Genetics Flashcards
1
Q
What does genome mean?
A
ALL THE genetic material found in one cell, it being nuclear or mitochondrial.
2
Q
Which part of the DNA is included in the final messenger RNA during transcription; introns or exons?
A
Introns.
3
Q
When are introns removed from dna
A
RNA splicing, they direct where the splicing machinery should go.
4
Q
What is the sense strand and which direction does it move in?
A
The strand that gets transcribed. Moves from the 5’ to the 3’ direction.
5
Q
What is gene density?
A
How many genes can be found in a certain length of DNA. The more the genes, the higher the DNA density.
6
Q
What is a tandem repeat
A
A tandem repeat is a sequence of two or more DNA base pairs that is repeated in such a way that the repeats lie adjacent to each other on the chromosome. Tandem repeats are generally associated with non-coding DNA.
7
Q
What are the 3 types of tandem repeats
A
Satellites (5 Base pairs to 5 kilo base pairs) Mini satellites ( 6 to 64 base pairs) Micro satellites (1 to 5 base pairs)
8
Q
What is the difference between mitochondrial and nuclear DNA?
A
Mitochondrial DNA is naked, i.e not covered in histones. Also, mitochondrial DNA contains mainly coding dna and not much junk protein
9
Q
How do you calculate genotype/ phenotype frequency?
A
Number of individuals with specific phenotype/ total individuals
10
Q
How do you calculate allele frequency?
A
Homozygous individuals + heterozygous individuals/ total number of people.
11
Q
What is meant by hardy weinberg’s equilibrium
A
It is a state in which no genetic microevolution occurs, a genetic equilibrium
12
Q
What equations can we use for hardy weinberg’s equilibrium
A
P squared + 2pq+ q squared.
P+q=1
13
Q
What is a translocation mutation?
A
The exchange of genetic material between two chromosomes
14
Q
What is a insertion mutation?
A
Part of a chromosome being inserted into another chromosome (not exchanged)
15
Q
What is a transposition mutation.
A
The change of the place of DNA within the gene
16
Q
What is a substitution mutation?
A
When a base pair changes from one type to another, example AGG to ACG
17
Q
What are the two types of substitutions and what do they mean?
A
- Transition (purine to purine or pyramidine to pyramidine)
2. Trans version (purine to pyramidine or vice versa)
18
Q
What is a tautomeric shift
A
The abnormal binding of purines to pyramidines
19
Q
What is the major mutagen found in food? What does it do to cause the mutation? What type of cancer does it lead to?
A
Aflatoxin B, binds to guanine residues and causes their removal. It leads to liver cancer.
20
Q
What happens in the normal splicing process
A
normal splicing process, introns are removed and exons are placed close together to undergo translation
21
Q
What are intercalators at what can they lead to
A
Flat molecules that insert themselves in the middle of base pairs. Can lead to insertions and deletions
22
Q
What is Mosiacism and how does it occur
A
When there are two different genetic lines in an organism. It caused by a mutation that happens in the developmental stage. The earlier in the mutation happens, the more the mocaisim will be which may eventually lead to disease,
23
Q
What meant by halpoinsufficiency
A
Where we have one faulty copy and one normal copy, however the normal gene is incapable making up for the faulty copy leading to formation of disease.
24
Q
What happens in hereditary hemorrhagic Telacgentasia
A
Mutation in chromosome 9 in gene coding for endolgin, a growth hormone receptor. This leads to insufficient amounts of endoglin being formed. This results in aretriovenous malformations and arterial and venous blood get mixed
25
What is the dominant negative effect, give an example of a disease with this effect.
When we have one mutant and one faulty copy, the product of the defective gene interferes with the fucntioning of the normal allele. Osteogenesis imperfecta
26
What is an autosome?
A non sex chromosome.
27
What is epistasis
When the action of a gene masks the effect of another.
28
What is the H antigen?
The antigen needed in RBCs to be able to add A or B antigens. If antigen is not present, it cannot add nor A nor B antigens so will present as blood type O, even if both parents do not posses the O allele.
29
What is pleiotropy
The result of a gene mutation which can have many different forms (eg tourretes)
30
What is the opposite of pleiotropy? Explain it
Genetic heterogeneity. This means that a specific symptom can be the result of many different gene mutations
31
What is penetrance?
