Biochemistry Exam 2

Front 1

HATs

Back 1

DNA loosen
Increase Transcription
Add Acetyl group

Front 2

HDACs

Back 2

DNA tighten
Decrease Transcription
Lose Acetyl group

Front 3

Prophase

Back 3

Chromosomes condense
microtubules rearrange

Front 4

Prometaphase

Back 4

Nuclear envelope breaks down
mitotic spindle starts to form

Front 5

Metaphase

Back 5

chromosomes line up

Front 6

Anaphase

Back 6

Sister chromosomes pull to opposite sides

Front 7

Telophase

Back 7

Chromosomes decondense
membrane reforms

Front 8

Cytokinesis

Back 8

Contractile ring tightens to form two daughter cells

Front 9

Mitosis

Back 9

2n diploid --> 4n (after replication) --> 2n diploid

Front 10

Meiosis

Back 10

2n diploid --> 4n (after replication) --> n haploid

Front 11

Point Mutations

Back 11

Incorrect base is inserted into a growing DNA strand, permanently altering the base identity at that position

Front 12

Base Insertions or Deletions

Back 12

frame shift mutation

Front 13

Three ways errors in DNA replication can be reduced

Back 13

1. Conformational change in DNA polymerases
2. 3' to 5' Exonuclease proofreading
3. Strand-directed mismatch repair

Front 14

MSH

Back 14

binds to bulge (mismatch) in DNA

Front 15

MLH

Back 15

binds to Msh, triggers degradation of nicked strand

Front 16

DNA glycosylases

Back 16

remove unnatural DNA bases
flip-out each nucleotide to probe for damage

Front 17

Base Excision Repair

Back 17

Single-stranded repair
1.DNA glycosylase cleaves bond on damaged base
2. AP endonuclease removes super-phosphate backbone
3. DNA polymerase fills in gap

Front 18

Nucleotide Excision Repair

Back 18

Removes several nucleotides
1. multienzyme complex scans for distortion
2. nuclease cleaves backbone on both sides
3. helicase separates damaged DNA from undamaged, complimentary DNA
4. Gap is repaired by DNA polymerase and DNA ligase

Front 19

Homologous Recombination

Back 19

Double-stranded DNA repair
during cell division when duplicated chromosomes have yet to separate
1. exonuclease-mediated removal of 5' ends of double-stranded break
2. single-stranded 3' ends invade double helix of sister chromatid or homologous chromsome
3. final product is fully restored & accurately repaired

Front 20

Nonhomologous End-joining

Back 20

Double-strand DNA repair
1. 3' ends of broken strand base pair as best they can with each other
2. loss of one or more bases
3. changes reading frame

Front 21

Deamination

Back 21

pairs with different partner during DNA replication

Repair: Base excision repair

Front 22

Depurination

Back 22

leaves ribose sugar without a base
can result in deletion mutation

Repair: Base excision repair

Front 23

Oxidation Damage

Back 23

cause mispairing, loss of a base, single and double-stranded breaks

Front 24

UV Irradiation

Back 24

induce pyrimidine dimer, creates kink which can block relication and transcription

Repair: Nucleotide excision repair

Front 25

Chemical Carcinogens

Back 25

Alkylation of base, changes H-bonding ability

Front 26

DNA Adducts

Back 26

add bulky adducts to DNA

Repair: Nucleotide excision repair

Front 27

mRNA

Back 27

messenger RNA
contains coding sequence for majority of cellular proteins

Front 28

rRNA

Back 28

Ribosomal RNA
strands of RNA incorporated into ribosomal proteins to form mature ribosomes

Front 29

tRNA

Back 29

Transfer RNA
Dock in a sequence-specific manner at the mRNA/ribosome to deliver amino acids to growing polypeptide chain

Front 30

snRNA

Back 30

small nuclear RNA
only found in nucleus
involved in mRNA splicing and transport of proteins to ER

Front 31

RNA polymerase I

Back 31

rRNA "Rampant"

Front 32

RNA polymerase II

Back 32

mRNA "Massive"

Front 33

RNA polymerase III

Back 33

tRNA "Tiny"

Front 34

5' Cap

Back 34

provides stability to RNA molecule by protecting it from degradation by nucleases

Front 35

poly(A) tail

Back 35

not encoded by the genome
provides stability to mRNA and is a signal for export of mRNA from nucleus to cytoplasm

