Genetics Test #3

Front 1

Describe GAL4 transcription process in yeast.

Back 1

No Galactose--> Gal 80 binds to GAL 4-->no activation

W/Galactose-->Galactose binds GAL 80
-GAL80 releases GAL4
-GAL4 activates transcription again

Front 2

Positive inducible

Back 2

Normal state-
transcription off; inactive activator.

Substrate present-
product binds to activator and makes it active;transcription on

Front 3

Positive Repressible

Back 3

Normal-
Transcription on; active activator

Substrate present--
Product binds to activator to leave DNA, transcription off.

Front 4

Negative Inducible

Back 4

Normal-
Inducer absent, repressor bound to operator.

Inducer present-
Inducer binds to repressor and leaves DNA.

Front 5

Negative Repressible

Back 5

No product-
Repressor is inactive, cant bind to operator. transcription on.

Product present-
Corepressor (product) binds to repressor then can bind to operator. No transcription.

Front 6

What are the 3 principle elements of mRNA sequences in bacterial cells?

Back 6

1)5' untranslated region which contains the shine-delgarno sequence
2) Protein-encoding region
3) the 3' untranslated region

Front 7

What is the Shine-Delgarno sequence and what does in contain?

Back 7

It is the ribosome binding site for transcription in bacteria and is in the 5' untranslated region.

Front 8

analog of Shine-Delgarno sequence in eukaryotes

Back 8

The 5' cap end plays a critical role in the initiation of translation in eukaryotes.

Front 9

What is an operon? What is its purpose?

Back 9

An operon is a group of bacterial structural genes that are transcribed together (along with their promoter and additional sequences that control transcription).
-->it regulates expression of structural genes by controlling transcription.

Front 10

start codons

Back 10

usually AUG

Front 11

non-overlapping

Back 11

means that one nucleotide cant be used cant be used in more than one codon.

Front 12

degeneracy of the genetic code

Back 12

means that more than one codon can specify the same amino acid

Front 13

How is the reading frame of a nucleotide sequence set?

Back 13

By the initiation codon

Front 14

How are tRNAs linked to their corresponding amino acids?

Back 14

By tRNA charging; done by enzymes called aminoacyl-tRNA synthetases. Each synthetase recognizes a single amino acid.

Front 15

What events bring about termination of translation?

Back 15

Termination occurs when the ribosomal unit reaches a stop codon. The first nucleotide enters the A site and no tRNA encodes for the stop codon. A release factor binds to the A site and breaks the polypeptide chain.

Front 16

similarities in protein synthesis between bacteria and eukaryotes.

Back 16

1)Charging of tRNA molecules w/AA
2)Both have large and small ribosomal subunits
3)elongation and termination are very similar but different factors are used.

Front 17

differences in protein synthesis between bacteria and eukaryotes

Back 17

1)initiation codon-bacteria->N-formyl methionine; eukaryotes--> methionine
2)transcription and translation are isolated temporally and spatially.
3)ribosomal subunits differ in size and composition
4)Shine-Delgarno sequence vs. 5'cap until first start codon

Front 18

What are the steps in initiation of translation?

Back 18

1)mRNA
2)small and large subunits assemble
3)a set of three initiation proteins called initiation factors
4)initiator tRNA with N-formylmethionine attached (fMet-tRNAfmet)
5)GTP

Front 19

3 major steps in initiation of translation?

Back 19

1)mRNA binds to small subunit
2)initiator tRNA binds to mRNA by bp b/t codon and anticodon
3)large subunit joins initiation complex

Front 20

Type of operon system displayed by the lac operon and the process

Back 20

negative inducible-->transcription is off unless lactose is present. product (allolactose) binds to repressor and leaves operator-->transcription on

Front 21

What is the concept of colinearity?

Back 21

It suggests that the number of nucleotides in a gene is proportional to the number of amino acids in the protein encoded by that gene.

Front 22

Bacterial promoter sequences

Back 22

Usually adjacent to RNA coding sequences. Include 2 common consensus sequences
1)-10 TATAAT
2)-35 TTGACA

Front 23

Eukaryotic promoter sequences

Back 23

TATA box--> TATAAA usually -25 to -35 upstream

Front 24

What forms the basal transcription apparatus in eukaryotes?

Back 24

1)accessory proteins made up of transcription factors
2)along with RNA polymerase

Front 25

What is the core promoter?

Back 25

is located immediately upstream of the gene and is the site where the basal transcription apparatus binds.

Front 26

What are transcriptional activator proteins?

Back 26

a class of accessory proteins that bind to specific DNA sequences and increase transcription levels

Front 27

Termination procedure in eukaryotes

Back 27

RNA continues to be transcribed sometimes long after termination sequence is transcribed. RNA is cleaved and RAT1 attaches to the 5'end of the RNA and degrades remaining RNA until it reaches the transcription bubble

Front 28

Substrate for transcription

Back 28

rNTPs--> ribonucleoside triphosphates. Does not require a primer.

Front 29

Haloenzyme

Back 29

Made up of sigma factor and the core enzyme.

Front 30

Purpose of the sigma factor

Back 30

Sigma is required for promoter binding and initiation.

Front 31

Processes of transcription initiation

Back 31

1)promoter recognition
2)formation of transcription bubble
3)creation of first rNTP bonds
4)escape of transcription apparatus from promoter

Front 32

What is the primary reason some genes are transcribed at different frequencies?