How likely it is for a patient carrying a diseased allele to actually get the disease. Some diseases have low penetrance, meaning that a patient might not express symptoms of the disease, despite showing symptoms.
32
Why does a mother with a mitochondrial mutation transmit the disease to all of her offspring but a father does not?
Mitochondrial genes are X LINKED. Therefore if a mother has a mitochondrial disease, she will transmit it to all of her children. However, her sons will not be able to transmit it to his children.
33
What is a wild type allele
Normal allele
34
What is uniparental disomy
When a child takes both copies of a gene from one parent only and not one from each parent.
35
What are the two rules of Mandelain inheritance
1. Segregation (alleles split and only one is inherited by a child)
2. Independent assortment (different genes are inherited independently of each other)
36
Summarize all exceptions of madeleine inheritance
```
Lethal alleles
Incomplete dominance
Codominance
Silent alleles
Epistasis
Pleiotropy
Genetic heterogeneity
Variable expressivity
Incomplete penetrance
Phemocopies
Incomplete ascertainment
Germaine mosaicism
Mitochondrial inheritance
Uniparental disomy
Linkage
```
37
What are phenocopies?
When an environmentally causes disease mimics a genetic disease, example is when a mum takes a pill during pregnancy that she was not supposed to leading to abnormal embryo.
38
How many hydrogen bonds do the purines(A and G) /pyrimidines(C and T) form with each other?
```
Purines= 2.
Pyramidines= 3
```
39
What is a nucleosome?
A single histone with DNA wrapped around it.
40
State the steps of DNA Replication
1. Helicase separates the two DNA strands
2. Primase adds a primer to initiate the addition of bases in the 5’ to 3’ end by DNA polymerase. The new strand being formed is called leading and the other is called lagging.
3. On the anti sense (3’ to 5’) strand, DNA polymerase adds Okazaki fragments after primase adds primers as it cannot work in thus direction
4. DNA ligament seals the two new DNA strands.
41
From which direction is the DNA strand read?
From left to right (upstream to downstream)
42
What is a DNA library?
A collection of recombinant DNA kept for research purposes.
43
What is the function of restriction endonuclease?
Breaks down DNA into smaller fragments after a specific recognition site of base pairs. It produces sticky ends. This allows us to take a closer look at the DNA structure.
44
What are the two types of DNA libraries?
1. Genomic DNA library
| 3. cDNA library
45
Describe how DNA in genomic library is formed and what it is used for
1. Normal DNA strand. Add restriction nuclease to it
2. DNA will be broken up into many small fragments
This always scientists to study to study the DNA sequence
46
Describe how DNA in cDNA library is formed and what it is used for
1. We get a DNA strand and allow it to undergo transcription forming mRNA
2. mRNA will contain introns, so it will undergo splicing to have only the exons present in the strand and contain only the protein coding portion
3. This mRNA is then taken and undergoes reverse transcription by reverse transcriptase to produce a single stranded complementary dna (cDNA) that can then be cloned.
This method is done to be able to study the PROTEINS produced by a certain gene.
47
Explain the process of recombinant DNA.
It is the process that creates a target new DNA by combining DNA molecules from two different species. This new DNA is then inserted into a host organism to produce many copies.
Example: inserting DNA into fruits to make them last longer
48
Where do we get the DNA required for recombinant DNA technology?
ccDNA and genomic libraries.
49
What are the 4 requirements of recombinant DNA technology
1. Extract DNA sequence of interest by the action of a restriction nuclease
2. Insert the DNA into a Vector e.g. plasmid or bacteriophage and seal with DNA ligase
3. Insert plasmid with recombinant DNA into bacteria and culture it.
4. Kill the remaining bacteria which do not have the recombinant DNA by antibiotics
5. Extract the DNA to use again.
50
What is plasmid
A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently.
51
What are the two types of PCR
Qualitative, tells us if a specific sequence is present or not and produces many copies
Quantitative: tells you how much of a specific DNAu have.
52
What is Taq polymerase and why do we use it in PCR?
It is a DNA polymerase extracted from bacteria that can able to withstand very high temperatures without getting denatured.
