Block I Flashcards
1
Q
In the miller-urey exp. that sougth to explain how organic compounds formed under prebiotic conditions, voltage was applied to mix of methane, ammonia, water and hydrogen. Which compounds were found in the condensate that resulted from this procedure?
A
adenine, fatty acids, glycine, hexases. NOT RNA, amino acids, carboxylic acids, nucleic acid bases, sugars
2
Q
genetic deficiency of what enzymes results in alkaptonuria?
A
homogentisic acid oxidase
3
Q
What sequence motifs might you expect to be present in a protein that activates a gene at the chromosomal level during fetal development?
A
DNA binding motif; homeodomain
4
Q
what is the diff btw an ortholog and a paralog?
A
ortholog: two homologous genes in the different organism/species
paralog: two homologs from the same species
5
Q
what is the appox. percentage of the humane genome represented by Alu sequences?
A
13%
6
Q
What is the approx. percentage of the human genome represented by coding sequences?
A
2%
7
Q
What is the approx. percentage of the human genome represented by LINE sequences?
A
20%
8
Q
What is the approx. pecentage of the human genome represented by satellite DNA?
A
13%
9
Q
what is the approx. percentage of the human genome represented by singl-copy sequences?
A
45%
10
Q
what is the approx. percentage of the human genome represented by non-coding repetitive sequences?
A
55%
11
Q
What are the sizes, roughly, of alpha satellites, lines, sines, microsatellites, minisatellites?
A
microsatellites: 1-13 bp alpha-satellites- 171 bp mini satellites 14-500 bp SINE 90-500 bp LINE 900-7000 bp
12
Q
What is the name for chromosomal regions, a few kb in length, that are repeated in a dispersed fashion on the same or different chromosomes?
A
segmental duplications
13
Q
How big is the haploid human genome?
A
3 billion base pairs (3,000,000)
14
Q
What are some mechanisms that give rise to psuedogenes?
A
deleterious mutations of the promotor or coding sequence so that gene expression is not possible.
2. processed pseudogenes- have no intron. some pseudogenes arose from reverse transcription of processed mRNAs into cDNAs, which were re-integrated into a random location in the human genome .
15
Q
What is horizontal gene transfer?
A
transfer of genes from the genome of one species into ththat of another
16
Q
What is a nucelosome?
A
a nucleosome consists of some DNA wrapped around a histone protein core
17
Q
how big is the “beads on a string” DNA structure?
A
10 nm
18
Q
Put these terms in order of size: chromatid, coils, metaphase chromosome, rosette, 30nm fiber
A
30 nm fiber, rosette, coil, chromatid, metaphase chromosome
19
Q
What DNA repeat element protects a chromosome from being inserted into another chromsome through random recombination?
A
telomere
20
Q
What does the ARS1 sequence do in a YAC?
A
It is responsible for helping the YAC replicate during the S-phase cell cycle. Think of it as the origin of replication!
21
Q
In what cell cycle phase do cells prepare for DNA synthesis?
A
G1
22
Q
Where do we see high GC content?
A
in regions of the chromosome that are gene-rich
23
Q
What are the characteristics of chromosomes stained with Q-banding?
A
Similar patter to G-banding (heterochromatin dark, euchromatin light), but requires fluorescent microscope
24
Q
What is R-banding?
A
heat-denatured chromsomes that are then steined with giemsa give a patter that is opposite of typical G-stains
25
What is C-banding?
a type of stain where chromosomes are treated with base before giemsa staining to show the chromatin near the centromeres
26
how does a chromosome preparation obtained early in metaphase differ from one obtained during late metaphase after G-banding?
in the prometaphse prep, the chromsomes appear longer and the banding resolution is higher
27
what do we call chromsomes 13,14,15,21,22?
acrosomic chromosomes
28
What are some common clinical complications of Down's syndrome?
cardiac septal defects, cataracts, duodenal atresia, myeloid leukemia, early onselt Alzheimers
29
A couple has a child with Down's syndrome who has a karyotype of 47,XY,+21. The probability for their next child to have Downs is _
1%
30
What is the name for the genotype 47,XXY? What are some clinical manifestations?
klinefeller: hypogonadism with small testes, tall stature and long extremities, gynecomastia, less body hair/muscle mass, infertility, some behave probs and learning disabilities
31
What are some clinical manifestations of 47,XYY?
tall stature, long extremities, some behavioral probs/learning disabilities. NO INFERTILITY.
