Micro Bio Test 2

Front 1

Functional unit of genetic information is the _____. This is composed of _____.

Back 1

1. Gene
2. DNA

Front 2

What are the 3 informational macromolecules in the cell?

Back 2

1. DNA
2. RNA
3. Protein

Front 3

List in the order in which they are produced:

RNA
DNA
Protein

Back 3

1. DNA
2. RNA
3. Protein

Front 4

Each gene is transcribed individually in

Back 4

Eukaryotes

Front 5

Introns and exons are not found in _____.

Back 5

Bacteria (nothing is ‘cut out’ like in eukarya)

Front 6

The sequence of nucleotides is aka a ____.

Back 6

Gene

Front 7

What codes for RNA?

Back 7

Gene

Front 8

What codes for the Amino Acid sequence?

Back 8

mRNA

Front 9

What codes for polypeptides?

Back 9

Amino Acid sequence (which folds into protein

Front 10

What are the 4 nucleotides found in DNA?

Back 10

1. Adenine (to T)
2. Guanine (to C)
3. Cytosine (to G)
4. Thymine (to A)

Front 11

Which bases melt at a higher temperature?

Back 11

Guanine and Cytosine because they have 3 hydrogen bonds vs. 2

Front 12

Which type of RNA is coded for on DNA?

Back 12

All 3 types (mRNA, tRNA, rRNA)

Front 13

What is transcription?

Back 13

DNA to RNA

Front 14

All cells and some viruses contain DNA in what type of structure?

Back 14

Double stranded (double helix)

Front 15

How are the two strands of DNA arranged according to one another?

Back 15

Anti-parallel

Front 16

The two strands of DNA form a what?

Back 16

double helix

Front 17

What type of bond holds the 2 strands of DNA together?

Back 17

Hydrogen bond

Front 18

This bond is strongest between what?

Back 18

Guanine and Cytosine (3 hydrogen bonds=higher melting point)

Front 19

The backbone of DNA is composed of:

Back 19

Phosphates & deoxyribose (pentose sugar)

Front 20

DNA’s backbone is held together by what?

Back 20

Covalent bonds (phosphodiester bonds)

Front 21

Compare DNA to RNA:

Back 21

DNA:
- double stranded
- contains deoxyribose (no OH at position #3)
- contains thymine
RNA:
- single stranded
- contains ribose
- contains uracil

Front 22

How many strands of DNA are transcribed and in what direction?

Back 22

Only ONE strand in 5’ to 3’

Front 23

What does translation facilitate?

Back 23

RNA to polypeptides

Front 24

Where does translation occur in:
1. bacteria (prokaryotes)
2. fungi (eukaryotes)
What about transcription:

Back 24

Bacteria:
- lack a nucleus so transcription and translation occur in the cytoplasm

NOTE: bacteria has no nucleus therefore transcription and translation may occur simultaneously

Fungi:
- transcription in nucleus
- translation in cytoplasm

Front 25

Replication always occurs ___ to ___.

Back 25

5’ to 3’

Front 26

PCR is an example of the _____.

Back 26

Denaturation (caused by high heat which breaks hydrogen bonds b/w bases)

Front 27

Which DNA melts at a higher temp?
GC rich OR AT rich?

Back 27

GC rich b/c 3 hydrogen bonds b/w bases.

Front 28

What physical configuration does DNA undertake to be able to fit inside the space allocated?

Back 28

Supercoiling

Front 29

Double helix = underwound is an ex. of:

Back 29

Negative supercoiling

Front 30

Double helix = overwound is an ex. of:

Back 30

Positive supercoiling

Front 31

Which type of supercoiling is most common in bacteria?

Back 31

Negative supercoiling

Front 32

Where can we find overwound supercoiling

Back 32

Archaea (overwound double helix = positive supercoiling)

Front 33

What enzyme is responsible for the supercoiling of DNA?

Back 33

DNA Gyrase

Front 34

T or F: histones in eukaryotes are the same as histones in prokaryotes.

Back 34

False. These do not indicate the same thing.

Front 35

What enzyme allows for the DNA to unwind at the replication fork?

Back 35

Helicase

Front 36

What holds the DNA apart so that it does not go back together

Back 36

Stabilizing proteins

Front 37

T or F: Viruses contain either RNA or DNA.

Back 37

TRUE. (viruses NEVER have both; this is why they need a host to survive)

Front 38

How many genes does the chromosome contain?

Back 38

All genes (= DNA = full genome of bacteria)

Front 39

Are viruses linear or circular?

Back 39

Can be both

Front 40

Are viruses single or double stranded?

Back 40

Can be both

Front 41

Are plasmids linear or circular?

Back 41

Most are circular

Front 42

Are plasmids single or double stranded?

Back 42

Most are double stranded

Front 43

What do plasmids carry?

Back 43

1. antibiotic resistance
2. gene for toxin
3. gene for capsule

Front 44

Are viruses intracellular or extracellular?

Back 44

Extracellular

Front 45

Are plasmids intracellular or extracellular?

Back 45

Intracellular

Front 46

Which genetic element has “housekeeping” genes?

Back 46

Chromosome (ie: glycolysis, etc = things the cell has to do again and again)

Front 47

T or F: A plasmid is self-replicating?

Back 47

FALSE. Plasmids are not self-replicating and only carry a couple of genes

NOTE: Plasmids are NOT part of chromosome

Front 48

The leading strand replicates continuously from _____ to _____.

Back 48

5’ to 3’

Front 49

The lagging strand replicates discontinuously from _____ to _____.

Back 49

3’ to 5’

Front 50

What does primase do?

Back 50

Makes RNA primers on both DNA strands

Front 51

_____ polymerase can start on its own.

Back 51

RNA

Front 52

_____ polymerase needs an –OH group on end to start.

Back 52

DNA

Front 53

What does DNA polymerase do?

Back 53

Copies DNA

Front 54

Is DNA replication conservative or semiconservative?

Back 54

Semiconservative = 1 old strand (parent) + 1 new strand

Front 55

Why does replication always proceed from 5’ to 3’?

Back 55

Because of free –OH group needed on 3’ end to add nucleotide.
NOTE: 3’ end is the “growing point”

Front 56

DNA synthesis begins at the what?

Back 56

Origin of replication

Front 57

The zone of unwound DNA where replication occurs is the what?

Back 57

Replication fork

Front 58

What enzyme unwinds the DNA?

Back 58

DNA helicase

Front 59

What is uniquely found on the lagging strand

Back 59

Okazaki fragments = pieces of DNA created by discontinuous replication
(= approx 1000 nucleotides)

Front 60

What connects the DNA pieces together?

Back 60

Ligase

Front 61

What cuts the RNA primer out and why is this important?

Back 61

RNAase; cuts RNA primer out to make DNA (imp. b/c RNA primer has uracil which may cause mutation if not cut out)

Front 62

Is RNA primer needed for the leading or lagging strand during replication?

Back 62

Both

Front 63

What winds and unwinds supercoils of DNA?

Back 63

DNA gyrase

Front 64

What connects Okazaki fragments?

Back 64

Ligase (each requires its own RNA primer)

Front 65

What unwinds DNA for replication?

Back 65

DNA helicase

Front 66

What holds DNA apart for copying?

Back 66

Single strand binding protein

Front 67

Which strand requires RNA primer during replication (leading or lagging)?

Back 67

Both

Front 68

In which direction does the leading strand replicate? Lagging?

Back 68

1. 5’ to 3’
2. 3’ to 5’

Front 69

In bacteria, because they have _____ chromosomes, replication occurs in the _____ direction with _____ origin(s) of replication and _____ replication fork(s) which makes replication _____.

Back 69

1. circular
2. bi-directional
3. one
4. two
5. faster

Front 70

A complex of multiple proteins involved in replication is called a _____.

Back 70

Replisome

NOTE: DNA moves (pulled through replisome) = replisome does not move

Front 71

What is the theta structure and what is it unique to?