53
Describe the steps of PCR
1. Denaturation by strong heat
2. Annealing by lowering temperatures to allow addition of RNA primer
3. Elongation by taq polymerase and dNTPs
BUFFER OF OH AND MAGNESIUM
54
In gel electrophoresis, why do DNA fragments go to positive electrodes?
DNA is negative charged. The smaller the molecule the closer to the positive electrode it will be
55
What is the stain that can be used to further visualize DNA in gel electrophoresis by UV light?
Ethidium bromide
56
What are the two types of agarose gels
Agarose- separates large DNA fragments
| Acrylamide- can separate small DNA fragments up to 1 base pair difference
57
How do we know the size of the fragments on DNA on gel electrophoresis
Compare the size to known standards
58
Which type of PCR Should be done to determine viral load in the blood?
Real time PCR (quantitative)
59
What a probe
A ssDNA labeled with fluorescent dye used to test for a specific DNA sequence.
60
What does RFLP mean?
Restriction fragment length polymorphisms. This means that the fragments of DNA produced by a restriction enzyme I’ll differ in number in size from an individual to an individual
61
What do we use RFLP in?
DNA fingerprints, sickle cell anemia (Beta subunit will be a larger size than normal)
62
What is southern blotting?
The process by which a specific DNA pattern is detected by labeling it with a fluorescent DNA probe on a membrane.
63
Write out the steps of southern blotting
1. DNA is broken down into smaller fragments by restriction enzymes
2. Separated based on size by gel electrophoresis
3. DNA is denatured (strands are separated) and blotted into a membrane by placing it in a bugger
4. Probe is placed on membrane to hybridize, then is washed.
5. The areas with the target DNA will show fluorescence
64
What is the molecule found in DNA that allows for the elongation of the sugar phosphate backbone?
OH.
65
What is the difference between dNTPs and ddNTPs?
dNTP: deoxynuceloside triphosphate, aka. AGCT. These are the base pairs we use to elongate a DNA sequence because they posses an OH group
ddNTP: dideoxynucleoside triphosphate. These do not have an OH group so are called CHAIN terminators.
66
What is Sanger’s method?
The method we use for DNA sequencing. We add a fluorescently labeled primer, ddNTPs and dNTPs, DNA polymerase. The chart produced is read from bottom to top (3’ to 5’). The actual DNA sequence will b the one complementary to it.
67
What is lyonisation
The inactivation of one of the two X chromosome on a cellular level in females to prevent over expression
68
What is primary prevention
The prevention of disease before it occurs
69
What is secondary prevention
Halt the progression of the disease and identifying it at its earliest stage
E.g Pap smear for HPV virus
70
What are ways in which the X chromosome is inactived?
DNA methylation
| Low levels of Histone acetylization
71
What is the gene that determines gender?
SRY
72
If a man has an x linked dominant disorder, who will inherit it?
All of his daughters but non of his sons. They will take the Y chromosome so no disease, but the daughters will take the faulty x and get the disease
73
Who usually inherits recessive x linked disorders?
It is usually a male inheriting it from a carrier female(only one faulty copy needed for the disease as they only have one x). A female will rarely get two faulty copies
74
Both angelman syndrome and prader Willi syndrome are caused by deletions on chromosome 15. How do we tell them apart?
Prader willi: paternal chromosome 15
| Angelman syndrome: maternal chromosome 15
75
In general, should you assume x linked disorders are dominant or recessive?
Recessive, as x linked dominant are VERY rare.
| Females will need 2 faulty gene copies wheras males will need 1.
76
Why are females less severely affected that males in x linked dominant diseases?
Females have another X chromosome to make up for the faulty one, but males do not.
77
Why can we not say with 100% certainty that a woman of an affected linked recessive disorder son was a carrier of the disease?
One third of cases of X linked recessive lethal diseases such as DMD are new mutations it is sometimes not obvious what are the odds of a woman being a carrier are.
78
What is a karyotype
Karyotyping is the process by which photographs of chromosomes are taken in order to determine the chromosome complement of an individual, including the number of chromosomes and any abnormalities. The term karyotype is also used for the complete set of chromosomes in a species or in an individual organism for a test that detects this complement or measures the number.
79
At what phase of the cell cycle is karyotyping done?
Metaphase
80
What is giemsa banding?
