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Cell Bio
Exam #2
113
Biology
Undergraduate 4
10/11/2015

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Term
Complex eurkaryotic genomes include...
Definition
Large amounts of non-coding sequences
Term
Gene
Definition
Segment of DNA that is expressed to yield a functional product
Term
Spacer sequences
Definition
Long DNA sequences that lie between genes
Term
Exons
Definition
Coding sequence
Term
Introns
Definition
Noncoding sequences
Term
UTRs
Definition
Untranslated regions at 5' and 3' of mRNA
Term
Average size of human gene
Definition
56 kb
Term
Alternative splicing
Definition
Occurs when exons of a gene are joined in different combinations
Term
Simple-sequence repeat
Definition
Tandem arrays of up to 1000s of copies of short sequences
Term
How much of the human genome is protein coding sequence (exons)?
Definition
1.2%
Term
Chromatin
Definition
Complexes between euk. DNA and protiens
Term
Basic unit of chromatin?
Definition
Nucleosome
Term
How many bp of DNA does a nucleosome contain?
Definition
145
Term
Nucleosome is made up of...
Definition
Two molecules of each H2A, H2B, H3 and H4
Term
Chromatosome
Definition
166 bp of DNA wrapped around the histone core and held in place by H1
Term
What facilitates histones binding to DNA
Definition
The fact that they contain a large percentage of basic AAs (positively charged) to bind to negatively charged DNA
Term
Euchromatin
Definition
Decondensed transcriptionally active interphase chromatin
Term
Heterochromatin
Definition
Condensed chromatin
Term
Centromere
Definition
Specialized region of chromosome that connects sister chromatids
Term
Kinetochore
Definition
Specialezed DNA/protein structure to which spindle fibers attach
Term
Telomeres form a...
Definition
Loop/chromosome cap
Term
Human telomere sequence
Definition
TTAGGG
Term
Telomerase uses BLANK to replicate telomeric DNA sequences
Definition
Reverse transcriptase
Term
Number of genes in humans
Definition
20k - 25k
Term
SNP
Definition
A single base change in a DNA sequence that occurs in a significant proportion of a large population
Term
Alternative splicing
Definition
Allows for more than one protein isoform from a single gene locus by removal of specific introns via spliceosomes
Term
SNPs occur...
Definition
at high frequency (1 in 1000)
Term
What happens when a SNP is close to a particular gene
Definition
It acts as a marker for that gene
Term
Why are SNP profiles important?
Definition
For identifying response to drug therapy and diagnosing diseases
Term
All polymerases synthesize DNA in the BLANK direction
Definition
5' -> 3'
Term
How does DNA polymerase differ from RNA polymerase?
Definition
RNA polymerase can initiate synthesis of a new strand in the absence of a primer
Term
After proofreading there are how many mutations?
Definition
Less than one/10^8-10^9
Term
Exonuclease activity occurs in what direction?
Definition
3' -> 5'
Term
Deamination results in...
Definition
Loss of a NH3 (cytosine -> uracil, adenine -> guanine lookalike)
Term
Depurination results in...
Definition
Loss of an A or G
Term
What occurs during exposure to UV light?
Definition
Pyrimidine dimer occurs, which blocks DNA replication
Term
Photoreactivation
Definition
A process where energy derived from visible light is utilized to break the pyrimidine dimer structure (DNA repair not present in mammals)
Term
Translesion DNA synthesis
Definition
Specialized DNA polymerases can replicate across a site of DNA damage (can occur after replication)
Term
How does E. coli respond to UV irradiation?
Definition
Polymerase V is induced to synthesize a new DNA strand across from a TT dimer
Term
Alkylation
Definition
A form of DNA damage that changes a guanine to O6-methylguanine with the addition of a CH3 (allows G to pair with T instead of C)
Term
Role of O6-methylguanine methyltransferase
Definition
Direct repair of O6-methylguanine that removes methyl group
Term
What can happen to DNA exposed to auto exhaust or tobacco smoke?
Definition
Guanine can react to form benzoapyrene via the addition of a bulky group
Term
BER
Definition
Base-excision repair
Term
NER
Definition
nucleotide-excision repair
Term
TCR
Definition
Transcription-coupled repair
Term
MMR
Definition
Mismatch repair
Term
A restriction enzyme is what kind of enzyme?
Definition
Endonuclease
Term
Endonuclease
Definition
Found within poly-nucleotide chain
Term
Exonuclease
Definition
Found at the end of poly-nucleotide chain
Term
Excinuclease
Definition
Protein complex in nucleotide-excision repair used to repair UV damage
Term
Excision Base Repair
Definition
A process where a single damaged base is recognized and removed from the DNA molecule
Term
DNA glycosylase
Definition
Enzyme that cleaves the bond linking a base to the deoxyribose backbone
Term
AP endonuclease
Definition
DNA repair enzyme that cleaves adjacent apyrimidinic or apurinic sites in DNA
Term
Enzymes needed for base excision repair
Definition
DNA glycosylase and AP endonuclease
Term
Nucleotide-Excision Repair
Definition
Damaged bases are removed from a DNA molecule (such as thymine dimers)
Term
XP
Definition
Xeroderma pigmentosum, which is a disease that causes extreme sensitivity to UV radiation resulting from a deficiency in NER
Term
How are thymine dimers recognized?