Back 71

Theta structure = when DNA of bacteria is half-way through replication = unique to bacteria b/c DNA is circular forming this structure which resembles the Greek letter ‘theta’.

Front 72

In the process of DNA replication in bacteria, the _____ will unwind the DNA going in both directions, the _____ proteins will be there to prevent the DNA from re-bonding, the _____ _____ will come in and begin copying the leading and lagging strands. The leading strand is transcribed _____ and the lagging strand _____. The fragments formed by discontinuous replication are called _____ _____.

Back 72

1. helicases
2. stabilizing
3. DNA polymerase
4. continuously
5. discontinuously
6. Okazaki fragments

Front 73

Why is bacteria DNA replication called semiconservative?

Back 73

The parent acts as template and synthesizes new DNA for complimentary strand.

Front 74

What must happen first for binary fission to take place?

Back 74

Chromosomes must duplicate which takes about 40 minutes (60 minutes for entire binary fission process)

Front 75

What do DNA Helicases do?

Back 75

Separate the strands for replication

Front 76

What do Primases do?

Back 76

Catalyzes primer on each strand

Front 77

Are mutation rates in cells common?

Back 77

NO = only 10 to -8 or 10 to -11 errors per base inserted.

Front 78

What performs the ‘proofreading’ activity in eukaryotes, prokaryotes, and viral DNA replication systems?

Back 78

Polymerase

Front 79

What’s happening during transcription?

Back 79

Making RNA from DNA (mRNA, tRNA, and rRNA)

Front 80

In what direction does transcription occur?

Back 80

5’ to 3’

Front 81

What makes transcription happen?

Back 81

RNA Polymerase

NOTE: ‘POLYMERASE’ always = copy

Front 82

How many strands is transcribed

Back 82

One strand

Front 83

Where the RNA polymerase binds =

Back 83

Promoter (begins transcription)

Front 84

Where repressor protein binds =

Back 84

Operator (stops transcription)

Front 85

What is the job of the promoter?

Back 85

To start transcription

Front 86

What is the job of the operator?

Back 86

To stop transcription

Front 87

What is located after the promoter and the operator and what does it code for?

Back 87

Structural Genes which codes for mRNA

Front 88

The structural genes in bacteria are _____.

Back 88

Polycistronic = mRNA will code for multiple genes

EX: Lac operon has 3 diff. structural genes for one mRNA (all 3 controlled by 1 promoter and 1 operator)

Front 89

What does the Lac Operon code for?

Back 89

The enzymes used in lactose metabolism

Front 90

What is the last thing that is found on a gene?

Back 90

Terminator

Front 91

Where is the stop codon located?

Back 91

On mRNA strand to stop translation

Front 92

What does the terminator do?

Back 92

Stops transcription

Front 93

What would happen if no terminator?

Back 93

Transcribe entire chromosome

NOTE: not useful b/c don’t need everything all at one time; ie: cell does not always need enzymes for lactose fermentation b/c it really wants to use glucose (lactose = glucose + galactose), genes for glycolysis expressed all the time

Front 94

Where does the polymerase bind?

Back 94

Promoter

Front 95

What controls whether the transcription happens or not?

Back 95

Operator

Front 96

What will happen if the repressor protein is not there? What is this called?

Back 96

It can keep going so transcription can happen. This is called induction = take the protein off = induce the gene = turn the gene on.

NOTE: turn the gene off = repressing it = stopping it

Front 97

Where does the polymerase bind?

Back 97

Promoter

Front 98

What binds to the promoter region to help the polymerase to get everything situated to be able to do transcription?

Back 98

Sigma factors

Front 99

What ends the transcription process?

Back 99

Terminator

Front 100

Transcription happens where there is no _____.

Back 100

Repressor protein

NOTE: this is a PHYSICAL thing = the repressor protein binds to the DNA causes the polymerase to physically run into it effectively stopping transcription

Front 101

Transcription happens where there is no _____.

Back 101

Repressor protein

NOTE: this is a PHYSICAL thing = the repressor protein binds to the DNA causes the polymerase to physically run into it effectively stopping transcription

Front 102

Where does the repressor protein bind?

Back 102

Operator site

Front 103

Where does mRNA go once created by transcription?

Back 103

Ribosome

NOTE: 70s in bacteria (80s in eukaryotes)

Front 104

Information stored in DNA is copied to RNA during

Back 104

Transcription (this info used to synthesize specific proteins)

Front 105

What are the 3 types of RNA used to cells?

Back 105

1. mRNA = carry info for making specific proteins from DNA to ribosomes
2. tRNA = deliver A.A. to ribosomes
3. rRNA = used to form ribosomes

Front 106

What are the 3 stages in the process of transcription?

Back 106

1. initiation
- RNA polymerase binds to promoter site on 3’ end of DNA and breaks H-bonds holding DNA strands together on both sides
- Binds to different promoter sites differently
2. elongation
- RNA Polymerase moves along DNA opening up bubble in DNA
- As it moves, RNA Polymerase adds bases to the 3’ end of the growing RNA transcript
3. termination
- RNA Polymerase and newly synthesized RNA transcript are released from DNA
- Can occur through 2 mechanisms
- 1. self termination
- 2. enzyme dependent termination

Front 107

Does RNA polymerase bind to all promoter sites the same way?

Back 107

NO. It binds to some more strongly than others = one way that cells can control gene expression = more strongly is more likely gene is to be transcribed

NOTE: in general, higher levels of transcription leads to higher levels of translation which leads to higher levels of concentration of that polypeptide

Front 108

Which strand of DNA is the RNA transcribed from?

Back 108

Template strand

Front 109

In what ways can termination occur?

Back 109

1. self termination = the RNA sequence transcribed to the terminator causes the RNA to hydrogen bond to itself pulling the RNA Polymerase off the DNA
2. enzyme dependent termination = a termination protein binds to the terminator and pushes RNA Polymerase off the DNA

Front 110

The sigma factors bind with the _____ at the _____ and recognize 2 sites on the promoter called the _____ and _____. These sites are considered _____.

Back 110

1. Polymerase (helps to hold Polymerase to DNA)
2. promoter
3. Pribnow box (10 bases b/4 transcription = -10 region)
4. -35 region (approx. 35 bases upstream of transcription)
5. conserved = the same over and over again throughout diff. generations = sequences stay the same

NOTE: “-“ = to left and “+” = to right

Front 111

The Pribnow box is aka the what?

Back 111

TATAAT box

Front 112

When does the sigma factor get released during the process of transcription?

Back 112

Stays on the whole time until terminator reached.

Front 113

What will end the gene for transcription?

Back 113

Terminator

Front 114

Why is polycistronic important in bacteria and what is it called when they are grouped together?

Back 114

An mRNA bacteria, very seldom code for just one protein but will have multiple ones and when grouped together they are called operons.

Front 115

Translation = _____ to _____.

Back 115

mRNA to polypeptide

Front 116

How many possible codons?

Back 116

64

Front 117

How many Amino Acids?

Back 117

20

Front 118

What is the start codon?

Back 118

AUG (“ALL U GO!”) = codes for methionine = every protein starts with methionine but may not necessarily keep the methionine (may get chopped off)

Front 119

What stops translation? What is another name for this?

Back 119

Stop codons aka non sense codon = do not code for amino acid (nothing there = stop)

Front 120

What does a sense codon code for?

Back 120

Amino acid

Front 121

Non sense codons code for what?

Back 121

Stop codons = do not code for an A.A.

NOTE: recall sense mutations = changes the A.A. and non sense mutations = causes a stop codon = stops transcription

Front 122

What is the ‘wobble’?

Back 122

What is the ‘wobble’?

Front 123

What does the anti-codon bond to?

Back 123

mRNA

Front 124

Is RNA double or single stranded?

Back 124

Single

NOTE: tRNA shaped like a ‘T’ b/c of complimentary base pairing

Front 125

Stop codons include:

Back 125

UGA
UAG
UAA

Front 126

The order that the codons are in is called the what?

