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67 Cards in this Set
- Front
- Back
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What are the phases of interphase? each specifically |
G1 (gap 1): cellular contents excluding the chromosomes are duplicated S (synthesis): chromosomes are duplicated into sister chromatids G2 (gap 2): Cell prepares for mitosis |
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What is the function of ORC? and what does it stand for? |
Origin Recognition Complex. Binds to the origin spot of DNA and marks each initiation site (recognizes lots of A's and T's) for DNA replication recruits other proteins such as MCM |
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How is origin licensing regulated? |
Once the proteins are used once, they are ubiquitinated and targeted for proteasome degradation
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What is a ribonucleoprotein? |
An enzyme that contains RNA and protein components |
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What is Telomerase? How does it work? |
Enzyme that removes RNA primer from lagging strand at very end of DNA strand RNA component creates template for telomeric sequence; protein component is like reverse transcriptase (turns DNA from RNA) |
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What is the relationship between mutation rate and genome size? |
The larger the genome form, the less amount of mutation experienced |
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What is Cohesin? |
Protein that holds newly-replicated chromosomes together |
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How are the three ways cells reduce mutations? |
1. Inherent accuracy of duplication 2. Proofreading 3. Surveillance and repair |
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What are the two functions of DNA Polymerase 1? |
1. 5' to 3' chews primers and other debris 2. 3' to 5' proofreads for accuracy. If wrong base is incorporated, kinetics get thrown off and strand gets sent down to editing site |
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What is an indel mutation? |
It's an insertion/ deletion of bases |
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What does UV radiation to do your DNA? |
Creates free radicals on thymines, which cause them to make C-C bonds with adjacent thymines. This distorts the backbone of DNA by shortening the length by almost one half Cause of skin cancer |
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How do bacteria cope with this? mechanism and cofactors |
Have an enzyme called DNA photolyase solar-powered enzyme that has THF that absorbs electron, transfers it to FAD+ which transfers is to the new dimer and restores the thymines |
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What is nucleotide excision repair? |
Mechanism to correct mutations detects the damaged bases, cuts them out along with others around them and then fills the empty spaces back in with Polymerase 1 and ligase removes base, sugar, and phosphate along with neighboring pairs |
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What is xeroderma pigmentosum? |
Genetic disease of excision repair enzymes |
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What is DNA mismatch repair? And mechanism |
Way E coli correct mismatched base pairing on newly-synthesized strand. Enzyme called MutS binds to mismatched sequences, recruits MutH and MutL which fix it. Deciphers new strand from old strand by methylating OG strand on adenines in GATC sequences |
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What do alkylating agents do? and way to fix it |
Add alkyl group to guanine, which then can BP with thymine or cytosine MGMT is a one-time use protein that removes methyl group and places it on cysteine residue |
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What do chemical mutagens (oxidizers) do? and what causes them |
Hot dogs and processed meat contain nitrites which lead to deamination of adenine and cytosine leads to incorrect base pairing |
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What is the mechanism behind Base excision repair? enzyme name |
only defective or incorrect base is removed by DNA Glycosylase, which breaks bond between sugar and base, creating an abasic site (AP) backbone is cleaved at the AP site by and endonuclease Polymerase removes nake sugar/phosphate group |
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How does bacterial RNA polymerase recognize promoter sequence on DNA? |
Sigma factor subunit of polymerase directs the polymerase to the promoter Once it binds to the promoter, it releases the sigma factor which increases the affinity of enzyme to DNA |
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What are the three types of RNAs? And what do they make? |
RNAP-1: ribosomal RNA (rRNA) RNAP-2: messenger RNA (mRNA) RNAP-3: translational RNA (tRNA) |
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What are GTFs? and function And what do they form with the form what complex? |
General Transcription Factors; do what the sigma factor does in bacteria, which is recognize promoter sequences Forms with RNAP2 to make Pre-initiation complex (PIC) |
