Molecular Biology Exam 2

Front 1

______ is the flow of information from DNA to RNA; Then RNA to protein.

Back 1

translation

Front 2

_____ is the actual synthesis of a protein under the direction of mRNA.

Back 2

translation

Front 3

What are the four primary components of RNA translation?

Back 3

1. mRNA
2. tRNA
3. rRNA and ribosome
4. Aminoacyl-tRNA synthetase

Front 4

_____ carry code for protein from DNA.

Back 4

mRNA

Front 5

_____ is an ordered series of three-nucleotide-long unit in the protein coding region of the mRNA.

Back 5

Codon

Front 6

The protein coding region of mRNA located within the mRNA is called what?

Back 6

Open reading frame (OFR)

Front 7

The ____________ defines the reading frame; first amino acid.

Back 7

start codon

Front 8

The __________ defines the end of the OFR; termination.

Back 8

stop codon

Front 9

What is the untranslated sequence located in eukaryotic mRNA called?

Back 9

UTR- Untranslated region

Front 10

The following are characteristics of what:
-Transports amino acids to ribosomes during translation
- Provide the physical interface between the amino acids being added to the growing polypeptide chain and the codons in the mRNA.

Back 10

tRNA

Front 11

RNA + proteins form what?

Back 11

functional ribosome

Front 12

___________ provides a mechanism for decoding mRNA into amino acids and interacts with tRNAs during translation by providing peptidyl transferase activity.

Back 12

rRNA

Front 13

rRNA catalyzes protein synthesis by facilitating the binding of ____ to ____.

Back 13

tRNA to mRNA

Front 14

Is this the small or large subunit of the ribosome?

Contains the peptidyl transferase center for the formation of peptide bonds.

Back 14

large subunit

Front 15

Is this the small or large subunit of the ribosome?

Contains the decoding center for charged tRNAs read or decode the codon units of mRNA.

Back 15

small subunit

Front 16

Ribosomes are named by the velocity of their sedimentation called ____.

Back 16

S

(The larger the S value, the faster the sedimentation velocity and the larger the molecule.)

Front 17

_______ is the unit for measure sedimentation velocity and named after the inventer of the ultracentrifuge.

Back 17

S=Svedberg
(Theodor Svedberg)

Front 18

_________ catalyzes the esterification of a specific amino acid to one or more its compatible cognate tRNAs to form an aminoacyl-tRNA. This is sometimes called "charging" the tRNA with the amino acid.

Back 18

Aminoacyl-tRNA synthetases

Front 19

Once the tRNA is charged, a ribosome can transfer the amino acid from the ______ onto a growing peptide, according to the genetic code.

Back 19

tRNA

Front 20

What are the two steps of Aminoacyl-tRNA synthetases?

Back 20

1. Adenylylation of amino acid: amino acid react with ATP to become adenylylated with release of AMP.

2. Transfer of the adenylylated amino acid to tRNA

Front 21

_____ is the template for translation. (information)

Back 21

mRNA

Front 22

_______ coordinate recognition and catalyze bond formation.

Back 22

ribosomes

Front 23

_____ is the physical interface between protein and codon.

Back 23

tRNAs

Front 24

________ couple amino acid to tRNAs.

Back 24

Amioacyl-tRNA synthetases

Front 25

What step of translation is this:

-results in the formation of an initiation complex in which the ribosome is bound to the specific initiation (start) site on the mRNA while the initiator tRNA is annealed to the initiator codon and bound to the ribosome.

Back 25

The first step- initiation

Front 26

What step of translation is this:

-consists of joining amino acids to the growing polypeptide chain according to the sequence specified by the message. Incorporation of each amino acid occurs by the same mechanism. Thus, the same steps are repeated over and over again until the termination codon is reached in the message.

Back 26

The second step- elongation

Front 27

What step of translation is this:

- termination codon gives the signal for the protein synthesis, in which the ready-made protein is released from the ribosome.