Back 32

Promoter binding by polymerase

Front 33

Process of Rho-dependent termination-

Back 33

1)DNA sequences that produce a pause in transcription
2)A DNA sequence that encodes a stretch of RNA upstream of the terminator that is devoid of any secondary structures

Front 34

Features of rho-independent termination-

Back 34

1)contain inverted repeats causing hairpin structures to form-->slow down or pause
2)a string of usually six A nucleotides follows the second inverted repeat in template DNA-->A-U bonding weaker

Front 35

trp operon process (negative-positive, repressible-inducible)

Back 35

negative repressible

Front 36

process of trp operon

Back 36

Tryptophan low->normally inactive repressor, transcription on.

Tryptophan is high->tryptophan binds to repressor and makes it active. Repressor binds to operator to turn transcription off.

Front 37

Differences in Bacteria and eukaryotic gene regulation

Back 37

1)eukaryotic genes are usually not organized into operons and are rarely transcibed together

2)Chromatin structure affects transcription

3)presence of a nuclear membrane in eukaryotes

Front 38

How does acetylation of histone proteins affect chromain structure?

Back 38

Acetylation usually stabilizes charge of histone tails and allows transcription factors to reach DNA

Front 39

Difference between repressors in bacteria and eukaryotes-

Back 39

Most eukaryotic repressors don't usually directly block RNA polymerase but rather compete with activators for DNA binding sites

Front 40

How do viruses affect T cells?

Back 40

Exposure to an anitgen (virus) causes an increase in the availability of transcription factors->increases protein synthesis and makes more T cells

Front 41

Base substitution mutations (2 types)

Back 41

Is the change of a single nucleotide in the DNA.
1)transition-like for like
2)transversion-purine for pyrimidine

Front 42

3 types of mutations

Back 42

1)Base Substitution
2)Insertion
3)Deletions

Front 43

What change happens in an insertion and deletion?

Back 43

is the addition or removal of one or more nucleotide pairs.

Front 44

Missense mutation

Back 44

Is a base substitution that results in a single amino acid change

Front 45

Nonsense mutation

Back 45

Is a base substitution that changes an amino acid to a stop codon

Front 46

Silent mutation

Back 46

Creates a different DNA sequence but the same amino acid (redundancy)

Front 47

Neutral mutation

Back 47

Changes the amino acid sequence of the protein but not the function

Front 48

Difference between spontaneous and induced mutations

Back 48

Induced mutations result from environmental chemicals or radiation

Front 49

Base analogs

Back 49

Is a class of chemical mutagens that chemically resemble any of the 4 normal bases of DNA and can be incorporated into newly synthesized DNA

Front 50

Intercalating agents

Back 50

Produce mutations by sandwiching themselves in between adjacent bases in DNA.
-->cause single nucleotide insertions and deletions in replication and FRAMESHIFTS

Front 51

Ionizing radiation and its results-

Back 51

X-rays, gamma rays, and cosmic rays-->dislodge electrons from the atoms in DNA and change these stable molecules into free radicals and reactive ions->alter structure of bases and break phosphodiester bonds.
-->also causes double stranded breaks in DNA

Front 52

UV radiation and its effects

Back 52

Bases absorb energy and can form bonds between adjacent pyrimidine molecules on the same strand of DNA-->pyrimidine dimers

-->blocks replication

Front 53

SOS system and what is results from-

Back 53

SOS system is put into place in bacteria after replication blocks from UV light. Allows replication to continue but makes MANY mistakes.

Front 54

Mismatch repair

Back 54

Corrects incorrectly inserted bases and also unpaired loops in DNA.
->Enzymes cut out distorted region and place in new nucleotides by using template strand. Ligase fills in nicks.
->differentiate between old and new strands by presence of methyl groups.
->methylation is delayed, so right after replication, old strand is methlated and new is not

Front 55

Direct repair

Back 55

Does not replace altered nucleotides but changes them back into original (correct) structures
->Some bases have incorrect methyl groups on them, methyl transferase removes methyl group and restores base.

Front 56

Base-excision repair

Back 56

A modified base is first excised and then the entire nucleotide is replaced
->Double strand DNA is pulled apart and new nucleotide is inserted by DNA polymerase and DNA ligase seals nick

Front 57

3 steps to incorporate foreign genes

Back 57

1)isolate and amplify gene of interest

2)Cutting and joining DNA fragments (put gene into vector(plasmid))

3)Transformation

Front 58

How is a a gene placed into a vector?

Back 58

Restriction enzymes (restriction endonucleases) recognize and make double stranded cuts in DNA at specific places.
->The new DNA is placed in high concentration to be incorporated into the plasmid to make recombinant plasmid

Front 59

What is a response element and what does it do?

Back 59

Response elements are DNA regulatory sequences that are at some distance away from the gene being regulated and provide binding sites for transcriptional activators

->During times of stress, transcriptional activators proteins bind to this regulatory element and elevate transcription

Front 60

What do poly (A) binding proteins do?

Back 60

They bind at the poly (A) tail and contribute to the stability of the tail and protect the 5' cap through direct interaction.

Front 61

How do eukaryotic repressors differ from bacteria repressors?

Back 61

Repressors in eukaryotes that bind to silencers block transcription activator proteins from binding to an activator site rather than blocking RNA polymerase

Front 62

Describe process of strand slippage and what results from it

Back 62

Strand slippage is a spontaneous mutation that results from one nucleotide stand forms a small loop.

->deletions and insertions can arise after replication