino terminus (tail)
29
What are the core histones that make up octamers?
H2A, H2B, H3, H4
30
What is the fifth histone that doesn't contribute to octamers? What does it do instead?
H1 is called the linker histone
Binds to DNA in the linker region
Less tightly bound to DNA than core histones
May help compact adjacent nucleosomes
31
At moderate salt concentrations, H1 ______
is removed
The result is the classic beads-on-a-string morphology
32
At low salt concentration, H1 _____
remains bound
Beads associate together into a more compact morphology
33
CCCTC binding factor (CTCF)
One of the proteins that helps facilitate loop domain formation
binds to 3 regularly spaced repeats of the sequence CCCTC
34
Structural maintenance of chromosome (SMC) proteins
One of the proteins that helps facilitate loop domain formation
wrap around themselves and 2 DNA segments to form a loop
35
Loop domains contain _____ and _______ that are available to cells
genes and other regulatory elements
Contain genes that the cell is using, remains accessible
36
What are the two ways in which the attachment of loop domains is important?
1. It plays a role in gene regulation
2. It serves to organize the chromosomes within the nucleus
37
During what phase are chromosomes compacted as euchromatin and heterochromatin?
interphase
38
Which is more condensed, euchromatin or heterochromatin?
Heterochromatin is tightly compacted (loop domains compacted even further), euchromatin is less condensed (30 nm fiber forms loop domains)
39
Which is transcriptionally active, euchromatin or heterochromatin?
Euchromatin, heterochromatin is transcriptionally Inactive (in general)
40
Constitutive heterochromatin
Regions that are always heterochromatic
Permanently inactive with regard to transcription
Usually contain highly repetitive sequences
41
Facultative heterochromatin
Regions that can interconvert between euchromatin and heterochromatin
42
By the end of prophase, sister chromatids are entirely _________
heterochromatic
Two parallel chromatids have an overall diameter of 1,400 nm
These highly condensed metaphase chromosomes undergo little gene transcription
43
In metaphase chromosomes, the loop domains are highly compacted and stay anchored to a ________
scaffold, the scaffold is formed from nuclear proteins including SMC proteins
44
What are the two multiprotein complexes that help to form and organize metaphase chromosomes?
Condensin - plays a critical role in chromosome condensation
Cohesin - plays a critical role in sister chromatid alignment
Both cohesin and condensin contain SMCs (structural maintenance of chromosomes)
SMCs use ATP to facilitate compaction
45
How many origins of replication are in eukaryotes vs. prokaryotes?
Prokaryotes: 1, sequence that is just a few 100 base pairs in length
Eukaryotes: many origins of replication per chromosome
46
The number of linkage groups is ________
the number of types of chromosomes of the species
For example, in humans there are 24 linkage groups - 22 autosomal linkage groups, an X chromosome linkage group, a Y chromosome linkage group
47
T/F: Genes that are far apart on the same chromosome may independently assort from each other
True, this is due to crossing over
48
During what phase of meiosis does crossing over occur?
Prophase I (bivalent formation)
49
Crossing over produces __________
non-parental phenotypes
Non-sister chromatids of homologous chromosomes exchange DNA segments
50
In diploid eukaryotes, linkage can be altered during meiosis as a result of ______________
crossing over
51
Recombination between two genes is more likely if the genes are ___________
farther apart
Recombination is essentially proportional to distance
52
Morgan's three hypotheses
1. The genes for body color, eye color, and wing length are all located on the X-chromosome (therefore parental alleles tend to be inherited together)
2. Due to crossing over, homologous X-chromosomes can exchange pieces of chromosomes (in females) (recombining the parental alleles)
3. Likelihood of crossing over depends on distance between the two genes (crossing over is more likely to occur between two genes that are far apart from each other)
53
Chi square analysis formula
x^2 = (observed - expected)^2/expected
54
Gene mapping attempts to:
determine the linear order of linked genes along each chromosome
55
In what ways are genetic maps useful?
1. They allow us to understand the overall complexity and genetic organization of a particular species
2. They improve our understanding of the evolutionary relationships among different species
3. They can be used to diagnose and potentially treat inherited diseases
4. They can help predict the likelihood that a couple will produce children with certain inherited diseases
5. They provide helpful information for improving agriculturally important strains through selective breeding programs
56
Genetic maps estimate the relative distances between _________
linked genes
based on the likelihood that a crossover will occur between them
57
Experimentally, the percentage of recombinant offspring is correlated with the _________________
distance between the two genes
If the genes are far apart → many recombinant offspring (too far apart and the genes look like they are sorting independently)
If the genes are close → very few recombinant offspring
58
What is the formula for map distance?