Back 126

Reading frame

NOTE: look at this with mutations

Front 127

What, on mRNA, base pairs with rRNA helping to hold mRNA in place?

Back 127

Shine-Dalgarno sequence = keeps reading frame in place b/c if reading frame changes = mutation (ie: sickle cell anemia is caused by a 1-base mutation)

Front 128

What has the anti-codon and carries the amino acid?

Back 128

tRNA

Front 129

What does the anti-codon base pair with?

Back 129

Codon which is on mRNA

Front 130

Where does protein synthesis happen?

Back 130

Ribosomes

Front 131

How many ribosomes does bacteria have?

Back 131

70s (eukaryotes have 80s)

NOTE: “S” = Svedberg units which is measured by use of a centrifuge

Front 132

E.Coli has ___ dinstict ribosomal proteins.

Back 132

52

Front 133

What are the 3 main stages of translation?

Back 133

1. initiation = start
2. elongation = peptide getting longer
3. termination

Front 134

What is happening during elongation?

Back 134

Polypeptides being formed by the addition of peptide bonds b/w A.A.

NOTE: Amino group on one end and carboxyl group on other = dehydration rxn to form peptide bond = happening during elongation

Front 135

What kind of a bond is a peptide bond?

Back 135

Covalent bond

Front 136

Once 2 A.A. are bonded together, what happens to the tRNA?

Back 136

It goes away and can be used again.

Front 137

Why does transcription stop when it reaches a stop codon?

Back 137

b/c stop codon does not have A.A. attached so there’s nothing to make peptide bond.

Front 138

Many antibiotics kill the bacteria because they interfere with _____ at the _____.

Back 138

1. translation
2. ribosome

Front 139

Why are translation and transcription coupled in bacteria?

Back 139

b/c no nucleus

NOTE: translation can begin before transcription is completed

Front 140

Multiple ribosomes on one mRNA is what?

Back 140

Polysome

NOTE: this helps them grow faster

Front 141

What is polycistronic?

Back 141

Multiple genes on one mRNA

Front 142

A polypeptide (protein) sometimes needs help from what to reshape or refold into its correct shape?

Back 142

Chaperonin

Front 143

T or F: protein folding is very important to its function.

Back 143

TRUE

Front 144

What are found on proteins that allow transport out of the cell?

Back 144

Signal sequences

NOTE: bacteria secrete enzymes (lipases) to break down lipids into fatty acids and glycerol so that it can transport them in…but to be able to secrete the proteins, it’s gotta be able to go through the PM and also the outer Cell Wall.

Front 145

What are we really talking about when we talk about gene expression? (GIVE EXAMPLE OF LAC OPERON)

Back 145

EX: lac operon expressed = enzymes for lactose fermentation made and lactose gets fermented

Front 146

An operon that can be turned on and off is called a what?

Back 146

Inducible operon

Front 147

The operons for the genes in glycolysis are called what?

Back 147

Constitutive enzymes = constitutive genes = constitutive proteins b/c made all at the same time (constantly made at a basic level the cell needs to survive)

Front 148

Why would we want to turn some genes on or off?

Back 148

b/c we don’t need everything all the time

EX: glucose available = do not need enzymes to break down other sugars

Front 149

What are the 2 major levels of regulation in the cell?

Back 149

1. control the activity of pre-existing enzymes
2. control the amount of an enzyme

Front 150

Where is the gene found?

Back 150

Chromosome

Front 151

What causes transcription to happen?

Back 151

RNA Polymerase

Front 152

What causes transcription to happen?

Back 152

RNA Polymerase

Front 153

What does this do?

Back 153

DNA to mRNA

Front 154

DNA to mRNA is called what

Back 154

transcription

Front 155

Where does translation happen?

Back 155

At ribosome

Front 156

What is the allosteric effect?

Back 156

When something binds to an enzymes changing the shape (recall feedback inhibition) preventing proper binding of substrate = not able to make end product we are looking for = controlled by enzyme activity

Front 157

Where does RNA Polymerase bind?
What happens after this?
What binds here?

Back 157

Promoter sequence on DNA
Operator
Repressor protein

Front 158

What makes or blocks transcription from happening?

Back 158

What makes or blocks transcription from happening?

Front 159

What can happen when protein binds to DNA?

Back 159

1. may catalyze a specific rxn (ie: transcription by RNA Polymerase)
2. may block transcription = negative regulation (control)
3. may activate transcription = positive regulation (control)

Front 160

Protein binding to DNA and blocking transcription = _____ control.

Back 160

Negative

Front 161

Protein binding to DNA and activating transcription = _____ control.

Back 161

Positive

Front 162

Negative control is talking about _____.

Back 162

Repression (= repressor protein binds to the operator and PHYSICALLY blocks RNA P-ase from passing/transcribing the gene)

Front 163

In what stage do the cells grow?

Back 163

Log (or exponential) phase

Front 164

“Cell makes it when it needs it but when it doesn’t, it turns those genes off “ is an example of what?

Back 164

repression

Front 165

What is an operon made of?

Back 165

1. promoter
2. operator (regulatory element)
3. multiple structural genes

Front 166

All of the structural genes of an operon are transcribed into what?

Back 166

Single mRNA molecule which is then translated into proteins

Front 167

What type of operon is not transcribed unless they are activated? What are they activated by?

Back 167

1. Inducible
2. activated by an inducer

Front 168

What type of operon is always transcribed? How do these get turned off?

Back 168

1. Repressible
2. when deactivated by a repressor

Front 169

Multiple genes controlled by one promoter is called what?

Back 169

Polycistronic

Front 170

Repression =

Back 170

Blocking

Front 171

Induction =

Back 171

Making

Front 172

Many bacterial genes are regulated in groups called what? What are the elements of this?

Back 172

1. operon
2. promoter, operator, and a string of structural genes (3 in Lac operon)

Front 173

What type of operon is the lac operon? Why is this important?

Back 173

1. inducible (meaning the genes are usually not transcribed)
2. b/c it wouldn’t be efficient to have enzymes made all the time to catabolize lactose when lactose is not available

Front 174

The inducer acts by doing what?

Back 174

By turning off the repressor…not by actively stimulating the genes to be transcribed.

Front 175

What promoter and operator together form the what?

Back 175

Control region

Front 176

When is the lac operon induced or stimulated to produce proteins of lactose catabolism? How does this happen?

Back 176

When is the lac operon induced or stimulated to produce proteins of lactose catabolism? How does this happen?

Front 177

Since allolactose stimulates transcription of the lac operon, it is called what? This acts by turning off the ____ and not by actively stimulating the genes to be transcribed.

Back 177

1. inducer
2. repressor

Front 178

What does E.Coli chromosome have near the lac operon that helps to control the production of enzymes to catabolize lactose?

Back 178

A regulatory gene that is constantly transcribed and translated to produce repressor protein which binds to the operator DNA at the operator physically preventing RNA Polymerase from moving beyond the promoter = no enzymes to catabolize lactose

Front 179

What does regulatory gene code for?

Back 179

Repressor protein

Front 180

TQ repressor proteins are made by the regulatory gene of a repressible operon, once made, are active or inactive?

Back 180

Inactive (unless – for ex. – activated by binding of excess tryptophan to them which then binds to the trp operator to stop transcription of structural genes coding for tryptophan biosynthesis.

Front 181

What is an example of a repressible operon found on E.Coli.

Back 181

Trp operon = promoter, operator, and 5 structural genes = codes for biosynthesis of tryptophan

Front 182

In the case of the trp repressor protein, what does it need attached to it?

Back 182

Tryptophan and then can bind to the operator (attached to repressor when excess tryptophan in cell = blocks gene for tryptophan biosynthesis = not blocking genes for tryptophan but blocking genes for the enzymes to make tryptophan)

Front 183

What will happen to the repressor protein in E.Coli when there is not excess tryptophan available to the cell?

