biochemistry 2

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Makes 2 cuts on either side of DNA & utilizes helicase & polymerase I to remove pyrimidine dimers: uvrABC
Uses UV light to cleave pyrimidine dimers (THF & FADH2 cofactors): DNA photolyase
tags oldest DNA strand: DAM Methylase
Removes uracil produced by deamination of cytosine: Uracil-DNA glycosidase
mechanism turned on by autolysis of LexA repressor: SOS response
Increased mutation % as a result of increased protein production: SOS response
Catalyzes pairing of ssDNA w/ complimentary dsDNA: recA
coprotease for LexA: recA
List correct order of recBCD generation of ssDNA for recombination: A)hits chi site & releases D B)enters at free ends C)BC unwinds DNA using 2 ATP/base pair D)ssDNA coated w/ DNA-binding protein: bacd
Stabilizes ssDNA during replication: SSB protein
DNA repair system utilizing Dam methylase, MutH, L, & S proteins, DNA helicase II, SSB, DNA polymerase III, Exonuclease I, & DNA ligase: Mismatch repair
Repair system that corrects abnormal bases, alkylated bases, & pyrimidine dimers: Base-excision repair
DNA repair mechanism that utilizes DNA glycosylases, AP endonucleases, DNA polymerase I, & DNA ligase: Base-excision repair
DNA repair mechanism that utilizes ABC excinuclease, DNA polymerase I, & DNA ligase: Nucleotide-excision repair
DNA repair mechanism that corrects DNA lesions that cause large structural changes (pyrimidine dimers): Nucleotide-excision repair
DNA repair mechanism that utilizes DNA photolyases & O6-methyllguanine-DNA methyltransferase: Direct repair
DNA repair mechanism that corrects pyrimidine dimers, O6-methylguanine: direct repair
DNA repair mechanism that corrects errors left by polymerase III: Mismatch repair
8-oxoguanine DNA glycosylase-1 correlates strongly (x5-10) w/ what kind of risk?: cancer (both smokers & nonsmokers)
Why does DNA have Thymine instead of Uracil?: It would be impossible to distinguish uracil from deaminated cytosine
DNA repair mechanism lacking in xeroderma pigmentosa patients: nucleotide excision repair
condition with skin lesions, cancer, photosensitivity (allergy to light): xeroderma pigmentosa
DNA absorbs light at a wavelength of:: 260 nm
activated when RNA polymerase stops at a deformity, which recruits excision repair enzymes: Transcription Coupled Repair (TCR)
gene for susceptibility to breast and ovarian cancer: BRCA1
responsible for accumulation of mutations causing a large proportion of breast and ovarian cancers: BRCA1-altered TCR
inhibits recombination when mismatches are high, inducing apoptosis: P53
type of recombination that occurs mostly during meiosis (eukaryotes) and conjugation (prokaryotes): homologous recombination
type of recombination that doesn't change the order of genes but determines which alleles will be linked.: homologous
List in order the steps of the Holliday model: 1-homologous DNA are alligned
2-breaking of strands for crossing-over
3-heteroduplex DNA extended by branch migration
4-two strands of intermediate are cleaved, gaps are filled
catalyzes strand assimilation reaction (forms d-loop) at the expense of ATP: recA
hydrolyzes ATP and unwinds dsDNA for ssDNA production: recB
nuclease that recognizes a chi site: RecD
resolvase that cuts the holliday intermediate in one or the other plane: RuvC
produced by the process of recombination: multimers & concatemers
type of recombination used by bacteriophage λ integration: site-specific recombination
Diversity of genes depends on communication between. . .: antibodies
Serve to inactivate antibiotics, metabolize natural products, and produce toxins: Plasmids
Encodes conjugation function, found in male bacteria: F-factor plasmid
Resistant Transfer Factors (RTF): R-factor plasmids
upon integration they duplicate recipient DNA (not inverted): Transposons (jumping genes)
coded by transposons and makes staggered cuts in DNA: transposase
A double-stranded nucleic acid that exhibits semiconservative replication has heavy nitrogen at all positions. After heavy nitrogen source is taken away, the strand is replicated through 3 generations. what is the composition of the strands?: 7 strands with no N14, 1 strand with half N14 (12.5%)
Enzyme that unwinds the DNA strands at the growing replication fork: DNA helicase
Relaxes tension in DNA by breaking one strand, unwinding it, and then ligating it. Alters DNA by a single linking number: Topoisomerase I
Relaxes tension in DNA by breaking both strands, unwinding them, and then ligating them. Changes the linking number in steps of 2: Topoisomerase II
Generates negative supercoils (requires ATP) in E.coli as well as relaxes the tension associated with helicase activity: DNA gyrase
Prevent DNA strands from reforming their base pairs after helicase passes until the polymerase synthesizes the new strand.: SSB proteins
Measure of level of supercoiling in DNA= Linking number of completely relaxed =: =Linking number