Back 27

The third step- termination

Front 28

What step of translation is this:

-ribosomal recycling after the release of polypeptide chain

Back 28

the critical last step

Front 29

Which initiation factor blocks ribosome A site

Back 29

IF1 and eIF1A

Front 30

Which initiation factor facilitates initiator tRNA binding to the P-site of the 40s subunit?

Back 30

IF2, eIF2, e1F5B

Front 31

Which initiation factor prevents ribosomal subunit association?

Back 31

IF3 and eIF3

Front 32

Which initiation factor prepares mRNA template form ribosome binding?

Back 32

eIF1, eIF4A, eIF4E, eIF4G, eIF4B

Front 33

Initiation of translation begins with the amino acid ______.

Back 33

methionine

Front 34

Which site is the binding site for aminoacylated tRNA?

Back 34

A site

Front 35

Which stie is the binding site for peptidyl tRNA?

Back 35

P site

Front 36

Which site is the exit site?

Back 36

E site

Front 37

_____ is when RNA translation shifts into elongation stage.

Back 37

Once the ribosome is assembled with the charged initiator tRNA in the P site, polypeptide synthesis

Front 38

What are the three factors that control elongation events?

Back 38

1. EF-Tu
2. EF-G
3. EF-Ts

Front 39

mRNA are usually translated by a series of ribosomes spaced at intervals of about ________ nucleotides.

Back 39

100-200

Front 40

Translation can also be regulated by a host of proteins that interact with ______, ________ or _______.

Back 40

5' ends
3' ends
The translation factors themselves

Front 41

Prokaryotic or Eukaryotic translation?

-Shine-Delgarno sequence or ribosome binding site (RBS) base pairs with the 3’ end of 16S rRNA (small subunit)
-Precedes the AUG initiation codon (codes for methionine)
-the initiator tRNA that is charged with a modified form of methionine(fMet-tRNA) is annealed to the initiator codon and enters the P site in the ribosome
-Three translation initiation factors (IF1,IF2,IF3) involve in initiation event in prokaryotic cell
-2 initiation complexes form in initiation events
30S initiation complex and 70S initiation complex

Back 41

prokaryotic

Front 42

Prokaryotic or Eukaryotic translation?

-mRNA is bound to the 40S subunit by the 7methylG cap
-Ribosome scans along until it finds an AUG
-At least 8 translation initiation factors involve in initiation event in Eukaryotic cells
-3 initiation complexes are formed in initiation events
43S preinitiation complex,48S preinitiation complex and 80S initiation complex

Back 42

Eukaryotic

Front 43

What are the four steps of translation?

Back 43

1. Initiation
2. Elongation
3. Termination
4. Ribosome recycling

Front 44

____ is the coding sequences in eukaryotic genes.

Back 44

Exon

Front 45

____ is the non-coding or intervening sequences in eukarytoic genes.

Back 45

Intron

Front 46

____ is the primary transcript of DNA.

Back 46

Pre-mRNA

Front 47

____ is the process of introns removal from the pre-mRNA.

Back 47

RNA splicing

Front 48

____ is a complex of specialized RNA and protein subunits that removes introns from pre-mRNA.

Back 48

Spliceosome

Front 49

_____ is the process of the re-combination of different exons in eukaryotes.

Back 49

Alternative splicing

Front 50

What is a major source of genetic diversity in eukaryotes?

Back 50

Alternative splicing

Front 51

What are the three classes of RNA splicing?

Back 51

1. Nuclear Pre-mRNA splicing (Spliceosome mediate intron removal)
2. Group 1 introns
3. Group 2 introns (Intron itself folds into a specific conformation within the pre-mRNA and catalyzes the chemistry of released by itself and the exon ligation)

Front 52

This pathway is mediated by spliceosome and involved in assembly, rearrangement and catalysis within the spliceosome:

Back 52

Nuclear pre-mRNA splicing

Front 53

Spliceosome compromises about ____ proteins and ____ RNAs.

