Microbial Genetics: Chapter 10

Front 1

What is a Genome?

Back 1

All the DNA present in a cell

Front 2

Genotype

Back 2

genes that are not visibly expressed or observed

Front 3

Phenotype

Back 3

genes that are observable

Front 4

What does the Central Dogma consist of?

Back 4

1. DNA Replication

2. Transcription

3. Translation

Front 5

What is Transcription?

Back 5

the production of mRNA from genes of DNA. A template DNA strand is used to produce a complimentary RNA strand

Front 6

What is Translation?

Back 6

the production of proteins from mRNA

Front 7

Differences in DNA and RNA strand numbers?

Back 7

DNA: double stranded

RNA: single stranded

Front 8

Type of sugars in DNA

Back 8

deoxyribose

Front 9

Type of sugar in RNA

Back 9

ribose

Front 10

Nucleotides present in DNA

Back 10

A, T, C, and G

Front 11

Nucleotides present in RNA

Back 11

A, U, C, and G

Front 12

Number of bonds between nucleotides C and G

Back 12

3 Hydrogen bonds

Front 13

Number of bonds between nucleotides A and T or A and U

Back 13

2 hydrogen bonds

Front 14

What are histones?

Back 14

proteins that DNA wraps itself around

Front 15

What are Nucleosomes?

Back 15

protein + DNA combination

Front 16

What is chromatin?

Back 16

compact structure made of many nucleosomes bound together

Front 17

What does semi-conservative mean in DNA replication?

Back 17

the template strand is used + newly synthesized complimentary strand = new DNA double helix

Front 18

What is the role of Dna A?

Back 18

binds to the origin of replication to begin DNA replication. breaks the hydrogen bonds between the nitrogen bases to separate the 2 strands. Local region becomes single stranded. This breaking requires ATP.

Front 19

What is the role of Dna B Helicase?

Back 19

It unwinds the 2 strands from each other and "opens" up the double helix.

Front 20

What is the role of Dna Gyrase?

Back 20

Creates little notches in the sugar-phosphate backbone to relieve stress due to supercoiling. Prevents the backbone from breaking during replication. It is a form of topoisomerase found in E.coli

Front 21

What does SSB stand for in SSB proteins?

Back 21

Single strand binding proteins

Front 22

What is the role of SSB proteins?

Back 22

prevent the separated DNA strands from joining back together

Front 23

What is the role of DNA Primase?

Back 23

produces the RNA primer. Short RNA strands made of 10 nucleotides that are complimentary to the template DNA strand

Front 24

What is the role of DNA Ligase?

Back 24

Joins the DNA fragments together using phosphodiester bonds between 3' hydroxyl of the growing strand and the 5' phosphate of an Okazaki fragment

Front 25

True or False: Most prokaryotes have a bidirectional replication from a single origin of replication.

Back 25

TRUE

Front 26

True of False: Archaea just have one origin of replication

Back 26

FALSE. Some archaea have more than 1 origin of replication

Front 27

What are replicaton forks?

Back 27

replication forks are a complex of the entire DNA replication process

Front 28

what is a replicon?

Back 28

a segment of DNA that contains a single origin of replication. Eukaryotes have multiple origins of replication therefore have multiple replicons whereas prokaryotes have a single origin of replication so the entire DNA strand is considered a replicon.

Front 29

What direction does DNA synthesis occur in?

Back 29

5' to 3' direction

Front 30

What directs the direction of replication?

Back 30

template strand

Front 31

What does DNA polymerase III contain?

Back 31

10 proteins & 2 core enzymes

Front 32

What do core enzymes do?

Back 32

1. proof read

2. bind both strands of DNA at the same time

Front 33

What is a replisome?

Back 33

A protein complex including DNA polymerase III

Front 34

What is the role of Topoisomerase?

Back 34

relives tension caused by rapid unwinding.

Front 35

What is a primosome and what is it involved in?

Back 35

It is a combination of primase + other proteins and is involved in primer preparation

Front 36

Explain the term Leading Strand

Back 36

- Leading strand (5'-3') direction is synthesized starting from the 3' end. DNA polymerase follows the helicase as it unwinds the helix and adds complimentary nucleotides. Polymerase needs a single RNA primer to help it begin DNA synthesis.

Front 37

What direction is the lagging strand synthesized in?