=0
103 kDa, 3'-5' exonuclease, 5'-3' exonuclease, processes 200 nucleotides, functions in replication & repair: DNA polymerase I
88 kDa, 3'-5' exonuclease, processes 10000 nucleotides at a rate of 10 bases/sec, functions in DNA repair: DNA polymerase II
900 kDa, 3'-5' exonuclease, processes 500000+ nucleotides at a rate of 1000 bases/sec, functions in DNA replication: DNA Polymerase III
Located in eukaryotic nucleus, has exonuclease, functions in replication, primase complex: DNA polymerase α
Specific change in DNA nucleotide sequence: mutation
Located in eukaryotic nucleus, doesn't have exonuclease, functions in replication and repair: DNA Polymerase β
Located in eukaryotic mitochondria, has exonuclease, functions in replication and repair: DNA Polymerase γ
Located in eukaryotic nucleus, has exonuclease, functions in replication and repair: DNA Polymerase δ
Generates the primer in the initiation complex, resulting in an RNA-DNA hybrid: Primase
Enzyme that joins 3' OH to a 5' phosphate to restore integrity of DNA strands: Ligase
Strand that appears to move 3' to 5', but actually moves 5'-3' creating Okasaki fragments: Lagging Strand
DNA replicates in what phase of the cell cycle: Synthesis phase
Primers needed for leading strand= Primers needed for the lagging strand=: =1

=many
E.coli replication constituent=SSB Eukaryotic replication constituent=: RPA
E.coli replication constituent=primase Eukaryotic replication constituent=: primase/polymerase α
E.coli enzyme that removes primer=Pol I/RNase II Eukaryotic enzyme that removes primer=: MFI/RNase II
Process in which mutations manifest: mutagenesis
Organism altered by mutation: mutant
Single mutation at a single base site (actually two after replication): Point mutation
mutation that results in an amino acid change; a change in the codon triplet that is unmasked by degeneracy: Missense
Mutation that changes an amino acid codon triplet into a stop codon: Nonsense
Mutation in which one or more nucleotides are deleted: Deletion
Mutation in which one or more nucleotides are inserted: Insertion
Point or missense mutation that is silent except under certain conditions: conditional mutation
mutation that permits the phenotype of the mutant to revert back to the wild-type: reversion
One purine is changed to the other or one pyrimidine is changed to the other: transition
A purine is substituted for a pyrimidine or vice versa: transversion
Mutation seen in sickle cell anemia: point mutation (Glutamate switched to
Valine)
Mutation seen in Marfan's syndrome: Point mutations in the fibrillin gene (FBN1)
autosomal dominant disorder affecting fibrous connective tissue (FBN1 gene): Marfan's syndrome
Change in the register in which amino acid sequence is read: frameshift
mutations that occur in non-gamete cells (not inherited): somatic
mutations that occur in gametes (inheritable): germinal
test for detection and classification of mutagens and carcinogens: Ames test
In an Ames test, S. typhimurium supplemented with histidine is cultured. Plates A and B are given a possible carcinogen. Plate C is a control. Plate A shows growth of colonies. Is the substance carcinogenic?: Yes
First predictor of longevity= Second predictor of longevity=: =DNA repair capacity

