Cell Biology Exam Ii

Front 1

What does DNA polymerase do?

Back 1

Forms phosphodiester bonds at the 3’ end of the growing chain using deoxynucleotide triphosphates (dATP, dCTP, dTTP, dGTP)

Has ability to PROOFREAD previous nucleotide and make sure it is properly basepaired before proceeding. If it is incorrectly paired it will remove the deoxynucleotide triphosphate and replace it with the correct one.

Front 2

Is the formation of phosphodiester bonds at the 3' end of the growing DNA chain an energetically favorable process? Why?

Back 2

Yes. Due to hydrolysis of phosphate bonds.

Front 3

The error rate of DNA polymerase is:

Back 3

1:10^7 nucleotides

Front 4

DNA helicase and DNA primase make up:

Back 4

the primosome

Front 5

The primosome is made up of:

Back 5

DNA helicase and DNA primase

Front 6

This builds an RNA primer that polymerase uses to start a DNA strand:

Back 6

primase

Front 7

Primase does this:

Back 7

builds an RNA primer that polymerase uses to start a DNA strand

Front 8

Does leading strand synthesis require a primer?

Back 8

No. Primase builds an RNA primer that polymerase uses to start a DNA strand. This is unnecessary in the leading strand.

Front 9

This is a specific DNA sequence approximately 100base pairs long which is rich in adenine and thymine.

Back 9

origin of replication

Front 10

Origin of replication is:

Back 10

A specific DNA sequence approximately 100 base pairs long which is rich in adenine and thymine.

Front 11

DNA synthesis cannot begin unless:

Back 11

there is a nucleotide to attach to

Front 12

Why does replication require primase?

Back 12

DNA synthesis cannot begin unless there is a nucleotide to attach to

Front 13

What does the single strand binding protein do?

Back 13

binds to the lagging strand template to keep it from reforming dsDNA, until the polymerase can begin a new fragment.

Front 14

This binds to the lagging strand template to keep it from reforming dsDNA, until the polymerase can begin a new fragment:

Back 14

single strand binding protein

Front 15

This attaches lagging strand fragments to each other after removal of an RNA primer by a nuclease:

Back 15

ligase

Front 16

Ligase does this:

Back 16

attaches lagging strand fragments to each other after removal of an RNA primer by a nuclease

Front 17

Why is replication carried out in the 5’ → 3’ direction?

Back 17

If elongation was 3’→ 5’, there could be no PROOFREADING!

Front 18

Explain why sickle-cell anemia occurs.

Back 18

A single nucleotide is mutated in the β-globin gene. This results in the production of β-globin with a valine instead of a glutamic acid in the sixth amino acid position. This causes it to form polymers of hemoglobin which distort the shape of the cell into sickle shapes. These RBC's do not carry oxygen well and makes the person anemic.

Front 19

How does the cell repair DNA?

Back 19

mismatch-pair

Front 20

This removes replication errors that are missed by polymerase:

Back 20

mismatch-pair

Front 21

Mismatch pair does this:

Back 21

removes replication errors that are missed by polymerase.

Front 22

Mismatch repair is carried out by several proteins that scan the new DNA strand for mismatches. T/F

Back 22

T

Front 23

With mismatch-repair, mistakes are repaired prior to the next round of replication: T/F

Back 23

T

Front 24

deamination does this:

Back 24

mutates DNA by changing C to U resulting in replication making U:A

Front 25

depurination does this:

Back 25

mutates DNA by the loss of G and A. Will be lost at replication.

Front 26

UV Radiation does this:

Back 26

mutates DNA by creating Thymine dimers. Interferes with replication

Front 27

Each type DNA mutation damage is detected by a different set of enzymes that repair the problem prior to DNA replication: T/F

Back 27

T

Front 28

What is a genome?

Back 28

The entire compliment of genetic material in an organism

Front 29

How many distinct chromosomes comprise the human genome?

Back 29

24

Front 30

How many base-pairs does the human genome span?

Back 30

3 x 10^9 nucleotide-pairs

Front 31

How many chromosomes are found in a typical human cell?

Back 31

46

Front 32

How many chromosomes are found in human sperm or egg cells?

Back 32

23

Front 33

What is chromatin?

Back 33

The combination of DNA and histone proteins where the proteins compact the DNA into a coiled and linked structure like "beads on a string"

The compacted DNA structure formed by histone proteins which coil the DNA

Front 34

What is a nucleosome?