Back 183

No tryptophan will bind to repressor protein preventing it from binding to the operator which allows for RNA Polymerase to bind to the promoter and synthesize all genes to synthesize tryptophan (5 total) = this is polycistronic b/c 5 genes (multiple genes) which are all needed for same thing (tryptophan biosynthesis) controlled by one promoter

Front 184

repression =

Back 184

Blocking

Front 185

Induction =

Back 185

Making it happen (ex. Lac operon)

Front 186

Enzymes are synthesized only when they are needed in what? What type of control is this?

Back 186

1. induction
2. negative control

Front 187

What is a regulatory mechanism the stops transcription called?

Back 187

Negative control (ie: repression and induction)

Front 188

What is a regulatory mechanism the stops transcription called?

Back 188

Negative control (ie: repression and induction)

Front 189

What does allolactose do?

Back 189

Binds to repressor protein turning it off which blocks its ability to bind to the operator which induces (by allowing RNA Polymerase to physically pass this point on chromosome) the transcription of the 3 genes to produce lactose for the cell.

Front 190

The collective term for inducers and repressors is what?

Back 190

effectors

Front 191

TQ The regulatory gene is aka the _____ and codes for the _____ protein. It is located _____ from the promoter.

Back 191

1. I-gene
2. repressor protein
3. upstream (before)

Front 192

What is the inducer for the lac operon?

Back 192

Allolactose (binds to repressor protein)

Front 193

What is lactose broken down into? What enzyme helps to do this?

Back 193

1. glucose + galactose
2. B-galactosidase (this will be referred to in mutation lecture also)

Front 194

The binding of allolactose to the repressor protein causes a what?

Back 194

Allosteric change in the repressor protein (shape change) which prevents the repressor protein from binding to the operator enabling the transcription of genes necessary to form enzymes to break down lactose.

Front 195

A substance that represses enzyme synthesis is what?

Back 195

Corepressor (refer tryptophan video)

Front 196

A substance that induces enzyme synthesis is what?

Back 196

Inducer

Front 197

What is an operon?

Back 197

Cluster of genes arranged in a linear fashion whose expression is under control of a single operator (ie: lac operon = 3 genes for 1 mRNA)

Front 198

TQ What does negative control do?

Back 198

Stops / blocks transcription

Front 199

TQ What does positive control do?

Back 199

Proteins will bind (usually along w/ polymerase) to allow transcription to happen (MALTOSE CATABOLISM AN EXAMPLE OF +)

Front 200

What is an example of negative control?

Back 200

Lac operon / tryptophan

Front 201

What is an example of positive control?

Back 201

Maltose

Front 202

TQ In positive control, the activator protein binds to the what?

Back 202

Activator binding site (not operator)

Front 203

TQ In positive control, the activator protein binds to the what?

Back 203

Regulon

Front 204

T or F: Different signals help cells to know what it needs?

Back 204

TRUE. For example: temp, pH, nutrients, etc)

Front 205

TQ A mechanism by which bacteria assess their population density is what?

Back 205

Quorum sensing = helps determine if enough bacteria around to do something (ie: 1 cell making a toxin vs. 1 million cells making toxin)

Front 206

Where can luciferase be found?

Back 206

In lightning bugs (this enzyme allows them to light up = bioluminescence)

Front 207

P. aeruginosa switches from free living to growing as a biofilm is an example of what?

Back 207

Quorum sensing

Front 208

What is a biofilm?

Back 208

When bacteria grow together and can grow all the way across a surface (ie: mop bucket or teeth day after)

Front 209

What is chemotaxis?

Back 209

Moving from pt. A to pt. B (toward or away from something)
Due to Chemicals

Front 210

TQX What is used to describe the phenomenon that cells use glucose first?

Back 210

Catabolite repression (represses other things to use glucose 1st)

Front 211

TQX What kind of curve is observed when a cell uses all glucose available then starts to break down different sugar?

Back 211

Diauxic growth curve (NOTE: flat area in curve = when glucose is exhausted and cell producing enzymes to catabolize other)

Front 212

What do heat shock proteins produced by cells help with?

Back 212

Repair after being exposed to high temps.

Front 213

TQX What is an example of differentiation?

Back 213

Making of endospores when cell runs out of food, water, etc.

Front 214

TQX What are 2 examples of this found in Caulobacteria?

Back 214

1. Swarmer cells = disperser role
2. Stalked cells = reproductive role

Front 215

TQX When RNA folds back onto itself to block transcription (instead of repressor protein) is called what?

Back 215

Attenuation

Front 216

How do bacteria control what protein is getting expressed?

Back 216

1. activity of enyme
2. controlling the amount = blocking transcription(+ or -)

Front 217

Why would a cell want to control what protein is expressed?

Back 217

To conserve NRG = only make what needs

Front 218

what binds at an operator site

Back 218

Repressor protein

Front 219

What makes the repressor protein

Back 219

I-gene or regulatory gene

Front 220

What does the repressor bind to? What does it do?

Back 220

1. operator
2. blocks polymerase from going forward

Front 221

What happens what lactose is present?

Back 221

Allolactose binds to repressor protein causing shape change = falling off of operator = transcription possible = induction

Front 222

What happens what lactose is present?

Back 222

Allolactose binds to repressor protein causing shape change = falling off of operator = transcription possible = induction

Front 223

TQ What is catabolic repression?

Back 223

Block genes for anything else but glucose utilization and once used up make genes to use other things = way cells use glucose 1st

Front 224

TQ Where does the inducer bind?

Back 224

Repressor protein

Front 225

TQ What is the inducer for the lac operon?

Back 225

Allolactose

Front 226

TQ Where do repressor proteins bind?

Back 226

Operator

Front 227

TQ What is the difference b/c + and – control? Give an example.

Back 227

+ : starts transcription (example is gene for maltose)

Front 228

What causes bacteria to fluoresce?

Back 228

Luciferase

Front 229

TQ What is an diauxic growth curve?

Back 229

Two growth curves in one (ie: glucose used up then lactose used up)

Front 230

TQ What is an diauxic growth curve?

Back 230

Two growth curves in one (ie: glucose used up then lactose used up

Front 231

TQ How does attenuation work?

Back 231

RNA folds up onto itself to block transcription (repressor not used) (ie: in case of excess tryptophan)

Front 232

Why are RNA viruses more dangerous?

Back 232

They mutate very easily

Front 233

What causes SARS?
Where did it come from?
What made it possible to be transmitted?

Back 233

Coranavirus (RNA virus)
Savant cats (birds to savant cats to people)
Close proximity of animals and humans in markets, etc.

Front 234

Why can viruses be used to treat bacterial infections and/or cancer?

Back 234

1. bacteriaphage
2. virus looks for protein receptor that’s different on cancer cells that’s not on normal cells so it will infect cancer cells and lyse them and not normal cells.

Front 235

What is a bacteriaphage? Why does it infect the bacteria and not other cells?

Back 235

1. Virus that infects a bacteria.
2. Viruses are very specific. They have receptors that only fit certain cells (ie: bacteriaphage will lyse anthrax cells and not affect other cells = able to target specific cells like using a virus instead of drug)

Front 236

Why are viruses not considered living cells?

Back 236

Because they can NOT replicate on their own

Front 237

Virology is the …

Back 237

Study of viruses

Front 238

The protein coat around a virus…

Back 238

Capsid

Front 239

Inside the protein coat is…

Back 239

DNA or RNA

Front 240

How is a virus host specific?

Back 240

It has specific receptors

Front 241

What is the difference between viruses that infect bacteria and animals

Back 241

Viruses that infect bacteria do not enter the cell, they only inject genetic material. Viruses that infect animal cells the whole virus goes into the cell.

Front 242

What are the two ways a virus can exit the cell?

Back 242

Lyse cell or buds out

Front 243

What does HIV infect

Back 243

T Cells

Front 244

Does a bacteriophage have an envelope?

Back 244

No, they

Front 245

Where are enveloped viruses seen primarily?

Back 245

Animals

Front 246

Where does the envelope come from?

Back 246

Host cells phospholipid bilayer

Front 247

TQ What are the three shapes of viruses?