Back 53

150
5

Front 54

What are the 5 small nuclear RNAs (snRNAs)?

Back 54

U1
U2
U4
U5
U6
100-300 nt

Front 55

What are the 3 roles of snRNPs in splicing?

Back 55

1. Recognizing the 5' splice site and the branch site.
2. Bringing those sites together.
3. Catalyzing the RNA cleavage

Front 56

A few rare introns can remove themselves from pre-mRNA, this process is called ______.

Back 56

self splicing

Front 57

What is it called when two exons carried different RNA molecules can be spliced together?

Back 57

Trans-splicing

Rare but occurs in almost all the mRNAs of trypanosome and nematode worm.

Front 58

The process of ______ is vital to creating mature RNA, which is then able to undergo translation. It is a specially altered nucleotide on precursor mRNA and some other primary RNA transcripts as found in eukaryotes.

Back 58

5' capping

Front 59

The process of 5' capping generally serves what four functions?

Back 59

1. Regulation of nuclear export.
2. Prevention of degradation by exonucleases.
3. Promotion of translation
4. Promotion of 5' proximal intron excision

Front 60

The enzymes for capping can only bind to ________ ensuring specificity to only these transcripts, which are almost entirely mRNA.

Back 60

RNA polymerase II

Front 61

________ is the covalent linkage of a polyadenlylyl moiety to mRNA molecule.

Back 61

Polyadenylation (poly (A) tail)

Front 62

The following are functions of what:

-Protects mRNA from degradation by exonucleases.
-Transcription Termination.
-Export of the mRNA from the nucleus.
-mRNA translation

Back 62

Poly (A) tail

Front 63

________ occurs during and immediately after transcription of DNA into RNA. After transcription has been terminated, the mRNA chain is cleaved through the action of an endonuclease complex associated with RNA polymerase. After the mRNA has been cleaved, around 250 adenosine residues are added to the free 3' end at the cleavage site.

Back 63

Polyadenylation

Front 64

Polyadenylation reaction is catalyzed by _________.

Back 64

polyadenylate polymerase

Front 65

What is any heritable change in the base sequence of a DNA molecule called?

Back 65

Mutation

Front 66

A ______ is an individual, organism or new genetic character that is different from the normal organism or gene. Also referred to as a wild type.

Back 66

Mutant

Front 67

What is an agent that causes mutation called?

Back 67

Mutagen
(may be a chemical or physical agent)

Front 68

_____ is the process of producing a mutation.

Back 68

mutangenesis

Front 69

This type of mutation occurs in nature without the addition of a mutagen:

Back 69

spontaneous mutation

Front 70

The mutation is caused by a mutagen and the process is called _________.

Back 70

induced mutagenesis

Front 71

In this type of mutation a single base is replaced by another: Base substitution can be transition and transversion:

Back 71

Point mutation-Base substitutions

Front 72

In this type of mutation one or more base are inserted or deleted in the DNA. Results in a change in the reading of codons:

Back 72

Frame shift mutations

Front 73

In this type of mutation mobile pieces of DNA sequence are inserted or deleted in the DNA molecule. Results in rearrangements in the host chromosome (chromosome mutations):

Back 73

Transposable elements

Front 74

This type of mutation involves a single base change, frequently refer to base substitutions:

Back 74

Point mutation

Front 75

Frequently ______ mutation cause a stop codon to produce a truncated protein.

Back 75

frame shift

Front 76

This type of mutation occurs in nature in the absence of mutagen: Under physical condition and occasional mistakes in DNA replication.

Back 76

Spontaneous mutations

Front 77

Spontaneous mutations all generally occur in which four events?

Back 77

1. Deamination
2. Depurination
3. Methylcystosine
4. Error in replication

Front 78

____ is the removal of an amine group from a molecule. Often occurs in the base cytosine, adenine and guanine. About 100 times per day.