Back 34

Consists of the DNA wrapped around a histone octamer which consists of two copies each of the core histones H2A, H2B, H3, H4. It also includes the linking DNA which connects it to the next nucleosome to makeup the "beads on a string" structure. The nucleosome has about 200 nucleotide pairs with 146 of them wrapped around the histone octamer. The size of the histone octamer with coiled DNA is 11nm.

Front 35

How many nucleotide pairs of DNA are there in a nucleosome?

Back 35

about 200

Front 36

How many nucleotide pairs of DNA are there wrapped around the histone octamer of a nucleosome?

Back 36

about 146

Front 37

What is the size of the histone octamer of a nucleosome with the coiled DNA?

Back 37

11nm

Front 38

How can nucleosomes be dissasembled for study?

Back 38

Using nucleases to digest the linker DNA strands and a high concentration of salt to dissociate the coiled DNA and the histone octamer

Front 39

Which amino acids are replete in histones? Why?

Back 39

Arginine and lysine because they are basic (+ charge). DNA has a negatively charged sugar-phosphate backbone so the basic amino acids attract to it.

Front 40

What causes the nucleosome structure to dissociate so that the cell can access the DNA for replication, transcription, etc.? How?

Back 40

Histone proteins. They have a long N-terminal amino acid tail which extends out from the DNA-histone core. They are subject to several types of covalent modification that control many aspects of chromatin structure.

Front 41

Describe the steps to complete replication.

Back 41

Open the DNA
Recruit Proteins
Prime DNA Synthesis (PRIMASE)
Synthesize DNA (POLYMERASE)
Proofread
Connect Fragments (LIGASE)

Front 42

Copying of ONE stand of DNA into a complementary strand of RNA:

Back 42

transcription

Front 43

Describe transcription:

Back 43

copying of ONE stand of DNA into a complementary strand of RNA

Done by RNA Polymerase.

Energy from nucleoside triphosphates

Front 44

List the Similarities Between Replication and Transcription

Back 44

carried out by several enzymes including a POLYMERASE

produces a linear polymer of nucleotides connected by phosphodiester bonds.

synthesis is 5’ → 3’

Uses 4 distinct nucleotides: A, U, C, and G

Front 45

List the Differences Between Replication and Transcription

Back 45

Nucleotides used are ribonucleotides
Uracil instead of thymine

RNA is SINGLE STRANDED

Strands of RNA can self-pair

RNA itself can function as an enzyme

Front 46

RNA that is TRANSLATED into protein

Back 46

mRNA

Front 47

Describe mRNA

Back 47

RNA that is TRANSLATED into protein

Front 48

Describe rRNA

Back 48

makes up ribosomes, used for TRANSLATION

Front 49

RNA that makes up ribosomes, used for TRANSLATION:

Back 49

rRNA - Ribosomal RNA

Front 50

RNA that carries amino acids for TRANSLATION:

Back 50

tRNA - Transfer RNA

Front 51

RNA used for Splicing, transport etc.

Back 51

snRNA - Small nuclear RNA

Front 52

Describe tRNA

Back 52

RNA that carries amino acids for TRANSLATION:

Front 53

Describe snRNA

Back 53

RNA used for Splicing, transport etc.

Front 54

Each type of RNA is synthesized by a distinct RNA Polymerase: T/F

Back 54

T

Front 55

Each type of RNA is synthesized by:

Back 55

a distinct RNA polymerase

Front 56

How does the RNA polymerase know where to start and stop transcription of a gene?

Back 56

RNA polymerase binds weakly to the DNA strand and slides along it until it finds the promoter region which contains a sequence of nucleotides indicating the starting point for RNA synthesis. Once it reaches the terminator site it will stop and release both the DNA template and the newly made RNA chain.

Front 57

How does the RNA polymerase know in which direction to go?

Back 57

The promoter indicates the DIRECTION that transcription will proceed because the sequence is asymmetrical.

Front 58

Describe promoter

Back 58

Sequence of DNA that specifies where transcription will start

indicates the DIRECTION that transcription will proceed because the sequence is asymmetrical.

also supplies CONTROL to the process

Front 59

Describe terminator

Back 59

Sequence of DNA that specified where transcription will stop

Front 60

Why is direction of transcription important?

Back 60

During transcription, only ONE strand of DNA is copied.

Once bound to DNA, the polymerase could move either LEFT or RIGHT.

Only ONE direction will produce the correct RNA!

Front 61

Describe the transcription process in prokaryotes.