Back 247

Rod Shaped – (Helical Symmetry)
Spherical – (Icosahedral symmetry)
Complex – (Mix of both)

Front 248

Why does a bacteriophage need lysozyme?

Back 248

To get through the cell wall when entering and exiting the cell.

Front 249

TQX What are neuraminadases?

Back 249

Enzymes that cleave glycosidic bonds in sugars; allows viruses to exit host,

usually associated with the spread of viruses throughout host tissue.

Front 250

What polymerase does viruses carry

Back 250

Reverse transcriptase

Front 251

TQ To grow a virus in the lab you must…

Back 251

grow the host (bacterium first)
Infect with virus
Look for clear areas = placques
plaques = # of bacteria in original sample

Front 252

What is a lawn of bacteria?

Back 252

When bacteria grow across the entire medium

Front 253

Why would this process not work for identifying lysogenic viruses?

Back 253

Because lysogenic viruses won’t form placques

Front 254

Animal viruses must be grown in ______ cultures

Back 254

Tissue

Front 255

How diagnose a viral infection?

Back 255

Indirect diagnosis: Look for specific antibodies instead of growing tissue cultures (difficult)

Front 256

TQ Titer is

Back 256

Number of infectous units per sample

Front 257

Placque Assay

Back 257

Analogous to the bacterial colony; one of the most accurate ways to measure virus infection.

Front 258

What are the steps to the replication cycle of a bacterial virus?

Back 258

1. Attachment
2. Penetration (Injection)
3. Synthesis of Nucleic acid and protein
(transcription & Translation)
4. Assembly & packaging (Cytoplasm)
5. Release (Lysis & budding)

Front 259

Burst Size = ?

Back 259

Number of virions released after one cycle (NOTE: “virion” = virus INSIDE host = infectious whereas virus OUTSIDE host = “virus particle” = usually not infectious)

Front 260

Bacteriophage T4 is what kind of virus?

Back 260

lytic virus

Front 261

What does a restriction enzyme do?

Back 261

Cuts DNA at a specific seuence

Front 262

How can a host cell stop infection from a virus?

Back 262

By having restriction enzymes in its cytoplasm (which would chop up the DNA injected by virus)

Front 263

What does the virus do to resist the hosts Restriction enzymes/

Back 263

Methylation of Viral DNA
Restriction Inhibitory Proteins

Front 264

The __________ system is used to name viruses.

Back 264

Baltimore System

Front 265

What is a +RNA and a –RNA virus

Back 265

Positive Strand RNA virus: single strand RNA used directly as mRNA

Negative Strand RNA virus: Single strand RNA that must transcribe – strand into + strand of mRNA.

Front 266

How does the naked virus get in

Back 266

Inject DNA

Front 267

Envelope virus gets in by

Back 267

phagocytosis (Cell eating)

Front 268

How does ssDNA and dsDNA infect its host?
AKA?

Back 268

ssDNA (+): synthesis of (-) strand, then transcription of (-) strand into mRNA (+)
dsDNA (+): (-)strand transcribed into mRNA (+)

Front 269

What is the temperate mode of the viral life cycle.

Back 269

The virus DNA has been inserted into the host DNA and both are replicated, does not kill host (Method of multiplying virus)

AKA – Lysogenic or Latent Stage

Front 270

What is the temperate mode of the viral life cycle.

Back 270

The virus DNA has been inserted into the host DNA and both are replicated, does not kill host (Method of multiplying virus)

AKA – Lysogenic or Latent Stage

Front 271

What is an example of a temperate virus?

Back 271

Lambda

Front 272

T4 is ___________ that infects _____________.

Back 272

Bacteriophage E-Coli

Front 273

What is the portion that holds the DNA and what is it made out of?

Back 273

Capsid (Proteins)

Front 274

What are the extensions that look like legs called? What is their importance?

Back 274

Tail fibers – Have receptors that match up with the host cell wall.

Front 275

When the cell lyses that is called what stage?

Back 275

The release stage AKA Lysis Stage (hello)

Front 276

What happens when it lysis the host?

Back 276

Kills the cell

Front 277

Whats that clear space on the culture.

Back 277

Placque

Front 278

What is the difference between a virus that infects bacteria and one that infects a human?

Back 278

Animal virus has to enter the cell, the capsid has to be uncoated, releasing the DNA into the cell.

Front 279

What does the virus have that allowed it to inject its DNA into the host?
All this is part of what phase of the lifecycle

Back 279

It had lysozymes that broke the beta 1,4 linkages of the cell wall.
Eclipse

Front 280

DNA Polymerase will

Back 280

Copy the DNA (Including the Phages DNA)

Front 281

It will go through _______ & _________ to make more proteins.

Back 281

Transcriptions / Translation

Front 282

Why will it make more lysozyme?

Back 282

To break out of host cell

Front 283

What is this a lytic virus?

Back 283

B/c it lysis the cell.

Front 284

__________ is the number of viruses released after one cycle of infection?

Back 284

Burst Size

Front 285

What is a temperate virus?

Back 285

They don’t kill the cell b/c they incorporate the viral DNA into the host DNA (ie Lambda)

Front 286

What is a prophage?

Back 286

when the Lambda DNA goes into the host chromosome

Front 287

Temperate viruses are also called ______________ ___________ ____________.

Back 287

AKA Lysogenic, dormant, latent

Front 288

How does the viral DNA of temperate viruses get copied?

Back 288

When the cell goes through binary fission, it will duplicate the viral DNA.

Front 289

Once the viral DNA is incorporated into the E-Coli bacteria it is now called _________________.

Back 289

Lysogenized Bacteria.

Front 290

What does a restriction endonuclease do?

Back 290

Cut DNA at very specific sequences/

Front 291

What is the importance of the sticky ends of DNA.

Back 291

Allows for the incorporation of the cut plasmid into the host DNA

Front 292

What does ligase do?

Back 292

Seal the gap where sticky ends come together

Front 293

Why does a prophage stay in the lysogenic stage?

Back 293

The reason that a prophage stays in the lysogenic stage is that there are repressor proteins that inhibit lytic stage

Front 294

What could we eventually use phages for?
What kind of problem could this cause?

Back 294

Fight infection
If it’s a gram negative bacteria, Lipid A in the LPS is a toxin. Too many cells lyse at once could poison the host.

Front 295

How do we know most of the animal viruses are enveloped?

Back 295

The animal cell does not have cell wall

Front 296

Papoloma virus causes

Back 296

Warts

Front 297

Adenovirus

Back 297

Infects adenoids, causing upper respiratory infections

Front 298

Parvovirus

Back 298

Infects Dogs

Front 299

What is a Reovirus

Back 299

Respiritory Enteric Orphan
Associated with upper respiratory or colon/gut infection that did not fit into other categories.

Front 300

Rhabdovirus causes…

Back 300

Rabies

Front 301

Coronavirus causes …

Back 301

SARS

Front 302

What is unique about a Retroviruses?

Back 302

Has Reverse Transcriptase…RNA  DNA

Front 303

_____ viruses tend to mutate more often.

Back 303

RNA

Front 304

When you get infected with any of these viruses you build up what?

Back 304

Antibodies

Front 305

How do you build up antibodies?

Back 305

Body recognizes protein as foreign, makes antibodies, next exposure antibodies bind to virus and blocks attachment.

Front 306

How long does it take to make antibodies?

Back 306

1 week to 10 days

Front 307

How does a vaccine work?

Back 307

It introduces your body to the virus, and you make a secretory antibody (IGA), that I in your secretions and it never comes into body.

Front 308

How do viruses normally get out of host cell?

Back 308

Bud out

Front 309

Transformation means to do what?

Back 309

Change

Front 310

What is contact inhibition? And why is it important in tumors.

Back 310

Cells grow to certain density then stop, tumors acquire a mutation that renders contact inhibition unproductive

Front 311

Retroviruses

Back 311

Enveloped, RNA virus, contains reverse transcriptase, also have integrase and protease.