=Immunological capacity
uvrABC removes pyrimidine dimers by making two cuts; ___ nucleotides from the 5' end and ___ nucleotides from the 3' end: =8

=4
=Removal of pyrimidine dimers =defective DNA displacement =patch (two enzymes): =uvrABC

=helicase

=Polymerase I & Ligase
Enzyme that uses UV light to cleave pyrimidine dimers (uses THF & FADH2 cofactors): Photolyase
enzyme that methylates the oldest DNA strand: Dam methylase
consequence of the action of Dam methylase: old strand recognized by Mut H & S; new strand is repaired
Enzymes that recognize methylated strands of DNA: Mut H & S
Nucleoside produced by cytosine deamination: Uracil
Enzyme that removes uracil produced by deamination of cytosine via glycosidic bond-cleavage: Uracil-DNA glycosidase
Process by which a cell deems it more necessary to stay alive than to prevent mutation: SOS response
Enzyme that represses SOS response: LexA
Recogize 4,6,or 8 base-pair palindromes: Restriction Enzymes
Sequence with bilateral symmetry (read the same 3'-5' as 5'-3'): Palindrome
Source of restriction enzymes: Prokaryotes
Limits foreign DNA integration into cells, made from restriction endonuclease & Dam methylase: Restriction enzymes
Copy sections of DNA, then inserts desired gene: Vectors
Monitors extent of DNA damage in humans and induces apoptosis (inhibits recombination) if there is too much mismatch: p53
Technique for separating DNA fragments by size: Electrophoresis
In electrophoresis, phosphate groups move toward what?: anode (+)
State of plasmid that replicates independently of the chromosome: relaxed
State of plasmid that replicates only when the chromosome does: stringent
_____ plasmids produce continuously (high copy number): Relaxed
Vectors that provide larger fragments (~20kb) and more efficient delivery to the host: viral vectors
Vectors (~1mb) that contain Autonomously Replicating Sequences (ARS), Centromeres, Telomeres, Selectable markers, and a MCS: Yeast Artificial Chromosomes (YACs)
Chromosome digested with restriction enzymes & ligated with a plasmid, so each vector will have only one piece. The genome is represented by many pieces each in a different cell: Genomic Library
Enzyme that mRNA converted to dsDNA in order to assemble a cDNA library: Reverse Transcriptase
Formed when products of Reverse Transcriptase are cloned into vectors, displaying only expressed sequences of genes: cDNA library
Central dogma of molecular biology: DNA ->(Trasncription)->RNA->(Translation)->Protein
=nondiscriminatory (copies everything) =selective transcription (certain genome parts): DNA replication=

RNA replication=
Two functions of DNA in prokaryotes=: =structural information (genes)

=regulatory signals (promoters, terminators, etc.)
Requirements for RNA polymerases: -DNA template
-4 ribonucleotide triphosphates
-divalent cations (Mg++)
Three required steps for RNA synthesis: -initiation
-elongation
-termination
step in which RNAP finds a promoter & unwinds DNA (most regulated step): initiation
=site of eukaryotic transcription: nucleus
=site of eukaryotic translation: cytoplasm
Primary sigma factor for most genes (housekeeping): 70
Sigma factor involved in transcribing nitrogen-regulated genes: 54
Sigma factor responsible for heat shock genes: 32
stationary phase Sigma factor: 38
Sigma factor that regulates expression of flagellar genes: 28
Unique polymerase in that it can initiate de novo synthesis (no primer required, but it needs a promoter): RNAP
Makes only ribosomal RNA and actually synthesizes a long preribosomal rRNA transcript that is a precursor for the 18S, 5.8S, and 28S rRNAs (Eukaryotic): RNAP I
does most of the work associated with transcription; makes all mRNA (Eukaryotic): RNAP II
makes all tRNAs and the 5S rRNA (Eukaryotic): RNAP III
Regulatory element located outside the promoter that decrease higher-order DNA structure (chromatin): Enhancer
Transcription factor that can be cut out & spliced in somewhere else without functional loss: enhancer
Step that most transcription factors operate: Initiation
Serve to increase higher order DNA structure (chromatin): silencers
___________ acetylate histones (loosen chromatin) ___________ de-acetylate histones (tighten chromatin): =activators

