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Flashcards in Midterm 1- Lec 1-5 Deck (134):
1

What are the three stages of replication

Initiation, Elongation and termination

2

What is the initiation stage of replication

At origins recognized by initiator protein; recruits DNA helicase

3

What is the elongation stage of replication

Beginning with RNA primer, polymerase synthesizes in 5'-3' direction, causing leading and landing strand

4

What is the termination stage of replication

At the ter site in bacteria, or when two forks meet, or when end of linear chromosome is reached

5

How many origins are in prokaryotes?

Only one

6

How many origins are in eukaryotes

Thousands, because there is much more genetic material

7

What is transcription

Produces a copy of DNA coding strand using ribonucleotides (RNA)

8

What is replication

Semi-conservative production of DNA

9

What is the initiation stage of transcription

RNA polymerase binds to promoter and separates DNA strands; synthesizes first few bases before leaving promoter region

10

What is the elongation stage of transcription

maintains transcription bubble of unwound ssDNA

11

What is the termination stage of transcription

RNA polymerase encounters a terminator and stops

12

What is translation

Polypeptide chain synthesis according to RNA instructions

13

What are the four stages of translation

Initiation, Elongation, termination and ribosome recycling

14

How is replication regulated in prokaryotes

regulated by initiation factor DnaA in ATP- bound state, and availibility of ori state

15

How is replication regulated in eukaryotes

it is linked to the cell cycle which helps regulate it

16

How is transcription regualted

mostly in initiation stage, RNA folding into structured regions can inhibit or promote transcription

17

How is translation regulated

Down regulated by amino acid starvation

18

What are some specific requirements of all cells

-establish and maintain a barrier (membrane)
-store and utilize genomic information (transcription and translation)
-replicate and pass information
-source of energy (ATP)

19

What direction does DNA lie?

5' -> 3', "head to toe"

20

What are the three components of a nucleotide

a phosphate, a sugar and a base

21

DNA is packaged into linear or circular units called _________

chromosomes

22

In eukaryotes, DNA is wrapped around packing proteins called ______

histones

23

What is the difference between DNA and RNA

DNA lack an oxygen atom (deoxy-)

24

What is the role of mRNA

encode information to produce a protein

25

T or F: The length of the cell cycle varies depending on the organism

T

26

T or F: different cell types are all regulated the same

F

27

What step prevents cell cycle progression if problems are present

"quality control"

28

What do tumor cells lack that normal cells have

growth controls and regulatory mechanisms (checkpoints)

29

what are oncogenes and name an example

can promote tumor growth, the "gas" that makes the car go faster. ex. EGF (epidermal growth factor

30

What are tumor suppressors

normally halt the cell cycle but fail to do so in cancer, the "brakes" that stop the car, ex. p53

31

What are alkylating drugs

indicate a drugs action: inhibit DNA synthesis

32

What are antimetabolites

Indicate drugs action: act as substitute form normal metabolic products, and inhibit essential reactions

33

What is aminopterin

An antimetabolite that binds in active site of dihydrofolate reductase and blocks the active site of the enzyme. Used in 1947 for children with leukemia (then fatal)

34

What is the mutation that causes breast cancer?

BRCA1, a tumor supressor

35

What are the key regulatory points in the bacterial cell cycle

Initiation of DNA replication and cell division

36

What indicates the start and finish sites in translation

distinct sequences in mRNA

37

what is the role of tRNA in translation

the 'adaptor' between codon and amino acid

38

T or F: expressing human genes in bacteria can help us produce large quantities of purified protein

T; ex. insulin production

39

What are missense mutations

alter the encoded amino acid

40

What are nonsense mutations

introduce a premature stop codon

41

What are silent mutations

do not change the amino acid sequence

42

What are frameshift mutations

an insertion or deletion of a nucleotide shifts the reading frame

43

If a mutation in a single gene causes a disease, this is called ________

monogenic

44

If a mutation results from changes in several genes, it is called ________

polygenic

45

What is penetrance

the percentage of people with the mutation that will develop the disease

46

T or F: Mitochondria and chloroplasts have their own genomes

T

47

What is forward genetics

mutant phenotype is observed, THEN the gene causing phenotype is discovered

48

What is reverse genetics

known gene of interest is deliberately mutated, then phenotype observed

49

What does the term 'ploidy' mean?