Map distance = number of recombinant offspring/total number of offspring x 100
The units of distance are called map units (mu) or centiMorgans (cM)
One map unit is equivalent to 1% recombination frequency
59
What is the formula to predict the likelihood of a double crossover from the individual probabilities of each single crossover?
Product rule
P(double between A-C) = P(single between A-B) x P(single between B-C)
60
Interference
when the presence of a single crossover alters the frequency of a second crossover occurring nearby
61
Positive interference
when the first crossover DECREASES the probability that a second crossover will occur nearby (this is the most common type of interference)
62
Negative interference
when the presence of the first crossover INCREASES the probability that a second crossover will occur nearby (this rarely occurs)
63
What is the formula for interference (I)?
I = 1 - C
C = (observed number of double crossovers)/(expected number of double crossovers)
If I is positive, it is positive interference
64
T/F: Mitosis does not involve homologous pairing of chromosomes to form bivalents
True, therefore crossing over in mitosis is expected to be much less likely than during meiosis
Nevertheless, crossing over does occur on rare occasions
In these cases, it may produce a pair of recombinant chromosomes that have a new combination of alleles
This is known as mitotic recombination
65
Crossing over occurs ______ during mitosis
Occasionally
If mitotic recombination occurs during an early stage of embryonic development
Daughter cells containing recombinant chromosomes continue to divide
This may ultimately result in a patch of tissue with characteristics that are different from those of the rest of the organism
66
Cytogenetic mapping (aka cytological mapping)
Relies on microscopy - with the aid of dyes/fluorescence
Genes are mapped relative to bands/fluorescence on locations on chromosomes
Crude maps with a resolution of ~5 million bp
67
Linkage mapping
Relies on frequency of recombination genetic crosses
Genes/regions of chromosome are mapped relative to each other
Distances computed in map units (mu or centiMorgans)
Geneticists have realized that regions of DNA, which need not encode genes, can be used as genetic markers
68
Physical mapping
Relies on DNA cloning/sequencing techniques
Genes are mapped relative to each other
Distances computed in number of base pairs between genes
Has the best resolution of the genetic maps
69
What is a molecular marker in linkage mapping?
A particular DNA segment that is found at a specific site and can be uniquely recognized
As with alleles, the characteristics of useful molecular markers may vary from individual to individual (polymorphic)
Therefore, the distance between linked molecular markers can be determined from the outcome of crosses
70
What are the seven traits of molecular markers?
1. Particular DNA segments found at specific sites in the genome
2. These sites can be uniquely recognized
3. Useful markers are polymorphic
4. Useful markers are interspersed throughout the genome
5. Sometimes markers are parts of a gene, but often they are not
6. Distance between markers can be mapped
7. Unlike dominant and recessive genes, molecular markers are co-dominant
71
Restriction fragment length polymorphisms (RFLPs)
Restriction enzymes recognize specific DNA sequences and cleave the DNA at those sequences
Along a very long chromosome, a particular restriction enzyme will recognize many sites
These are randomly distributed along the chromosome
When comparing two individuals, a given restriction enzyme may produce certain fragments that differ in length
72
Microsatellites or short tandem repeats (STRs)
newer method of generating molecular markers that is now used more frequently
Short, repetitive sequences
Abundantly dispersed throughout a species’ genome
Variable in length among different individuals
73
What is the most common human microsatellite?
The sequence (CA)n, where n may range from 5 to more than 50
(CA)n found about every 10,000 bases in the genome
74
By following the transmission of many microsatellites
in a large family tree which also shows the transmission
of a disease or trait, it may be possible to:
identify a microsatellite marker linked to the disease causing gene
75
What is a key difference between RFLPs and microsatellites?
RFLPs use restriction enzymes and Southern blots (rather difficult)
Microsatellites use PCR (relatively easy)
76
Haplotypes
refers to the close linkage of alleles or markers on single chromosome
rarely changed by mutation, but can change in a few generations due to crossing over
77
What are the three main types of mutation?
