Exam 1 Review Flashcards
(110 cards)
1
Q
What is an allele?
A
Alternative forms of a DNA sequence making up a gene. Can be dominant or recessive.
2
Q
What is a genotype?
A
The alleles present in the nucleus of a cell. Can be heterozygote (Dd) or homozygote (DD, dd)
3
Q
What is a phenotype?
A
The physical expression of the genotype
4
Q
What is penetrance?
A
The proportion of those with a mutation that display clinical symptoms
In other words, the percentage of those with a genotype that express the corresponding phenotype.
5
Q
What does Epigenetic mean?
A
Epigenetics cause differences between individuals that are not due to differences in DNA sequence.
Some examples include: methylation, alternative splicing…etc.
6
Q
What is the difference between soft determinism and strong determinism?
A
Soft determinism acknowledges that the environment, history and epigenetic modification whereas strong determinalism says that health and disease are driven primarily by genes and their variants
If strong determinism is true: then all schizophrenics would have the same mutant genes
7
Q
What types of bonds hold nucleotides together in DNA?
A
Phosphodiester bonds
8
Q
What type of bonds are responsible for the stability of the DNA helix?
A
H-bonds hold the complimentary bases together in the DNA double helix
9
Q
What is the difference between ribose and deoxyribose?
A
Ribose has a 2’ OH group whereas deoxyribose does not
10
Q
What nucleotide is only found in RNA and which nucleotide does it replace?
A
Uracil is foound only in RNA and it replaces Thymine
11
Q
Which end of the DNA chain is ALWAYS the next site for polymerization?
A
The 3’ end
12
Q
Which end of the DNA chain contains the oldest nucleotide?
A
The 5’ end is the oldest nucleotide
13
Q
How many DNA strands are in one DNA molecule?
A
2: Double helix
14
Q
Which base pair takes more energy to break down?
A
G-C because there are 3 H-bonds between each nucleotide whereas there are only 2 H-bonds between A and T
15
Q
What effect does temperature have on the structure of the DNA double helix?
A
It destroys the H-bonds, thus eliminating the double helix structure. Covalent (phosophodiester) bonds remain intact.
16
Q
Which base pair is most common in DNA molecules?
A
A-T is found about 60%, whereas G-C is about 40%
17
Q
How many bases are found in one complete turn of DNA? What is the distance (in angstroms) between turns?
A
10 bases and 34 A per complete turn
18
Q
Why are nucleic acids unique in their method of replication?
A
They can serve as a template for their own replication due to the complimentary pairing nature within the double helix
19
Q
What does Semi-conservative DNA replication mean?
A
With each round of replication, one of the strands is conserved, and a new complimentary strand is synthesized.
20
Q
Which direction does DNA polymerization occur?
A
5’ to 3’
One direction is discontinuous
21
Q
Describe how DNA is packaged
A
The DNA helix spools around histones that are made up of 8 subunits. The DNA-histone complex is called a nucleosome.
22
Q
How does the condensation of chromosomes change throughout the cell cycle?
A
DNA is not condensed during Interphase, but begins to condensed to a maximum in Metaphase/Anaphase.
This is why karyotypes are typically done for cells in pro-metaphase or metaphase
23
Q
Describe G-banding
A
Methylene blue stains regions of the DNA backbone that are accessible.
Stains A-T rich regions dark
Sister chromatids act as their own staining control
24
Q
Describe metacentric, submetacentric, acrocentric, and telocentric chromosomes
A
Metacentric: p=q
Submetacentric: p~=q
Acrocentric: p<q></q>
<p>
Telocentric: p~=0, all q</p>
</q>
25
Why are karyotypes often performed in pro-metaphase instead of metaphase?
Slightly less condensed chromosomes allow for higher resolution for visualizing smaller bands.
26
What is an Alu element?
a short RNA sequence that has been reverse transcribed into the human genome many times; make up ~10% of the human genome
27
What chromosome has the highest gene density?
Chromosome 19
28
What are the steps in the mitotic cell division cycle?
Interphase: G1, S, G2
G1: cell growth, normal functioning
S: DNA replicates
G2: Cell grows and prepares for mitosis
Mitosis: Prophase, Metaphase, Anaphase, Telophase, Cytokinesis
29
What is the copy number of DNA in metaphase? What about the diploid number?