=repressors
tightly controlled genes in E.coli to be "on" only when lactose is present: lac operon
states of lac operon: =glucose present, lactose absent =glucose present, lactose present =glucose absent, lactose present: lac operon "off"=

lac operon "on"=

lac operon "highly on"=
set of genes in tandem that are regulated by a single promoter: operon
Site bound by repressor to prevent transcription: operator
small molecule that relieves repression allowing RNAP access to the promoter: inducer
required to turn lac operon "highly on" by activation: CAP (catabolite activator protein) or
CRP (cAMP receptor protein)
HIV-1 promoter: LTR
protein RNAP I binds to in Termination: Reb1p
termination that involves only an interaction between RNA and RNAP: rho independent (intrinsic)
Pause site hit by hairpin loop that signals termination is rich in what base pair?: AU
forms a hexamer that binds to RNA at a hairpin pause structure; moves along RNA and unwinds RNA-DNA duplex to terminate transcription: rho
contains a 5' cap structure and a 3' poly A tail: mRNA
consists of methylated guanine triphosphate attached to the OH group on the ribose at the 5' end of mRNA: cap
200 adenine nucleotides attached to 3' OH end of mRNA: poly A tail
associate with proteins to form ribosomes: rRNA
16S, 23S, and 5S rRNA is derived from __________, while 18S, 28S, 5S, and 5.8S rRNA is derived from ___________.: =Prokaryotic

=Eukaryotic
cloverleaf strux, contains modified nucleotides including thymine: tRNA
The primary tRNA transcript is shortened at both ends via: cleavage
_____ cleaves 5' end of tRNA _____ cleaves 3' end of tRNA (both ribozymes): =RNase P

=RNase D
sequence at 3' end of tRNA that binds the amino acid: CCA
adds CCA to 3' end of tRNA after RNaseD cleavage: terminal deoxytransferase (nucleotidyl transferase)
___________ have operons ___________ have introns and exons: =prokaryotes

=eukaryotes
type of RNA processing that differs between prokaryotes & eukaryotes: mRNA
prevents mRNA degradation & allows translation; linked by 5'-5' triphosphate: 5' cap
enzymes required for 5' cap addition:: 1- phosphohydrolase (P cleavage)
2- guanylyltransferase (5'-5'
phosphate attack using GTP)
3- guanine-7 methyltransferase
(protects 5' end)
4- 2'-O-methyltransferase (unique to
RNA)
process by which introns are removed and exons are linked to encode a functional polypeptide: splicing
Self-splicing introns= Spliced via lariat structure=: =Groups 1 & 2

=Group 3
RNA-protein complexes contain ______ made by RNAP III that enable lariat structure formation: small nuclear RNAs (snRNAs or Snurps)
The lariat structure is created when the _____ end of ribose attacks the phosphodiester bond at the ______ forming a covalent link Finally, the ______ nucleophilically cleaves the intron.: =2' OH