Front 312

What does + orientation mean when speaking of RNA viruses

Back 312

Everything is the same as mRNA, which means translation of protein and copied to make more of RNA

Front 313

Viroids are…

Back 313

only RNA that infects plants.

Front 314

Prions are…

Back 314

infectious proteins that cause normal proteins to change shape.

Front 315

Prions

Back 315

Infectious Protein: Normal protein changes into mis-shaped protein, causing plaques in brain

Front 316

Prions disease in generally called:

Back 316

Spongiform Encephalopathy

Front 317

Diseases caused by Prions and what animal it affects…

Back 317

1. Scrappies (Sheep)
2. Cruchfeld-Jacobsen Disease (Humans)
3. Kuru (Humans – Papua New Guinea Tribe)
4. Mad Cow Disease (Cows Duh)
5. Chronic Wasting Disease (Deer)

Front 318

First prion found…

Back 318

First prion found… Sheep, called scrappies b/c they would scrape off their coats, transmitted to cows b/c sheep brain was fed to cows in feed.

Front 319

Primary workhorse for bacterial genetics

Back 319

E-coli

Front 320

What do you see when you look at the E-coli Chromosome?

Back 320

LAC Operon
TRP Operon
Histodine

Front 321

Origin of Replication

Back 321

Where replication starts

Front 322

What is a Plasmid?

Back 322

Made out of DNA, Circular, with few genes, Can be passed between bacteria.

Front 323

How can you cut a plasmid?

Back 323

With restriction enzyme (Endonuclease)

Front 324

Plasmids are used to…

Back 324

Transfer genes into other bacteria

Front 325

To clone something one would…

Back 325

Cut plasmid with restriction endonuclease, insert gene of interest, insert plasmid into bacteri, allow bacteria to transcribe & translate cloned product

Front 326

Plasmids have origin of replication so they can…

Back 326

make multiple copies within the cell

Front 327

Taking the plasmids out is called…

Back 327

Curing

Front 328

What was it about the temperate phages, what did they?

Back 328

They incorporated their DNA via a plasmid into the host cell or chromosome.

Front 329

Is the plasmid essential for cell function?

Back 329

No, but it does enhance the bacteria in some way. (May be a toxin, capsule or resistance gene)

Front 330

_______________ is used in bioremediation b/c it can break down octane & camphor.

Back 330

Psuedomonias

Front 331

What are the things that bacteria produce via plasmid that can make them more virulent?

Back 331

Resistance
Tumor Formation
Bacteriosin
Hemolysin
Toxins and Capsules

Front 332

______________ means the antibiotic won’t kill the organism.

Back 332

Resistance

Front 333

Bacteriosins are…

Back 333

Proteins produced by bacteria that inhibit or kill closely related species or even different strains of the same species (similar to antibodies)

Front 334

Cloning is …

Back 334

when you take a gene from one place, put it in a bacteria and get the gene product back.

Front 335

Mutation is …

Back 335

a heritable change in the genetic sequence, can be positive, negative or neutral.

Front 336

Wild type is the organism found in ________.

Back 336

Nature

Front 337

Two types of radiation that can cause damage to DNA

Back 337

Ionizing and Non Ionizing

Front 338

Examples of Ionizing radiation

Back 338

x-rays & Gamma rays

Front 339

How do Ionizing radiation cause damage?

Back 339

Cause free radicals that break DNA because of the short wavelength which penetrate causing cancer.

Front 340

Examples of non-ionizing radiation.

Back 340

UV Light and Microwaves

Front 341

Non-ionizing radiation causes the DNA strand to form ______.

Back 341

Thymine–Thymine Dimers, (more exposure causes more dimmers and the cell can’t repair.)

Front 342

Thymine–Thymine Dimers, (more exposure causes more dimmers and the cell can’t repair.)

Back 342

Skin Cancer

Front 343

Skin Cancer

Back 343

Amino Acid ; protein

Front 344

What are nucleoside analogs?

Back 344

Chemical mutagens that look like a regular nucleotide base but have a different side chain. When incorporated into the DNA strand it will cause the base pairing to be wrong.

Front 345

What are nucleotide analogs?

Back 345

Chemical mutagens that look like a regular nucleotide base but have a different side chain. When incorporated into the DNA strand it will cause the base pairing to be wrong. exampleAZT – (aids treatment)

Front 346

Example of frameshift mutations are…

Back 346

Ethidium bromide – (stain that incorporates itself into the DNA used for Gel Electrophoresis)

Front 347

Why would you want to know that ethidium bromide could cause a frame shift?

Back 347

Duh, wear your gloves when handling…can cause cancer

Front 348

A ________________is one that you can look for.

Back 348

selectable mutation

Front 349

Antibiotic resistance is a selectable mutation and if a bacteria is resistant to penecilin it will________ on a penecilin media.

Back 349

GROW

Front 350

______________ are things that you have to screen for by looking at a multitude of things to find certain characteristics

Back 350

Nonselectable Mutation

Front 351

What are some examples of nonselectible mutations?

Back 351

Pigment Production, Loss of pigment

Front 352

What are some examples of nonselectible mutations?

Back 352

Pigment Production, Loss of pigment

Front 353

Replica Plating looks for mutants that are _____________.

Back 353

Auxotroph

Front 354

________ is a mutant with a nutritional requirement (example; Histodine)

Back 354

Auxotroph

Front 355

____________ media has all of its ingredients and ____________ media lacks one ingredient.

Back 355

Complete Minimal

Front 356

____________ media has all of its ingredients and ____________ media lacks one ingredient.
Why does everything grow on the complete media?

Back 356

Complete Minimal
B/c all of the nutrients are there,

Front 357

Why are there some colonies that do not grow on the incomplete media?

Back 357

B/c those are the auxotrophs that required the missing ingredient from the complete media.

Front 358

How do you determine which are the mutants?

Back 358

Compare the two colony growths from the complete and incomplete medias and see which did not grow on the incomplete media. Those are the mutants.

Front 359

If you induce something you …

Back 359

make it happen or force it to happen

Front 360

Induced mutation…

Back 360

One that we force to happen by exposing the bacteria to a mutagen

Front 361

Spontaneous mutation

Back 361

Happen in nature as a result errors in replication or the exposure to natural radiation.

Front 362

Spontaneous mutation

Back 362

Happen in nature as a result errors in replication or the exposure to natural radiation.

Front 363

DNA to mRNA is what?

Back 363

Transcription

Front 364

mRNA to amino acid sequence is?

Back 364

Translation

Front 365

Where does the mutation happen?

Back 365

on DNA strand

Front 366

Silent mutation

Back 366

When base pair substitution occurs and resulting mutation does not change the amino acid
(Example: AAA AAG both code for Phe)
Change in Genotype NOT Phenotype

Front 367

Missence Mutation

Back 367

The base pair substitution created a different codon that coded for a different amino acid. Results in a protein with a different conformation (shape).

Front 368

The codons that code for amino acids are called _____________?

Back 368

Sense codons

Front 369

Nonsence Mutation

Back 369

A base pair substitution that causes a stop codon to occur, instead of an amino acid, forming an incomplete protein. Likely to be most lethal.

Front 370

Frameshift Mutation

Back 370

When nucleotides are inserted or deleted which causes a change in the reading frame. This changes all of the codons that are downstream.

Front 371

Reversion

Back 371

Change that occurs when the mutation goes back to the wild type. (reverses of previous mutation)

Front 372

Non-Ionizing radiation causes ______________ to occur.

Back 372

Thymine – Thymine Dimers

Front 373

Ionizing radiation causes …

Back 373

free radicals which break DNA causing serious mutations

Front 374

What is the SOS system?

Back 374

What is the SOS system?

Front 375

What is the SOS system?

Back 375

Take salmonella bacteria that is an auxotrophic mutant, expose it to potential carcinogen, if back mutation occurs, the chemic may be carcinogen.

Front 376

Transformation by definition is…

Back 376

the uptake of free DNA

Front 377

Where did free DNA come from?