C=4 4 DNA helixes (2 copies of each of 2 homologs)
2n=4 because still only have 2 chromosomes
30
What step of mitosis do chromatids become chromosomes?
Anaphase: the sister chromatids are pulled apart by the spindle apparatus and become individual chromosomes
31
Does heterozygosity change in mitosis?
No. The daughter cells are genetic twins.
32
Is every cell in the body genetically identical?
No. Mitosis is a mutagenic process, so there are differences between cells.
33
Which stage of meiosis is considered the reductional division?
Meiosis I: 2n--\>1n
One homolog ends up in each daughter cell
34
What is the difference between Meiosis 2 and Mitosis?
Meiosis 2 only has half of the chromosomes of mitosis. The homolog pairs are no longer in the same cell after meiosis 1.
35
Does pairing occur in Meiosis II?
No. There are no homologs after Meiosis I.
36
What proportion of female gametes that are formed are thrown out?
3 out of 4 gametes are thrown out as polar bodies
37
Describe the female meiotic division.
A primary oocyte (2n) undergoes meiosis one, forming a secondary oocyte (n). It begins meiosis II and stays in metaphase unless it is fertilized.
38
Describe the meiotic division in males.
Several generations of spermatogonia multiply via mitosis. These primary spermatocytes undergo meiosis 1 and meiosis 2 with incomplete cytokinesis forming cytoplasmic bridges. These bridges develop into the 'tails' of the sperm.
39
Explain mutual exclusivity
2 alternatives with one outcome OR another
If one happens, then the other cannot occur
40
Explain statistical independence
ex: 2 coins being flipped; the result of one does not determine the other
AND
41
Describe the stucture of a tRNA molecule
They made up of a single RNA strand that folds up with itself to form a clover leaf shape. At one end, the anticodon can bind to mRNA in the Ribosome, and at the other end, the amino acid (corresponding to the anticodon) can bind.
42
Describe the path a tRNA takes through a ribosomal subunit during translation
"tRNAs go APE"
## Footnote
1) Amino binding site
2) Peptidyl binding site (amino acid binds to growing polypeptide chain)
3) Exit site
43
What is the only aminoacyl amino acid found at the P site of a ribosome?
Methionine because it is the first amino acid of every peptide, so when it enters the P site, it still has a free N and C terminus
44
How does translation stop?
A stop codon signals the end of translation. No normal tRNA molecule will bind to stop codons, but a release factor enters the A site and causes the ribosome to detach from the mRNA
45
Which of the three bases in a codon are the 'characteristic bases'?
The first two are characteristic of the specific amino acids, whereas the third one can change and still produce the same amino acid.
46
What is unique about the inheritance of mitochondrial DNA?
It is only passed down maternally.
47
What are the major methods for specific amplification (DNA cloning)?
1) Cell based DNA cloning
2) Polymerase chain reaction (PCR)
48
What is gene cloning?
The phenomenon of isolating and making many copies of a specific gene
49
What is the advantage of cell-based DNA cloning over PCR?
You can clone a genome from a completely unknown sequence with cell based cloning, whereas with PCR you need to know the sequence of interest.
50
Explain recombinant DNA technology
You cut a piece of chromosomal DNA and paste it into another molecule, usually a vector DNA
These recomninant molecules can be introduced into living cells like E.Coli for amplication
51
What are the basic steps of gene cloning?
1) Isolate your gene of interest (YGI) from among thousands of genes
2) Link YGI to bacterial or phage DNA
3) Introduce into bacterial or phage host
4) Separate individual cells/clones
5) Make sufficient amounts of YGI's DNA for further analysis
52
What are restriction enzymes?
Enzymes used to cut DNA at specific locations on each DNA strand
53
What is the difference between an endonuclease and an exonuclease?
Endonucleases will cut within an entire strand, whereas exonucleases just cleave peptide bonds at the end of the peptide chain.
54
Describe how a restriction enzyme cleaves a DNA strand.
The sequence around the point of cleavege is palindromic (symmetrical about it's center point). When the r.e. cleaves, the two strands are each left with a 5' overhang and a recessed 3' end.
The complimentary ends can fit back together
55
What is the purpose of DNA ligase?
DNA ligase fills the nicks that remain when complimentary DNA sequences join back together creating a continuous phosphodiester backbone throughout the polypeptide
56
What are the steps of cloning a piece of DNA?