32
What are some clinical manifestations of 47,XXX?
decreased ferlitiy, menstrual instability, slight developmental probs.
33
What is the name of the genotype for 45,X? Clinical manifestations?
turner's syndrome
significant fetal detha, lymphedema, aortic coarctation and bicuspid aortic valve, short, ovarian dysgenesis and amenorrhea, behavioral probs and learning disabilities.
34
What gene is responsible for the short stature of turner's syndrome patients? In what region is it located?
SHOX gene in the pseudoautosomal region
35
What is the difference between apericentric inversion and and a paracentric inversion?
pericentric inversion occurs across the centromere; paracentric inversion occurs all on the same side of the chromsome
36
what is an isochromsome?
example of chromsomal duplication when an entire chromosome arm is duplicated, and this duplication replaces the other chromosome arm
37
exposure to what causes pyrimidine dimers to be formed in DNA?
UV radiation
38
What are common phenotypes associated with DNA repair disorders?
severe growth deficiencies, premature aging, photosensitivity of skin immunodeficiency and hematological defects, and cancer predisposition
39
What are the three main ways in which nucleotide bases can be damaged?
oxidation, chemical adducts, and deamination
40
Describe base excision repair. What is the name of the only genetic defect known to involve base excision repair?
glycosylase removes the damaged base, leaving only the sugar backbone (aka a apurinic/apyrimidinic nucleotide. apurinic/apyrimidinic nucleotide is excised by an AP endonucease, which excises the sugar. then the gap is filled in to pair with the complementary strand, and the strands are ligated. This can happen as either short-patch (single-base damage) or long-patch (2-10 base damage). disorder: hyper-IgM syndrome
41
What mechanism repairs pyrimidine dimers?
nucleotide excision repair
42
How does nucleotide excision repair work?
this mechanism repairs pyrimidine dimers. these dimers cause a bulky distortion of the double helix that is detected, leading to the removal of about 25 bases, including the buly bases. The gap is repaired using DNA polymerase delta, proliferating cell nuclear antigen (PCNA), and DNA ligase
43
What are the two recognition systems for distortions caused by pyrimidine dimers?
global genome pathyway and the transcriptional-coupled pathway
44
What are some of the clinical manifestations of xeroderma pigmentosum (XP)? How is XP usually inherited?
Most importantly: extreme sunburns after minimal sun exposure, freckling, and high risk of skin cancer. Some eye involvement, especially in the parts of the eye exposed to the sun.
Other possible complications include CNS and neurological complications like microcephaly, progessive hearing loss, and cognitive impairment. usually autosomal recessive
45
In mismatch repair, what protein recognizes single nucleotide mismatches?
MSH6
46
In mismatch repair, what protein recognizes small insertions and deletions?
MSH3
47
What causes Lynch syndrome? What is the clinical manifestation?
Lynch syndrome is caused by defects in the MMR genes (genes for mismatch repair). Patients are usually heterozygous for these defects. Lynch syndrome leads to very high levels of risk for GI, urinary, and endometrial and ovarian cancers. Many of these tumors demonstrate microsatellite instability.
48
What is microsatellite instability? Where might we observe microsatellite instability?
Microsatellite instability means that the microsatellite loci are highly variable in the length of the alleles at microsatellite loci. This is frequently seen in the tumors of patients with Lynch syndrome as a result of mutations in the genes for mismatch repair.
49
What enzyme is involved in single-strand break repair? What does this enzyme do?
PARP (poly-ADP ribose polymerase). PARP detects single-stranded breaks and then tags them for repair by sythesis of a poly ADP ribose chain. Inhibition of PARP may help treat cancer.
50
What are the two types of double strand break repair?
non-homologous end-joining and homologous recombination repair
51
How does non-homologous end joining work?
