Genetics Exam 2

Front 1

The table above gives the results from intercrossing beetles with seven forms of mutant elytra (striated, punctate, rugose, wrinkled, fuzzy, glabrous, shiny, rough, scapose). An + in the table indicates that the offspring had a wildtype phenotype, a - indicates non-wildtype elytra. On these results, the cross between glabrous and fuzzy is best explained as:

Back 1

complementation

Front 2

In a human population the genotype frequencies at on locus are f(aa) = 0.51, f(Aa) = 0.43, and f(AA) = 0.06. The frequency of the A allele is_____?

Back 2

0.285

Front 3

In Drosophila the sv/+ locus is normally located at the end of a chromosome arm. The recessive allele sv shortens and flattens the bristles. In a certain
sv/+ heterozygotes, the + allele is relocated next to the centromere by an inversion. This fly showed patches of shaven and wild type bristles on its body.
This is an example of:

Back 3

position effect variegation

Front 4

When an autotetraploid is backcrossed to its parent species, sterile offspring are produced. Such sterile offspring can be best represented by:

Back 4

3n

Front 5

In a particular strain of tomato, fruit color is determined by the following three alleles: R = red, r = albino, and rm = albino (R with Te inserted). A cross
is made between rm/r Te+/Te+ and R/r Te/Te+. What will be the phenotypic ratio in the progeny? [Assume that Te does not jump into the non-inserted R
allele or break the chromosome containing the R allele.]

Back 5

1/2 red, 1/4 albino, 1/4 albino with red spots

Front 6

The norm of reaction is important because:

Back 6

the range of phenotypes produced by a genotype will vary depending on the environment

Front 7

Suppose you have a large population of flour beetles. Red body color is due to a dominant allele, R; individuals who are genotypically RR or Rr are red.
Individual which are homozygous recessive rr have black body color. If the population is in Hardy-Weinberg equilibrium, with f(R) = 0.55 and f(r) = 0.45, what are the expected frequencies of the red and black phenotypes?

Back 7

80% red, 20% black

Front 8

What is the name of the enzyme that, during DNA replication, extends the lagging strand from the 3' end of each RNA primer?

Back 8

DNA polymerase III

Front 9

What would happen during DNA replication in a cell lacking topoisomerase?

Back 9

DNA ahead of the replication fork would become increasingly tightly coiled.

Front 10

What observation(s) were crucial in allowing Watson and Crick to propose the double helix structure of DNA?

Back 10

Chargraff's rules concerning the relative frequency of different nucleotides and Franklin's X Ray diffraction of the DNA molecule.

Front 11

Which of the following distinguishes RNA from DNA?

Back 11

RNA has an oxygen at the 2’ position of ribose.

Front 12

In what way did the Avery, MacLeod and McCarty experiment build on Griffith’s experiment? They:

Back 12

Identified DNA as the transforming factor through a process of elimination.

Front 13

This parental helix of DNA is replicated in a test tube containing all the proteins necessary for DNA replication, GTP (guanosine triphosphate) and radioactive CTP (cytosine triphosphate - 32P):

5’-GGGGGGGGGGG-3’ 3’-CCCCCCCCCCC-5’

What pattern of radioactivity would you expect among the new helices?

Back 13

Only 1 of the new helices would be radioactive it is possible to predict which one

Front 14

In E. coli, what do sigma factors do during transcription?

Back 14

Help the holoenzyme to bind to the promoter

Front 15

In prokaryotes, the functional equivalent of the TATA binding protein is:

Back 15

Sigma factor.

Front 16

You delete a gene coding one of the proteins required for splicing (removing) introns from pre-mRNA. This deletion mutation stops growth of a yeast cell. Why?

Back 16

Failure to remove introns will lead to non-functional proteins because their primary sequence will be derived from introns as well as exons.

Front 17

Which answer combines the correct responses to the questions below?
(i) What is the name of the structure shown below?
(ii) What is its function in transcription?
(iii) What is the probable base composition of the region marked by the “A” arrow?
(iv) What is the probable base composition of the region marked by the “B” arrow?

Back 17

(i) Hairpin loop; (ii) Termination of transcription in prokaryotes; (iii) G/C rich; (iv) string of U’s.

Front 18

In this picture of DNA, which number identifies the leading strand and how can you tell?

Back 18

1 because the 3’ end is extended in the same direction as the replication fork

Front 19

What is the name of the sequence region recognized by the bacterial ribosome?
A. -10 and -35 consensus sequences.

Back 19

Shine-Dalgarno

Front 20

Which of the following constitutes the primary structure of a protein?

Back 20

The linear sequence of amino acids in a polypeptide chain.