1) Cut both vector and DNA with same restriction enzyme
2) Ligate pieces together
3) Transform ligated DNA mix into bacterial host (usually E.Coli)
4) Grow E. coli on antibiotics to screen for clones/colonies with recombinant DNA.
57
What is a host cell?
The cell that harbors the vector
Usually E.Coli for recombinant DNA
58
What are the main components of cloning plasmids?
1) Origins of replication
2) at least one antibiotic resistance gene to use as a selectable marker
3) a number of unique restriction sites where DNA fragments can be inserted.
59
What is the significance of the lacZ gene for DNA cloning.
A gene found in the pUC19 vector
DNA can be insterted into the middle of this gene, thus disrupting the ability of the cell to produce B-galactosidase.
This allows for colonies with the recombinant DNA to be identified by color when XGal is added: those with the added DNA will be white, and those without will be blue.
60
What are the two ways that gene amplification occurs during cell based cloning?
1) The vector gets replicated many times by the host cell because the origins of replication fire repeatedly.
2) The bacterial cell divides every ~30 minutes
Can generate many million copies of a gene overnight.
61
Why is it advantageous to limit the amount of time that restriction enzymes cleave a genome when building a genomic library?
If the enzymes are allowed to run to completion, they will splice all of the same sites in each copy of the gene. The useful parts of the genes are the overlapping segments, which can be used to reconstruct the genome sequence. By only exposing the gene to restriction enzymes for a limited amount of time, random cleavages will occur on each copy.
62
Why are centromeres and telomeres very poorly sequenced?
They contain a high percentage of repetitive DNA, which confounds the overlapping method for sequencing because many different overlaps are possible from repetitive DNA.
63
By what factor does PCR amplify a DNA molecule during each round of PCR?
2
multiply by 2 over and over and over....millions
64
What components do you need to perform PCR?
1) Template DNA
2) Primers complimentary to sequences at the beginning and end of fragments to be amplified.
3) Heat stable DNA polymerase
4) Nucleotides (dNTPs)
5) A PCR machine (thermal cycler)
65
Describe the thermal cycling that takes place during PCR
During each cycle:
95° to separate/denature the strands
50° to add primers
72° for polymerase to extend/synthesize the strands
REPEAT!
66
After 20 PCR cycles, by what factor will the DNA sample increase by?
220 (~1 million fold)
67
Explain what a probe is used for.
A probe is a labeled known sequence that can complementary pair with target DNA.
The complimentary DNA will then be labeled due to its association with the probe.
68
Which probe has the highest affinity for DNA?
DNA, RNA or Oligonucleotide
RNA
69
Describe nick translation
DNase I is used to break the phosphodiester bond between two adjacent nucleotides leaving behind a 'nick'.
DNA Polymerase can then attach to the nick and replace the existing molecules downstream. In the presence of a labeled dNTP, the DNA strand will be labeled after DNA polymerase finishes.
70
Describe random primed labeling.
Random hexanucleotide primers can bind to complimentary sequences on DNA. Because these oligonucleotides have free 3'OH groups, DNA polymerase can be used to synthesize from these primers, adding labeled dNTPs
71
How does end labeling work?
An enzyme called polynucleotide kinase catalyzes the exchange of cold 5' P for P32 , a radioactive phosporous isotope.
72
What is fill-in end labeling?
After a restriction enzyme leaves behind recessed 3'ends, they can be filled in using Klenow DNA polymerase, which recognizes the 3' ends. This can be used to added labeled nucleotides.
73
What is run-off transcription?
A DNA sequence can be inserted into an RNA plasmid, which can be replicated by RNA polymerase. The desired sequence can be replicated with radiolabeled nucleotides numerous times with this method.
74
What is autoradiography?
DNA is first cut with restriction enzymes and run through PAGE. Then the contents are transfered to the appropriate backing, and labels can hybridize to the bands, making them visible with X-ray or other methods.
75
What is the basic principle behind nucleic acid hybridization?
Base complementarity between the probe and target
76
What are homoduplexes? Heteroduplexes?
During nucleic acid hybridization:
homoduplexes form when target binds with target, or probe binds with probe
heteroduplexes form when probe binds with target (this is what you want to happen)
77
What is the relationship between base composition and melting point?
Higher G-C base composition will lead to higher melting points because of 3 H-bonds instead of 2
78
What is the structure of a sample of DNA at exactly it's melting temperature?