1. Chromosome mutations - changes in chromosome structure
2. Genome mutations - changes in chromosome number
3. Single-gene mutations - relatively small changes in DNA structure that affect a particular gene
78
Point mutation
A point mutation is a change in a single base pair (involves a base substitution)
Transition - change of a pyrimidine (C,T) to another pyrimidine or purine (A, G) to another purine
Transversion - change of a pyrimidine to a purine or vice versa
79
Silent mutations
base substitutions that do not alter the amino acid sequence of the polypeptide (due to the degeneracy of the genetic code)
80
Missense mutations
base substitutions in which an amino acid change does occur (ex: sickle-cell anemia)
If the substituted amino acids have similar chemistry, the mutation is said to be neutral
Can also be extremely deleterious (causing harm or damage)
81
Nonsense mutations
base substitutions that change a normal codon to a termination codon
82
Frameshift mutations
involve the addition or deletion of nucleotides in multiples of one or two
This shifts the reading frame so that a completely different amino acid sequence occurs downstream from the mutation
83
Can gene mutations in noncoding sequences still affect gene expression?
Yes, a mutation may alter the sequence within a promoter
Mutation can also alter splice junctions in eukaryotes
84
Up promoter mutation
make the promoter more like consensus sequence (repetitive, recognizable sequences like TATA box)
may increase rate of transcription
85
Down promoter mutations
make the promoter less like the consensus sequence (repetitive, recognizable sequences like TATA box)
may decrease the rate of transcription
86
Position effect
A chromosomal rearrangement may affect a gene because the break occurred in the gene itself
Gene may be left intact, but expression may be altered because of its new location
87
What are the two common reasons for position effects?
1. Movement to a position next to regulatory sequences
2. Movement to a position in a heterochromatic region
88
Mutation rate
likelihood that a gene will be altered by a new mutation
It is commonly expressed as the number of new mutations in a given gene per generation
It is a range of 10^-5 to 10^-9 per generation
89
Is the mutation rate for a given gene constant?
No, it can be increased by the presence of mutagens
Mutation rates vary substantially between species and even with different strains of the same species
Within same individual, some genes mutate at a much higher rate than other genes
90
The bigger a gene is, the ____ likely mutations will accumulate per generation
more
91
Hot spots
Some genes have locations within the chromosome that make them more susceptible to mutation
Can also be found within a single gene
92
Spontaneous mutations
Result from abnormalities in cellular/biological processes
Errors in DNA replication, for example
Occur because of normal biological processes
93
Induced mutations
Caused by environmental agents
94
Mutagens
Agents that are known to alter DNA structure
Can be physical or chemical agents
95
What are the three main types of molecular changes to DNA structure that can lead to spontaneous mutations?
Depurination (most common), deamination, tautomeric shifts
96
Depurination
involves the removal of a purine base (guanine or adenine) from the DNA
The covalent bond between deoxyribose and a purine base is somewhat unstable
97
Apurinic site
Location in DNA that has neither purine nor pyrimidine base, either spontaneously or due to DNA damage
DNA occasionally undergoes a spontaneous reaction with water that releases the base from the sugar
Fortunately, apurinic sites can be repaired
However, if the repair system fails, a mutation may result during subsequent rounds of DNA replication
98
____% of the time, if DNA replication occurs at an apurinic site, mutation will occur
75%
Because a base is missing, a random one is put in, and ¾ of the bases are the incorrect one
99
Deamination
involves the removal of an amino group from the cytosine base
The other bases are not readily deaminated
DNA repair enzymes can recognize uracil as an inappropriate base in DNA and remove it
However, if the repair system fails, a C-G to A-T mutation will result during subsequent rounds of DNA replication
Deamination of 5-methyl cytosine can also occur
100
How do methylated cytosine bases tend to create hot spots for mutation?
Deamination of methylated cytosine creates thymine
Thymine is a normal constituent of DNA, which poses a problem for repair enzymes - cannot determine which of the two bases on the two DNA strands is the incorrect base
101
Tautomeric shift
involves a temporary change in base structure
These rare forms promote AC and GT base pairs
Must occur immediately prior to DNA replication to cause a mutation
102
Why are we concerned by mutagens (two reasons)?
1. Mutagens are often involved in the development of human cancers
2. Mutagens can cause gene mutations that may have harmful effects in future generations
103
What are the three main types of chemical mutagens?
