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Flashcards in Section 7: Molecular Genetics Deck (140):
1

Describe the structure of DNA

Double helix with major and minor grooves

2

This carries the hereditary information of the cell

DNA

3

What is the DNA backbone made of?

5' to 3' phosphodiester bonds form a phosphate backbone

4

What are the nitrogen bases in DNA?

In RNA?

ATGC in DNA

AUGC in RNA

5

DNA replication begins at special sites in the middle of the DNA molecule (not the end) called

DNA strands separate to form __________ that expand in both directions

Thousands of them happen to speed up relication of 3 billion BP molecule in eukaryotic cells. How many origins of replication do prokaryotes have?

Origins of replication

Replication bubbles

One

6

In DNA replication, when is the second chromatid containing a copy of DNA assembled?

Interphase (S phase?)

7

During interphase, DNA is unzipped and each strand serves as a template for complementary replication

This is term means one strand of the two is old, the other is new, occurs in DNA replication of all known cells

Semi Conservative Replication

8

What is the enzyme that unwinds DNA?

It forms a Y shaped replication fork

Helicase

9

Single stranded binding proteins attach to each strand of uncoiled DNA to keep them separate

What break and join the double helix, allowing the prevention of knots?
(if you unwind a twist, the ends will get extra tight and knot up)

Topoisomerases

10

In what direction does DNA polymerase move?

Is the new strand parallel or antiparallel?

3'-->5'

Antiparallel (5'---->3')

11

On this strand, the DNA polymerase works continuously as more DNA unzips

In this strand (the 5'-->3' strand), the DNA polymerase has to go back to the replication fork and work away from it

What are the fragments that it produces called?

What connects these fragments?

Leading Strand

Lagging Strand

Okazaki Fragments

DNA ligase

12

In DNA replication, this is an enzyme that creates a small strip of RNA primer off which DNA polymerase can work since it can only add to an existing strand

Primase

13

What does DNA replication require at the start?

RNA primer

14

Every okazaki fragment has an RNA primer, these RNA strips are later replaced by...

DNA Polymerase 1

15

Other than replacing BPs from RNA primers, what else does DNA pol 1 do?

This polymerase is pure replication

DNA repair

DNA polymerase 3

16

DNA poly 1 and 3 have 3'-->5' _____, it breaks phosphodiester backbone on a single strand of DNA and removes a nucleotide. It can only remove from 3' end (in this case_ of the chain

Exonuclease

17

Which can also do proofreading, DNA poly 1 3, or both?

Which also has a 5'-->3' exonuclease to take off the primer

both

Pol 1

18

in sum:

DNA Pol ______ mainly replicates the DNA 5’ to 3’ but can also proofread via 3’ to 5’ exonuclease.

DNA Pol ______ primarily breaks down RNA primer via 5’ to 3’ exonuclease and replaces it with DNA (laid down between Okazaki fragments mainly) via 5’ to 3’ polymerase while proofreading as it goes, can proofread
via 3’ to 5’ exonuclease as well

DNA polymerase 3

DNA polymerase 1

19

In prokaryotes, what happens to the good strand if there is an error in replication, so it doesn't repair the wrong strand?

It is methylated

20

In all cases of repair, what must come seal the backbone afterward?

Ligase

21

Energy for elongation is provided by two additional ________ attached to each new nucleotide. Breaking the bonds
holding the two extra _________ provides chemical energy for the process (same w/ transcription!). Human rate 50n/s

Phosphates (both blanks)

22

A region of repetitive nucleotide sequences at each end of a chromatid, which protects the end of the chromosome from deterioration or from fusion with neighbouring chromosomes.

telomere

23

What two problems can occur in the replication of a telomere?

Not enough template strand where primase can attach

The last primase is removed

24

Do prokaryotes have telomeres?

