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genetics exam 3 (SI notes)

front 1

What did Rosalind Franklin do?

back 1

She used X-Ray diffraction to see crystal structure of DNA

front 2

What did Watson and Crick do?

back 2

They figured out the Double Helix Structure of DNA

front 3

What di Erwin Chargaff find?

back 3

found that A and T pair and G and C pair

front 4

What did Meselson and Stahl discover?

back 4

That DNA replicates Semiconservatively. They also found out that it was NOT conservative or dispersive

front 5

What did Frederick Griffith discover?

back 5

that there is a “Transforming Factor” responsible for heredity

front 6

What did Avery and MacLeod suggest?

back 6

That DNA was the transforming factor in hereditary material

front 7

What kind of expirement did Avery hold?

back 7

Recreated Griffith experiments but destroyed (1 at a time) proteins, lipids, RNA, and DNA

front 8

Hershey and Chase proved what?

back 8

That DNA is hereditary material and is found in viruses too

front 9

How did Hershey and Chase prove their theory?

back 9

They tagged the Sulfur of a bacteriophage (proteins) and the phosphorus (DNA). Thus phage infected a cell, and all new viruses created had that P tag. NOT the S one.Proving finally that DNA was the genetic material

front 10

What does semiconservatively mean?

back 10

only one strand of new DNA comes directly from parent molecule

front 11

How did Meselsohn Stahl rule out conservative replication?

back 11

He labeled both strands of DNA and let it replicate. Through this they discovered that there was one strand of parent DNA in each new molecule

front 12

How did Meselsohn Stahl rule out dispersive replication?

back 12

By replicating the 2 molecules again and again found there were just the two original strands, and 6 new strands

front 13

What did the fred griffith experiments discover?

back 13

There was a Transforming Principle responsible for heredity

front 14

What were the 3 results from the free griffith experiment?

back 14

SIII virus kills mice, RII lets mice live, SIII heat killed lets mice live.

This means that some transforming principle passed from the shocked SIII to the RII

front 15

Why does the transforming principle happen a lot in bacteria?

back 15

Because DNA is super stable so is hard to get rid of, so in
bacteria if it can jump to a cell with working organelles, it will, and then will become a part of that cell

front 16

DNA runs in what direction?

back 16

It runs in 2 antiparallel strands. (5'-3')

front 17

How are the DNA strands held together?

back 17

By hydrogen bonds between A-T and G-C

front 18

A-T have how many bonds?

back 18

2

front 19

G-C have how many bonds?

back 19

3

front 20

The DNA backbone is held together

back 20

phosphodiester bonds

front 21

DNA is found in what form?

back 21

The B form naturally in living organisms

front 22

Base Stacking leads to what?

back 22

the turns in the DNA double helix which forms major and minor grooves

front 23

In Eukaryotes DNA Replication is what?

back 23

Bidirectional and proceeds from multiple replication origins

front 24

In bacteria DNA replication is what?

back 24

bidirectional but has ONE replication origin

front 25

Consensus Sequences are what?

back 25

Unique in prokaryotes and eukaryotes, conserved across species, and essentially tell DNA polymerase where to bind and start replication

front 26

What does the helicase enzyme do?

back 26

It breaks DNA hydrogen bonds and unwinds DNA

front 27

These unwound strands are stabilized by what?

back 27

SSBs

front 28

DNA polymerase is the enzyme that does what?

back 28

Extends DNA strands to replicate DNA

front 29

DNA polymerase requires what?

back 29

RNA Primer made by primase

front 30

On bacteria DNA polymerase III is the what?

back 30

main replication enzyme

front 31

In replication, the 5-3 new strand will always be elongated...

back 31

continuously and it makes the leading strand

front 32

The 3-5 strand is elongated in short sections called

back 32

Okazaki fragments

front 33

Okazaki fragments are later joined together by what?

back 33

ligase

front 34

What does DNA polymerase I do?