the number of copies of its genome that the organism has

50

In nucleotides, nitrogenous base is joined to sugar by _______ ______

glycosidic bond

51

What is the difference between a nucleotide and a nucleoside

Nucleoside lacks a phosphate group

52

What are the purines and the pyridimines

Purines- Adenine and Gualnine
Pyrimidines- Cytoisne, Thymine and Uracil

53

What is a tautomer

molecule in which a proton migrated to a different place

54

How are nucleotides attached

Phosphodiester bond between 3' hydroxyl and the phosphate on the 5' P

55

What are the Watson-Crick bas pairs

A with T
G with C

56

How is DNA stabilized

stablilized by Van der Waals interactions

57

What is the most common type of DNA

B-DNA

58

What is A-DNA and Z-DNA

A-DNA is a right handed helix and Z-DNA is an unusually left handed helix

59

is B-DNA right or left handed

left handed

60

What is supercoiled DNA

DNA under tension and twists in on itself

61

How does supercoiled DNA occur

Circular molecule is cut and held while the other end is twisted, changes the number of bases per turn

62

What is the difference between left and right hand supercoiling

Left handed- positive supercoiling = overwinding
Right haded- negative supercoiling = underwinding

63

What does the Twist (Tw) represent?

The number of turns in a DNA fragment

64

What does the Writhe (Wr) represent

supercoiling of closed circular or constrained linear DNA

65

What does the Linkage Number (Lk) represent?

The number of times one strand wraps around the other

66

What is the supercoiling equation

Lk = Tw + Wr

67

What do topoisomerases do

add or remove supercoiled from DNA, requires energy

68

What is DNA Electrophesis

Samples are loaded into wells of an agarose or acrylamide gel and subjected to an electric field, causing the negatively charged nucleic acids to move toward the positive electrode.

69

T or F: Supercoiled DNA runs faster than linear DNA

T

70

What are the three steps in purifying genomic DNA

1. Lyse the cells and solubilize the DNA
2. remove contaminants (RNA, protein)
3. precipitate the DNA in wash

71

What are the two ways in which DNA is used as a template?

Used in replication, only dNTPs used
Used in transcription, only NTPs used

72

T or F: RNA can base pair with DNA

T

73

What happens to non-coding RNAs

Fold in on themselves and usually fold back on themselves and fold into a hairpin structure

74

how do non-coding RNAs fold

Three of the double-helices are formed by hairpins and one is formed from distant complementary regions

75

T or F: RNA often has some non-Watson-crick pairs

T

76

when do RNA tertiary structures form

formed when short double stranded helices interact with each other and with single stranded regions

77

how does chromosome shape vary in prokaryotes vs eukaryotes

in eukaryotes chromosomes are linear whereas in prokaryotes they are circular

78

Cells must copy ___ and separate the ________ before they can divide

DNA, chromosomes

79

What counteracts the negative charges on the DNA backbone?

small positively charged histones

80

What are the four core types of Histones

H2A, H2B, H3 and H4

81

what are the steps in eukaryotic DNA packaging

2 H3-H4 dimers associate with the DNA, Two H2A and H2B dimers associate to form an octamer.
DNA is wound around the histone in a left handed direction

82

What are histone tails

Interact with other nucleosomes to help compact DNA

83

What histone is needed in order to pack chromatin

histone H1

84

What is the difference between euchromatin and heterochromatin

Euchromatin is decondensed and stains light
Heterochromatin is more compact and stains dark

85

what regions are high in heretrochromatin

regions with highly repetitive DNA sequences, including telomeres and centromeres

86

What the four types of histone modification

Acetylation, methylation, phosphorylation and ubiquitination

87

what is acetylation

Lys residues
promotes an open euchromatic state, and is associated with active transcription

88

what is methylation

uses lys or arg residues, activity depends on lovation, monomethylation activates

89

T or F: Chromatin packing creates a barrier to proteins that need to access DNA

T

90

T or F: replication and transcription can occur when chromatin is packed

F

91

what is the role of the centromere

necessary for correct chromosome segregation during cell division

92

centromeres bind specific proteins to form a structure called a ________

kinetochore

93

what is the diference between a point centromere and a regional centromere

point centromeres- small and have defined sequences
regional centromeres- have hundreds of kilobases