It is a way of dealing with a double stranded break. Most of the time, the ends are uneven. First, the protruding end is cleaved (which results in loss of DNA material). Then, rhwew is limited base pairing between the two double stranded DNA strands are filled in, joined by ligation.
52
What is double strand break repair by homologous recombination?
In homologous recombination repair, a segment of the undamaged chromosome is transferred to over to replace the damaged segment-- homologous recombination. One potential consequence is loss of heterozygosity.
53
What are the four main examples of diseases caused by defects in homologous recombination repair?
Bloom syndrome, Werner syndrome, fanconi anemia, and familial breast and ovarian cancer syndrome
54
What are clinical manifestations of Bloom's syndrome, and what is the general cause of bloom's syndrome?
homologous recombination repair
growth restriction, hypersensitivity to light, infections due to immunodeficiency, chromic pulmonary disease and diabetes mellitus. possible learning disability, male infertility, and early menopause. high risk for cancer. autosomal recessive.
55
What is the genetic cause of bloom's syndrome?
defect in BLM gene that codes for DNA helicases. can also cause loss of heterozygosity during mitosis. BS patients show hyper recombination detected by the sister chromatid exchange test.
56
What is Werner syndrome (general cause, inheritance pattern, clinical manifestation)
Symptoms: premature aging, cataracts and retinal degeneration, skin ulcers and scleroderma, atherosclerosis, diabetes mellitus, hypogonadism, osteoporosis and increased cancer risk (esp.soft tissue sarcomas). bird like facial features. it is autosomal recessive and caused by defects in double stranded break repair
57
What genes cause Werner syndrome?
WRN, a DNA helicase. Without WRN, cells have decreased recombination repair. also leads to shortened telomeres.
58
What are the clinical symptoms associated with FAconi Anemia?
Bone marrow failure, birth defects, short stature, pigmentation abnormality and an increase in cancers, especially of lymphoreticular origin. it is autosomal recessive and caused by problems with double stranded break repair
59
What are the clinical manifestations of dyskeratosis congenita? What is the inheritance pattern?
reticular pigmentation of the skin, dystrophic nails, oral leukoplakia (white patchy lesions), bone marrow failure. maybe pulmonary fibrosis, ataxia, strictures of GI, growth delay and malignancy. can be inherited as autsomal dominant, autosomal recessive, or X-linked recessive!
60
What are the two main components of telomerase? What other proteins are also required?
telomerase RNA component and telomerase reverse transcriptase. dyskerin also required
61
What is the breakage fusion bridge cycle?
After telomeric shortening, we see chromosomal and genome instability because of the formation of fusion bridges when cromosomal ends are more exposed. then, fused chromsomes are broken, leading to more chromsomal arrangement and genome instability.
62
What is the role of RNA pol I?
exclusively transcribes a single rRNA
63
What is the role of RNA pol II?
transcribes all mRNA
64
What is the role of RRNA III?
transcribes all but one rRNA and all tRNA
65
What does alpha-amanitin do?
inhibits RNA pol II to a high degree (RNA Pol II makes mRNA); inhibits RNA pol III a little (makes tRNA and most rRNA). from a mushroom!
66
What does actinomycin D do?
intercalates in DNA and inhibits transcription, especially directed against RNA pol I
67
What are the three core promoter elements?
initiator, which encompasses the transcription start site. the TATA box, 26-31 bps upstream of initiator, and the DPE, which is 28-33 bp downstream of the start site.
68
What is involved in the formation of the pre-initiation complex (PIC) for transcription?
1. TBP (TATA binding protein) binds to the TATA site. It is a part of the PIC even if the gene doesn't have a TATA box.
2. TBP forms part of a larger complex called TFIID made of additional factors called TAFs. TAFs can recognize DPE and initiator sites.
3. TFIID is bound by TFIIB. TFIIB binds to DNA near the TATA box.
4. RNA Pol II is rectruited and binds to TFIIB through a factor called TFIIF.
5. TFIIE and TFIIH bind to the complex
69
Through wat factor does RNA pol II bind to the pre-initiation complext (PIC)
TFIIF
70
What factors bind to the PIC/RNA Pol II complex just before initiation of transcription?
TFIIE and TFIIH.