A technique used to analyze chromosomes by creating a karyotype. A dye stains chromosomes according to the GC content (guanine, cytosine) of the chromosome. The more the GC content, the darker the color of the stain at that part of the chromosome. This is done to be able to split each chromosome into certain areas to be able to refer to it and analyse it.
81
What is the use of single locus probes?
Can detect if there have been deletions from areas of thr chromosome
82
What is meant by aneuploidy?
Abnormal number of chromosomes
83
What method can we use to check for aneuploidy prenatally?
FISH (fluorescent in situ hybridization) or chorionic villus sampling
84
Which pcr method can be used to detect excess genetic material?
Quantitative real time pcr
85
Describe how we can carry out direct FISH
1. Get a probe complementary to a specific DNA we’re looking for ( may be abnormal to detect for disease)
2. denature DNA and allow probe to bind to it
86
What is the difference between peri centric and paracentric inversions.
Pericentric: involves centromere
Paracentric: happens in one of the arms of the chromdome
87
What is a translocation and what are its types?
Translocation: the exchange of genetic material between 2 chromosomes.
Balanced: no loss of genetic material
Unbalanced: loss of genetic material. Usually occurs in the child of a parent with a balanced translocation
88
prader Willi vs angelman?
Both due to deletions on chromosome 15
Prader Willi: paternal chromosome
Angelman: maternal chromosome
89
What disease occurs as a result of a deletion on the terminal part of chromosome 5?
Cri di chat
90
What is mean by an Acrocentric chromosome. Name the 5 acrocentric chromosomes
A chromosome which has its centromere closer to one side than the other.
13,14,15,21,22
91
What type of chromosomes undergo roebrtsonian translocations?
Non homologous, acrocentric chromosomes.
92
How can a robertsonian translocation be dangerous?
A carrier of a balanced robertsonian translocation is normal. However, the offspring of a person who is normal and person with a balanced robertsonian translocation may be at risk of trisomies.
93
What is an isochromosome
A chromosome made up of two long arms or two short arms
94
What is meiotic non disjunction
An incorrect division during meiosis (failure to separate homologous chromosomes in meiosis 1, or failure to separate sister chromatids in meiosis 2)
95
What is the main cause of most trisomy 21 cases?
Non disjunction in the first meiotic division (failure to separate homologous chromosomes)
96
What is the name of the disease occurring with trisomy 13?
Patau syndrome. Fused eyes, baby dies within the first month. Caused by meiotic non disjunction
97
What is trisomy 18
Edward’s syndrome. Meiotic disjunction.Abnormal head, clenched fists
98
Why are allosome aneuploidies not as dangerous?
1. X inactivation (lyonization)
| 2. Y chromosome carried only 500 genes, compared to 900 on X chromosomes, so Y aneuplodies are not harmful
99
Describe turner’s syndrome
45X. Normal IQ and life’s pain, however short stature, no gonad development, webbed neck
100
How do we treat turner’s syndrome
Estrogen and progesterone for secondary sexual characters, growth hormone for short stature.
101
What is meant by senescence
Aging of the cells.
102
What are the substances associated with aging in non diving cells?
Amyloid plaques
| Lipofuscin pigment
103
How does telomere length change with age?
Shortens.
104
What is p53 and what happens when it is mutated?
Tumor suppressor gene, G1 to S checkpoint. Inhibition of apoptosis
105
What does exposure to high ROS cause?
DNA damage and inhibition of mitochondrial function
106
How does a cancer cell evade apoptosis
1. No contact inhibition
2. No apoptosis
3. Produce cell activation signals
107
What are proto onco genes and tumor suppressor genes?
Both are genes that regulate cell cycle and control cell proliferation
108
How many mutations in Porto oncogenes are needed to cause cancer?
Only 1 mutation needed
109
How many mutations in tumor suppressor genes are needed to cause cancer?
2 mutations needed
110
What is a virus’s mechanism to cause cancer?
Integration of viral genome into host cell, activating proto oncogene
111
What is the name of the epidermal growth factor receptor that is over expressed in breast cancers?
Her2/ERBB2. The more the it is over expressed, the worse the prognosis
112
What happens when the RAS proto oncogene becomes an oncogene?
Protein becomes constitutively active
113
How many mutant copies of the retinoblastoma gene are needed to develop retinoblastoma?