No, circular DNA

25

enzyme that attaches to the end of template strand and extends the template strand by adding short sequence
of DNA over and over (not important code), allowing elongation of lagging strand to continue

For reference: https://www.youtube.com/watch?v=AJNoTmWsE0s

Telomerase

26

Telomerase carries an
RNA template: binds to flanking _____ end of telomere that compliments part of its RNA template, synthesizes to fill in over
the rest of its template

binds to 3' end

For reference: http://upload.wikimedia.org/wikipedia/commons
/3/3b/Working_principle_of_telomerase.png

27

In protein synthesis, one-gene-one-polypeptide hypothesis defines a _____ as the DNA segment that codes for a particular polypeptide.

Also, genetic code is universal for nearly all organisms and most AAs have more than one codon specifying them. This concept is called

gene

redundancy/degeneracy

28

This type of RNA is a Single stranded template. Since there are 64 possible ways (4x4x4) ways that four nucleotides can be arranged
in triplet combinations, there are 64 possible codons. 3 of them are stop codons. Therefore, only 61 codes for amino acids

mRNA

29

This type of RNA has a C-C-A-3' that attaches to an AA, and the other portion is the anticodon which base pairs with the codon in mRNA

tRNA

30

What part of tRNA base pairs with the codon of mRNA?

What fragment of tRNA attaches to an AA?

anticodon

C-C-A-3'

31

This is the term for the concept that the exact bp of the 3rd nucleotide in the anticodon and the 3rd nucleotide in the codon is often not required, allowing 45 different tRNA’s base-pair with 61 codons that code for amino acid. There is space for the 5' anticodon on tRNA to move or...

Wobble

32

This type of RNA transports an AA to its mRNA codon

tRNA

33

Together w/ proteins, this type of RNA forms ribosomes

How many binding sites do ribosomes have? What are they?

rRNA

3, one for mRNA, tRNA that carries a growing polypeptide chain (Psite) and one for 2nd tRNA that delivers the next aa (A site)

34

The nucleolus is an assemblage of DNA being actively transcribed into..

rRNA

35

What are the termination sequences on mRNA?

UAA, UGA, UAG

36

Where is the ribosome assembled?

Where is it exported?

The nucleolus

Cytoplasm (large and small subunits separately)

37

The is the creation of RNA molecules from a DNA template

Prokaryotes are MONOCISTRONIC/POLYCISTRONIC

Eukaryotes are MONOCISTRONIC/POLYCISTRONIC

Transcription

Prokaryotes POLYCISTRONIC (each mRNA can create multiple polypeptide chains)

Eukaryotes MONOCISTRONIC (each mRNA creates a single polypeptide chain)

38

In this phase of transcription, the RNA polymerase attaches to a promoter region on DNA and unzips the DNA into two strands

The promoter region often contains what sequence?

Initiation

TATA (TATA box)

39

The most common sequence of nucleotides at the promoter region is called the _____ sequence

Variations from it cause what?

Consensus

less tight RNA polymerase binding and a lower transcription rate

40

In this phase of transcription, RNA polymerase unzips DNA and assembles RNA nucleotides using one strand of DNA as template.

Elongation

only ONE strand is transcribed!

41

This phase of transcription occurs when RNA pol reaches a special sequence, often AAAAAAA in eukaryotes

Termination

42

In what direction of the DNA strand is transcription occurring?

3' to 5' (synthesized RNA is 5' to 3')

43

In mRNA processing, before leaving the nucleus, pre-mRNA undergoes several modifications

First this sequence is added to the 5' end of the mRNA. It's a guanine with three phosphate groups, also called ___, providing stability at the point of attachment for ribosomes

5' cap (-P-P-P-G-5')

GTP

44

In mRNA processing, before leaving the nucleus, pre-mRNA undergoes several modifications

After the 5' cap is added, this sequence is attached to the 3' end of the mRNA. It provides stability and control of movement across the nuclear envelope

How many AAs is it?

A poly-A tail (AAA...AAA-3')

200

45

What does the A poly A tail facilitate in prokaryotes?

Degradation

46

After the A poly A tail is attached to the 3' end of the mRNA, this occurs to remove nucleotide segments from mRNA, deleting introns and splicing exons

RNA splicing

47

During DNA splicing in mRNA processing, before the mRNA moves into the cytoplasm, what delete the introns and splice the exons?