Back 37

still 5' to 3', but it is synthesized in fragments since the parental strand is 5' to 3'

Front 38

Describe synthesis of DNA in the lagging strand

Back 38

There are new RNA primer is needed for every Okazaki fragment. New DNA polymerases are also needed. DNA fragments are joined by ligase to form a complete strand. RNA primers and primosomes are then removed.

Front 39

Describe the proofreading that is carried out by DNA polymerae III

Back 39

using exonuclease the mismatched bases are removed off where it is easiest to remove them, the 3' end

Front 40

Codons

Back 40

sequence of 3 nitrogen bases and code for a single amino acid. Found in mRNA

Ex: AUG: start codon and codes for Methionine

Front 41

Name the codon that intiates the completion of DNA replication.

Back 41

Stop codon. This signals a trailer sequence that contains a terminator sequence used to stop transcription. Termination needs the aid of rho factors sometimes.

Front 42

What happens before the start codon?

Back 42

coding region begins with the DNA sequence 3' TAC 5' which produces AUG

Front 43

Name the 3 types of RNA and their functions

Back 43

1. mRNA: messanger RNA: carries the gene for protein synthesis

2. tRNA: transfer RNA: carries amino acids to different sites during protein sythesis

3. rRNa: ribosomal rNA: make up ribosomes

Front 44

What is Polycistronic mRNA?

Back 44

mRNA found in prokaryote cells. They are mRNA that can code for several different polypeptide chains.

Front 45

what is a sigma factor?

Back 45

helps the core enzyme of RNA polymerase to recognize the start of genes

Front 46

holoenzyme

Back 46

core enzyme + sigma factor. only the holoenzyme can begin transcription

Front 47

Name all the steps in Transcription

Back 47

1. Initiation

2. Elongation

3. Termination

Front 48

Describe Initiation

Back 48

RNA polymerase binds to a sequence on the DNA called the TATA box or the Pribnow box.

Front 49

Describe Elongation

Back 49

A bubble is created through the separation of the two strands. The RNA polymerase follows the bubble until transcription is complete.

Front 50

Describe Termination

Back 50

RNA polymerase dissociates. Termination factors (specific sequence of codons) use the aid of rho factors to signal this

Front 51

What are the differences in transcription of eukaryotes?

Back 51

1. have 3 RNA polymerases

2. promoters have combinations of many elements

3. RNA polymerase II is a large aggregrate containing 10 + subunits

Front 52

RNA polymerase II function?

Back 52

catalyzes production of hereogeneous nuclear RNA (hnRNA) also known as pre-mRNA which undergoes post-transcriptional modification to generate mRNA

Front 53

What modifications are made during transcription?

Back 53

Pre-mRNA is altered to mature mRNA when it has it's 3' poly A tail attached to it, its 5' cap of 7 methylguanosine, and the introns removed by splicing

Front 54

What do the cap and tail do?

Back 54

protect the mRNA from degradation and signal it is ready for transport to the cytoplasm. The cap also helps ribosomes recognize it in the cytoplasm

Front 55

What do spliceosomes do?

Back 55

a large complex where splicing of the pre-mRNA occurs

Front 56

Alternative splicing

Back 56

sometimes pre-mRNA is spliced so different patterns of exons remain

Front 57

What is different about transcription in archaea?

Back 57

introns are left in the mature mRNA

Front 58

Code degeneracy

Back 58

up to 6 different codons can code for the same a.a.

Front 59

sense codons

Back 59

61 codons can code for a.a

Front 60

stop (nonsense) codons

Back 60

do not code for codons, just signal the start, stop and termination of transcription

Front 61

Name the direction of synthesis of translation

Back 61

N terminal (amino) --> C-terminal (carbonxyl)

Front 62

What is the site of translation?

Back 62

ribosome

Front 63

What is a polyribosome?

Back 63

a combination of mRNA and ribosomes. Used in translation

Front 64

What is tRNA's role in translation?

Back 64

tRNA attaches to the a.a and helps build the protein

Front 65

Aminoacyl-tRNA synthetases

Back 65

a type of catalyst that helps change precursor a.a.'s to amino acyl tRNA

Front 66

What is the minimum number of aminoacyl tRNA synthetase enzymes needed to attach a.a's to all the various tRNA molecules? Why?

Back 66

20. The aa-tRNA deliver a specific a.a to the ribosome to add to the polypeptidechain that is being produced. But a specific tRNA can only pick up its related a.a.

Front 67

What is amino-acyl tRNA?

