Human Genome Flashcards
What are the 2 subunits of TF2D?
TBP & TF2H
What is the function of TBP in TF2D?
- binds to TATA box
- recognizes methylation of histone 3, K4
What is the function of TATA box in TF2D?
establishes where the primary transcript will begin
What is the function of TF2H in TF2D?
- opens/exposes DNA for RNA polymerase 2
- phosphorylates a subunitof rNA polymerase to start transcription
What is the function of RNA polymerase 2?
transcribe and used for protein coding genes
What is primary transcript?
defines the egene space in the genome browser
that mostly gets processed to mRNA
What does the primary transcript include?
- 5’UTR
- 3’UTR
- introns
- exons
Does the primary trancript include the regulatory sequence?
no
Are primary transcripts RNA or DNA?
RNA
What is translation?
using RNA code to add amino acids to make a protein
What is mRNA?
RNA that leaves to nucleus, goes to cytoplasm, and gets translated into a protein
What is a tRNA?
bring in amino acids
What are the key components in translation?
- mRNA
- tRNA
- AUG
What is AUG?
start codon that codes for Met
What are the assigned terminus to the 5’ and 3’ ends?
- 5’: N temrinus (has AUG)
- 3’: C terminus
What occurs with V600E?
- valine at position 600 mutates into glutamate
- gains a negative charge
What is the BRAF protein?
- pro-proliferative kinase that is active when phosphorylated
- gets things going
What does each gene include?
- regulatory sequences
- exons
- introns
- 5’ UTR
- 3’ UTR
In genes, what is the charge of the coding and template strands?
- coding = +
- template = -
What are the important numbers to know about gene sizing?
- SRY = .9 kb
- HBB = 1.6 kb
- TP53 = 39 kb
- F8 = 186 kb
- CFTR = 250 kb
- DMD = 2400 kb
Whatis the trend in mutagenesis in gene sizing?
- random
- bigger the gene -> more likely for mutation
What are the characteristics of a gene family?
- 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
What are examples of a gene family?
globins & Ig families
What are the 2 types of globin families?
- fetal -> high affinity to O2 in placenta
- adult -> lower O2; release of O2 in tissues
Genes must be atleast what percentage to be considered the same family?
70%
Amino acids must be at least what percentage to be homologs?
20%
What is BLAT?
- shorter
- only nucleotides used to match sequence to genome
What is BLAST?
- longer
- can compare using nucleotides or amino acids
What are the types of immunoglobulins?
- IgG
- IgM
- IgE
- IgA
- IgD
What are the characteristics of immunoglobulins?
- homologous
- similar biochemical functions
What are the 2 types of genes in immunoglobulins?
35 V & 5 J
What genes are in heavy and light chains?
- heavy -> V, D, J
- light -> V & J
How are gene families formed?
from duplication & mutations
What is the main difference between gene and supergene families?
- gene -> related by biochemical functions
- supergene -> related by physiological function
What can cause a supergene family?
- exon shufling
- reverse transcriptase making DNA from RNA
Supergene families are composed of what percentage of homologous genes?
50%
What is an example of a supergene family?
immunoglobulins
What are the characteristics of a single copy DNA sequence?
- one or few copies per haploid genome (< 100)
- no upper or lower size
What are the characteristics of a moderately-repetitive DNA sequence?
- 100-1 million copies
- clustered or dispersed
- can be code or non-code
What are the characteristics of a highly-repetitive DNA sequence?
- 10^6
- clustered
- non-coding
What are examples of highly-repetitive DNA sequences?
telomeres & centromeres
What are examples of a moderately-repetitive DNA sequence?
LINEs & SINEs
What are LINEs?
- longer DNA that can encode proteins
- reverse transcriptase
What are SINEs?
too short to encode proteins
Where are polyT tails located?
on cDNA to have A-T rich sequences as integration site targets
What is exon shuffling?
downstream exon with cDNA inserts itself at new position
What is an important number to remember for rRNA?
Man is 280
What are the 2 ribosomal units?
18S & 28S
What are intervening sequences?
remnants after ribosomal subunits are cleaved
How do intervening seuqences differ from introns?
not spliced together
How many base pairs are in our genome?
3 billion
How many times can mRNA be used?
many times
What are variable number tandem repeats?
same sequence at the same location but different number of repeats
finger printing
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
How many protein coding genes are there?
about 20,300
What are transposons?
- DNA that has moved due to reverse transcriptase
- moves around exons
What are CpG islands?
- associated with regulatory regions
- roles gene regulation (gene slicing)
What does CpG methylation lead to?
gene inactivation
What is cbioportal.org?
- useful for bioinformatics studies
- shows gene mutations in tumors of cancer patients
What is COSMIC?
- user friendly for basic info regarding cancer related genes and genome changes in cancer
- catalog of somatic genes in cancer
What is TCGA?
cancer genome atlas (data types = mutations)
What is OMIM?
data base showing DNA mutations in individuals that can cause disease states
What is SNPS?
simple difference in ones genome with no medical impact
What is cons 100 verts?
refers to exon sequence for 100 vertebrates