Do prokaryotes have introns?

Small nuclear ribonucleoproteins (snRNPs) and splicosome

No

48

After RNA splicing in mRNA processing, this occurs, which allows different mRNA to be generated from the same RNA transcript by selectively removing differences of an RNA transcript into different combination, coding for a different product

Alternative Splicing

49

EUKARYOTES/PROKARYOTES generally have ready to go mRNA upon transcription

Only in EUKARYOTES/PROKARYOTES do you need mRNA processing

Prokaryotes have ready to go mRNA, translation can occur immediately

eukaryotes require proessing,

50

In which can multiple RNA polyermases transcribe the same template simultaneously, prokaryotes, eukaryotes, or both?

Both

51

This process is the assembly of AAs based on reading of new RNA

What is the energy source?

Translation

GTP

52

This is located in the cytoplasm for translation, the amino acid attaches to it at the 3' end requiring 1 ATP

Aminoacyl-tRNA

53

In this phase of translation, the small ribosome unit attaches to the 5' end of mRNA, the tRNA-methionine attaches to the start sequence of mRNA and the large ribosomal unit attaches to form a complete complex

What is the start sequence of mRNA

Initiation

AUG

54

During the initiation of translation, the small ribosomal subunit attaches to what end of mRNA?

The large ribosomal subunit binds...

For reference: http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter
15/translation_initiation.html

5'

The small subunit

55

During this step of translation, the 2nd tRNA binds to the A site for peptide bond formation. This 1st tRNA is released without methionine. The 2nd tRNA moves to the p site and the next tRNA comes into A site to repeat process

Elongation

56

The movement of tRNA from the A site to the P site during elongation during translation is referred to as

Translocation

57

During this step of translation, the complex encounters a stop codon (UAG, UAA, UGA). The polypeptide and two ribosomal units all release once the release factor breaks down the bond between tRNA and the final AA of the polypeptide.

Termination

58

While a polypeptide is being translated, AA sequences determine the folding conformation. Folding is assisted by

Chaperone Proteins

59

After translation, signal peptide at the beginning of the translated polypeptide may
direct the ribosome to attach to the ER, in which case the polypeptide is injected into the

If injected, the polypeptide may be secreted from the cell via

ER lumen

Golgi

60

In general, post translational modifications may occur with the addition of sugars, lipids, phosphate groups, etc. They may be subsequently processed by the ___ before it is functional

Golgi

61

Amino Acids are placed starting from the ____ end of the mRNA and move all the way down to the ____ end

tRNA codons for matching are ___ to _____

5' end, move all the way down to the 3' end

tRNA codons for matching 3' to 5'

62

Multiple ________ may simultaneously translate 1 mRNA

Ribosomes

63

In bacteria the start codon is _____ rather than methionine

n-formylmethionine

64

This is a mutation where the new coon still codes for the same AA

This is a mutation where there is no change in protein fxn

Silent mutation

Neutral mutation

65

his is a mutation where the new codon codes for a stop codon

Nonsense mutation

66

This is a mutation where a new codon codes for a new AA. Can be minor or fatal, like sickle cell (val substituted for glu)

Missense mutation

67

What are the three repair mechanisms?

Proofreading
Mismatch repair
Excision repair

68

Proofreading of DNA is conducted by _______ which checks base pairs

This type of DNA repair has enzymes repair things DNA polymerase missed

This type of repair has enzymes remove nucleotides damaged by mutagens

DNA polymerase

Mismatch repair

Excision Repair

69

This is DNA coiled around bundles of 8/9 histones like beads on a string

Nucleosome

70

When it's not division, chromatin exists as either of two types

This type is loosely bound to nucleosomes, actively being transcribed

This type is areas of tightly packed nucleosomes where DNA is inactive

Euchromatin

Heterochromatin

71

Heterochromatin has a lot of ____________, which are large tandem repeats of noncoding DNA

Satellite DNA

72

There are DNA segments that can move to new location on same/different chromosome

Transposons

73

This type of transposon consist of only one gene that codes for enzyme that just transports it (transposase)

These code for extra: replication, antibiotic resistance, etc.