Definition
Family of XP proteins
Term
Role of XP proteins
Definition
XPB and XPD act as helicase to unwind 25 bp around the site of damage and then XPG and XPF act as endonucleases that cleave the damaged region
Term
Transcription-coupled repair
Definition
NER specifically dedicated to repairing damge within actively transcribed genes using XP and CS family protein
Term
CS
Definition
Cockayne syndrome
Term
CSB
Definition
Protein that recognizes stalled RNA polymerase and recruits repair proteins
Term
Mismatch repair
Definition
Identifies and excises mismatched bases, conformationally dependent
Term
What does regulation of gene expression allow?
Definition
Adapting to environmental changes and is responsible for the distinct activities of differentiated cell types
Term
What is the first step in gene expression?
Definition
Transcription
Term
RNA and DNA are made up of
Definition
Multiple polypeptide chains
Term
Promoter
Definition
DNA sequence to which RNA polymerase binds to to initiate transcription
Term
When is transcription regulated?
Definition
Mainly during initiation, but a little at elongation
Term
Repressor
Definition
Regulatory molecule that blocks transcription
Term
Inducer/activator
Definition
Regulatory molecule that stimulates transcription
Term
Cis-acting control elements
Definition
Regulatory sequences that affect the expression of only linked genes on the same DNA
Term
Trans-acting factors
Definition
Transcriptional regulatory proteins affecting expression of genes located on different chromosomes
Term
What is the main difference between prokaryotic and eukaryotic transcription in regards to RNA polymerase?
Definition
Prokaryotes only use a single core RNA polymerase and eukaryotic cells use three different RNA polymerases
Term
RNA polymerase II synthesizes...
Definition
mRNA, snRNA and miRNA
Term
RNA polymerase III synthesizes...
Definition
tRNA and rRNA (5S)
Term
CENP-Q normal function
Definition
Allows microtubules to attach to the kinetochore
Term
What happens if CENP-Q is non-functional?
Definition
The entire group of proteins is non-functional so microtubules will not attach (NONDISJUNCTION)
Term
RNA polymerase I synthesizes
Definition
rRNA (5.8S, 18S, and 28S)
Term
What synthesizes mRNA?
Definition
Polymerase II
Term
What synthesizes miRNA?
Definition
Polymerase II
Term
What synthesizes tRNA?
Definition
Polymerase III
Term
How many subunits in euk. RNA polymerase?
Definition
12-17 (9 are conserved, 5 are related to bacterial polymerase)
Term
Transcription factors
Definition
Proteins that are required to initiate transcription
Term
TATA box
Definition
Regulatory DNA sequence in promoters of euk. genes
Term
TAFs
Definition
TATA-binding protein associated factors (TFIID)
Term
Promoters of rRNA genes are located...
Definition
150 bp upstream
Term
Canonical promoter consists of
Definition
CAAT box (-75), GC-rich box (-50) and TATA box (-25)
Term
Role of enhancer
Definition
Stimulates transcription even if located several kb from promoter
Term
Are enhancers dependent on distance from start site?
Definition
No
Term
How do distant enhancers interact with RNA polymerase?
Definition
DNA looping
Term
Enhancers contain...
Definition
Multiple functional sequence elements, which bind response elements
Term
How many TFs?
Definition
2500 (10%)
Term
What are DNA-binding domains associated with?
Definition
Transcription factors
Term
Zinc finger domain
Definition
Contains repeats of cysteine and histidine that bind sinc ions and fold into looped structures that bind DNA
Term
Steroid hormone receptors
Definition
TFs that regulate gene transcription in response to hormones that binds to the zinc-finger domain
Term
Helix-turn-helix
Definition
3-4 helical regions that contact DNA formed by the dimerization of 2 polypeptide chains
Term
Homeodomain proteins
Definition
Play critical role in embryonic development
Term
How do coactivators stimulate transcription?
Definition
Modifying chromatin structure
Term
HAT
Definition
Histone acetylytransferases, acts to acylate lysines which are rich in histones, activates chromatin
Term
HDAC
Definition
Histone deacetylases, deactivates chromatin
Term
HDIs
Definition
Inhibitors of deacetylases, inhibit the deactivation of chromatin
Term
Which AA in histones are/is methylated?
Definition
K and R
Term
Which AA in histones is/are phosphorylated?
Definition
S
Term
Which AA in histones are small residues added to?
Definition
K
Term
Post-transcriptional modifications?
Definition
Spicing, addition of a 7-methylguanosine cap to 5' end and addition of poly-A tail to 3' end (polyadentylation)
Term
Splicing process
Definition
Cleave at 5' and form a loop with intron, then cleavage at 3' and excision of loop
Term
What are spliceosomes composed of?
Definition
Protein and RNA
Term
snRNPs
Definition
Small nuclear ribonucleoprotein, complex of snRNAs with proteins that play a role in splicing process
Term
snRNAs
Definition
Small nuclear RNAs that are 50-200 bases
Term
First step in splicesome assembly
Definition
Binding of U1 snRNP to the 5' splice (formation of lariat)
Term
How is RNA degradation initiated?
Definition
De-adenylation by RNAse
Term
Aminoacyl tRNA synthetases
Definition
Group of enzymes that recognize a single amino acid to the correct tRNA
Term
How many ribosomes in mammals?
Definition
10 milli
Term
How many ribsomes in E. coli?
Definition
20,000
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