Micro2 Chaps. 7, 8

Front 1

The ____ strand encodes the genetic info while the ______ strand is read by RNA pol to make mRNA. ________ base pairing allows this.

Back 1

Plus, Minus, Complementary

Front 2

The promotor region is _______ of all genes.

Back 2

Upstream

Front 3

Upstream vs Downstream

Back 3

Upstream = towards the 5' end
Downstream = towards the 3' end

Front 4

Transcription Factors

Back 4

Sequences of DNA within the promotor that are recognized by regulatory proteins.

Front 5

TF's are analogous to a _________ switch.

Back 5

Dimmer
Some promote, some repress

Front 6

During initiation of transcription, the _______ ________ on the RNA pol recognizes the _________ region.

Back 6

Sigma Factor, Promotor

Front 7

After the RNA pol binds to the promotor region, the _______ _______ falls off, leaving the RNA pol _______ ________.

Back 7

Sigma Factor
Core enzyme

Front 8

mRNA is synthesized _____ to ____.

Back 8

5' to 3'

Front 9

A _________ sequence in the DNA displaces the RNA pol from the gene, ending transcription.

Back 9

Termination

Front 10

Define UTR's. What does it stand for, what do they do and where are they located on the mRNA?

Back 10

Untranslated regions. Each mRNA has a short 5' UTR and a long 3' UTR. They contain regulatory elements that control several aspects of mRNA activities including the 1/2 life.

Front 11

The genetic code is __________ because more then one codon can encode some aa. The _____ position is where the degeneracy occurs.

Back 11

Degenerate, 3rd

Front 12

__________, composed of RNA's and proteins, are the site of polypeptide synthesis.

Back 12

Ribosomes

Front 13

The ________-_________ sequence is found in the __' UTR of bacterial RNA's.

Back 13

Shine-Delgarno
5'

Front 14

Define the Shine-Delgarno sequence.

Back 14

It assures proper alignment of the mRNA on the ribosome, allowing the ribosoe to find the AUG start codon.

Front 15

tRNA's have two important features:

Back 15

1. The anti-codon that is complementary to the codon
2. An amino acid that is specific for the codon.

Front 16

Define the wobble hypothesis:

Back 16

The reason why the 3rd position is degenerate is because the 3rd position can't make as close contact between the tRNA and the mRNA and can therefore be misread fairly easily.

Front 17

A ribozyme is a __________ RNA molecule.

Back 17

Catalytic

Front 18

A ribozyme called ________ _________ forms a peptide bond between the COOH of the 2st amino acid and the NH2 of the 2nd amino acid.

Back 18

Peptidyl transferase

Front 19

Eukaryotic mRNA is usually _______cistronic while prokaryotic mRNA is usually _______cistronic.

Back 19

Monocistronic
Polycistronic

Front 20

When a gene is continually expressed, it is said to be __________ expressed.

Back 20

Constituatively

Front 21

A _________ gene is one that is affected by repression or activation.

Back 21

Modulated

Front 22

Define repressors:

Back 22

They bind to the DNA between the promotor and the transcriptional start site, thus blocking RNA pol.

Front 23

Define activators:

Back 23

They interact with the promotor region to facilitate RNA pol binding.

Front 24

The lac operon is a sensing pathway for __________.

Back 24

Lactose

Front 25

Define the lac operon:

Back 25

The presence of lactose and the absense of glucose in a culture media stimulates the expression of genes that metabolize lactose.

Front 26

Describe the first step of the lac operon pathway:

Back 26

1. As glucose levels drop, cyclic AMP increases (cAMP)

Front 27

Describe the second step of the lac operon pathway:

Back 27

2. cAMP binds to catabolite activating protein (CAP), allowing it to bind to the promotor. It can't bind without cAMP.

Front 28

Describe the third step of the lac operon pathway:

Back 28

3. Allolactose, an isomer of lactose, binds to the lac repressor, preventing it from binding to the DNA.

Front 29

Ligation to specific macromolecular receptors on the surface of cells creates what kind of response within the cell?

Back 29

This induces a series of signal transduction events inside the cell that results in a change in gene expression profile.

Front 30

Staphylococcus aureus is a common Gram ________ bacteria

Back 30

Positive

Front 31

There are multi-drug resistant strains of Staph in hospitals, how do they survive the antibiotics and what are these strains called?

Back 31

They are called methicillin-resistant Staphylococcus aureaus (MRSA), they evolved a pump system to export the antibody.

Front 32

True or False:
Antibiotic resistance is a genetic event.

Back 32

True

Front 33

What are the two mechanisms of mutagenesis?

Back 33

1. Spontaneous mutation of the DNA
2. Horizontal gene transfer (bacteria sex)

Front 34

What are the two main causes of mutagenesis?

Back 34

1. Chemicals and radiation
2. Mutases

Front 35

What are mutases?

Back 35

Enzymes that are expressd during times of stress that increase rates of mutations. They are modified DNA polymerases, this is a last ditch effort.