Insertion of transposons into another region could cause...

Insertion Sequence

Complex transposons

mutation (little to no effect)

74

What are the 3 parts of a virus

Nucleic acid
Capsid
Envelope

75

In viruses, can the nucleic acid be DNA, RNA or either?

Can it be double stranded, single stranded, or either?

It can be one or the other

It can be one or the other

(remember big table in microbio?)

76

This is the protein coat that encloses the nucleic acid

What assemble and form the nucleic acid?

Capsid

Capsomeres

77

This part of the virus surrounds the capsid of some viruses, it encorporates phospholipid/protein obtained from cell membrane of host

Envelope

78

This is a virus that only attacks bacteria

Bacteriophage

79

Are viruses usually specific or nonspecific to type of cell and species?

Highly specific

80

This is the range of organisms that a virus can attack

Host range

81

In this type of viral replication, this occurs when the virus penetrates the cell membrane of the host and uses host machinery to produce nucleic acids and viral proteins that are then assembled to make new viruses

The viruses burst out of the cell and infect other cells

Lytic Cycle

82

In a DNA virus, DNA is replicated and forms new viral DNA which is transcribed to produce...

Viral proteins (they assemble to form new viruses)

83

For this type of virus, RNA serves as mRNA, it is translated into protein

RNA virus

84

These are viruses that use reverse transcriptase to make a DNA complement of their RNA, which can manufacture RNA or enter the lysogenic cycle

Retroviruses

85

In this type of viral replication, viral DNA is incorporated into the DNA of the host cell

When in this state, it remains inactive until external stimuli triggers it to enter the lytic cycle

What the virus called if it enters lysogenic cycle?

Lysogenic Cycle

Dormant State

Provirus or prophage (bacteria)

86

What are on the cell wall of bacterium that are used as recognition and binding sites by bacterial viruses? They also provide cell wall rigidity

What type of bacteria are they found on?

Techoic Acids

ONLY on gram positive

87

These are not viruses or cells. They are misfolded versions of proteins in brain that cause the normal proteins to misfold as well. They are fatal.

Prions

88

How do bacteria reproduce?

Binary fission

89

This type of replication has the chromosome replicating and the cell dividing into two cells, each with one chromosome

Do bacteria have a nucleus? Microtububles? Spindle? Centriole?

Binary Fission

Nope not needed for replication

90

These are short, circular DNA segments outside the chromosome. They carry genes that are beneficial but not necessary for survival

Plasmids

91

Do plasmids replicate with the host cell?

These are plasmid that can integrate into bacterial chromosome

No, they replicate independently

Episomes

92

This is a method of genetic variation among bacteria where one bacterial cell produces a bridge (pilus) and connects to a recipient bacteria. It sends chromosome/plasmid and recombination to occur

Conjugation

93

The conjugative plasmid, it is an episome that can integrate itself into the bacterial chromosome..

Once the recipient receives it, it is now ____ and can donate as well

This type of plasmid provide bacteria with antibiotic resistance

F Plasmid/F factor

F+

R plasmids

94

What can be used for cell adhesion in bacterial cells?

Pili

95

This method that produces genetic variation in bacteria introduces DNA into the genome by a virus via the lytic cycle.

When the virus infects another host, the bacterial DNA part that it delivers can recombine with resident DNA

Transduction

96

This method of genetic variation in bacteria where bacteria absorb DNA from surroundings and incorporate it into its genome

Transformation

97

In the regulation of prokaryotic gene expression, these control gene transcription

What do they consist of? 4 things

Operons


Promoter

Operator

Structural Genes

Regulatory Genes

98

This part of the operon (prokaryotic gene expression regulation) is a sequence of DNA where RNA polymerase attaches to begin transcription

Promoter

99

This part of the operon (in prokaryotic regulation of gene expression) is the region that can block action of RNA polymerase if occupied by a repressor protein

Operator

100

This part of the operon (prokaryotic regulation of gene expression) is DNA sequences that code for related enzymes

This part is located outside of the operon region, produces repressor produces and activator proteins which assist in the attachment of RNA polymerase to promoter region

Structural Genes

Regulatory Genes

101

In the regulation of prokaryotic gene expression, this is an operon that has a regulatory gene that controls the breakdown of lactose

The regulatory gene produce an active repessor called ______ and blocks RNA polymerase. When lactose is available, it binds the repressor and inactivates it, RNA polymerase can now transcribe.