Back 61

RNA polymerase finds a DNA strand and binds weakly. It slides down the strand until it finds the promoter and it begins transcribing at the start site of the gene. After about 10 nucleotides the sigma factor comes out of RNA polymerase so that it can continue transcribing. When the RNA polymerase reaches the end of the gene, the terminator stop site, it breaks its bond with the DNA, releasing itself and the newly made RNA strand, then rebonds with the sigma factor.

Front 62

Genes can exist anywhere on the DNA strand and can run in opposite directions: T/F

Back 62

T

Front 63

Bacterial and eukaryotic organisms use essentially the same RNA polymerase for transcription: T/F

Back 63

T

Front 64

Bacterial and eukaryotic organisms use different enzymes for transcription: T/F

Back 64

F

Front 65

RNA polymerase and an associated SIGMA FACTOR (protein) slide along the DNA until association at the START SITE. This occurs in:

Back 65

prokaryotes

Front 66

Transcription in these require Appropriate DNA structure and a binding of specific proteins within the promoter and at other DNA sites.

Back 66

eukaryotes

Front 67

eukaryotic transcription requires:

Back 67

Appropriate DNA structure and a binding of specific proteins within the promoter and at other DNA sites.

Front 68

prokaryotic transcription requires:

Back 68

RNA polymerase and an associated SIGMA FACTOR (protein) slide along the DNA until association at the START SITE.

Front 69

Once a eukaryotic mRNA is synthesized in the nucleus it must be:

Back 69

processed

Front 70

Once a eukaryotic mRNA is synthesized in the nucleus it must be PROCESSED: T/F

Back 70

T

Front 71

These are types of processing a eukaryotic mRNA can undergo:

Back 71

Capping

Poly-adenylation

Splicing

Front 72

Describe Capping:

Back 72

Addition of a methyl guanine nucleotide to the 5’ end of the mRNA.

FOR: export from the nucleus and stability.

Front 73

Bacterial mRNAs can contain the instructions for several different proteins whereas eukaryotic mRNA nearly always contains the information for only a single protein: T/F

Back 73

T

Front 74

Bacterial mRNAs can contain the instructions for only a single protein whereas eukaryotic mRNA contains the information for several different proteins: T/F

Back 74

F

Front 75

Describe polyadenylation:

Back 75

Addition of adenine residues to the 3’ end of the mRNA: poly-A tail.

Usually a few hundred A’s.

FOR: export, stability, identification of the transcript as an mRNA.

Front 76

Prokaryotic mRNA must undergo processing before it can be used to translate proteins: T/F

Back 76

F

Front 77

Describe splicing:

Back 77

The REMOVAL of specific mRNA sequences (introns - the non-coding regions)

Carried out by specialized enzymes - small ribonucleoprotein particles (snRNPs) - that recognize “splice signals” in the mRNA sequence.

Front 78

These are marked by specific sequences that are recognized by splicing machinery.

Back 78

intron-exon junctions

Front 79

What is a spliceosome made up of?

Back 79

proteins and snRNAs

Front 80

Intron-exon junctions are marked by specific sequences that are recognized by splicing machinery: T/F

Back 80

T

Front 81

How do snRNAs recognize introns?

Back 81

through complementary base pairing

Front 82

What does the spliceosome do?

Back 82

Recognizes the splicing signals on a pre-mRNA molecule, brings the two ends of the intron together and provides the enzymatic activity for the two reactions necessary to complete the splicing (removal of the intron and joining of the two remaining exons)

Front 83

What is the significance of introns?

Back 83

make genetic recombination more likely

alternative splicing

Front 84

What is the relationship between exons and protein domains?

Back 84

Exons generally specify DOMAINS

Front 85

This can produce several different mRNAs from a single gene:

Back 85

splicing

Front 86

All exons will not be used to build the final mRNA: T/F

Back 86

T

Front 87

All exons will be used to build the final mRNA: T/F

Back 87

F

Front 88

This produces several different proteins from the same gene:

Back 88

splicing

Front 89

Splicing produces several different proteins from the same gene: T/F

Back 89

T

Front 90

Splicing produces one protein from each gene: T/F

Back 90

F

Front 91

Multiple transcripts can be produced simultaneously from a gene: T/F

Back 91

T

Front 92

One transcript at a time can be produced from a gene: T/F

Back 92

F

Front 93

Describe transcription:

Back 93

regions of the DNA (genes) are transcribed into ss RNA

Front 94

What is the genetic code?