Front 36

Alternative Splicing

Back 36

different patterns of splicing to give rise to different mRNA sequences

Front 37

Apo-B100

Back 37

liver: unedited mRNA is translated to yield Apo-B100

Front 38

Apo-B48

Back 38

intestine: mRNA is edited such that C becomes U and produces stop codon
Synthesis of shorter protein (48% of Apo-B100)

Front 39

Start Codon

Back 39

AUG
dictates reading frame for translation

Front 40

Stop Codons

Back 40

UAA, UAG, UGA

Front 41

Missense Mutation

Back 41

base substitution results in an amino acid change

Front 42

Nonsense Mutation

Back 42

Base substitution results in introduction of STOP codon

Front 43

Silent

Back 43

Base substitution does not change identity of amino acid

Front 44

Frameshift Mutation

Back 44

Insertion or deletion not divisible by three alters rest of translated mRNA reading frame

Front 45

Aminoacyl-tRNA synthetase

Back 45

uses energy of two phosphate bonds to catalyze the attachment of amino acids to their corresponding tRNAs via an ester linkage

Front 46

eIF-2

Back 46

recuits initiator tRNA to 40S subunit

Front 47

eIF-4G and eIF-4E

Back 47

binds to 5' cap, helps position mRNA on small ribosomal subunit

Front 48

eIF1-alpha

Back 48

elongation factor bound to aminoacyl tRNA, hydrolysis of GTP allows for incorporation into polypeptide chain

Front 49

Polysome

Back 49

Polyribosome:
group of ribosomes bound to mRNA molecule, each synthesize separate polypeptide chain

Front 50

Streptomycin

Back 50

Inhibits initiation and causes misreading

Front 51

Tetracycline

Back 51

Inhibits binding of aminoacyl tRNAs (1st step of elongation)

Front 52

Chloramphenicol

Back 52

Inhibits peptidyl transferase (peptide bond formation during elongation)

Front 53

Erthromycin

Back 53

Inhibits translocation (during elongation)

Front 54

Protein Disulfide Isomerase

Back 54

rearrange incorrect disulfide bonds
located only in ER
stabilizes folded structures

Front 55

Transcriptional Regulation: cis-elements

Back 55

specific DNA sequences where transcription factors bind

Front 56

Transcriptional Regulation: Trans-elements

Back 56

gene regulatory proteins (activators or repressors)

Front 57

Four major DNA-binding domains

Back 57

1. zinc-finger
2. helix-turn-helix
3. leucine zipper
4. helix-loop-helix

Front 58

Activation Domain

Back 58

Interact with other transcription regulatory proteins of the transcriptional machinery (RNApol or coactivators)

Front 59

RNAi

Back 59

regulation of translation
silence expression of target gene
triggered by the presence of dsRNA

Front 60

Translational regulation via eIF2

Back 60

can be phosphorylated by kinases
blocks exchange of GDP to GTP
inhibits initiation

Front 61

Blunt Ends

Back 61

cleave both strands of DNA in same position, no unpaired bases

Front 62

Sticky Ends (Cohesive Ends)

Back 62

staggered cuts on two strands
2 to 4 unpaired nucleotides at each end

Front 63

DNA ligation

Back 63

Glue sticky ends together

Front 64

Molecular Cloning

Back 64

covalent insertion of DNA fragment from one type of cell into another

Front 65

Multiple cloning site

Back 65

several palindromes
ligation of DNA fragment

Front 66

Gel Electrophoresis

Back 66

charged molecules are separated based on rates of migration through gel meshwork

Front 67

Sanger Method

Back 67

relies on dideoxyribonucleotides (lack of 3'-hydroxyl group)
four different reactions

Front 68

PCR

Back 68

amplifies specific region a million-fold within a few hours

Front 69

Reverse transcriptase

Back 69

uses mRNA as template to synthesize DNA

Front 70

Southern Blot

Back 70

DNA

Front 71

Northern Blot

Back 71

RNA

Front 72

Western Blot

Back 72

Protein

Front 73

In situ hybridization

Back 73

used to detect DNA or RNA sequences in chromosomes or intact cells

Front 74

DNA Microarrays

Back 74

allows analysis of thousands of genes at the same time

Front 75

Genotyping

Back 75

DNA
"What kind of protein is being made?"

Front 76

Gene expression profiling

Back 76

mRNA converted to cDNA
"How much mRNA is being made?"