50% of the molecules are double helix and 50% are single stranded.
79
How does a single mismatch affect the probe binding stability in nucleic acid hybridization?
A probe with a single mismatched base can still be stable if it is long enough that the bases on either side are able to complimentarily pair with the adjacent regions.
Shorter probes with higher hybridization stringency will be unstable.
80
What does high stringency mean?
Low salt concentration, increased temperature
Encourages dissociation of mismatched top
81
Does Northern blotting look at DNA or RNA?
RNA
82
Does the intensity of the signal in a microarray matter for identifying the gene?
No, only the color content is important
83
What is FISH?
Fluorescent in Situ Hybridization
allows you to visualize macromutations of chromosomes using a mixture of chromosome 'paints', which are fluorescent DNA probes
84
What is SKY?
Spectral Karyotyping
Useful for imaging rearrangements, deletions and inversions
Visible karyotype with different color for each chromosome
85
What determines the binding pattern of a chromosome?
The base composition and the condensation of the chromosome
Less condensed, more bands, more information
86
What is the difference between a constitutional and a somatic chromosome abnormality?
Constitutional: present in all tissues, probably arrose from sperm/egg mutation or early mitotic catastrophe
Somatic: Present in only certain cells/tissues. Produces "mosaics"
87
What is usually the cause of aneuploidy?
Nondisjunction that occurs during anaphase of mitosis.
88
How can you determine if nondisjunction occured in meiosis I or meiosis II?
Look at the alleles.
Meiosis I will create 2 n+1 gametes, and 2 n-1 gametes
Meiosis II will create an n+1 gamete, an n-1 gamete and 2 n gametes
89
Which produces more viable offspring: autosomal chromosome aneuploidy or sex chromosome aneuploidy?
Sex chromosome aneuploidy
90
What is trisomy 21?
Down syndrome
91
What is trisomy 13?
Patau syndrome
92
What is trisomy 18?
Edwards syndrome
93
What are the major changes that can occur in chromosome structure?
1. Deletion/Deficiency
2. Duplication
3. Inversion
4. Translocation (non-homologous exchange)
94
Describe why an inversion loop occurs.
When a portion of one homolog is inverted, it still tries to align with it's homolog. In order to do so, the chromosome forms a loop in order for proper pairing to occur.
If a crossover occurs in the loop, this will lead to duplication/deletion of certain DNA regions
95
How does microdeletion and duplication occur?
Repeated sequences can misalign with eachother. If recombination occurs, duplications and deletions can occur
96
What is the difference between a monogenic and a polygenic trait?
Monogenic only has one gene that encodes for the trait, whereas polygenic has many genes that code for a single trait.
97
What is a 'de novo' mutation?
When a sporadic mutation occurs in an individual with 2 wildtype parents.
98
What is the assumption that is made about out-of-family individuals for pedigree analysis?
They have wildtype genomes
99
Which type of mutations usually result in a "Loss of Function" mutation?
Recessive mutations
The presence of a broken gene can be compensated for by one copy of the wildtype allele.
100
What are the major characteristics of an autosomal-dominant trait in a pedigree?
Every generation has a mix of males and females with the trait and about 50% of all offspring have it.
101
What are the major characteristics of autosomal recessive in a pedigree?
Trait often skips generations.
Consanguinity leads to higher prevalence.
~1/4 of offspring of 2 carriers will have the trait.
102
What are the major characteristics of an X-linked trait in a pedigree?
Only females can be carriers (because they have 2 X chromosomes)
1/2 of male offspring of female carriers will have the trait
103
What are the major characteristics of an X-linked DOMINANT trait in a pedigree?
No sons of affected males will be affected; son can only get the affected X chromosome from mother
Affected fathers pass to ALL daughters
104
What are the major characteristics of Y-linked traits in a pedigree?
All male offspring of affected male will have the trait because they will all have the same Y chromosome.
105
If 8 out of 10 individuals with a specific genotype display the corresponding phenotype, what is the penetrance of that trait?
80% Penetrance
106
What is Locus Heterogeneity?
When the same phenotype occurs from mutations at different genes
107
What is clinical heterogeneity?
Penetrance and expressivity.
108
What is Epistasis?
When the effects of one gene are influenced by one or more different genes.
Mutations in any one of these related genes could lead to the same phenotype.
109
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