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What is the TBP? |
TATA-binding protein, recognizes TATA sequence (found upstream of promoters) introduces 45 degree bend in helix which helps unwind it |
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What is the difference between heterochromatin and euchromatin? |
Heterochromatin is condensed chromatin that is repressed and inactive Euchromatin is dispersed and active |
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What do Nucleosome remodeling complexes do? |
Motors that use ATP to move nucleosomes around, which exposes genes |
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What are the post-translational modification of chromatin? |
N-terminal tails w/ basic residues on chromatin get marks added to them by writers, taken off by erasers. Reader proteins interpret the marks; reads whether or not to allow chromatin condensation/de-condensation, transcription activator binding, etc |
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Types of marks |
Writers: methylations, acetylations erasers: deacetylations and demethylations |
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What are the post-translational modifications of DNA? |
methylation of bases (methyl cytosine) Enzyme: DNA Methyltransferases |
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What are the specific post-translational modifications of histones? and their effects |
1. Phosphorylation (on serine and threonine): makes charge negative, which reduces binding to DNA 2. Acetylation (on lysine): neutralizes it; related to transcriptionally-active chromatin 3. Methylation (Lysine and arginine): no effect on charge, has effect on how reader proteins interpret it tho. Methyl donor is SAM |
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What do active genes have on them? What do silenced genes have on them? |
They are heavily acetylated They are heavily methylated |
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What signals transcriptional elongation? |
phoshorylation of the RNAP 2 CTD (c-terminal domain) 52 repeats of YTPS, serine gets phosphorylated and enables polymerase to know it's in elongation phase |
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What are the steps of mRNA processing? |
1. adding the 5' cap
2. adding the 3' poly-A tail 3. intron splicing |
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What is the mechanism of capping mRNA? and enzyme |
capped by 7-methylguanosine; done by capping enzyme1. Hydrolysis removes 5' gamma Pi. guanine attaches via 5' to 5' triphosphate bridge (releases PPi)3. methylation of guanosine at position 7. methyl donor is SAM |
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What is the poly-A tail? and enzyme |
Poly-A-polymerase (PAP) attaches many A's in a row to 3' end |
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What is the enzyme that carries out mRNA splicing? |
Sliceosome, made of snRNPs (small nuclear ribonucleoproteins) |
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What is the lariat mechanism? |
nucleophilic attack of 2' OH group from intron that attacks at exon/intron joining area. frees exon Makes a lasso |
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What is tRNA? and last 3 bases on it |
Single-stranded RNA that BP with itself. BP with mRNA and adds aa to 3' end last three are always CCA, A attaches to amino acid |
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What is the Wobble effect? |
3' end of codon matches with: U,C: G G: C A, G: U A,U,C: I |
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What is tRNA Synthetase? and abbreviation |
Enzyme that attaches appropriate amino acid onto its tRNA (aaRS) |
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What has to happen to an amino acid for it to be added to a tRNA? and process |
needs to be activated
carboxyl O nucl. attacks alpha Pi on ATP, released PPi to create adenylated amino acid tRNA synthetase attaches aminoacyl-AMP to 3' end of adenine on tRNA, releases AMP |
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What are the three sources of error in translation? |
1. aaRS uses wrong aa as substrate 2. aaRS uses wrong tRNA as substrate 3. ribosome selects wrong aa-tRNA for codon |
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How does proofreading work in tRNA synthetase? |
Analogous to 3'5' polymerase 1. If mismatch is present, then it gets sent to editing site to get hydrolyzed kinetics control this. if it doesn't fit, then it flops around to editing site |
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What happens if there are errors in proofreading mechanisms? |
Wrong aa's get incorporated into proteins, proteins can't fold correctly and genetic diseases ensue |
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What is a ribosome? |
Complex on mRNA of ribosomes |
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What are the three stages of translation? |
1. Initiation: ribosome is placed on start codon 2. elongation: mRNA-templated polypeptide polymerization 3. Termination: polypeptide and mRNA are released |
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What is the Shine-Dalgarno Sequence? |