Back 78

Deamination

Front 79

_____ is the cleavage of the N-glycosidic bond between a base and deoxyribose. As a result the base "falls out" leaving an abasic site or apurinic site in the DNA.

Back 79

Depurination

Front 80

What is the most common form of DNA damage?

Back 80

Depurination

Front 81

Depurination of adenine and guanine creates ______.

Back 81

Apurinic deoxyribose

Front 82

What are the types of environmentally induced mutations?

Back 82

1. Chemical- Alkylating agents, base analogs, deaminating agents and intercalating agents.
2. UV radiation- Formation of pyrimidine dimers.
3. Ionizing radiation- Single and double-strand breaks and formation of free radicals. Cross linking.

Front 83

What are the four consequences of the change in terms of the effect on the amino acid sequence?

Back 83

1. Silent or neutral mutations
2. Missense mutations
3. Nonsense mutations
4. Frameshift mutations

Front 84

Base change results in no change of the amino acid sequence of the translated protein or do not yield mutant phenotype (often occur base substitutions)

Back 84

silent or neutral mutations
(Don't alter protein structure)

Front 85

This mutation is also called chain termination mutations.
-A nucleotide change has inserted a stop codon into the middle of the protein.
-These lead to the production of a nonfunctional or truncated protein to eliminate protein activity completely.

Back 85

Nonsense mutation

Front 86

In this mutation the base change results in the change of an amino acid in the translated protein:

Back 86

missense mutation
(Can cause sickle cell)

Front 87

__________ can change the structure of a chromosome by moving from site to site in the host DNA and then cause chromosome mutations.

Back 87

transposable elements

Front 88

Genetic variation (caused by mutation) is necessary for evolutionary change of the species:

Back 88

beneficial mutation

Front 89

Mutation may cause change in the genotype which may or may not affect the phenotype.
-nutritional mutations
-temp sensitive

Back 89

neutral mutation

Front 90

-Lethal mutations (RNA polymerase mutation)
-Morphological mutations (strep pneumo)
-Too much genetic change

Back 90

Harmful mutation

Front 91

Direct remove damaged DNA by enzymes:
-Photolyase directly reverses the formation of pyrimidine dimers ( found in E. coli and also found in yeasts and plants)
-A methyltransferase removes the methyl group from the O6methylguanine

Back 91

Reversing base modifications

Front 92

This system works by recognizing distortions to the shape of the double helix rather than recognizing any particular lesion:

Back 92

nucleotide excision repair

Front 93

What are the three steps of nucleotide excision repair?

Back 93

1. Distortions trigger a chain
of event that lead to removal
of a short single-strand
segment.
2. the resulting a single-strand
gap in the DNA is filled in
by DNA polymerase using
the undamaged strand as a
template
3. DNA ligase restore the
original nucleotide
sequence

Front 94

______ is a system for recognizing and repairing erroneous insertion, deletion and mis-incorporation of bases that can arise during DNA replication and recombination.

Back 94

DNA mismatch repair

Front 95

What are the 3 mechanisms to repair double-strand breaks (DSBs)?

Back 95

1. Homologous recombination repair
2. Non-homologous end joining NHEJ
3. Microhomology-mediated end joining MMEJ

Front 96

_____ is a repair system in which sequence information will retrieve from nearly identical sister chromosome by exchange and finishing the repair of DNA.

Back 96

Homologous recombination repair

Front 97

________, also knowns as translesion synthesis, is a DNA damage tolerance process that allows the DNA replication machinery to replicate past DNA lesions such as thymine dimers or AP sites.

Back 97

SOS repair system

Front 98

The sequence of nucleotides in DNA or mRNA that determines the specific amino acid sequence in the synthesis of proteins:

Back 98

genetic code

Front 99

The genetic code features ___ possible codons, which must code for 20 different amino acids and ___ stop codons.

Back 99

61
3

Front 100

Many amino acids are specified by more than one codon

Back 100

degenerate

Front 101

Signals the start or translation (start codon)

Back 101

AUG

Front 102

All proteins are initially translated with _____ in the first position.