Back 94

The rules specifying the correspondence between nucleotide triplets (codons) in DNA or RNA and amino acids in protein

Front 95

The sequence of nucleotides in an mRNA is read how?

Back 95

consecutively in groups of three

Front 96

Describe codon:

Back 96

Each triplet sequence that encodes an amino acid

Front 97

Describe anti-codon

Back 97

The sequence within the t-RNA that recognizes the CODON

Front 98

mRNA is read in this direction:

Back 98

5’→ 3’

Front 99

In translation this usually specifies the start of the reading frame:

Back 99

AUG

Front 100

Describe the open reading frame (ORF)

Back 100

The sequence of nucleotides that specify a specific protein

Each mRNA has the potential to be “read” in three distinct frames

Front 101

How does the translation machinery know where to start?

Back 101

Use a Specific Sequence To
Start All Proteins

AUG - methionine

Front 102

What components are needed
for translation?

Back 102

tRNA
amino acids
ribosome

Front 103

Describe tRNA

Back 103

~ 80 nucleotide RNA

contains an anticodon that base-pairs with mRNA
“charged” with a specific amino acid

a high energy bond between a.a. and tRNA!

Front 104

61 codons encode amino acids, but humans have only 48 different tRNAs. What makes this possible?

Back 104

tRNA's recognize more than 1 codon

‘wobble’ base-paring can occur in 3rd codon position

Front 105

What joins an amino acid to tRNA? How?

Back 105

Aminoacyl tRNA synthetase

covalently attaches an amino acid to a specific tRNA, by ATP hydrolysis.

The high energy bond between the amino acid and tRNA will drive protein synthesis!

Front 106

Where does the energy come from to power protein synthesis?

Back 106

The high energy bond between the amino acid and tRNA will drive protein synthesis!

Front 107

Describe ribosomes:

Back 107

provide the machinery that allows for protein synthesis

Large Subunit
3 rRNAs
49 proteins

Small Subunit
1 rRNA
33 proteins

Each subunit is constructed in the nucleus.

Front 108

What are the ribosome's tasks?

Back 108

Find RNA and know WHERE to start

Associate with tRNA 1
Associate with tRNA 2
Form peptide bond
Release the ‘uncharged’ tRNA

Cycle along, maintaining FRAME
Know where to stop
Do all this at 2 peptide bonds/sec!

Front 109

List the ribosomal binding sites:

Back 109

RNA binding site

3 tRNA binding sites:
A = amino acyl tRNA-binding
P = peptidyl tRNA-binding
E = exit

Front 110

How does the Ribosome know where to begin translation?

Back 110

Initiator tRNA - Special tRNA that Associates with AUG. Carries methionine.

Binds to small subunit along with other initiator proteins BEFORE it associates with RNA.

Front 111

Describe initiator tRNA:

Back 111

Special tRNA
Associates with AUG
Carries methionine

Front 112

Why is the place where the ribosome begins translation so critical?

Back 112

Specifies correct reading frame.

Last point at which the cell can decide to go through with translation.

Speed of initiation of translation determines speed of generation of protein.

Front 113

What is the difference between eukaryotic and prokaryotic translation? What does this mean?

Back 113

Eukaryotes: 1mRNA = 1 open reading frame. Therefore each mRNA species encodes for one protein.

Prokaryotes: 1mRNA = >1 open reading frame. Therefore each mRNA can encode for several proteins.

Front 114

How does the ribosome know when to stop?

Back 114

STOP CODONS:

UAA, UGA, UAG

A release factor binds in the A site and the whole complex will be released.

Front 115

Each mRNA will be translated by multiple ribosomes: T/F

Back 115

T

Front 116

Each mRNA will be translated by multiple ribosomes: Polyribosomes. This means that:

Back 116

1 mRNA will lead to the synthesis of many identical peptides.

Front 117

1 mRNA will lead to the synthesis of many identical peptides. This is because:

Back 117

Each mRNA will be translated by multiple ribosomes: Polyribosomes.

Front 118

How is translation controlled?

Back 118

Very complicated, but consider that every aspect is REGULATED at some level.

mRNA is broken down
Protein is broken down
Transcription is turned on and off

Front 119

This sequence of DNA is from the middle of a gene and was used as a template to make mRNA:

5’- T T A C G C G G A T A T C C C - 3’

1) What is the sequence of the mRNA?
2) What are the amino acid sequences coded?

Back 119

5’- G G G A U A U C C G C G U A A - 3’

GISA
GYPR
DIRV