Back 377

A Plasmid of a cell that lysed

Front 378

Cells that take up DNA are called ____________.

Back 378

Competent

Front 379

How could you make that were competent?

Back 379

By growing in calcium

Front 380

Explain Griffiths Experiment

Back 380

Two strains of Streptococcus pneumonia,
Smooth (S) and Rough (R) strains
R = not virulent
S = Virulent (due to capsule)
Heat killed S strain = not virulent
Mix Heat Killed S and Live R = Virulent
Live S cells found in blood of this rat.
Tells us that the R strain picked up plasmid from S strain and develop capsule.

Front 381

What’s the difference between repression and induction?

Back 381

Repression = when you have repressor protein bond to operator that stops transcription.

Induction = when inducer binds to repressor protein so that it falls off and allows transcription to happen.

Front 382

Do bacteria have histones?

Back 382

No. Histones are found in eukaryotic cells and hold DNA together.

Front 383

What is the uptake of free DNA called?

Back 383

transformation

Front 384

Cells have to be what for transformation? What does this mean? How is this accomplished?

Back 384

1. competent
2. able to uptake free DNA
3. some naturally occurring competent like streptococcus but to make most competent =
- grow in high levels of calcium OR
- electroporation (hitting bacteria w/ electrical pulses that makes them uptake some DNA)

Front 385

What is diff b/w transfection and transduction?

Back 385

Transfection = transformation with DNA naked by itself taken from bacteriophage Transduction = transfer of DNA using a replicating virus (aka phage) itself

Front 386

A virus that infects bacteria is called a ?

Back 386

Bacteriophage OR phage

Front 387

What are the 2 types of transduction?

Back 387

1. generalized transduction
- initiated during lytic cycle of virulent bacteriophage
- donor DNA can be any fragment of bacterial chromosome
2. specialized transduction
- initiated during lysogenic cycle of temperate bacteriophage
- donor DNA is very specific part of chromosome adjacent to prophage

Front 388

When is generalized transduction initiated?

Back 388

During the lytic cycle of virulent bacteriophage

Front 389

When is specialized transduction initiated?

Back 389

During lysogenic cycle of temperate bacteriophage

Front 390

What is a transducing phage?

Back 390

Composed of phage proteins filled with bacterial DNA (carrying DNA from bacteria that was infected)

Front 391

When is specialized transduction initiated?

Back 391

During lysogenic cycle of temperate bacteriophages.

Front 392

What happens
During lysogenic cycle of temperate bacteriophages.

Back 392

Phage DNA becomes incorporated into bacterial chromosome

Front 393

What is the phage DNA called once it becomes incorporated into a bacterial chromosome?

Back 393

prophage

Front 394

A recipient bacterial cell incorporates new injected DNA into its own chromosome through what?

Back 394

Recombination (bacterial cell is now recombinant)

Front 395

The prophage is cut out from the host chromosome during what?

Back 395

Induction (this may take with it some of the host bacterial genes therefore new recipient will have prophage + new bacteria genes)

Front 396

What can specialized transduction be used for?

Back 396

Transferring antibiotic resistant from one bacterium to another

Front 397

What does the phage end up with during generalized transduction?

Back 397

Bacterial DNA = new recipient cell able to make proteins that this codes for

Front 398

What is transduction?

Back 398

Transfer of DNA by phages

Front 399

What is transduction?

Back 399

Transfer of DNA by phages

Front 400

In conjugation, the cells must do what?

Back 400

Touch each other to transfer DNA

Front 401

Touch each other to transfer DNA
What are the short ones called?

Back 401

Pilli
fimbrae

Front 402

What is the F factor?

Back 402

Fertility factor aka F plasmid (E.Coli that have this = F+ = able to have conjugation pilus and serve as DNA donors during conjugation

Front 403

What does a cell do once it has pilus?

Back 403

Rolling replication = copy one strand of DNA which goes through pilus to F- which turns F- into F+

Front 404

What’s special about F+ cells?
What is coded for on the plasmid?

Back 404

Has F factor (aka plasmid which can be self replicating)
Ability to make pilus

Front 405

What is a cell called when the F factor goes into the chromosome?

Back 405

High frequency recombinant

Front 406

What basically happens during Hfr factor?

Back 406

Adding to diversity. Recipient cell remains F- because it does not get full copy of F+ genes but has new genes added to its chromosome.

Front 407

It is called the _____ ______ replication when a bacterial cell goes from F+ to F-.

Back 407

Rolling circle replication

Front 408

When the F plasmid goes into the chromosome, the cell is called what?

Back 408

Hfr cell (high frequency of recombination cell)

Front 409

What are transposons and insertions sequences used to do? In what are they most commonly found in use?

Back 409

1. another way to move DNA around
2. in eukaryotes

Front 410

What is the simplest transposable element?

Back 410

Insertion sequence

Front 411

What is an insertion sequence?

Back 411

Series of nucleotides in a certain order that go into chromosome

Front 412

What moves DNA b/w inverted repeats?

Back 412

Transposons (these are larger than I.seq.)

Front 413

The process of conjugation can be used to help geneticists do what?

Back 413

Map the genome of bacteria

Front 414

What is a nutritional mutant called?

Back 414

auxotroph

Front 415

The technique used to look for nutritional mutants is called what?

Back 415

Replica plating (this involves the minimal (=has minimal) and the complete media (=has everything)

Front 416

What is a segment of DNA that can moved from one location to another called? How does this happen?

Back 416

1. transposon
- simple = contain only elements necessary for transposition
- complex = also carry other elements (ie: gene for antibiotic resistance)
2. the segment of DNA also has the gene coding for transposase (enzyme that cuts out of one location and inserts in another and also forms covalent bond b/w itself and new host DNA)

Front 417

What is the simplest transposon called?

Back 417

Insertion sequence = tranposase gene flanked by inverted repeat

Front 418

What is the simplest transposon called?

Back 418

Insertion sequence = tranposase gene flanked by inverted repeat

Front 419

What do complex transposons consist of?

Back 419

Consists of 2 simple transposons with another sequence of DNA b/w them

NOTE: this DNA is often a gene that gives some selective advantage to the organism containing transposon (ie: antibiotic resistance)

Front 420

What are the simplest transposable element?

Back 420

The insertion sequence

Front 421

Transposae moves any DNA between what?

Back 421

Inverted repeats

Front 422

“in-vitro” means what?

Back 422

In a test tube

Front 423

Following are the basic techniques at alter genetic material. What does each one do?
1. restriction enzymes
2. gel electrophoresis
3. nucleic acid hybridization
4. nucleic acid probes
5. molecular cloning
6. cloning vectors

Back 423

1. enzymes that cut DNA (blunt ends and sticky ends)
2. get different bands (use + and – poles to pull DNA through gel)
3. hybrid = combine from 2 sources (complimentary base pairing)
4. single stranded used to look for complimentary strands (usually put radioactive label on that probe)
5. cut gene from source (with restriction genes) and then cut and paste into plasmid (cut plasmid and gene with same restriction enzymes) and they hybridize. Transformation technique is used to put plasmid in bacteria which will undergo transcription / translation for the gene (ie: insulin)
6. carry the gene (DNA) = plasmid or phage

Front 424

Does DNA/RNA need to be in single strand or double stranded form to hybridize?

Back 424

Single stranded form

Front 425

What is the reason DNA/RNA hybridize?

Back 425

Complimentary base pairing

Front 426

What do vectors do?

Back 426

Carry things

Front 427

What is the vector for:
1. lyme disease?
2. malaria?

Back 427

1. tick
2. mosquito

Front 428

What are the two primary vectors used in recombinant DNA technology?

Back 428

1. plasmids
2. phages

Front 429

What do restriction enzymes do?

Back 429

Cut DNA

Front 430

What do you end up with after restriction enzymes are used?

Back 430

either
1. sticky ends = single stranded DNA at each end = can easily recombine / base pair with another single strand which end up with blunt ends
2. blunt ends

Front 431

What is the 1st restriction enzyme found?