Front 21

What experimental observation addressed the likelihood of the genetic code being overlapping?

Back 21

A mutation changing a single nucleotide changed one amino acid in the corresponding protein.

Front 22

Which of the following is an important feature of the genetic code?

Back 22

-It is a triplet code.
-Each codon specifies no more than one amino acid.
-It is degenerate.
-It is non-overlapping.

Front 23

What answer represents the most likely order of the severity of the phenotypic effect resulting from the different types of mutations listed below. (Answers are ranked from most to least severe.)

i. Insertion of a nucleotide causing a shift in the codon reading frame.
ii. Nucleotide substitution that does change the amino acid a codon codes for.
iii. Nucleotide substitution that does not change the amino acid a codon codes for.

Back 23

i>ii>iii

Front 24

A newly discovered set of genes – the hou operon – are transcribed from the same promoter. They allow the bacteria to use a rare sugar, houstose. This sugar doesn’t give much energy when it is broken down, but, when nothing else is available, it is better than nothing. In what combination of environmental conditions would you expect bacteria to express the hou operon? (Assume that conserving energy used in expressing a gene is important – if a bacteria does not need to express a gene, it won’t.)

Back 24

In the presence of houstose and the absence of any other more effective nutrient source.

Front 25

The lac repressor (LacI) binds to:

Back 25

Lactose and DNA.

Front 26

Does the lac repressor (LacI) act as a cis or a trans regulator?

Back 26

Trans.

Front 27

A mutant strain of E. coli has the following genotype at its lac operon (assume all other genes are functional): I+ P+ O- Z+ Y+ A+ (I = repressor; P = promoter; O = operator; Z,Y,A = structural genes). Which of the following answers best match the environments in which the operon will be expressed at a high level?

Back 27

Glucose is absent, regardless of the presence of lactose.

Front 28

What is the best explanation for both positive (cAMP-CAP) and negative (LacI) regulation being needed to ensure that the lac operon is only expressed when it is needed?

Back 28

Each control system (cAMP-CAP and LacI) is sensitive to only one environmental condition (glucose or lactose) – both controls are needed for regulation by both glucose and lactose.

Front 29

How does tryptophan inhibit transcription of the trp operon through attenuation?

Back 29

The ribosome NOT pausing at two consecutive trp codons in the leader region causes mRNA to fold in a way that terminates transcription by RNA polymerase

Front 30

In yeast, the Gal structural genes are controlled by the regulatory proteins Gal4, Gal80 and Gal3. Gal4 is a positive regulator which binds to activation sequences upstream of the Gal structural genes. Gal80 binds to Gal4 and inhibits the ability of Gal4 to activate gene expression. In combination with galactose, Gal3 reduces Gal80 inhibition and allows Gal4 to activate Gal structural gene expression. How would you expect the expression of Gal structural genes to depend on galactose in a Gal80- mutant?

Back 30

Expression of Gal structural genes would be ON, regardless of the presence of galactose.

Front 31

What are the base (default) positions of bacterial and eukaryotic promoters – that is, will gene transcription be ON or OFF in the presence of RNA polymerase and any accessory proteins but in the absence of any specific transcription factors?

Back 31

Bacterial promoters are ON and Eukaryotic promoters are OFF by default

Front 32

The hunchback gene has an enhancer containing 3 binding sites for the transcription factor Bicoid. How could the loss of a single DNA binding site – leaving 2 others intact – act to reduce gene expression of hunchback by more than 1/3?

Back 32

Bound Bicoid transcription factor molecules interact cooperatively to cause maximal gene expression.

Front 33

Which of the below are types of analyses that you could perform if you knew the entire sequence of a genome?

Back 33

All of the above

Front 34

Which of the following is a key advantage of reverse genetics in comparison with forward genetics? (Reverse genetics: observing the phenotypic consequence of disruption of a specific gene. Forward genetics: Identifying the genetic changes that are associated with a particular phenotype.)

Back 34

Only reverse genetics can establish cause and effect between a genetic change and a phenotypic consequence.

Front 35

Central Dogma

Back 35

DNA is information coding molecule
-it gets replicated (DNA->DNA)
-passes on information to intermediary (DNA->RNA) *transcription
Translation- information is conversion of the RNA information to Protiens

Front 36

Bacterial Transcription

Back 36

2 dna strands separate (replication bubble) - one strand acts as template.
RNA polymerase assembles an RNA strand using DNA template strand.
RNA (U, A, C, G vs. A, T, G, C for DNA)

Front 37

RNA Replication assembly proceeds at

Back 37

5' to 3' (new nucleotides to 3' end)

Front 38

In DNA replication the DNA strand that is not used as a template is called the _____ __________.

