Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

Genetics 431: Molecular Genetics > quiz #2 > Flashcards

quiz #2 Flashcards

(76 cards)

Start Studying
1
Q

why do histone proteins migrate anomalously?

A

histones don’t migrate because they are very charged

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what does B-mercaptoethanol do in SDS gels?

A

breaks disulfide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

epitope tags for protein detection and isolation

A

GST- binds to glutathione
6HIS- 6 histidines in a row: binds to nickel chelate resin
peptide (epitope) tags: FLAG, myc, HA: bind to specific antibodies
GFP: small protein
TAP: sequentially uses 2 different epitopes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what are epitopes?

A

tags for protein detection and isolation
antibody binding sites

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

TAP tags

A

tandem affinity purification tags
very low background of non-specific interactions
1. purify target protein and interactors using IgG beads, which bind protein A
2. TEV protease removes protein A
3. purify target and interactors a second time using Calmodulin beads

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what is ChIP used to detect?

A
  • proteins-DNA interactions, binding
  • binding sites and distribution of transcription factors
  • gene transcription and polymerase activity
  • modifications to histone that influence chromatin structure and gene expression
  • nucleosome architecture and regulation of chromosomal maintenance
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what can ChIP-exo identify?

A

protein-DNA interactions with near base pair precision by incorporating exonuclease digestion

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

-

Chromatin Endogenous Cleavage-Seq (ChEC-seq)

A
  • uses micrococcal nuclease (MNase) attached to protein of interest (YFP) via a flexible linker (completly inactive until Ca2+ ions are added)
  • introduce YFP-MNase into live cells
  • permeabilize cell membrane and add Ca2+
  • DNA near (but not bound by) YFP cleaved by MNase
  • isolate and sequence small fragments of DNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

omics

A

Genomics: DNA sequencing
Transcriptomics: RNA-seq
Proteomics: Protein/complex purification and MS
Metabolimics: MS and NMR

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what was used in typical large genome projects?

A

promoters as landmarks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

size of human map unit

A

1,000,000 bp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

how many map units in humans is more than all DNA of E. coli

A

4 map units

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

high-resolution recombination mapping

A

landmarks for anchoring sequence information
1cM = 1 Mb DNA
1cm = 1% chance of recombination during meiosis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

how identical are humans at sequence level?

A

99.9

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

how many SNPs are between any 2 individuals?

A

3 million

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

FISH

A
  • fluorescent in-situ hybrid
  • cloned DNA with fluorescent dye
  • hybridize to denatured metaphase or polytene chromosomes
  • chromosome locations
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

physical maps

A

based on bp, not recombination
maps of purified pieces of genome (cloned DNA)
clones with large inserts are most useful
overlapping clones are assembled into contigs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Contigs

A

long continuous stretches of chromosome DNA
BAC sequences

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

what is the purpose of integrating genetic and physical maps?

A

to know which chromosome is which
order of markers is the SAME on genetic and physical maps
physical distance (base pairs) is NOT THE SAME as map distance in % recomb

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

evidence that physical evidence (bp) IS NOT the same as map distance in % recomb

A
  • frequency of recombination can differ 100 fold
  • recombination rates are influenced by chromatin structure
  • in humans, there are 30,000 recombination hot spots spaced every 50-100 kb
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

genome sequencing

A

one consensus sequence per chromosome
<1 error/ 10,000bp
usually 10 independent reads of each ntd

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

what are the 2 basic genome sequencing strategies

A

ordered clone sequencing- clones make up a physical map; requires the mapping of each chromosome prior to DNA splitting.
whole genome shotgun sequencing- randomly sequenced clones are assembled; best suited for small (bacterial) genomes; gaps filled by primer walking

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

ordered clone-by-clone genome sequencing

A
  • overlaps allow fragments to be assembled
  • requires the mapping of each chromosome prior to DNA splitting.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

first draft of the human genome sequence?