71
Which two complexes for DNA transcription intiation include DNA helicases? What do they do?
TFIIF and TFIIH. they unwind DNA at the promoter in a process called promoter melting.
72
What is special about the C-terminal domain of human RNA pol II?
it has 52 repeats of a heptapeptide (YSPTSPS, but you don't need to know this sequence)
73
How does synthesis of the nascent transcript begin?
the TFIIH complex has a kinase that phosphrylates the C-terminal domain of RNA pol II. this event is called promoter clearance.
74
What happens immediately after phosphorylation of the c-terminal domain of RNA pol II during transcription? Why?
transcription is paused by the binding of DSIF and NELF. This happens so that the mRNA transcript can undergo 5' capping
75
What does positive transcription elongation factor b (PTEF-b) do?
It allows transcription to go on after 5'capping of mRNA transcripts. It does this by further phosphorylating the c-terminal domain of RNA Pol II and by phosphorylating DSIF. DSIF phosphorylation leads to release of RNA pol II by DSIF and NELF so that RNA pol II can be released from transcriptional pause.
76
What does TAT do?
TAT is part of the HIV genome. WIthout TAT, HIV replication begins, but RNA pol II gests stuck in the pauses and eventually falls off. With TAT, the HIV transcript is recognized and PTEF-b is recruited. PTEF-b phosphorylates the RNA pol II and HIV is propogated.
77
What is one drug that blocks TAT? How?
DRB inhibits the PTEF-b kinase.
78
Where does the recognition helix of the helix-turn-helix domain bind dna.
major groove
79
What are the important structural characteristics of zinc finger domains?
His and Cys residues coordinate a zinc molecule. they can be organized into repeating chains to increase specificity for given DNA sequences.
80
How do transcription factors work generally?
They bind to regions near the gene promoters. Then, they recruit general transcription factors. They can also recruit factors that modify chromatin structure.
81
What is a common chromosomal rearrangement in T-cell acute lymphoblastic leukemia?
SCL/TAL1, which is normally not expressed very much in differentiated T-Cells, is put under the promotor of the SIL gene (about 90 bps upstream), due to some kind of a deletion/rearrangement/translocation. because SIL is constitutively expressed, this results in over exprossion of the SCL/TAL1 transcription factor, which leads to misregulation of all the genes regulated by SCL/TAL1.
82
What is the classic example of a gene that is regulated by multiple promoters?
PBG deaminase, which helps make heme. One promoter active in erthyroid cells (strong promoter), and one cell active in all other cells (weak constitutive promoter)
83
What are the three potential consequences of a nonsense mutation?
1. unstable mRNA- if there is a stop codon about 50 bases upstream of the last splice junction, it is usually rapidly degraded via nonsense-mediated decay
2. truncated protein- rare event usually occurring in genes without introns
3. exon skipping: alternative splicing eliminates the premature stop codon
84
What happens if you mutate the 3' untranslated region of a coding DNA sequence? What about the 5' end?
3' end: RNA instability
| 5' end: difficulty initiating translation
85
What is the difference between haploinsufficiency and dominant negative mutations?
haploinsufficiency: heterozygotes don't make enough of the functional protein, so they show a phenotypic difference. follow dominant pattern of inheritance
dominant negative mutation: the "bad" gene actively disrupts the function of the "good" gene
86
Define the terms amorphi, hypomorphic and antimorphic alleles:
amorphic: no gene product made
hypomorphic: reduced amount of gene product made
antimorphic allele: activity of this allele antagonizes that of normal allleles
87
What is the difference between penetrance and expressivity?
penetrance: the probability that someone with the disease genotype will have the disease phenotypically
expressivity: the range of phenotypes resulting from a given genotype
88
What is genetic anticipation?
genetic diseases where the disease severity increases with successive generations
89
What is the molecular basis for fragile X syndrome?
trinucleotide repeats (CGG) in the 5' untranslated region of the FMR1 gene on the X chromosome. this makes lots and lots of CpG dinucleotides, which are easily methylated. Methylation leads to transcriptional silencing of the FMR1 gene.