Back 38

coding strand

Front 39

Classes of RNA

Back 39

INFORMATIONAL:
Messenger RNA

FUNCTIONAL:
transfer (tRNA)
ribosomal (rRNA)
small nuclear (snRNA)
micro (miRNA)
small interfering (siRNA)

Front 40

Informational RNA

Back 40

intermediate between DNA sequence and protien sequence

Front 41

Functional RNA

Back 41

carry out some physiological role as RNA molecules

Front 42

Central Dogma: Condensed

Back 42

DNA Polymerase - REPLICATION
RNA Polymerase - TRANSCRIPTION
Ribosome - TRANSLATION

Front 43

DNA:A
RNA:__

Back 43

U

Front 44

DNA:T
RNA:__

Back 44

A

Front 45

DNA:G
RNA:__

Back 45

C

Front 46

DNA:C
RNA:__

Back 46

G

Front 47

__________RNA polymerases can __________ transcribe a _______ gene.

Back 47

Multiple, simultaneously, single

Front 48

Three stages of Transcription

Back 48

-initiation
-elongation
-termination

Front 49

What suggested that RNA might serve a role as an intermediate between DNA and proteins?

Back 49

Scientists noticed a burst of RNA production immediately following bacteriophage infection.

Front 50

RNA is usually _______ stranded, but still able to base pair (with itself) through _________ _________, this usually happens '____-__________' which give RNA _____________ ________.

Back 50

single stranded (ssRNA), hydrogen bonds, 'intra-molecularly', specific shapes

Front 51

DNA has ______sugar and RNA has _______ sugar in each nucleotide

Back 51

deoxyribose, ribose

Front 52

RNA can do _______ _______ ______(as can protien) and DNA cannot.

Back 52

catalyze chemical reactions

Front 53

ribozyme

Back 53

RNA that catalyzes reactions

Front 54

U=______ -> for RNA
T=______ -> for DNA

Back 54

Uracil
Thymine

Front 55

DNA structure frame used to organize the flow of information transfer inside a cell was proposed by:

Back 55

Crick

Front 56

Step 1 of transcription:
DNA-DNA

Back 56

DNA strands locally separate (a bubble) - one strand acts as template the other is coding strand

Front 57

Step 2 of transcription: RNA
DNA-RNA

Back 57

An RNA strand is assembled using the template DNA strand as a guide. 5'-3' of the DNA (new nucleotides added to 3' end of RNA growing chain)
-assembly done by RNA polymerase

Front 58

Transcription: Initiation
(prokaryote transcription initiation)

Back 58

-promoter indicates, to RNA polymerase, where to begin RNA synthesis (promoters located upstream of the region of DNA to be transcribed

Front 59

Consensus

Back 59

average sequences that seems to be recognized by RNA polymerase - the sequences are the core of the promoter.
-TATAAT (-15)
-TTGACAT (-35)
Usually promoters with sequence close to the consensus will be better recognized by RNA polymerase and transcribed at a higher rate.

Front 60

Initiation:

Back 60

-RNA polymerase complex scans DNA and recognizes a promoter (specifically the -10 and -35 sequence stretches)
-DNA is unwound in this location to reveal single stranded DNA (ssDNA)
-Transcription begins from the +1 position - located just downstream of the promoter

Front 61

5' untranslated region

Back 61

(5' UTR) - upstream region of mRNA between transcription start and start of gene is called this. This has sequence important for translation that the ribosome recognizes.

Front 62

RNA polymerase holoenzyme

Back 62

multi-protein enzyme that consists of:
-2 alpha units, 1 beta unit, 1 beta' unit, 1 omega unit (core enzyme - nessasary for function)
-sigma factor: directs enzyme to promoter

Front 63

Sigma factor 70

Back 63

directs RNA polymerase to the promoter ( -10 and -35 upstream region before the start of transcription)
-sigma factor is released once the transcription begins

Front 64

RNA must _______ the _____ _______ as it travels down the gene being transcribed - forming a '_________ ______'

Back 64

unwind, DNA helix, 'transcription bubble'

Front 65

Single free RNA nucleotides are synthesized in other reactions in the cell. What happens when they com into contact with the RNA polymerase

Back 65

When complimentary match to the ss DNA occurs the RNA polymerase adds it to the 3' end of the RNA chain

Front 66

Signals that cause RNA polymerase to release from the DNA helix:

Back 66

Intrinsic and Rho-dependant

Front 67

Intrinsic

Back 67

strong hairpin/ stem-loop (intra molecular bonding) RNA pairs with itself. structure followed by a region of weak binding between RNA and DNA destablizies the RNA polymerase and it is released from the DNA helix

Front 68

Rho-dependant:

Back 68

rho protein binds to the RNA strand and travels down until it reaches the RNA polymerase and displaces it from the DNA helix

Front 69

which has more genes? bacteria or eukaryotes?