So the operon is induced by

The enzymes that the operon produces are said to be...

Lac Operon (E. coli)

Bind operator

Lactose

Inducible enzymes

102

Lac operon consists of three lac genes, Z, Y and A which code for.....

B-galactosidase, lactose perease, and thiogalactoside thransectylase

103

In lac operons, low gluose means high what levels? It binds to CAP binding site of promoter so RNA polymerase more efficiently transcribes in high lactose levels

cAMP

104

This operon produces an enzyme for trp synthesis

Regulatory genes prouce and inactive repressor, RNA polymerase produces enzymes. When trp is available, you no longer need to synthesize it internally. It binds to the inactive repressor and inactivate it. It then binds the operator and blocks RNA polymerase

Trp is a _______

Trp operon

corepressor

105

When structural genes stop producing enzymes only in presence of active repressor, the enzymes are called

Repressible enzymes

106

Unlike some repressible enzymes, some genes are _____ (constantly expressed) either naturally or due to mutation

Constitutive

107

In the regulation of eukaryotic gene expression, these are repressors and activators, they influence RNA polymerase's attachment to the ____ region

Regulatory Proteins'

Promoter region

108

In the nucleosome packing in regulation of eukaryotic gene expression, this induces tighter packing prevent transcription

This uncoils the nuclesome and allows transcription to proceed

Methylation of histones (also used in X inactivation on DNA bases to repress DNA activity)

Acetylation of histones

109

These block mRNA transcriptions, translation, or degrade existing mRNA in eukaryotic gene expression

This is mRNA which folds back into itself. It gets chopped up then made single stranded. The relevant strand will bind to DNA (prevent transcription) or mRNA (signals destruction)

Short interfering RNAs (siRNA)

dsRNA (double stranded RNA)

110

What percent of the human genome does not code for a protein product?

97%

Noncoding DNA includes

regulatory sequences, introns,
repetitive sequences never transcribed, etc. Tandem repeats abnormally long stretches of back to back repetitive sequences
within an affected gene (e.g. Huntington’s).

111

Tandem repeats are abnormally large back to back repetitive sequences within an affected gene, and play a role in this disease when expanded past normal.

Huntington's Disease

112

This DNA contains DNA segments or genes from different sources. It can come from viral transduction, bacterial conjugation, transposons, or artificial technology

Recombinant DNA

113

Crossing over during the ____ phase of meiosis produces recombinant moleculesPro

Prophase

114

For recombinant DNA, technology uses ________ to cut up specific segments of DNA and leave it with a ____ end (unpaired)

Restriction endonucleases

Sticky End

115

These restriction enzymes are normally used by bacteria to protect against viral DNA

They protect their own DNA via...

EcoRI, BamHI

methylation

116

This is a vehicle used to transfer foreign genetic material to another cell

What is an example of a DNA molecule that can be a vector?

Vector

Plasmid

117

To introduce foreign DNA into a plasmid, the plasmid is treated with the same ________ so the same stick ends bind from the previously cleaved DNA molecule

What stabilizes the attachments?

Then the plasmid is introduced into bacterium by

Restriction enzyme

DNA ligase

Transformation

118

In order for bacterium to take up a modified plasmid (treated with restriction enzymes), it must be made competent with

After this process, bacteria can be grown to produce product. What can be used to filter out the ones that don't have recombinant DNA?

Electroporation or heat shock + CaCl2

Antibiotic resistance/screen method

119

This is a technique that uses agarose gel under an electric field for the separation of proteins based upon charge and size

DNA moves toward the anode or cathode?

Does shorter DNA move further or less than longer DNA?