2
114
Normally, what is the function of the RB (retinoblastoma gene)
Tumor suppressor gene
115
How can a person have a genetic predisposition to developing retinoblastoma?
They can inherit a mutant rb gene from parent
116
How are growth factors receptors affected by cancer?
Increase in number and become hyper responsive to growth factors
117
What is the growth factor receptor that increase in squamous cell carcinomas of the lung?
ERBB1
118
What can be given to breast cancer patients with HER2 over expression?
HER2 antibody to block extra cellular domain of this receptor
119
What is the gene that is most commonly mutated in cancers?
RAS gene
120
What acts as a molecular brake on the uncontrolled RAS protein?
GAPS (GTP-ase activating proteins) by favoring hydrolysis of GTP to GDP
121
What intracellular signalling pathway does RAS protein activate
MAP Kinase pathway
122
Function of ABL protooncogene?
Promotion of apoptosis and has a high tyrosine kinase activity
123
In what disease do we get BCR-ABL translocation
Chronic myeloid leukemia
124
Which chromosome are BCR and ABL genes on?
BCR: 22
ABL:9
125
What changes occur in a cell because of BCR ABL translocation?
1. No inhibition of apoptosis since it cannot enter the nucleus
2. Activation of RAS-RAF pathway leading to potent, unopposed tyrosine kinase activity and growth autonomy
126
What is the drug given to the patients of the BCR ABL translocation and what is its mechanism of action?
STI 571 (Gleevec)
Promotes apoptosis by nuclear localization of ABL
Neutralizes tyrosine kinase activity, inhibiting growth
127
Function of myc gene
Promotes cell proliferation and levels return to basal again at the start of the cell cycle by INDUCINF THE TRANSCRIPTION OF CDKS AND CYCLINS
128
What happens in myc gene overexpression
Cancer
129
What are the molecules that drive a cell into starting thr cell Cycle?
Cyclins and cycling dependent kinases bound together .
130
Cyclin dependent kinases are constitutively synthesized, but in the inactive form. What leads to their activation?
Cyclins.
131
Which cyclins and CDKs become the most over expressed in cancers?
CDK4 and cyclin D
132
Where can the retinoblastoma gene be found?
Chromosome 13q14 (long arm, sub band 14)
133
What cancer have a mutant form of the RB gene
Breast, lung, bladder.
134
What is the active and inactive form of RB? Andd what is responsible for the phosphorylation.
Active: hypo phosphorylated
Inactive: hyper phosphorylated
135
Function of RB gene.
Regulation of G1 to S checkpoint
136
State the effect of these genes on the cell cycle
Myc gene: causes cell to start cycle
CDK/ cyclins: cause cells to start cell Cycle
Retinoblastoma: checks cell between G1 and S to control cell cycle. (Inhibitory).
137
State the mechanism of how the RB gene inhibits transcription
1. In the hypophosphrylated (active) state, RB binds to EW transcription factor preventing it from forming a complex inhibiting the genes required for the S phase of the cycle. CDK inhibitors allow them to be in the hypophosphorylates state by deactivating cyclins and CDKs.
138
State the mechanism of how the RB gene is made inactive
1. When CDKs and cyclins are active, the phosphorylate the RB gene inactivating it,therefore E2 is free to bind to DNA to stimulate the transcription factors of S phase. TRANSCRIPTION OCCURS
139
What is the gene mutated in 100% pancreatic cancers?
TGF- Beta
140
What effect does TGF-B have on cell cycle and how?
It inhibits cell cycle by activating CDK inhibitors and RB gene
141
What is the ligand releases by t cytotoxic cells to induce apoptosis in another cell?
Fas ligand
142
What is the name of the final protein produced by fas and fas ligand pathway which induces apoptosis?
Caspase 3
143
What is cytochrome c?
A substance released by the mitochondria which promotes apoptosis. It is a key event in the apoptosis pathway. Similar to it is also AFPAF-1
144
What mechanisms do the tumor cell use to evade apoptosis?
Lowered expression of fas ligand and do not release cytochrome c
145
How does BAX impact p53?
Increases its activation
146
What do caspases do?
PROMOTE APOPTOSIS
147
What does telomerase do?
