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Human Genome Flashcards

1
Q

What are the 2 subunits of TF2D?

A

TBP & TF2H

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2
Q

What is the function of TBP in TF2D?

A
  • binds to TATA box
  • recognizes methylation of histone 3, K4
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3
Q

What is the function of TATA box in TF2D?

A

establishes where the primary transcript will begin

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4
Q

What is the function of TF2H in TF2D?

A
  • opens/exposes DNA for RNA polymerase 2
  • phosphorylates a subunitof rNA polymerase to start transcription
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5
Q

What is the function of RNA polymerase 2?

A

transcribe and used for protein coding genes

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6
Q

What is primary transcript?

A

defines the egene space in the genome browser
that mostly gets processed to mRNA

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7
Q

What does the primary transcript include?

A
  • 5’UTR
  • 3’UTR
  • introns
  • exons
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8
Q

Does the primary trancript include the regulatory sequence?

A

no

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9
Q

Are primary transcripts RNA or DNA?

A

RNA

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10
Q

What is translation?

A

using RNA code to add amino acids to make a protein

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11
Q

What is mRNA?

A

RNA that leaves to nucleus, goes to cytoplasm, and gets translated into a protein

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12
Q

What is a tRNA?

A

bring in amino acids

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13
Q

What are the key components in translation?

A
  • mRNA
  • tRNA
  • AUG
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14
Q

What is AUG?

A

start codon that codes for Met

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15
Q

What are the assigned terminus to the 5’ and 3’ ends?

A
  • 5’: N temrinus (has AUG)
  • 3’: C terminus
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16
Q

What occurs with V600E?

A
  • valine at position 600 mutates into glutamate
  • gains a negative charge
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17
Q

What is the BRAF protein?

A
  • pro-proliferative kinase that is active when phosphorylated
  • gets things going
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18
Q

What does each gene include?

A
  • regulatory sequences
  • exons
  • introns
  • 5’ UTR
  • 3’ UTR
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19
Q

In genes, what is the charge of the coding and template strands?

A
  • coding = +
  • template = -
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20
Q

What are the important numbers to know about gene sizing?

A
  • SRY = .9 kb
  • HBB = 1.6 kb
  • TP53 = 39 kb
  • F8 = 186 kb
  • CFTR = 250 kb
  • DMD = 2400 kb
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21
Q

Whatis the trend in mutagenesis in gene sizing?

A
  • random
  • bigger the gene -> more likely for mutation
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22
Q

What are the characteristics of a gene family?

A
  • genes decended by duplication with a slight variation
  • homologous throughout entire length of sequence (70-80% similar)
  • clustered together or dispersed
  • similar nucleic and amino acid composition
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23
Q

What are examples of a gene family?

A

globins & Ig families

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24
Q

What are the 2 types of globin families?

A
  • fetal -> high affinity to O2 in placenta
  • adult -> lower O2; release of O2 in tissues
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25
Genes must be atleast what percentage to be considered the same family?
70%
26
Amino acids must be at least what percentage to be homologs?
20%
27
What is BLAT?
* shorter * only nucleotides used to match sequence to genome
28
What is BLAST?
* longer * can compare using nucleotides or amino acids
29
What are the types of immunoglobulins?
* IgG * IgM * IgE * IgA * IgD
30
What are the characteristics of immunoglobulins?
* homologous * similar biochemical functions
31
What are the 2 types of genes in immunoglobulins?
35 V & 5 J
32
What genes are in heavy and light chains?
* heavy -> V, D, J * light -> V & J
33
How are gene families formed?
from duplication & mutations
34
What is the main difference between gene and supergene families?
* gene -> related by biochemical functions * supergene -> related by physiological function
35
What can cause a supergene family?
* exon shufling * reverse transcriptase making DNA from RNA
36
Supergene families are composed of what percentage of homologous genes?
50%
37
What is an example of a supergene family?
immunoglobulins
38
What are the characteristics of a single copy DNA sequence?
* one or few copies per haploid genome (< 100) * no upper or lower size
39
What are the characteristics of a moderately-repetitive DNA sequence?
* 100-1 million copies * clustered or dispersed * can be code or non-code
40
What are the characteristics of a highly-repetitive DNA sequence?
* 10^6 * clustered * non-coding
41
What are examples of highly-repetitive DNA sequences?
telomeres & centromeres
42
What are examples of a moderately-repetitive DNA sequence?
LINEs & SINEs
43
What are LINEs?
* longer DNA that can encode proteins * reverse transcriptase
44
What are SINEs?
too short to encode proteins
45
Where are polyT tails located?
on cDNA to have A-T rich sequences as integration site targets
46
What is exon shuffling?
downstream exon with cDNA inserts itself at new position
47
48
What is an important number to remember for rRNA?
Man is 280
49
What are the 2 ribosomal units?
18S & 28S
50
What are intervening sequences?
remnants after ribosomal subunits are cleaved
51
How do intervening seuqences differ from introns?
not spliced together
52
How many base pairs are in our genome?
3 billion
53
How many times can mRNA be used?
many times
54
What are variable number tandem repeats?
same sequence at the same location but different number of repeats ## Footnote finger printing
55
What are the characteristics of gel electrophoresis?
* matrix where DNA moves towards the "+" end * heavy DNA moves slower -> more repeats * lighter DNA moves faster -> less repeats
56
How many protein coding genes are there?
about 20,300
57
What are transposons?
* DNA that has moved due to reverse transcriptase * moves around exons
58
What are CpG islands?
* associated with regulatory regions * roles gene regulation (gene slicing)
59
What does CpG methylation lead to?
gene inactivation
60
What is cbioportal.org?
* useful for bioinformatics studies * shows gene mutations in tumors of cancer patients
61
What is COSMIC?
* user friendly for basic info regarding cancer related genes and genome changes in cancer * catalog of somatic genes in cancer
62
What is TCGA?
cancer genome atlas (data types = mutations)
63
What is OMIM?
data base showing DNA mutations in individuals that can cause disease states
64
What is SNPS?
simple difference in ones genome with no medical impact
65
What is cons 100 verts?
refers to exon sequence for 100 vertebrates

Genetics (11 decks)

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