Gel electrophoresis

DNA moves towards the positively charged anode (DNA is a negative molecule, ANIONS MOVE TOWARDS THE ANODE)

Further

120

Can electrophoresis be done on proteins?

Yes. they have negative charges and positive charges to separate them based upon charge.

121

These can be identified between individuals, it is often used in paternity suits or to identify crime suspects as it's a result of Mendelian genetics

Restriction Fragment Length Polymorphism

(restriction fragments are compared and differ in length because of polymorphism)

122

This is used at crime scenes to compare the RLPs of suspects

DNA fingerprinting

123

This is a repeat of 2-5 nucleotides that differ between all individuals except identical twins

STR (short tandem repeat)

124

this enzyme makes DNA molecule directly from mRNA

DNA obtained in this manner is complementary DNA which lacks ______ that supresses transcription

Reverse Transcriptase

Introns

125

This technique uses synthetic primer (the primer may be RNA or DNA oligonucleotides) to clone DNA (rapidly amplify). Taq polymerase (heat stable) + nucleotides + primers + salts (buffer) necessary.

PCR

126

What are the 3 steps of PCR

1. Denaturation (>90degreesC)
2. Add primers + Anneal
3. Elongation (taq polymerase)

127

This is a technique used to ID target fragments on known DNA sequences in a large population of DNA. Electrophoresis is first, then the DNA fragments are transferred to nitrocellulose membrane, then a probe is added which will hybridize and mark it

Southern Blotting

128

This is a technique that is the same as Southern blotting but is used for RNA fragments

Northern blotting

129

This is similar to Southern blotting but for proteins. Electrophoresis, blot to membrane, primary antibody specific to protein added to bind to
that protein, then secondary anti-body-enzyme conjugate will bind to primary and mark it w/ enzyme for visualization

Western Blotting

130

Note: an easy way to identify all of the blotting methods is to use the phrase SNOW DROP. Match the letters in their order for each word, skipping O in both words

SNOW
DROP

131

The genome of humans differs roughly one of every _____ nucleotides

These differences are called

Nucleotide polymorphisms (SNPs)

132

Plasmids are circular DOUBLE/SINGLE stranded DNA

They have ______ sites for restriction enzymes.

If these sites are cut, what is the shape of the DNA?

Double stranded DNA

Restriction sites

linear

133

Do plasmids get reproduced during cell division?

It depends! They can or they cannot.

134

Do bacteria readily take up plasmids?

No, that's why there's antibiotic resistance screening to clone the one's that actually did take it up.

135

If you're making a prokaryotic gene product in a mammalian cell, what do you need to add for the mRNA to survive

If making a eukaryotic gene product in a prokaryotic cell, what do you need to make sure to not have?

PolyA tail (look it up)

Introns

136

This is the term for complementary bases annealing

Hybridization

137

If you want to test for a specific gene sequence in someone's DNA, this is the first method in the notes, testing for a single gene only.

take drop of blood, cut up DNA, use PCR
method w/ specific primer for that region. If that gene is there  lots of copies. Gene not there ---> no copies.

138

This is a second method of testing for a specific gene in someone'es DNA, and can test for many things at the same time.

take drop of blood, PCR it to amplify. We have a solid support w/ pieces of ssDNA w/ specific sequence covalently attached --> will hybridize to anything complementary (e.g. disease genes). On that same solid support we can put sSDNA pieces specific for other genes, can do this hundreds of times at different spots on this DNA microarray. Take desired amplified DNA, heat it to denature, add to DNA microarray, any DNA that hybridizes is a match. The amplified DNA we added is already fluorescently tagged --> hybridization wash to get rid of weakly bound sequences (e.g. not a complete match) -->add a dye that will show heavily if something has bound to our microarray. Can also do this starting w/ mRNA -->reverse transcriptase -->PCR amplify -->etc.

139

What can cleave the phosphodiester backbone to chunk out NTs in DNA?

What cut out just the NTs?

endonucleases

Exonucleases

140

This term means that a cell can give rise to any and all human cells, and even an entire functional organism

This term means a cell can give rise to a limited range of cells within a tissue type

Totipotent

Multipotent