Front 36

The three main types of mutations are:

Back 36

1. Nucleotide base substitution (AKA point mutation)
2. Deletion or insertion of nucleotides
3. Transposable elements ("jumping genes")

Front 37

Mutations are a _________ game with rates that usually fall between:

Back 37

Numbers
10^-4 and 10^-12

Front 38

Silent Mutation

Back 38

A base substitution mutation that has no effect on which amino acid is added to the polypeptide

Front 39

Missense Mutation

Back 39

A base substitution mutation resulting in an amino acid change (can be dramatic

Front 40

________ mutations can alter the 3D shape of a protein or compromise a critical amino acid.

Back 40

Missense

Front 41

Nonsense Mutation

Back 41

Results in a premature stop codon.

Front 42

Deletions or insertion mutations alter the _________ ________ of DNA.

Back 42

Reading frame

Front 43

Mutations that shift the reading frame on DNA are termed _________ mutations.

Back 43

Frameshift

Front 44

__________ elements are common in plants and often carry genes that alter the __________ of recipient bacteria, including antibiotic resistance.

Back 44

Transposable
Phenotype

Front 45

_______ are used to discover gene functions.

Back 45

Mutagens

Front 46

______ _________ change cases that are misread during DNA replication.

Back 46

Base modifiers

Front 47

______ _________ resemble normal bases but have different ___-_______ characteristics and are mismatched during replication

Back 47

Base analogs
H-Bond

Front 48

________ _______, such as ethidium bromide, insert btwn adjacent baes on a strand, which can lead to the __________ of a base pair

Back 48

Intercalating agents
Insertion

Front 49

Radiation thru UV light can create ________ ________ while X-rays induce ________ ________ _____ ________.

Back 49

Thymine dimers
Double strand DNA breaks

Front 50

What is proofreading?

Back 50

Some DNA polymerases can step backward and remove a misincorporated base.

Front 51

True or False:
Viruses can proofread their DNA looking for mutated DNA.

Back 51

False, viruses cannot proofread.

Front 52

_________ are enzymes that recognize inappropriate ____ _______ of DNA and remove mutant bases, which are corrected by DNA pol

Back 52

Endonucleases
3D structure

Front 53

The process of endonucleases removing mutant bases so DNA pol can replace them is called __________ repair.

Back 53

Mismatch

Front 54

After endonucleases recognize and remove a mismatched base, _____ _____ repairs it.

Back 54

DNA pol

Front 55

Thymine dimers can be repaired through ____________, which recognizes buldges in the DNA.

Back 55

Photoreactivation

Front 56

Photoreactivation harness light energy to break the _________ bonds btwn adjacent ___________.

Back 56

Covalent
Thymines

Front 57

The two types of thymine dimer repair are:

Back 57

1. Photoreactivation
2. Excision repair

Front 58

Explain excision repair:

Back 58

-Repairs thymine dimers
-Removes several adjacent bases
-DNA pol refills the gaps
-DNA ligase forms phosphodiester bonds

Front 59

________-_______ __________ recognize modified bases and remove them.

Back 59

Lesion-specific glycosylases

Front 60

Explain SOS repair:

Back 60

-System of 30+ genes for repair of highly damaged DNA
-System of desperation
-Highly prone to error

Front 61

What are the three events that evolution requires:

Back 61

1. Genetic variation
2. These variations must be inheritable
3. Natural selection of those traits most suitable for an environment

Front 62

Isolating a mutant is a ________-________ event.

Back 62

Statistically-unlikely

Front 63

List three important microbes that have been developed using artificial seletion:

Back 63

1. Oil-consuming bacteria
2. Heavy metal decompisition
3. Wines

Front 64

Cells that are receptive to DNA transfer are termed _________.

Back 64

Competent

Front 65

Competent cells allow DNA to pass through their _________ and ______ ______, this process is termed __________.

Back 65

Membranes
Cell walls
Transformation

Front 66

___________ are bacterial viruses.

Back 66

Bacteriophages

Front 67

The process of new genes in a bacterial genome "spread" by a bacteriophage is termed __________.

Back 67

Transduction

Front 68

Plasmids

Back 68

-Circular molecules of DNA
-They can be 100-1000 nucleotides long
-They often contain virulence factors

Front 69

Define virulence factors

Back 69

Often contained in plasmids and contribute to disease suseptibility with antibiotics and toxins.

Front 70

Plasmids are considered __________ because they can disseminate btwn species of bacteria.

Back 70

Promiscuous

Front 71

Competent cells acquire plasmids by ___________ __________.

Back 71

Random chance

Front 72

__________ is the direct transfer of plasmids (or chromosomes) btwn bacteria.

Back 72

Conjugation

Front 73

A recipient cell is denoted as _____, while a donor cell is donated _____

Back 73

Recipient = F-
Donor = F+

Front 74

Define a sex pilus

Back 74

A tubular structure that mediates contact btwn a donor cell and a reciepient

Front 75

A plasmid becomes __________ when an enzyme cleaves it.

Back 75

Mobilized

Front 76

At the end of conjugation both bacteria are F__.

Back 76

+

Front 77

Transposons

Back 77

Self replicating DNA molecules. AKA transposable elements, jumping genes

Front 78

All transposons encode DNA and/or RNA polymerase, termed ___________, that mediates jumping.

Back 78

Transposases