=5' cleavage site

=3' OH (on severed 5' exon)
allows for diversity of structure and function without duplication of genes, depending on environmental need: alternative splicing
function of the poly A tail=: protection and translatability
three steps of polyadenylation=: 1-precursor RNA cleavage via
polyadenylation signal
2-poly A tail addition via poly A
polymerase
3-unneeded 3' end material is degraded
genetic code: ____ bases ____ possible codons ____ reading frame ____ reading direction: =4
=64
=3 bases/amino acid
=5'-3', N-C
Start codon=: =AUG (codes for methionine)
define degeneracy.: the genetic code has more than one codon for each amino acid, differing in only the third base
Stop codons=: UGA
UAA
UAG
Steps of translation=: =Activation, Initiation, Elongation, Termination
=synthesis of aminoacyl-tRNAs: Activation
=assembly of mRNA and initiator aminoacyl-tRNA on the ribosome: =initiation
=Synthesis of peptide bonds in RNA translation: Elongation=
=Release of newly synthesized peptide bonds and disassembly of translation apparatus: termination
set by the start codon (AUG): reading frame
allows one tRNA to translate more than one codon: wobble
wobble pairing: U= G= I=: U=A or G
G=C or U
I=A, C, or U
E.coli ribosomes consist of __ and __. Eukaryotic ribosomal subunits are ___ and ____.: E.coli=50S and 30S (70S)

Eukaryotes=60S and 40S (80S)
measure of how rapidly ribosomal subunit migrates in an ultracentrifuge (dimensions of size & shape): Svedburg units
Site of protein synthesis: Ribosome
Activated intermediate for protein synthesis: Aminoacyl-tRNA
control gene expression by blocking mRNA: RNAmi or RNAi
Unravels and seeks out mRNA to cleave at the attachment site: RNAmi or RNAi
Main problem of RNAi in treatment of disease: delivery
site of activation reaction: cytosol (not on ribosome)
tRNAs which have different sequences but carry the same amino acid: isoaccepting tRNAs
only tRNA recognized by eIF-2: tRNAi(Met)
When a methionine residue is to be located anywhere in a protein other than the N-terminus, it is brought to the ribosome by:: tRNAm(Met)
Euk. Prok. 1st AA= IF= Ribosomes=: Euk. Prok.
1st AA=Met Formyl Met
IF=12 3
Ribosomes=80S 70S
Aminoacyl-tRNAs are brought to the ribosome as a _________with GTP and the elongation factor eEF-1: ternary complex
Incoming aminoacyl-tRNA base pairs its anticodon with mRNA codon located in the ___ site of the ribosome: A
Elongation steps=: 1-binding (A site)
2-translocation (A->P; mRNA movement)
catalyzes formation of peptide bond: peptidyl transferase
occurs when stop codon moves into the A site: termination
recognizes stop codons and triggers the hydrolysis of newly sythesized protein from tRNA at the P site: Release factor
complex that translates mRNA by several ribosomes at the same time: polysome
binds the small ribosomal subunit and causes incorrect anticodon-codon pairing: streptomycin
blocks the A site: tetracycline
inhibits peptidyl transferase (also affects mitochondria): chloramphenicol
causes premature termination of translation: puromycin
inhibits EF-2 (translocation) via ADP-ribosylation: Diptheria toxin
activated under conditions of low heme levels in order to prevent protein synthesis: heme-regulated inhibitor (HRI)
Kinase phosphorylates (with ATP) the ___ inhibiting protein synthesis: eIF-2-GDP complex