Back 69

eukaryotes (1-10 times as many)

Front 70

Three RNA polymerase

Back 70

RNA Polymerase I
RNA Polymerase II
RNA Polymerase III

Front 71

RNA polymerase I

Back 71

transcribes ribosomal genes (rRNA)

Front 72

RNA Polymerase II

Back 72

transcribes protein coding genes

Front 73

RNA Polymerase III

Back 73

transcribes small functional RNA genes [e.g. transfer RNA genes - (tRNA)]

Front 74

In eukaryotes transcription occurs where?

Back 74

in the nucleus, where the DNA is

Front 75

Because transcription for eukaryotes occurs in the nucleus, how does this affect RNA transcripts.

Back 75

most RNA transcripts need to be exported outside the nucleus to the cytoplasm where translation takes place

Front 76

What must happen to RNA transcripts before exportation outside of the nucleus to the cytoplasm

Back 76

the transcripts must be processed

Front 77

pre-mRNA

Back 77

RNA before processing the transcript - in the nucleus

Front 78

mRNA

Back 78

RNA after transcript is processed-exported to the cytoplasm

Front 79

general transcription factors

Back 79

eukaryotes use to recognize promoter regions (similar to sigma factor in prokaryotes) protein that first identifies the promoter "TATA binding protein"

Front 80

GTF names are

Back 80

TFIIA, and TFIIB (transcription factor of RNA polymerase)

Front 81

Eukaryote transcription elongation and processing

Back 81

Capping, Cleavage and polyadenylation

Front 82

Capping

Back 82

5' -cap: cap is added to prevent degradation

Front 83

Cleavage and polydenylation

Back 83

3' poly(A) tail: when RNA polymerase II reaches a specific termination sequence it stops and a 150-200 adenine nucleotides are added

Front 84

Splicing

Back 84

section of the RNA transcript that are not meant to code for protein (introns) are removed to create a continuous stretch of coding RNA (exons)

Front 85

What does splicing cause in reference to the pre-mRNA?

Back 85

Protien predicted from a pre-mRNA differs from the protein that is actually observed.

Front 86

In different tissues can Alternative Splices be made?

Back 86

Yes, creating as much as 100 different proteins (an enormous variety from one gene)

Front 87

What identifies introns as regions of pre-mRNA to be removed?

Back 87

by comparing pre-mRNA with mRNA. regions ALWAYS missing are introns.

Front 88

snRNPs

Back 88

recruit additional proteins to form a complex called spliceosome

Front 89

spliceosome

Back 89

removes the intron and joins the exons together.

Front 90

siRNA

Back 90

prevent translation of mRNA- preventing expression of the corresponding protein

Front 91

DICER

Back 91

enzyme that produces siRNA in short 20-25 bp fragments

Front 92

RISC

Back 92

binds to ssRNA fragments and degrades mRNA that they pair with (complementary)

Front 93

What is the general structure of protein (amino acid polymers)?

Back 93

R group can be any of 20 that distinguish the different protein amino acids

Front 94

what are proteins

Back 94

proteins are polymers of amino acids

Front 95

How are amino acids formed

Back 95

through peptide bonds linking amino groups (NH2) of one group to the Carboxyl group (COOH) of another

Front 96

chain of amino acids called?

Back 96

polypeptide - called protein when complete

Front 97

What is the major type of functional molecule in cells?

Back 97

proteins

Front 98

what do proteins need in order to be functional?

Back 98

they need to be able to fold into a particular structure.

Front 99

Four Level of structures for proteins

Back 99

primary, secondary, tertiary, quaternary

Front 100

primary structure

Back 100

sequence of amino acids

Front 101

secondary structure

Back 101

particular shapes that local regions of a protein fold into (alpha helix and beta sheets)

Front 102

tertiary

Back 102

overall shape of protein

Front 103

quaternary

Back 103

multipe tertiary proteins (subunits) come together to make a functional protein

Front 104

What determines structure

Back 104

sequence

Front 105

what determines function

Back 105

structure

Front 106

One gene - one protein

Back 106

Beadle and Tatum - proposed each gene encodes (somehow) one protein

Front 107

Yanofsky-1963

Back 107

"changes in the gene were about the same position as the changes in the protein"
-Indicated that DNA and protein sequences were CO-LINEAR.