back 34

its 5-3 exonuclease activity to remove the primer and then its 5-3 polymerase activity to elongate the gaps in the strand

front 35

DNA is heavily coiled, so what enzyme helps alleviate the tension during replication?

back 35

topisomerase

front 36

Telomeres serve as what?

back 36

caps at the end of linear chromosomes. They help to combat the shortening of chromosomes in each replication
cycle

front 37

Telomeres are fomred by what?

back 37

They are formed by T loops and protected by the protein sheltrin

front 38

What are the 4 nucleotides of RNA?

back 38

adenine, uracil, cytosine, and guanine (no T)

front 39

Is RNA double-stranded or single-stranded?

back 39

single stranded (so it is way less stable)

front 40

RNA includes ribose sugar, what does this mean?

back 40

It includes an extra OH on the 2’ carbon

front 41

What does Messenger RNA (mRNA) do?

back 41

made by protein coding genes and is intermediate between
DNA and proteins

front 42

What does Ribosomal RNA (rRNA)?

back 42

NOT from protein coding genes...works with proteins to form ribosomes

front 43

What does Transfer RNA (tRNA) do?

back 43

NOT from protein coding genes...binds to amino acid to add it into growing protein chain

front 44

Telomerase RNA does what?

back 44

provides template for synthesizing telomeres

front 45

Small Nuclear RNA (snRNA) play a role in what?

back 45

In mRNA processing and splicing out introns

front 46

What does Micro RNA (miRNA) do?

back 46

pairs with mRNA to alter stability

front 47

Small Interfering RNA (siRNA) is cut from what?

back 47

double stranded RNA to also alter mRNA stability

front 48

The template Strand is what?

back 48

the strand of DNA that RNA polymerase binds to and assembles a complementary strand of nucleotides to

front 49

The other strand of DNA is called what?

back 49

coding strand. It is where the actual genes being transcribed

front 50

True or false. The Promotor Region is immediately upstream of transcription start site (more to the 5’ end)

back 50

true

front 51

RNA Polymerase is ninds to what?

back 51

The promoter region

front 52

What does the Transcription Region contain?

back 52

sequences to help stop transcription (close to 3’ end)

front 53

Describe the process of transcription? (for prokaryotes)

back 53

The sigma subunit actually identifies the promotor region and allows RNA Polymerase to bind. The RNA Polymerase holoenzyme complex then unwinds the DNA to form an open promotor complex. After 8-10 nucleotides have been transcribed, the sigma subunit then
dissociates from the complex

front 54

What does DNA do in transcription? (for prokaryotes)

back 54

the DNA continues to unwind in front of RNA Polymerase and reforms the double helix behind it

front 55

What happens in transcription termination? (for prokaryotes)

back 55

1. Intrinsic Termination happens in most prokaryotes

2. Rho-Dependent Termination needs the protein rho

front 56

What is intrinsic termination?

back 56

The termination sequence is a bunch of inverted repeats, followed by a tail of Adenines.

ex: GGGGGGCCCCAAAAAAAAA

front 57

What does the rho protein do?

back 57

Rho moves up the mRNA, forces it to form a loop, detaching it from the DNA and kicking RNA Polymerase off

front 58

In eukaryotic transcription RNA Polymerase I transcribes what?

back 58

rRNA

front 59

In eukaryotic transcription RNA Polymerase II transcribes what?

back 59

mRNA, miRNA, siRNA and snRNA

front 60

In eukaryotic transcription RNA Polymerase III transcribes what?

back 60

tRNA, miRNA, siRNA one snRNA, and one rRNA

front 61

Enhancer sequences can bind what?

back 61

proteins around the promotor to enhance the level of
transcription...i.e. gene expression

front 62

Silencer sequences bind proteins to bend what?

back 62

DNA so it can’t be transcribed as easily...decreases gene expression

front 63

What are some of the post-transcriptional modifications for eukaryotes?

back 63

1. Capping 5’ mRNA (Guanylyl transferase adds a special Guanine nucleotide to the 5’ end of the mRNA to
serve as a cap)

2. 3’ Poly-A tail (A polyadenylation sequence is at the 3’ end of the mRNA . The mRNA is cleaved after this sequence and then PAP and CPSF then add up to 200 As.)