Ribosomal binding site upstream of start codon on mRNA aligns ribosome with start codon pairs with 3' end of small subunit of ribosome |
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Difference between prokaryotic and eukaryotic mRNA? |
Prokaryotic mRNA can have multiple transcripts for protein on each mRNA Eukaryotic mRNA can only transcribe for 1 protein |
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What are the three sites of the ribosome? |
A, P, and E site A = aminoacyl-tRNA site (where tRNA w/ amino acid binds, where selection occurs) P = peptidyl-tRNA site (where growing protein chain attached to tRNA sits, where peptide bond is transferred to) E = exit site |
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What is the mechanism of elongation? |
aa chain is already in P site. Incoming aminoacyl-tRNA binds to A-site. Entire chain from P site gets added to the incoming aa-tRNA everything shifts, uncharged tRNA gets kicked out of E-site |
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What is the first amino acid always in protein synthesis? |
Methionine, but special kind, called formyl-methionine (fMet) in eukaryotes |
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What are the initiation steps in bacteria? |
Initiation factor (IF-1) occupies A-site. IF-2 bound to GTP brings in tRNA that is bound to fMet, matches initiation codon Once start codon bound, GTP is hydrolyzed and initiation factors fall off, large subunit moves in and now elongation can begin |
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What are the initiation steps in eukaryotes? |
No Shine-delgarno sequence, the small subunit loosely binds to 5' cap and moves and scans until it finds start codon; uses energy. initiation factor called elF4 complex binds 5' cap and 3' poly-A tail and creates a circular mRNA which brings everything close together |
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What is EF-Tu? |
elongation factor that moves aa around ribosome almost all aa-tRNA is bound to EF-Tu |
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What is the target for antibiotics?
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target elongation stages; tetracycline binds to A-site and inhibits aa-tRNAs from binding in A site; interrupts protein synthesis |
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What is the regulation of protein synthesis? |
1. anticodon and mRNA pair; if incorrect pairing occurs, the stability is really low so it flies off instead of incorrectly pairing |
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What are the three molecules doing the work at each of the three sites of elongation? |
A site: aa-tRNA: EF-Tu:GTP P-site: large subunit of ribosome E-site: EF-G:GTP |
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How is polypeptide synthesis terminated? |
Release factors (RF) bind to stop codon which inhibits transfer of aa bc there is no aa. Water hydrolyzes amino acid chain from tRNA in P-site |
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What is the effect of EF-G? |
Not only helps in translocation, but also uses energy that releases a message that dissociates the two subunits, recruits the initiation factors to bind back to small subunit and get it ready for next calling |
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What do macrolide antibiotics do? |
They plug the exit tunnel of the ribosome, so proteins cannot be released |
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What are the functions and other names of the ribosomal subunits? |
Small: decodes mRNA (bacteria: 30S; 16S) (eukaryote: 40S; 18S) Large: catalytic, makes the peptide bonds (bacteria: 50S; 23S) (eukaryote: 60S; 28S) |
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What is an SRP? and what is this for? and steps |
Signal Recognition Particle for creating transmembrane proteins 1. Recognizes signal sequence coming out of ribosome 2. Pauses translation 3. directs ribosome and polypeptide to ER, binds with SR (receptor) 4. SRP + SR bind, which then can hydrolyze GTP, which continues translation |
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What does it mean to be glycosylated? and where does this happen? |
Putting sugar on proteins, happens in ER and golgi |
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What is N-linked glycosylation? and where |
Sugar addition to asparagine (N) next to serine/threonine ER |
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What is an O-linked oligosaccharide? and where |
attachment of a sugar to an O of an amino acid, on serine or threonine happens in the golgi |
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How many phosphate bonds are used up in making a peptide bond? |
4 |
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What is the sense and antisense strands? |
Sense runs 5' to 3'; has same sequence as mRNA (coding strand) antisense runs 3' to 5' (template strand) |
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What does a chaperone protein do? |
Regulates folding of proteins, holds them together |
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What are the chaperone proteins? |
Calnexin, BiP, PDI |