Back 102

methoionine

Front 103

Which is a stronger pair:
G:C or A:U

Back 103

G:C

Front 104

what are the three stop codons? (nonsense codons)

Back 104

UAA
UAG
UGA

Front 105

3 stop codons are read not by tRNA but by specific proteins called _______.

Back 105

release factors

Front 106

UAG is called ____.

Back 106

Amber

Front 107

UGA is called ___.

Back 107

opal or umber

Front 108

UAA is called _____.

Back 108

ochre

Front 109

Most of organisms have fewer than 45 tRNAs. So, one tRNA may recognize several different codons.

Back 109

Wobble theory

Front 110

______ allows less stringent pairing between the 3' base of the codon and the 5' base of the anticodon. This allows fewer tRNAs to accommodate all codons.

Back 110

Wobble pairing

Front 111

What are the 5 anticodon bases?

Back 111

1. C
2. A
3. G
4. U
5. I (inosine-derived from adenine)

Front 112

_____ is the process by which information from a gene is used in the synthesis of a functional gene product.

DNA>RNA>protein>trait

Back 112

gene expression

Front 113

Gene expression DOES or DOES NOT depend on size of the genome?

Back 113

Does not

Front 114

The following are characteristics of:

-Necessary for the basic function of any cell
-Under minimal regulatory control
-Genes are expressed all the time at the same level

Back 114

housekeeping genes
(Actin, GAPDH and ubiquitin)

Front 115

The following are characteristic of:

-Provide the maximum growth rate under certain environmental stimuli
-Allows for cellular adaption, variation, differentiation and development

Back 115

Highly regulated genes

Front 116

The following are characteristic of:

-A consecutive gene is a gene that is transcribed
-A facultative gene is a gene which is only transcribed when needed
-An inducible gene is a gene whose expression is either responsive to environmental change or dependent on the position in the cell cycle.

Back 116

Highly regulated genes

Front 117

The following are characteristics of:

-DNA binding protein
-Positive regulation
-Increases gene transcription
-Up regulate

Back 117

Activators

Front 118

The following are characteristics of:

-DNA binding protein
-Negative regulation
-Decrease or eliminates gene transcription
-Down regulate

Back 118

Repressors

Front 119

_____ is several genes with related functions that are regulated together.

Back 119

operon

Front 120

___ is the DNA site where repressors bind.

Back 120

operator

Front 121

_____ code for the enzymes/proteins of interest.

Back 121

structural genes

Front 122

___ control the expression of structural genes by expressing regulatory proteins.

Back 122

Regulatory genes

Front 123

The ______ is located between the promoter and the first structural gene and involved in transcription of structural gene in prokaryotes.

Back 123

operator

Front 124

The following are characteristics of:

-First operon discovered
-contains 3 structural genes coding for E. coli proteins that permit the bacteria to use the sugar lactose in the lactose operon.

Back 124

lac operon

Front 125

_______ permeases which transports lactose into the cells (lacZ)

Back 125

galactoside

Front 126

______ cuts the lactose into galactose and glucose (lacY)

Back 126

Beta galactosidases

Front 127

__________ (lacA) rids the cell of toxic

Back 127

thiogalactoside

Front 128

The following are characteristics of:
-Regulatory element of Lac Operon
-Has its own promoter region
-Produced constitutively repressor protein
-When lactose is absent, repressor protein binds to the operator to inhibit transcription or turns transcription off

Back 128

lacI gene
(i)

Front 129

______ operon consist 3 genes (araA, araB ad araD) that code for three digestive enzymes involved in the breakdown of arabinose that are clustered together

Back 129

Arabinose

Front 130

The arabinose proteins (araA, araB and araD) are dependent on the initiation of transcription from _____.

Back 130

PBAD

Front 131

_____ acts as a repressor in the absence of arabinose and as an activator in the presence of arabinose.

Back 131

araC