94

T or F: all organsims have a defined centromere

F; some have no defined centromere

95

What is CENP-A in humans

Defined regions where nucleosomes have a histone H3 variant; crucial for centromere function

96

What is a telomere made up of

repeats one C-rich strand and one G-rich strand

97

In organisms with long telomeres, the ssDNA overhange be be processed into a _-____

t-loop

98

T or F: DNA polymerase can copy the ends of a DNA molecule

F

99

What is telomerase

Special DNA polymerase that has a protein and RNA component, active in stem and germline cells

100

What are telomeres

Bind proteins that protect the ends and help maintain the lenght

101

What are the three classes of telomere binding proteins

-End-binding proteins
-ds binding proteins
-Proteins that associate with the DNA binding proteins

102

What is non-chromosomad DNA in prokaryotes

plasmids- small circular DNA molecules

103

What are viruses

infectious agents that carry genetic information as small DNA or RNA chromosomes

104

DNA is converted to RNA in a process called

transcription

105

The DNA double helix is stabilized by weak hydrogen bonds between:

A and T bases and G and C bases

106

a fruit fly mutant with white eyes is observed. We sequence the genome to find the gene is mutated. What kind of study is this

Forward genetics

107

T or F: Bacterial chromosomes use different packaging proteins than eukaryotes do

T

108

T or F: Protein binding to DNA alters supercoiling

T

109

is there any non-chromosomal DNA commonly present in cells?

yes, in all domains of life

110

In which phase of replication does DNA ligase participate?

Termination

111

In which phase of replication does primase participate

Initiation

112

Which type of DNA polymerase would be best for replicating genomic DNA

Processive

113

Which end does DNA polymerase add nucleotides to

The 3' end

114

How do bacteria avoid the 'end replication' problem?

Their genome doesnt have ends

115

How are nucleosomes replaced on newly-replicated dsDNA?

Asfl/Cafl interact wtih the sliding clamp to direct histones H3 and H4 into place

116

Which option groups only bacterial replication proteins and genes?

DnaA, datA, oriC

117

T or F: DnaA can bind to ori or to datA sequences in the genome

T

118

At which stage of PCR are deoxynucleoside triphosphates incorporated into nucleic acids?

Extension

119

Which of the following would be used by bacterial RNA polymerase?

Sigma factor

120

Which is a characteristic of some eukaryotic promoters?

TATA box

121

In which groups are mRNA processing and chromatin remodelling observed (bacteria or eukaryotes)

Eukaryotes

122

What are intrinstic terminators

They encode a hairpin and have a poly-A sequence

123

In replication, elongation is when polymerase adds dNTP to 5' end (T or F)

F, adds dNTP to 3' end!

124

How is the nucleus of a eukaryotic cell similar to the nucleoid of a prokaryotic cell?

They both contain condensed DNA associated with binding proteins

125

Imagine that a mutant human cell has a deletion of the gene encoding CENPA. This cell proceeds through the cycle to the M stage. What do you expect to happen?

The sister chromatids will not separate during anaphase

126

When you mutate the gene and then test the amount of drug required to kill the wild type, what kind of genetics is this?

reverse genetics

127

Normally, this protein encourages progression through the cell cycle in an appropriate manner. Mutant versions of this gene promote increased cell proliferation and are a major risk factor for cancer. What kind of gene is this?

Oncogene

128

What occurs during the B period of the bacterial cell cycle?

Increase in mass and size

129

T or F: Histone tails can be chemically modified to regulate chromatin packing

T

130

The codons CUA and CCC are rare in E. coli. If you were trying to overexpress a bacterial gene with many of these codons, what would you expect?

translation problems

131

How does the acetylation of histone tails affect chromosome packing?

It promotes open, euchromatic DNA that is available for transcription

132

For a particular plasmid, the linking number is 340. If the twist is 420, what can you conclude?

The plasmid would be negatively supercoiled

133

At which point(s) can the expression level of a particular protein be regulated?

At multiple levels, replication, transcription and translation

134

T or F: negative supercoiling makes strand separation easier, thus allowing replication and transcription machinery access

T