A

2001
took 13 years and $100 million

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
how many bp and genes are in genome?
3 billion bp 20,000 genes
26
how many bp per cell?
60 billion
27
what % of the human genome codes for enzymes?
1.5%
28
haplotypes
set of DNA variants tat tend to be inherited together because they are close to each along a single chromosome (shared group of polymorphisms that are very close together, so stick together)
29
homolog definition
genes related by descent from a common ancestral DNA sequence ex: hemoglobin and myoglobin
30
2 types of homologs
**ortholog**- gene in different species that evolved from common ancestor. retain the same function during evolution; ancestors and progeny **paralog**- genes related by duplication within a genome. May evolve new functions; cousins
31
C-value paradox
* DNA value per nucleus * lack of correlation between genome size and developmental, metabolic, or behavioral complexity
32
what % of genome is transcribed?
more than 80%
33
what % of genome accounts for introns?
30%
34
microRNAs and long noncoding RNA
regulate gene expression at epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels
35
what things have acquired key roles in gene regulation, development, and diseases?
highly repetitive elements, remains of transposable elements, and pseudogenes (inactive genes) | basically, dead genes acquire function
36
when was the last common ancestor?
90 MYA
37
what approach is used for comparative genomics?
**synteny** * retain the same function during evolution organisms of relatively recent divergence * show similar content and organization of genes in the same relative positions in the genome (not necessarily in the exact same order) * one of the most reliable criteria for estabilishing the orthology of genomic regions in different species
38
how can humans and apes be related?
human chrom. 2 is the result of head-to-head fusion of telomers of chromosomes homologous to chrom 12 and 13 of apes (Robertsonian translocation)
39
what are hominids?
extint members of the human lineage (not our ancestors, but cousins)
40
human-specific changes
most proteins have only 1-2 amino acid differences (30% are identical) changes in conserved noncoding sequences (regulatory regions) 1. brain development (GADD45G) 2. ability to speak and use language (FOXP2) 3. decreased sensitivity to smoke derived toxins (AHR)
41
what percentage is neandertal geome identical to modern humans?
99.7
42
what percentage are chimps identical to modern humans?
99.0
43
most current humans from Europe and Asia but not .......have .......
not Africa 1-3% Neanderthal DNA
44
Neanderthal genes that show evidence of positive selection
genes that affect keratin function in skin and hair neanderthal version of some genes involved in immune system function
45
what could contribute to disease in modern humans?
neanderthal genes
46
how much Neanderthal genome is present in modern humans?
30% but some regions appear to be completly lacking
47
human DNA from --> ........ from --->.......
humans --> Tibetans --> Denisovans
48
Tibetans
high altitude adaptation caused by introgression of Denisovan-like hypoxia gene, EPAS1
49
Denisovans
sequences make up 5% of DNA from modern Melanesians, Papuans, and Aboriginals
50
what makes our brains different from Neanderthal's?
* 100 mutations that change protein structure are specific to modern humans (only 100 proteins have meaningful aa change) * TKTL1 active in frontal cortex of humans: glucose metabolism and cell cycle regulation (if add human version of gene to mice, mice grow more neurons) (less neurons formed with Neaderthal version of gene than with human) * induce brain organoid fromation in tissue culture, which is an organ made in the lab
51
how has the human genome continued to adapt and evolve?
* **lactase production**(evolved independently in Africa, Middle East, and Europe; associated with domestication of cattle, camels * **skin color**: fair skin allows vitamin D production under low light; light skin protects against skin cancer in high light * **G6PDH**: high levels defend against free radical damage; low levels provide partial protection against malaria * **alpha-amylase**: humans have between 1-9 copies of the gene; high numbers in societies with high starch diets (apes and most wild dogs only have 1, Dogs that have been with humans long time picked up additional copies)
52
what is measured in a northern vs southern vs western blot?
northern: RNA southern: DNA western: proteins
53
3 requirements for linear chromosome stability and inheritance
telomeres: protect chromosome ends and allow their complete DNA replication centromeres: facilitate segregation during mitosis and meiosis origins of replications
54
telomerase TER RNA TERT
**telomerase**: ribonucleoprotein enzyme (protein + essential RNA) **TER RNA**: template for the repeated addition of G-rich telomeric repeats to the chromosome 3' end **TERT**: reverse transcriptase that copies the TER template
55
how are the ends of chromosomes preserved during DNA replication?
telomerase has its own primer (uses DNA as the primer), uses reverse transcriptase because copies DNA telomeres promote T-loop structure, which protects DNA ends and blocks DNA damage response
56
what can telomere shortening lead to?
DNA damage response cell cycle arrest deletional recombination telomere fusion
57
dangers of telomerase inhibition and activation
**inhibition**: limited proliferation potential (stem cell disease like aplastic anemia) **activation**: unlimited proliferation potential (cancer)
58
what do telomeropathies cause?
premature telomere shortening --> stem cell disease (cant proliferate) mutations in telomere binding proteins can also cause cell death or genome instability
59
centromeres
* DNA sequences/regions where sister chromatids adhere to each other most strongly prior to anaphase * assemble at kinetichore, which is a large protein complex where microtubules of the spindle apparatus attach to the chromosome (trans-acting factors)
60
cis-acting factors vs trans-acting factors
cis: affect gene expression on same piece of DNA trans: diffuse through DNA and affect different genes
61
chromosome disjunction
cohesins- ring-like proteins that prevent premature separation separase- cleaves cohesin at anaphase
62
what is anaphase driven by?
APC and activator Cdc20 --> triggers both activation of separase and also degrades cyclins less CDK activity --> exit from M phase
63
by how much do chromosomes compact?
7000 fold
64
length of DNA wrapped around histones length of linker DNA
146 ALWAYS around 50 bp (varies)
65
nucleosomes
146 bp of DNA (-) wrapped around histone octamers (+)
66
what makes up nucleosome core?
H2A H2B H3 H4 made up of Lys and Arg core is highly conserved because highly specialized core has a well-ordered crystalline structure
67
what does DNA wrapped around nucleosome consist of?
relatively straight 10 bp segments that are connected by bends and the DNA is slightly underwound
68
A=T vs GC regions in nucleosomes
2 or more A=T at 10 bp spacing will tend to position nucleosomes GC tracts inhibit nucleosome placement arrange DNA to where nucleosomes want or dont want to park there
69
what mediates histone-DNA and histone-histone interactions?
Histone-fold motif
70
tails of histones
extend from core octamer unstructured and available for interaction and modification
71
how many DNA turns around core octamer?
1.65 turns
72
who has the least neanderthal DNA?
humans from Africa
73
by how much does chromosome compact from nucleosomes?
6 fold linear compaction
74
what does linker histone H1 do?
goes at the end and compacts nucleosomal arrays
75
what do N-terminal tails of histones do?
interact with adjacent nucleosomes compacting chromatin
76
Whole-genome shotgun sequencing (WGS)
sequence a large number of overlapping DNA fragments in parallel (**reads**) uses computers to assemble into largers **contigs** primer walking to get **scaffolds**

Genetics 431: Molecular Genetics (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions