Mol Bio Exam 2

Front 1

In Prokaryotic DNA replication, this enzyme binds the sequence at the ori C site containing 11 GATC/CTAG repeats

Back 1

DnaA

Front 2

In Prokaryotic DNA replication, this enzyme methylates Adenine sites

Back 2

Dam methylase

Front 3

Helicase enzyme in prokaryotic DNA replication

Back 3

DnaB

Front 4

Topoisomerase enzyme in prokaryotic DNA replication

Back 4

DNA gyrase (target for drugs)

Front 5

Major 'worker' of replication in prokaryotic DNA replication; responsible for building the new DNA strand

Back 5

Polymerase III

Front 6

Primase enzyme in prokaryotic DNA replication

Back 6

DnaG

Front 7

In prokaryotic DNA replication, these enzymes remove RNA primer and replace sequence with DNA

Back 7

Rnase H and DNA polymerase I

Front 8

What is type 2 topoisomerase used for in prokaryotic DNA replication?

Back 8

Unlink newly synthesized circular chromosomes allowing cell division to continue

Front 9

This enzyme binds the DNA sequence at the points of origin in Eukaryotic DNA replication

Back 9

Origin recognition complex (ORC)

Front 10

This enzyme binds DNA and ORC in Eukaryotic DNA replication

Back 10

Minichromosome maintenance proteins (MCM)

Front 11

What are SSBs named in Eukaryotic DNA replication?

Back 11

RPA

Front 12

In Eukaryotic DNA replication this wraps around the DNA and travels along the strand with DNA polymerase

Back 12

PCNA (sliding clamp)

Front 13

In Eukaryotic DNA replication this works with Primase to create 10 nucleotide RNA primer followed by 20 nucleotides

Back 13

Pol a

Front 14

What enzyme, in Eukaryotic DNA replication, continues DNA strand elongation on the leading strand?

Back 14

Pol e

Front 15

What enzyme, in Eukaryotic DNA replication, continues adding dNTPs to the Okazaki fragment on the lagging strand?

Back 15

Pol o

Front 16

In Eukaryotic DNA replication what is primer removed by?

Back 16

Flag endonuclease 1 (FEN1) and RNase H

Front 17

In Eukaryotic DNA replication what fills in missing DNA sequence?

Back 17

DNA polymerase o

Front 18

What is the purpose of Telomerase in Eukaryotic DNA replication?

Back 18

Lengthen 3' overhang by using built in primer that recognizes the TTAGGG sequence; Telomerase acts as a polymerase increasing the length of parental strand; allows primes to bind and new strand to lengthen

Front 19

What is the purpose of 3'-5' exonuclease?

Back 19

Excise mismatched nucleotide

Front 20

Missense mutation

Back 20

Changes a letter that changes the amino acid sequence

Front 21

Silent mutation

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Missense mutation that does not change the amino acid sequence

Front 22

Nonsense mutation

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Changing letter that makes sequence stop

Front 23

What gene mutation can cause disease?

Back 23

Triplet expansion

Front 24

What does UV radiation cause in DNA?

Back 24

Thymine dimers/cyclobutane ring

Front 25

What mechanism would be most efficient to correct deprivation?

Back 25

Base excision repair

Front 26

Core enzyme of prokaryotic polymerase

Back 26

5 subunits

Front 27

Holoenzyme of prokaryotic polymerase

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core enzyme + sigma (o) factor

Front 28

Process of Rifampin

Back 28

Inhibits transcription by binding to the B subunit of the RNA polymerase (stops phosphordister bond formation in the RNA)

Front 29

What is Rifampin used to treat?

Back 29

Rhodococcus, Mycobacteria, and Staphylococci

Front 30

In Eukaryotic Transcription, what is RNA polymerase II responsible for?

Back 30

protein-coding genes

Front 31

In Eukaryotic transcription, what is always used by RNA polymerase II to initiate transcription?

Back 31

General transcription factors

Front 32

In Eukaryotic transcription, what are the proteins involved for recruitment of general transcription factors and RNA polymerase to the promoter

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Regulatory transcription factors

Front 33

What is the mechanism of amanitin?

Back 33

Binds to RNA polymerase II and inhibits transcription

Front 34

What symptoms are exhibited after ingestion of Amanita phalloides?

Back 34

Gastrointestinal (vomiting, diarrhea, and cramps), recovery period prior to kidney and liver failure, eventually death

Front 35

What inhibits eukaryotic RNA polymerase II?

Back 35

a-amanitin

Front 36

What inhibits all of RNA polymerases?

Back 36

Actinomycin D

Front 37

What is Actinomycin D's mechanism of action?

Back 37

Stabalizes topoisomerase-I on the DNA and prevents RNA polymerase progression, also causing double-strand breaks

Front 38

What RNA polymerase is used as a chemotherapy drug for lymphomas and various sarcomas?

Back 38

Prevents transcription in both eukaryotes and prokaryotes

Front 39

What is inclusion or exclusion of a sequence in splicing lead to ?

Back 39

mutations; will interfere with production of the correct protein

Front 40

Your patient has a novel mutation disrupting the splice donor site of intron 2. Which of the following mRNAs is likely a result form this mutation?

Back 40

Front 41

What are protein isoforms?

Back 41

variations of a protein with slightly different functions (alternative splicing)

Front 42

What does alternative splicing allow?

Back 42

Allows the cell to tailor the protein for the desired job in that cell type

Front 43

What is alternative splicing?

Back 43

using different combinations of splice sites allowing for the production of different isoforms form the same gene

Front 44

Intron retention

Back 44

mRNA contains and will encode protein the sequence of this intron

Front 45

Exon skipping

Back 45

mRNA lacks and will not encode protein front the sequence of exon2

Front 46

Mutually exclusive exons

Back 46

Will allow either exon 2 or exon 3 to be included in the mRNA, but not both

Front 47

Alternative polyadenylation

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mRNA contains and will encode protein from the sequence from intron 2

Front 48

Proteolysis

Back 48

Cleavage and removal of amino acid residues in the protein

Front 49

Glycosylation

Back 49

Addition of oligosaccharides to proteins via a glycosidic bond to the hydroxyl or amine group of an amino acid side chain

Front 50

Methylation and acetylation

Back 50

addition and removal of methyl and acetyl groups at specific lysine and arginine residues controls gene expression

Front 51

Myristolylation

Back 51

myristoyl (C14) is added to the N-terminus at glycine residue (must cleave start methionine; results in protein association with intracellular vesicles)

Front 52

Palmitoylation and prenylation

Back 52

addition of a lipid on a cystein side chain

Front 53

Hydroxylation

Back 53

addition of hydroxyl group to amino acid (proline and lysine residues are hydroxylated on the a-chians of collagen)

Front 54

Carboxylation

Back 54

carboxyl groups are added to glutamate residues by a vitamin K dependent carboxylation (important for blood clotting factors

Front 55

Ubiquitination

Back 55

addition of small polypeptide ubiquitin to a protein via a lysine residue to target proteins for degradation in the proteasome

Front 56

Gated transport

Back 56

the nuclear pore complex facilitates protein transport from cytosol to nucleus

Front 57

Transmembrane transport

Back 57

membrane-bound protein translocators directly transport specific proteins across the membrane (proteins usually unfolded to undergo this transport)

Front 58

Vesicle transport

Back 58

membrane enclosed transport intermediates pinch off from other membrane-enclosed compartments

Front 59

Signal sequence

Back 59

short sequence in the protein that is used to direct proteins to the correct compartment of the cell; sequence can be cleaved from protein once transport has occurred

Front 60

Signal patches

Back 60

3-D arrangement of amino acids on the proteins surface that forms after the protein is folded; can be used for gated-transport

Front 61

Sorting receptors

Back 61

recognize corresponding signal sequences or patches and guide protein to the correct location

Front 62

What types of proteins are transported into the nucleus?

Back 62

Histones, transcription factors, polymerases

Front 63

Nuclear localization signal (NLS)

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signal sequence or signal patch that is rich is positively charged amino acids

Front 64

Nuclear import receptors

Back 64

soluble cystosolic proteins that bind the NLS as well as nucleoporins

Front 65

TOM complex

Back 65

translocase for the outer membrane

Front 66

TIM complex

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translocases for the inner membrane (TIM23 and TIM22)

Front 67

OXA

Back 67

translocase for inner membrane

Front 68

Proteins transported into ER

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transmembrane proteins, proteins found int he lumen of the ER or other membrane-bound organelles, and excreted proteins

Front 69

Free ribosomes

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remain in the cytoplasm synthesize proteins used in the cytoplasm

Front 70

Membrane-bound ribosomes

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start in the cytoplasm and are recruited to the surface of the ER during translation

Front 71

ER sequence

Back 71

contains a section of hydrophobic/nonpolar amino acid

Front 72

Signal-recognition particle (SRP)

Back 72

bind the ER signal sequence, temporally stalls translation

Front 73

Signal-recognition particle receptor (SRP-receptor)

Back 73

an integral membrane receptor on the cytosol side of the ER membrane. Bring SRP-ribosomes to the surface of the ER

Front 74

Sec61 complex

Back 74

ER protein translocator, donut-shaped, contains binding site for the ER signal sequence

Front 75

Processes within the Golgi

Back 75

Glycosylation, sulfation, phosphorylation, proteolsis

Front 76

Proteins that bind the cytosol side of the vesicles used to transport proteins to/from/within the Golgi

Back 76

Clathrin, COP I, COP II

Front 77

In protein transport to the lysosome, what targets the protein for the lysosome?

Back 77

the attachment of mannose 6-phosphate to a protein

Front 78

A deficiency of the ability to phosphorylate mannose leads to what?

Back 78

I-cell disease (mucolipidosis II)

Front 79

Symptoms of mucolidosis II

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skeletal abnormalities, restricted joint movement, coarse facial features, severe psychomotor impairment, death usually occurs by 8 years of age

Front 80

Symptoms of mucolidosis II in cats

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abnormal facial features, retarded growth, progressive hindlimb paresis, skeletal abnormalities (major thing) (mutation in gene encoding GIcNAc-phophotranserase)

Front 81

Constitutive secretion

Back 81

secretory vesicle travels from Golgi directly to the membrane

Front 82

Regulated secretion

Back 82

secretory vesicles remain in the cytoplasm util a signal triggers the fusion and release of contents

Front 83

What do clathrin-coated vesicles transport?

Back 83

macromolecules bound to specific receptors for import into the cell

Front 84

How is cholesterol imported into the cell?

Back 84

bound to low-density lipoproteins (LDL) by binding the LDL receptor (LDLR) and being transported to the lysosome via vsicles

Front 85

What is needed for translation?

Back 85

ribosomes (multiple proteins and rRNAs), aminoacyl tRNA (transport amino acids), mRNA (transported to the cytoplasm), translation factors (facilitate the process at each step)

Front 86

Shine Dalgarno sequence

Back 86

ribosome binding site ~10 bases upstream from the start codon, 5' AGGAGGU 3', base pairs with the 16S rRNA (30S)

Front 87

IF-1: initiation factor 1

Back 87

binds 30S subunit, prevents subunits joining prematurely

Front 88

IF-2: initiation factor 2

Back 88

binds initiator-tRNA, hydrolyzes GTP

Front 89

IF-3: initiation factor 3

Back 89

stabilizes free 30S subunit, prevents subunits from joining prematurely

Front 90

EF-Tu in elongation

Back 90

escorts aminocyl-tRNA to the ribosome and checks for correct codon-anticodon base pairing. hydrolyzes GTP

Front 91

Ribosomes in elongation

Back 91

catalyzes peptide bond formation through 23S rRNA acting as a ribozyme

Front 92

EF-G in elongation

Back 92

binds ribosomes to facilitate translocation. Hydrolyzes GTP

Front 93

Eukaryotic translation initiation factors

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Ternary complex, recruitment complex, eIF3, eIF5B

Front 94

eIF2

Back 94

binds the initiator tRNA (mehtionine) and GTP

Front 95

eIF4E

Back 95

binds 5' cap

Front 96

eIF4G

Back 96

binds eIF4E and poly-A binding protines (PABP)

Front 97

eIF4A

Back 97

helicase that unwinds seoncdary structure in the 5' UTR

Front 98

eIF3

Back 98

binds the 40S subunit, brings subunit to the pre-initiation complex

Front 99

eIF5B

Back 99

binds the 60S subunit, brings subunit to the initiation complex

Front 100

Ternary complex

Back 100

eIF2, GTP, aminoacyl-tRNA

Front 101

Recruitment complex

Back 101

eIF4E binds 5' cap of mRNA, eIF4G, POBP, eIF4A

Front 102

Enzymes in elongation

Back 102

eEF-1, ribosome, eEF-2

Front 103

eEF-1 in eukaryotic elongation

Back 103

escorts aminoacyl-tRNA to the ribosome and checks for correct codon-anticodon base pairing. Hydrolyzes GTP

Front 104

Ribosomes in eukaryotic elongation

Back 104

catalyzes peptide bond formation through 28S rRNA acting as a ribozyme

Front 105

eEF-2 in eukaryotic elongation

Back 105

binds ribosomes to facilitate translocation. Hydrolyzes GTP

Front 106

What is the mechanism of antibiotics?

Back 106

Inhibitors of prokaryotic translation and bind directly to the ribosome

Front 107

What is the mechanism of chemotherapeutics?

Back 107

eukaryotic translation inhibitors since translation is essential for cell survival and occurs at a higher rate in rapidly proliferating cells ex: targets for eIF4E, eIF4A

Front 108

Scientists are designing a new chemotherapeutic drug that will target translation initiation. What is a protein that is a likely target?

Back 108

eIF4E

Front 109

Transcriptional activators (genetic switches)

Back 109

turns genes on; increases transciriton by enhancing the binding of the polymerase to the promoter or opening the helix

Front 110

Transcriptional repressors (genetic switches)

Back 110

turns genes off; binds the operator, a sequence upstream of transcription, blocks access to promoter for RNA polymerase

Front 111

What are Lac operon and Trp operon?

Back 111

genetic switches

Front 112

Eukaryotic regulation of transription

Back 112

promote/prevents assembly of transcription initiation complex (modification of chromatin, DNA methylation, gene-spcific transcription factors)

Front 113

Purpose of chromatin modifications?

Back 113

transcription factors cannot bind the promoter if DNA is tightly wrapped n nucleosomes

Front 114

Mechanisms of chromatin modifications

Back 114

covalent histone modifications, nucleosome removal, nucleosome replacement, nucleosome remodeling

Front 115

Global regulation

Back 115

changes in the level of all protein synthesis in the cell

Front 116

Specific regulation

Back 116

changes in the translation level of specific mRNAs in the cell

Front 117

How do cells decrease protein synthesis in times of high stress?

Back 117

phosphorylation of eIF2

Front 118

What is the mechanism of ricin?

Back 118

binds and removes an adenine residue from 28S rRNA making the ribosome inactive