Base modifiers, base analogues, intercalating agents
104
Base modifiers
covalently modify the structure of a nucleotide
These modified bases do not pair with the appropriate nucleotides in the daughter strand during DNA replication
105
Base analogues
become incorporated into daughter strands during DNA replication
Not as stable as the normal base, so tautomeric shifts occur more often (promote mispairing)
106
Intercalating agents
contain flat planar structures that intercalate themselves into the double helix
Intercalate - insert (something) between layers in a crystal lattice, geological formation, or other structure
This distorts the helical structure
When DNA containing these mutagens is replicated, the daughter strands may contain single-nucleotide additions and/or deletions
107
Two main types of physical mutagens
ionizing and nonionizing radiation
108
Ionizing radiation
Includes x-ray and gamma rays
Has short wavelength and high energy
Can penetrate deeply into biological molecules (very detrimental)
Creates chemically reactive molecules termed free radicals
Can cause base deletions, single nicks in DNA strands, cross-linking, and chromosomal breaks
Can cause germ-line mutations because it can penetrate deeply enough
109
Nonionizing radiation
Includes UV light (sunlight)
Has less energy
Cannot penetrate deeply into biological molecules
Causes the formation of cross-link thymine dimers
Thymine dimers may cause mutations when that DNA strand is replicated
110
What are the 4 steps of DNA repair?
1. An irregularity in DNA structure is detected
2. The abnormal DNA is removed
3. Normal DNA is synthesized (invovlving DNA polymerase)
4. DNA ligase seals the newly synthesized DNA to the original strand
111
What do photolyases repair and how do they do so?
Photolyase can repair thymine dimers
It splits the dimers restoring the DNA to its original condition
Uses energy of visible light
112
What do O6-alkylguanine alkyltransferases repair and how do they do so?
O6-alkylguanine alkyltransferase repairs alkylated bases
It transfers the methyl or ethyl group from the base to a cysteine side chain within the alkyltransferase protein
Surprisingly, this permanently inactivates alkyltransferase
113
What does base excision repair (BER) do?
Base excision repair removes a damaged DNA base
Base excision repair (BER) involves a category of enzymes known as DNA N-glycosylases
These enzymes can recognize an abnormal base and cleave the bond between it and the sugar in DNA
Depending on the species, this repair system can eliminate abnormal bases such as
Uracil; thymine dimers
3-methyladenine; 7-methylguanine
114
What does nucleotide excision repair (NER) do?
Nucleotide excision repair removes damaged DNA segments
This type of system can repair many types of DNA damage, including:
-Thymine dimers and chemically modified bases
-Missing bases, some types of crosslinks
NER is found in all eukaryotes and prokaryotes
However, its molecular mechanism is better understood in prokaryotes
DNA polymerase and ligase finish the repair job
115
What are the four key proteins the NER system requires in E. coli
UvrA, UvrB, UvrC, and UvrD
Named as such because they are involved in Ultraviolet light repair of pyrimidine dimers
They are also important in repairing chemically damaged DNA
UvrA, B, C, and D recognize and remove a short segment of damaged DNA
116
What do mismatch repair systems do?
Mismatch repair systems detect and correct a base pair mismatch if the proofreading ability of DNA polymerase fails
Found in all species
Three proteins, MutL, MutH and MutS detect the mismatch and direct its removal from the newly made strand
The proteins are named Mut because their absence leads to a much higher mutation rate than normal
117
An important aspect of the mismatch repair system is that it is specific to the ________
newly made strand
118
How does MutH distinguish between the parental and the daughter strand?
Prior to replication, both strands are methylated
Immediately after replication, the parental strand is methylated whereas the daughter is not!
119
Double-stand breaks in DNA can be repaired by ______
Recombination
120
DNA double-strand breaks
Breakage of chromosome into pieces
Caused by ionizing radiation and chemical mutagens
Also caused by reactive oxygen species which are the byproducts of cellular metabolism
10-100 breaks occur each day in a typical human cell
Breaks can cause chromosomal rearrangements and deficiencies
They may be repaired by two systems known as homologous recombination repair (HRR) and nonhomologous end joining (NHEJ)
121
Actively transcribed genes in eukaryotes and prokarotes are ____ efficiently repaired than is nontranscribed DNA
more
Not all DNA is repaired at the same rate
122
What are the biological advantages of DNA repair enzymes targeting actively transcribing genes?
Active genes are more loosely packed (may be more vulnerable to DNA damage)
Transcription may make DNA more susceptible to damage
DNA regions that contain active genes are more likely to be important for survival than nonstranscribed regions