front 64

How does capping 5' mRNA help transcription?

back 64

This protects the mRNA molecule from rapid degradation and helps with later translation

front 65

How does a 3' poly-a tail help transcription?

back 65

This protects mRNA from degradation and helps with translation

front 66

What is intron splicing in eukaryotes?

back 66

Eukaryotic mRNA is unique in that intronic (non-coding) regions and spliced (cut) out of final transcript. This is important in correct protein formation

front 67

Describe intron splicing in eukaryotes?

back 67

In splicing, you have a 5’ splice site, 3’ splice site, and a branch
point. Introns are removed by an snRNA - protein complex called a spliceosome. The 5’ end is cut first, then 3’ end. They are then ligated together to form a lariat intron structure

front 68

How do we produce alternating proteins?

back 68

1. Alternative Intron Splicing

2. Alternative Processing

3. Alternative Polyadenylation

4. RNA Editing and processing

front 69

How many amino acids are there?

back 69

20 with unique chemical properties

front 70

What is the r group of amino acids?

back 70

They are distinct and give these amino acids their unique
properties

front 71

The ribosome catalyzes the formation of what?

back 71

a peptide bond between amino acids which forms a growing polypepetide chain

front 72

What is a codon and what does it code for?

back 72

A group of 3 nucleotides on an mRNA strand and they code for one amino acid

front 73

What are the start and stop codons of translation?

back 73

start codon: 5’ AUG (always)

end codon: UGA, UAG, UAA 3’

front 74

The starting codon AUG codes for what amino acid?

back 74

methionine (met)

front 75

What is before or after the start and end codons?

back 75

small Untranslated regions (UTRs) on the 5’ and 3’

front 76

What are ribosomes?

back 76

a combination of rRNA and proteins found in ALL living organisms

front 77

What doe ribosomes do?

back 77

They bind mRNA, facilitate pairing of correct tRNAs carrying amino acids to catalyze the formation of peptide bonds to
create proteins

front 78

Each ribosome has how many sites?

back 78

3 (A, P, E)

front 79

What is the A site?

back 79

where tRNAs carrying amino acids first bind to the ribosome (NOT THE FIRST ONE THOUGH)

front 80

What is the P site?

back 80

where the ribosome transfers amino acids into the polypeptide chain

front 81

What is the E site?

back 81

where the tRNA will leave the ribosome after dropping off its amino acid

front 82

Eukaryotic ribosomes have __ and ___ subunits to create a ___ ribosome

back 82

40s and 60s to create 80s

front 83

Prokaryotic ribosomes have ___ and ___ subunits to create a __ ribosome

back 83

30s and 50s to create 70s

front 84

What provides the energy for translation?

back 84

GTP

front 85

What are initiation factors (IF)?

back 85

proteins that facilitate mRNA and ribosome binding

front 86

What are elongation factors (EF)?

back 86

They use GTP hydrolysis to help create growing protein chains

front 87

What are charged tRNAs?

back 87

tRNA molecules WITH an amino acid attached to them

front 88

What are release factors?

back 88

They bind to the codon in the A site after the stop codon has been reached (basically end translation)

front 89

What sequence is in the 5’UTR? ( for prokaryotes)

back 89

a Shine-Dalgarno sequence found in all prokaryotic mRNAs

front 90

In prokaryotes the first amino acid ONLY is what?

back 90

N-formylmethionine (fMET) instead of normal methionine

front 91

The tRNA carrying the fMET amino acid will first bind to what site?

back 91

the p site (all other tRNAs will first bind to the A site)

front 92

For eukaryotes, the small ribosomal subunit (40s here) binds to what consensus sequence?

back 92

the Kozak Sequence. (everything else is similar to prokaryotes)

front 93

How is a tRNA charged?

back 93

aminoacyl-tRNA synthetase binds the correct amino acid to the tRNA with the correct anticodon (this uses ATP)

front 94

How does termination occur?