(inhibits formation of eIF-2-GTP)
mutation in exon 11 of the gene for the α-chain of β-hexoaminidase A: Tay-Sachs
Part of tRNA that reacts w/ mRNA: anticodon loop
Energy Requirements for AA synthesis: __ Activation __ Initiation __ Elongation __ Termination: 1 ATP/AA for Activation
1 ATP(E) & 1 GTP(P) for Initiation
[(# of AA-1)*2] GTP for Elongation
1 GTP for Termination
for 100 AA, 200 GTP, 100 ATP (P), 101 ATP(E)
The difference between SER & RER: RER has ribosomes
Oligosaccharides added to the amide N of an Asp residue: N-linked oligosaccharides
oligosaccharide attached to the O of a Ser or Thr residue: O-linked oligosaccharide
What type of oligosaccharide are mucus proteins?: O-linked
What type of oligosaccharides are Blood serum proteins?: N-linked
The core of all N-linked oligosaccharides consists of--: 2 glcNAc and 3 Man residues
A core oligosaccharide is derived from what lipid-linked oligosaccharide intermediate?: dolichol phosphate
The 14-hexose precursor of N-linked oligosaccharides is assembled on the dolichol phosphate starting with the transfer of glcNAc-1-phosphate from --: UDP-glcNAc (cytosolic side of ER membrane)
After the target sequence has been translocated into the lumen of the ER, the N-linked oligosaccharide precursor is transferred where?: Asn residue part of the sequence Asn-X-Ser or Asn-X-Thr
Dolichol-P + 2 UDP-GlcNAc------>UMP + UDP + Dolichol-PP-2GlcNAc is inhibited by what antibiotic? (first step of N-linked synthesis): tunicamycin
Translocation of N-linked oligosaccharide intermediates occurs at which step?: 3
signal that the protein is ready for transfer to the Golgi: removal of 3 glc and 1 man while glycoprotein is still in the ER
GalNAc transfer to a Ser or Thr residue from UDP-GalNAc takes place in what type of synthesis?: O-linked oligosaccharide
Most secreted proteins and membrane proteins are of what type?: glycoproteins
What sugar do glycoproteins never have?: Glc
Targeting sequence for the ER membrane: LysAspGluLeu
Targeting sequence to send proteins to mitochondria: N-terminal sequence
Targeting sequence to send proteins to nucleus: Basic amino acid rich
Targeting sequence to send proteins to lysosome: Man-6-P
Targeting sequence to send proteins to peroxisome: Carboxyl terminal SerLysPhe
The process by which proteins enter cells from the blood: endocytosis
Protein that coats transferin-filled vesicles: clathrin
reacts with a specific receptor and becomes incorporated into endosomes that deliver iron to ferritin: transferin
protein that stores iron in the cell: ferritin
determines the half-life of cytosolic proteins: amino-terminal residues
binds with protein, then binds with lysine residues to form an isopeptide linkage for degradation: ubiquitin
contain tryptic and chromotryptic-like proteases for degradation: proteosomes
type of linkage of salivary mucin: O-linkage
Sialic acid (NANA) attaches to what part of oligosaccharides?: terminal
dictates the structure of glycoproteins: transferase
target of transferase in protein glycosylation: nucleated sugar
site of completion of modifications to N-linked oligosaccharides: Golgi
Linkage of blood group glycoproteins to cells: O-linked to Ser
Terminal linkage of H blood group antigen: Fucose (alpha 1,2)

O-
Terminal linkage of A blood group antigen: GalNAc, Fuc (alpha 1,3)
Terminal linkage of B blood group antigen: Gal, Fuc (alpha 1, 3)
Phenotype:O Genotype: Reacts with antibodies: Antibodies:: Phenotype: O
Genotype: O/O
Reacts with antibodies: none
Antibodies: anti-A, anti-B
Phenotype: O Genotype: Reacts with antibodies: Antibodies:: Phenotype: O
Genotype: O/O
Reacts with antibodies: none
Antibodies: anti-A, anti-B
Phenotype: A Genotype: Reacts with antibodies: Antibodies:: Phenotype: A
Genotype: A/A, A/O
Reacts with antibodies: ANTI-A
Antibodies: anti-B
Phenotype: B Genotype: Reacts with antibodies: Antibodies:: Phenotype: B
Genotype: B/B, B/O
Reacts with antibodies: ANTI-B
Antibodies: anti-A
Phenotype: AB Genotype: Reacts with antibodies: Antibodies:: Phenotype: AB
Genotype: A/B
Reacts with antibodies: ANTI-A, ANTI-B
Antibodies: NONE (universal acceptor)
signal for golgi to send glycoproteins to vesicles: Man-6-P
enzyme defect in I-cell disease: GlcNAc transferase
GlcNAc transferase: enzyme defect in I-cell disease

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