Back 67

It is a specific type of tRNA that grabs its related a.a and brings it to the ribosome to match up with it's related codon during the formation of the polypeptide chain.

Front 68

What is missing in context to the amino-acyl tRNA?

a.a. + tRNA + _____ ----> aminoacyl- tRNA + AMP + PPi

Back 68

ATP

Front 69

What 2 molecules are needed to assist ribosomes with protein synthesis?

Back 69

Initiator factors and initiator tRNA

Front 70

Describe Initiation of Translation

Back 70

1. fMet tRNA binds to the 30S ribosomal subunit

2. the 30S ribosomal unit contains a 16s ribosome that is complimentary to the Shine Delgarno sequence on the mRNA. So when the mRNA comes in it binds to the ribosome in the correct location through hydrogen bonding

3. The 50S ribosomal subunit finally comes in and attaches to the 30S ribosomal subunit

Front 71

What is the Elongation cycle in Translation?

Back 71

the addition of amino acids to a growing polypeptide chain

Front 72

Name the 3 phases of Elongation

Back 72

aminoacyl tRNA binding, transpeptidation reaction, translocation. It also involves several elongation factors

Front 73

Describe ELongation in Translation.

Back 73

1. a.a. corresponding to the proper mRNA codon is added to the end of the polypeptide chain called the C-terminal end

2. tRNA binding sites are the A, P, E site

3. ribosome moves from codon to codon along the mRNA.

Front 74

A site

Back 74

in the A site the codon on the mRNA is matched with its anticodon which has an a.a. on it. This complex is brought in by an aminoacyl tRNA corresponding to the codon in the A site. Then moves to the P site

Front 75

P site

Back 75

the attached a.a. is added to a growing polypeptide chain and is detached from the anticodon

Front 76

E site

Back 76

the anticodon moves from the P site to the E site and leaves

Front 77

Peptidyl transferase

Back 77

catalyzes the bonding between adjacent a.a. called a transpeptidation reaction to form the a.a. chain

Front 78

Where does Termination of Protein synthesis take place?

Back 78

UAA, UAG, or UGA codons

Front 79

What are release factors?

Back 79

the help to recognize the stop codons

Front 80

There are ___ RF(s) in prokaryotes and ____ RF(s) in euaryotes

Back 80

3 and 1

Front 81

What do molecular chaperones do in protein folding?

Back 81

help to fold polypeptides, help to transport proteins across the membranes and protect the cells from thermal damage

Front 82

Domains

Back 82

structurally independent regions of polypeptide that are separate by less structured regions

Front 83

Protein splicing

Back 83

removes inteins of the polypeptide before folding and keeps the exteins

Front 84

housekeeping genes

Back 84

consecutive genes that are constantly being expressed. Necessary for life

Front 85

inducible genes

Back 85

genes that code for inducible enzymes and are only expressed when needed such as Beta galactosidase. Only if the levels of something are too high or too low is there repression of the gene (turned off) or induction (turned on)

Front 86

What is the cause of induction and repression?

Back 86

the rate of transcription

Front 87

Beta galactosidase

Back 87

an inducible enzyme that helps to break apart lactose (made of a molecule of galactose and and a molecule of glucose) through hydrolysis. By breaking apart these two molecules lactose is used to provide energy to the cell, when glucose levels are low

Front 88

What does an inducer do?

Back 88

a molecule that binds to the repressor protein. This doesn't allow for the co-repressor to bind to the repressor which means the repressor can't bind to the operator site on the DNA. This means RNA polymerase can come in and bind. It essentially promotes transcription.

Front 89

Repressor proteins

Back 89

a molecule that binds to DNA with the help of a molecule called the co-repressor (active). It takes up the binding site to where RNA polymerase usually binds and therefore blocks transcription from occurring.

Front 90

Activator proteins

Back 90

promote transcription by promoting the binding of RNA polymerase

Front 91

With the help of an inducer the activator protein can bind to the DNA. This promotes the binding of RNA polymerase even more to the DNA molecule

Back 91

if there is an inhibitor and it binds to the activator protein, the activator protein cannot bind to the DNA molecule. No transcription happens.

Front 92

What is an operon?

Back 92

sequence of genes that code for a protein. Contains a promoter region, a operator region, and a structural gene

Front 93

What is the role of DNA polymerase I?

Back 93

It removes the RNA primer and fills the gap in with a DNA primer