90
What is the molecular basis for Rfiedreich ataxia?
trinucleotide expansion in an intron of the gene frataxin that results in problems with transcription and gene splicing
91
What is the molecular basis for myotonic dystrophy?
trinucleotide repeat sequence in the 3' untranslated region of the DMPK region that prevents normal RNA handling and metabolism
92
What is the molecular basis of Huntingtons?
trinucleotide CAG repeat sequence in the coding region that leads to a long polyglutamine tract that preiptates in neurons and leads to neuronal cell death.
93
What is meiotic drive? Examples?
significant deviation from the 1:1 segregation of allels at a given locus. frequently seen in trinucleotide expansion diseases, often in a sex-specific manner. examples: fragile x and myotonic dystrophy expansion occurs only in females, while huntingtons expansion occurs only in males
94
What is the Lyon hypothesis?
In any given cell, there is only one active X-chromosome
95
When does X cell inactivation occur?
1000-2000 cell stage of the early embryo
96
What happens during X inactivation?
XIC (x inactivation center) contains the XIST gene. XIST produces an RNA that coats almost all of the chromosome. This recruits proteins that convert X euchromatin into heterochromatin
97
What are four main reasons for non-random X inactivation/
1. chance
2. monozygotic twinning
3. balanced X autosomal translocation
4. mutant allele affects survival, cells from females heterozygous for the allele will always have an active normal-allele-bearing X
98
What is the Sherman paradox?
refers to the fact that, for fragile X, daugthers of transmitting males often have affected kids, but their grandmothers don't usually. due to the fact that fragile x is only unstable in the female germ line
99
About how many RNA genes do we have?
3000
100
What do snRNAs do?
play a role in RNA splicing
101
What do snoRNAs do?
help in site-specific modification of rRNAs
102
describe the process of splicing in extremely vague terms
1. adenosine of the branch point attacks the phosphodiester bond on the 5' end of the dibir intron. this is the first transesterification. the loopy thing on the 3' end is called a lariat
2. in the second step, the 3'0H group attacks the receptor site of the intron. the lariat is excised and the exons are attached (second transesterification)
103
What makes up a spliceosome?
pre-mRNA and snRMPs
104
What are three important features of most snRNPs?
1. guanosine cap
2. Sm binding site
3. Some complementary sequences to certain conserved regions of pre-mRNA (like, the 5' splice site or whatever)
105
Describe the four steps of spliceosome assembly.
1. U1 binds to the 5' splice site in an ATP dependent manner.
2. U2 binds to the branch point. mismatch causes the A that will do the attacking of the first transesterification bulges out.
3. U4,5 and 6 join the complex to form a spliceosome.
4. The spliceosome is rearranged before becoming active.
106
What is 5' capping, chemically?
end of the 5' transcript of mRNA is modified by the addition of 7-methylguanosine in a 5' to 5' phosphodiester linkage
107
what are the two purposes of 5' capping?
1. initiation of protein synthesis
| 2. mRNA stability
108
What are the three purposes of the 3' polyA tail?
1. export from the nucleus
2. message stability
3. recogniction signal for the ribosome to increase efficiency of translation
109
What happens in the nucleolus?
rRNA processing, transcription, and modification
110
What molecules are responsible for removing spacer sequences of pre-rRNA?
snoRNPs
111
What modifications occur in rRNAs? what molecules are responsible?
methylation (2'-O-methylation)
and
psuedoruidylation
carried out by snoRNPs
112
what is the difference in function btw the large and small subunits of ribosomes?
smaller subunits: interations btw mRNA and tRNA
| larger subunits: peptide bond formation
113
What rna polymerase makes tRNAs?
RNA pol III
114
what molecule edits precurser tRNA 5' end?
RNaseP
115
what is special about the 3' end of tRNA?
it contains a CCA trinucleotide sequecnce that is added during tRNA processing
116
what enzyme attaches an amino acid to its given tRNA?
aminoacyl-tRNA synthetase
117
how much energy is required to activate a given tRNA? to incorporate it into a growing amino acid polypeptide chain?