Front 108

overlapping code prediction is that a ______ mutation will change _______ amino acids.

Back 108

single, multiple

Front 109

observation of overlapping code is?

Back 109

single mutations change a single amino acid and therefore the code is non-overlapping

Front 110

Genetic code is overlapping or nonoverlapping?

Back 110

non overlapping

Front 111

How can a sequence of 4 letters (DNA bases) be translated into one with 20 letters (amino acids)

Back 111

code length is 1 therefore the amino acids that can be coded for are 4 to the power of 1 = 4 and so forth. Therefore 4 to the power of 3= 64 so need a codon at least 3 nucleotides (bases) long to code all amino acids ( a triplet)

Front 112

frameshift

Back 112

nucleotide groups change in composition

Front 113

suppressed

Back 113

when a first mutation's effect is blocked by the position of the second mutation

Front 114

codon

Back 114

nucleotide triplets

Front 115

3 deletions or 3 insertions could do what

Back 115

restore the function of a protein that have codons that are thre nucleotides long. NOT 4 NUCLEOTIDES B/C 3 DELETIONS WILL NOT RETURN TO BEGINNING.

Front 116

STOP codon

Back 116

UAA, UAG, UGA 3 of 64 codes are stop codons the others are for 20 amino acids

Front 117

degenerate genetic code

Back 117

different codons can code for the same amino acid there are 61 codons and they only make a total of 20 amino acids (about 3 different codons per amino acid)

Front 118

tRNA charging

Back 118

adding the amino acid to tRNA through the synthetase.

Front 119

tRNA has a triplet of nucleotides called ________?

Back 119

anticodon located in the anticodon loop

Front 120

anticodons are complementary to?

Back 120

codons of mRNA (except for stop codons)

Front 121

aminoacyl-tRNA synthetase

Back 121

separate synthetase for each amino acid - many synthetases needs to recognize multiple tRNA's

Front 122

How many binding sites to synthetases have?

Back 122

2 binding sites - one that contains an amino acid, and the other recognizes appropriate tRNA's

Front 123

what is the complex that catalyzes protein synthesis?

Back 123

ribosome

Front 124

Ribosomes consist of how many units

Back 124

2 larger subunit has 2 RNA molecules (3 if prokaryotic) and the smaller subunit has 1 RNA molecule

Front 125

Ribosome facts

Back 125

1. bring together the components needed for protein synthesis
2. add the amino acid attached to the charged tRNA to the growing protein chain
A) aminoacyl - position that a charged tRNA enters the ribosome. a ribosome region called 'decoding center' ensures only the right charged tRNA is accepted.
P) peptidyl - position that the amino acid of a charged tRNA is joined to the protein chain. A ribosome region called the peptidyl-transferase center' catalyzes this reaction
E) exit- tRNA is ejected from the ribosome

Front 126

protein:enzyme
RNA:

Back 126

ribosome

Front 127

prokaryotes mRNA translation

Back 127

mRNA between the beginning of the transcription and the beginning of the gene called the 5' UTR contains a sequence that orientates the ribosome - called Shine Dalgarno

Front 128

Initiation factors (IF)

Back 128

promote the assembly of the complete ribosome

Front 129

what is the usual first codon for the special initiator for formyl-methionine amino acid

Back 129

AUG

Front 130

mRNA must be processed and exported from the nucleus to the cytoplasm before translation can begin in what type of cell

Back 130

eukaryotic cells

Front 131

elongation factor Tu vs EF-G

Back 131

a protein that brings charged tRNA to the A site of the ribosome while EF-G shifts the ribosome along the mRNA by one codon

Front 132

RF

Back 132

release factor

Front 133

operators and activator sites

Back 133

binding sites that influence the ability of RNA polymerase to bind and begin transcription for a given promoter

Front 134

positive regulation

Back 134

binding of some regulator proteins to activator binding sites and can increase RNA polymerase activity

Front 135

negative regulation

Back 135

binding of some regulator proteins to operators can decrease RNA polymerase activity

Front 136

allosteric effector

Back 136

signal molecule that binds to the allosteric site turning on or off gene expression

Front 137

lac operon

Back 137

model gene regulation

Front 138

three genes that are active as enzymes are called

Back 138

structural genes

Front 139

LacI - negative regulation

Back 139

inhibits gene expression by binding to operator and blockin the progress of RNA polymerase

Front 140

CAP-cAMP

Back 140

positive regulator

Front 141

constitutive

Back 141

always on, in reference to lac operon

Front 142

cis acting

Back 142

DNA operator only regulates genes on the same DNA molecule

Front 143

trans acting

Back 143

protein repressor regulates genes on any DNA molecule in the cell