back 94

The correct tRNA will have a complementary sequence to the correct codon in its anticodon stem. Once one of the three stop codons binds in the A site, a Release Factor (RF) will bind in the A site as well

front 95

How many different codons are for the 20 amino acids.

back 95

64 including the 3 stop codons

front 96

Our amino acid code is degenerate which means?

back 96

more than one codon can code for an amino acid ( but there are 3 exceptions - methionine and tryptophan)

front 97

What are the 2 synonymous codons?

back 97

methionine and tryptophan (helpful in protecting against mutations)

front 98

What is the Wobble Effect?

back 98

the third nucleotide in a codon is least important, and has the
flexibility to mutate and still bind the original amino acid

front 99

true or false. In prokaryotes, the f-MET amino acid is always removed

back 99

true

front 100

it is hypothesized that the first 15-20 amino acids act as what?

back 100

signal sequences to lead the new protein chain to other organelles for processing or packaging

front 101

Fraenkel-Conrat proved that there were no overlapping codes by...

back 101

by showing that a single nucleotide substitution only affected one amino acid

front 102

How do you read 3 base pairs at a time and what can it lead to?

back 102

by looking at the reading frame and it can cause frameshift mutations

front 103

What are somatic mutations?

back 103

Mutations that occur in somatic, body cells and they can NOT be passed down

front 104

What are germline mutations?

back 104

mutations that occur in egg/sperm cells and these CAN be passed on

front 105

Point mutations occur where?

back 105

only one specific place in the DNA (ex: one base pair was deleted)

front 106

Substitution Mutations occur when what happens?

back 106

when you swap one nucleotide for another

front 107

Transitions occur when...

back 107

a purine switches with a purine (or pyrimidine for pyrimidine)

front 108

Transversions occur when...

back 108

a purine and pyrimidine switch places

front 109

Frameshift Mutations occur when...

back 109

when you insert or delete nucleotides NOT in a multiple of 3 (they change the reading frame of the DNA sequence and can leave it nonfunctional)

front 110

What are the types of substitution mutations?

back 110

silent, missense, and nonsense

front 111

What is a silent mutation?

back 111

A nucleotide is substituted, but the amino acid does NOT change (Ex: UUU and UUC both code for Phe)

front 112

What is a missense mutation?

back 112

A nucleotide is substituted, and the amino acid DOES change
(Ex: UUU codes for Phe but UUA codes for Leu)

front 113

What is a nonsense mutation?

back 113

A nucleotide is substituted and creates a premature stop codon (Ex: UAU codes for Tyr and UAG is a stop codon)

front 114

Regulatory mutations do what?

back 114

alter the expression of the protein product but have no affect on the protein coding DNA sequence

front 115

What are promoter mutations?

back 115

any types of mutations that occur in the consensus sequences in the promotor region. They mainly affect RNA polymerase

front 116

RNA polymerase activity correlates to what?

back 116

the amount of protein produced

front 117

What are splicing mutations?

back 117

They occur in the specific splice sites of introns and they can actually change the protein produced

front 118

Cryptic Splice Site Mutations will create what?

back 118

new splice sites in mRNA, additionally changing the
protein produced (they can accidentally skip some exons)

front 119

What does forward mutations mean?

back 119

Going from wild type to mutant allele

front 120

True Reversion occurs when?

back 120

a codon receives a second mutation that restores the original amino acid

front 121

Intragenic Reversions are what?

back 121

reversions occurring somewhere else in the gene

(a frameshift fixing another frameshift mutation)

front 122

Second-Site Reversions occur where? (also known as suppressor mutants)

back 122

in a DIFFERENT gene that compensates for the original mutation

front 123

true or false. Most mutations in the genome are spontaneous and occur from errors in DNA replication or proofreading

back 123

true

front 124

What is depurination?

back 124

breaks the nucleotide from the backbone, if unprepared is replaced by an A

front 125

What is deamination?

back 125

occurs when an amino group is lost from a nucleotide