Back 431

EcoR1

Front 432

What are the following examples of?
EcoR1, Hind III, Hhal

Back 432

Names of restriction enzymes

Front 433

Where do restriction enzymes come from?

Back 433

Naturally from the cells and helps to protect cell from invasion from foreign DNA by cutting it up (NOTE: cell has to protect itself from its own restriction enzymes so it modifies the DNA to do that)

Front 434

What is gel electrophoresis?

Back 434

1. dye DNA
2. run charge through gel (DNA naturally negatively charged) (NOTE: gel has pores to physically allow passage of certain sized DNA)
3. stain with ethidium bromide

Front 435

What do you use to stain a gel electrophoresis? What does this cause and how?

Back 435

1. ethidium bromide
2. cancer b/c gets b/w bases causing a mutation

Front 436

What kind of light is needed to see the stain in gel electrophoresis?

Back 436

UV light

Front 437

What is the map of the location of restriction enzyme cuts on a segment of DNA called?

Back 437

Restriction map

Front 438

What is a nucleic acid probe used for and in what technique? Is it single stranded or double stranded?

Back 438

1. it is used in nucleic acid hybridization that is used to look for another complimentary piece of DNA
2. single stranded

Front 439

“Southern blot” and “Northern blot” are two names for what kind of technique?

Back 439

Nucleic acid hybridization

Front 440

What are the 3 main steps of gene cloning?

Back 440

1. isolation and fragmentation of source DNA (EX: source = pancreas cells for insulin) (NOTE: fragmented / chopped up by restriction enzymes and gel electrophoresis used to isolate whatever size DNA they want)
2. insert DNA into cloning vector (vector most likely plasmid but also could be phage) (NOTE: plasmid needs to be cut w/same restriction enzymes and it becomes hybridized)
3. introduction of cloned DNA into host organism (ie: E Coli)

Front 441

What is used to seal the DNA during the hybridization process?

Back 441

DNA Ligase

Front 442

What is the process by which scientists can modify the genome of an organism?

Back 442

Recombinant DNA technology (insert desirable or remove undesirable genes)

Front 443

A method that is used by scientists to screen for nutritionally defective mutants is called what?

Back 443

Replica plating

Front 444

Explain this process:Replica plating

Back 444

1. bacterial cells treated with X-rays or mutagen (NOTE can be radiation or chemical) to induce mutation in genome
2. cells grown on master plate (complete medium) w/ all necessary A.A., etc to form colonies on the plates
3. plates pressed onto blocks covered with sterile velvet (stamping)
4. imprint is stamped onto 2 other plates (one w/ complete medium and one w/ minimal medium)
5. replica plates are examined for differences in the growth of the colonies (NOTE: cells that grow on complete medium and not on minimal medium = mutants which can then be isolated from master colony for study)

Front 445

What is replica plating used to look for?

Back 445

Auxotrophs = mutant that has a nutritional requirement

Front 446

What is used to cut a plasmid at the gene?

Back 446

Restriction enzymes

Front 447

Why do the plasma and the gene go back together?

Back 447

Complimentary base pairing at the sticky ends?

Front 448

What enzyme allows it to seal off?

Back 448

Ligase

Front 449

How do we get plasmid into host cell?

Back 449

Transformation = uptake of free DNA

Front 450

The plasmid with the gene in it is called?

Back 450

Recombinant

Front 451

What are the 2 possible vectors?

Back 451

Plamids or phages

Front 452

Why do you want to cut them with the same enzyme?

Back 452

End up w/ same cut = increase chance of them coming together

Front 453

What is the host likely to be?

Back 453

Bacteria (E.Coli mostly)

Front 454

Why is it important that plasmids have selectable markers?

Back 454

To know if the plasmid picked up the gene or not (marker will help you know)

Front 455

What is pUC19?

Back 455

Example of a plasmid vector

Front 456

What does pUC19 have?

Back 456

Amphicillin resistance and lacZ gene (part of the lac operon)

Front 457

What does lacZ produce?

Back 457

B-galactosidase

Front 458

What technique is used to determine whether or not a colony has a vector with foreign DNA inserted = test for recombinants / mutants?

Back 458

Blue/White screening (have to get plasmid in there and also get gene in plasmid)

Front 459

What media is used to test for lactose utilization?

Back 459

X-gal = substitute for lactose

Front 460

If pUC19 makes B-galactosidase, what color will this media be?

Back 460

Blue

Front 461

If pUC19 makes B-galactosidase, what color will this media be?
If not, what color?
What color would the mutant be?

Back 461

Blue
White
White

Front 462

What are the markers for pUC19?

Back 462

Amphicillin and B-galactosidase

Front 463

What are the most common markers?

Back 463

Antibiotic resistance and the lacZ gene (because of X-gal)

Front 464

What is the most common method of sequencing?

Back 464

Sanger dideoxy method (invented by Sanger)

Front 465

What is sequencing?

Back 465

Order of nucleotides

Front 466

What does PCR do?

Back 466

Amplifies DNA (when need more copies of DNA)

Front 467

What polymerase is used for PCR?

Back 467

tAq polymerase

Front 468

What’s special about this Thermos aquaticus

Back 468

Doesn’t denature in high heat
Thermos aquaticus=thermophil =archaea

Front 469

What does high temp break?

Back 469

Hydrogen bond b/w bases to be able to separate DNA strands to replicate it

Front 470

What replicates DNA?

Back 470

DNA Polymerase

Front 471

What is the piece of DNA called that is being amplified by PCR?

Back 471

Target DNA

Front 472

What are steps of PCR?

Back 472

1. denaturing (=high temp=94 C)
-separates DNA strands
2. priming (=low temp=60 C)
3. extension (=int. temp=72 C)

Front 473

What is the machine called that changes the temperature during the PCR process?

Back 473

thermocycler

Front 474

Why does PCR require a primer?

Back 474

b/c DNA P.ase needs 3 prime end (-OH)

Front 475

What are the most common cloning hosts:

Back 475

1. E.Coli = Gram – rod
2. Bacillus subtilis = Gram + rod (has spores)
3. Saccharomyces = yeast (used to make bread)

Front 476

What is the disadvantage of using E.Coli for cloning?

Back 476

It is potentially a pathogen

Front 477

What is transfection? What are 4 ways transfection is accomplished?

Back 477

1. introduction of DNA into mammalian cells
2. accomplished by:
- phagocytosis of DNA by host cell
- using microinjection (like in vitro fertilization)
- by electroporation
- by gene gun

Front 478

What are the nucleic acid probes or antibodies labeled with?

Back 478

Radioactive dye (ie: P32)

Front 479

Xrays and Gamma rays are examples of what? What do they cause?

Back 479

1. ionizing reaction
2. highly reactive ions & free radicals which can then combine w/ bases on DNA resulting in errors (mutations) OR can react w/ sugar phosphate backbone causing breaks in chromosomes

Front 480

What is UV light an example of? What can it cause?

Back 480

1. non ionizing radiation
2. thymine dimmers

Front 481

What are the 2 main types of mutations?

Back 481

1. base substitution mutation
- silent = no change in A.A. seq. (affect genotype but not phenotype)
- missense = changes 1 A.A. = could be harmful or helpful
- nonsense = changes A.A. to stop codon = premature ending of protein = harmful
2. frameshift mutation (lead to nonfunctional protein)
- insertion = nucleotide base(s) inserted
- deletion = nucleotide base(s) removed

Front 482

What type of DNA repair mechanisms do cells have?

Back 482

1. light-repair enzymes = break bond b/w adjoining thymine nucleotides
2. excision-repair enzymes = cut out damaged DNA (DNA P-ase fills in)
3. mismatch-repair enzymes (NOTE: cannot repair once mutation becomes methylated)

Front 483

What is the most common form of mutation?

Back 483

Thymine dimmers caused by exposure to UV light

Front 484

A protein called a what binds to the A site when a ribosome reaches a stop codon during translation?

Back 484

Release factor