Maintain telomere length
148
How do cancers avoid senescence
Upregulation of telomerase which maintains telomere length
149
What are the two most important tumor associated angiogenic factors?
Basic fibroblast growth factor
| VEGF= vascular endothelial growth factor
150
How does the wild type p53 inhibit angiogenesis
By producing thrombospondin 1
151
Why does p53 not produce thrombospondin during cancer?
Usually p53 becomes mutated so no longer produces thrombospondin
152
What are the two genes mutations that account for most familial breast cancer?
BRCA1 and BRCA 2 (breast cancer gene)
153
Which gene mutation substantially increases the risk of developing epithelial ovarian and prostate cancer?
BRCA1
154
What mutagenic effects does radiation have
Chromosomal breaks, double stranded DNA breaks, translocations and point mutations
155
What is the difference between PGT and other prenatal diagnosis (CVS, AMNIOCENTESIS) methods?
PGT: Pre implantation testing. Genetic testing before implantation, however can only be done by IVF, NOT NORMAL PREGNANCIES
prenatal diagnosis: done after NORMAL pregnancy on implanted embryo of 12 to 16 weeks, after which parents can decide to abort or keep the baby
156
What are the two types of PGT
PGS: Preimplantation genetic screening. Done to test for aneuploidy
PGD: preimplantation genetic diagnosis. Tests for SINGLE chromosomes
157
What are the specific molecular techniques used with PGT
Fluorescent in situ hybridization (FISH)= test for specific chromosomes
Array comparative genome hybridization (aCGH)= chromosomal imbalances in a cell
PCR
NGS (next generation sequencing)
158
What is the Tumor Lysis syndrome
A group of symptoms experienced by a cancer patient due to the lysis of tumor cells and release of their contents into the bloodstream.
159
What is the epithelium of the ectocervix
Non keratinized Stratified squamous epithelium
160
What is the layer of the cervix that accumulates glycogen in response to insulin?
Ectocervix
161
What is the epithelium of the endocervix
Simple columnar mucin secreting epithelium
162
What is the cell responsible for squamous metaplasia of the endocervix in response to chronic cervicitis?
Endocervical progenitor cell
163
What is the name of the ectocervics, cell responsible for regeneration
Basal cell
164
How do we know ectocervixal cells have a lot of glycogen?
Clear cytoplasm under the microscope
165
The cells of extrocervix undergo keratinzation in which layer?
Intermediate and superficial
166
What is the SCJ
Abrupt transition between ectocervical stratified squamous epithelium and endocervical mucin-secreting columnar epithelium
167
What is the hormone responsible for the SCJ moving out into the Porto vaginalis at menarche?
Oestrogen
168
What type of cancer does the transformation zone predispose to?
Squamous cell carcinoma.
169
What are the low risk genotypes of HPV and what is their clinical presentation?
6 and 11. Non cancerous genital warts.
170
What are the high risk genotypes of HPV and what is their clinical presentation?
16 and 18. Cervical cancer.
171
Which area does the HPV target to cause cervical cancer ?
Transformation zone.
172
Are koliocytes a normal cell to be found in the cervix?
No. Koilocytes aka. halo cells are a type of epithelial cell that develops following a human papillomavirus (HPV) infection. Koilocytes are structurally different from other epithelial cells. For instance, their nuclei, which contain the cell's DNA, are an irregular size, shape, or color
173
What grade of dysplasia is the level of koliocytes associated with?
CIN 1 (cervical intraepithelial neoplasia 1)
174
What do we mean by cervical intraepithelial neoplasia levels 1 to 4?
The levels of dysplasia (non invasive) preceding squamous cell carcinoma (invasive)
175
What do we assess the grade of cervical intraepithelial
Look at the N/C ratio
176
In which layers of the cervix can koliocytes be found?
Superficial and middle layer after infection of HPV
177
How can we distinguish normal from abnormal cells during colposcopy (microscope for looking at cervix)
We add acetic acid which will stain the cells that underwent CIN white (aceto white)
178
What is a “cone” biopsy
A circular/cylindrical shaped excision from the cervix, containing areas from the TZ and endocervix
179
When is cone biopsy indicated?
CIN 2/3 by cytology and colposcopy or HSIL (high grade squamous intraepithelial lesion)