2 ATPs; 2 GTPs
118
describe translation initiation
1. eIF2 helps the 40S subunit bind to initiation tRNA
2. the mRNA cab binds cap binding protein
3. initiating tRNA/40S complex binds to AUG of mRNA
4. 60S joins the group
all this takes energy
119
In what site does enongation being? what happens next>
begins in the P site. then tRNA is bound to A site with the help of EF1alpha. if codon recognition happens, GTP is brought in and the chain is elongated
120
what is nonsense mediated decay? why is the useful (name a disease)
`mRNA transcripts containing premature ternination codons that are located more than 50 nts upstreat of the 3'most exon-exon junction are degraded. this prevents dominant negative proteins from being produced.
one example of why this is useful comes from a dominant version of thalessimia in which a truncated protein product is not caught by this mechanism (the premature termination codon is too close to the end) messes up hematopoiesis.
121
what are the four names of strategies employed to overcome nonsense mutations, and one limitation of each (except the last)
1. gentamicine/amnioglycoside antibiotics: promote read-through of premature AND normal termination codons
2. suppressor t-RNAs that match the termination codon- again, promote readthrough of both normal and premature termination signals
3. antisense 2'-O-methyl oligoribonucleotides: promote skipping of an exon
4. PTC124: can supposedly distinguish btw premature and normal termination sequences
122
what are the two planes of rotation in a peptide bond?
psi bond (btw carbonyl C and alpha carbon) and phi bond btw C and N
123
how do you estimate protein mw?
110 da X # amino acids
124
Describe keratin structure
made of two alpha helicies (right handed) into a left anded coiled coil where hydrophobic residues are matched up. lots of cysteine for disulfide bonds
125
describe collagen structure
three amino acids per turn of left-handed helix, usually rich in glycine and prline. forms a right handed triple helical bundle. good for strength and flexibility
126
what is the structure of silk?
mostly beta sheets with lots of ala and gly. resists longitudinal stretching but good for bending.
127
What is the difference between the cis-Golgi network and the trans golgi network?
cis: forming face: side of the golgi closest to the ER
trans: opposite of the cis face
128
How is stuff imported into the nucleus?
less than 40 kDa: imported passively
larger molecules/proteins: contain a nuclear localizing signal (NLS) which complexes with importin and enters the cell via nuclear pore complexes. undloading and recycling of importin requires GTP
129
How is stuff exported from the nucleus?
lots of proteins complex with stuff in the nucleus and then need to leave. they contain nuclear export signals and complex with exportin
mRNAs leave through an mRNP exporter
130
How does a protein end up being synthesized into the RER?
1. It contains a signal sequence (cationic and hydrophobic) called the ER signal seq.
2. ER signal sequence is recognized by cytoplasmic SRP (signal recognition peptide
3. SRP binds to SRP receptors in the ER with the help of GTP.
4. SRP and SRP receptors dissociate from the growing peptide as the peptide attaches to translocon channel
5. peptide synthesized into the the RER
6. signal peptidases cleave ER signal sequence
7. protein folds.
131
What two major modifications happen in the RER for secretory proteins and membrane proteins?
glycosylation and sulfide bond formation
132
What is N-glycosylation vs. O glycosylation?
N: an pentasacchride core is linked to the nitrogen of an Asn residue
O: linked to the Oxygen atom of the r groups of serine or threonine
133
What protein catalyzes disulfide bond formation?
rotein disulfide isomerase
134
What are two chaperone proteins with proofreading abilities? which one is membrane bound and which one is not?
calnexin (membrane bound) and calreticulin (soluable)
135
What do calnexin and calreticulan recognize, molecularly?
single terminal glucose residues
136
How are type I membrane proteins inserted into the membrane?
initially transported as in secretory proteins with continuted translation after the signal sequence has been cleaved. but they also have a stop-transfer anchor sequence that is highly hydrophobic and stops translation of the peptide while the peptide is still in the translocon channel.
137
What happens with the formation of transport vesicles?
GTP-binding coat proteins like clathrin are recruited to part of the donor compartment. this part also contains V-SNARE proteins. recruited proteins tend to bind with cargo. vesicles bud off.
clathrin falls off, and v-snares bind with t-snares (target snares) on the target membrane.
note: clathrin usually needs an adapotor protein complex to bind to the cargo protein receptors. dynamin is needed for vesicles to bud
