Bio 340 Exam 3

Proofreading removes approximately 99% of mismatches before DNA replication moves on. After proofreading what is the mutation rate for DNA replication in humans?

10^-6 mutations/base pair

Which activity of DNA polymerase is responsible for its ability to proofread newly synthesized DNA?

3' to 5' exonuclease

distance between base pairs

3.4 x 10^-10

Guanine starts at which prime end?

5 prime

Transcription occurs when in prokaryotic cell

5 to 9 base pairs after pribnow (TATAAAT)

Proofreading removes approximately 99% of mismatches before DNA replication moves on. How many mutations would you expect to see in the human genome if mismatches can be repaired by proofreading?

6,000

How many mutations would you expect to see in the human genome if mismatches could not be repaired?

600,000

What temperature does the denaturation step require?

95 degrees C

A tautomeric shift may result in:

A transition mutation

Purines

A, G

Shine Dalgarno Sequence

AGGAGGU-after Pribnow

The start codon in a eukaryotic cell is located:

AUG in Kozak sequence

Start codon is _____ and when does it occur in Prokaryotic DNA

AUG occurs after Shine Dalgarno (AGGAGGU)

What does wild type lacI protein do?

Acts as a repressor (inhibits transcription from the lacI operon)

Which of the following are true of epigenetic changes?

Allow DNA to be transcribed, move histones to open or close a chromosomal region, and are temporary

Regarding Sanger's sequencing method, why does the incorporation of a ddNTP in the growing complementary strand terminates the process of DNA replication?

Because the ddNTP cannot form a phosphodiester bond with the sugar from a newly recruited dNTP due to the missing hydroxyl group (-OH).

Order of enzymes in DNA replication

Binding to origin of replication, helicase, single stranded binding proteins prevent reannealing, synthesis of RNA primers, Proofreading, exonuclease, ligation

What kind of enzyme is primase?

DNA dependent RNA polymerase

The initial mechanism for repairing nucleotide errors in DNA is _________.

DNA polymerase proofreading

True or False: In gel electrophoresis, the DNA is attracted to negative electrode.

False

True or False: During PCR, two DNA strands are separated by breaking covalent bonds during the denaturation step.

False-hydrogen bonds

A transversion occurs in the coding DNA triplet GAA for Glu in the middle of the gene sequence and mutates to GAT. What would you expect during translation?

Glu would be substituted with Asp.

Explain how lacI operon works?

If lactose is present then lactose will bind to the repressor and prevent it from binding to the operator, and will allow transcription to occur to metabolize the lactose. If no lactose is present, the lac operon will will encode a repressor to bind to the operator to prevent transription.

Transcription and translation have what 3 steps?

Initiation, Elongation, Termination

Which of the following regarding the Ames Test is true?

It is used to identify mutants with restored biosynthetic activity.

Which of the following conditions leads to maximal expression of the lacI operon?

Lactose present, glucose absent

Which amino acid would you expect to be part of an alpha helix from the GPCR signaling protein?

Leucine

Which of the following components is not involved during the formation of the replication fork?

Ligase

Which of the following is responsible for repairing phosphodiester bond backbone of DNA molecular cloning?

Ligase

For hydrogen potential, who are acceptors and who are donors?

Nitrogen and Oxygen are acceptors, while H is donor

The __________ blot technique is used to find an RNA fragment within a sample that is complementary to a DNA probe

Northern

How many Shine-Dalgarno sequences can be found in a single mRNA?

One sequence per gene

Regulatory Proteins

Positive transcription factors which increase transcription, Negative transcription factors that decrease transcription

The ployA tail on a eukaryotic mRNA is important:

Protects mRNA from degradation, It is important for translation, it is important for transport of MRNA out of the nucleus

What does an operon consist of?

RNA Polymerase, Promoter, operator, LacZ, LacY, LacA

Which of the following enzymatic activities is not involved in DNA replication in eukaryotic cells?

RNA dependent DNA polymerase

Explain how an operon works?

RNA polymerase binds to promoter and will pass through the operator if there is not repressor bound to it, and will produce enzymes.

Transcribe the following DNA template sequence: 3' - GAC TTA AGC - 5'

RNA; 5' - CUG AAU UCG - 3'

Pyramidine

T, U, C

The TATA box in Eukaryotes is really

TATAAA

-10 consequence

TATAAT

Which sequence would you predict to be a promoter site?

TATAAT

-35 consensus sequence

TTGACA

Which of the following statements is false?

The TRP Operon is under positive control

What led to the commercialization of personal genomic products?

The increase in understanding genetics and the decrease in price of mapping a genome

How are genomic libraries created?

There are multiple methods - the main one uses molecular cloning to amplify fragments of genomes for further study and addition to a collection (the genomic library).

enol to ketone

Thymine and Guanine

In the absence of lactose, the lac operon I+OCZ+Y+A+ will be transcribed in an organism.

True

True or False: True/False: The codon AUG has two purposes: 1) Indicating the start of protein synthesis and 2)coding for the amino acid of Methionine.

True

Consider the DNA coding sequence: 5' - TAC GAG TTC - 3'. What is the correct amino acid sequence?

Tyr - Glu - Phe

List stop codon

UAG, UGA, UAA

What would the consequences of having DNA polymerase without 5' to 3' exonuclease?

Will not remove RNA primer

In positive control, a __________________ binds to DNA _________ gene transcription

activator, increase

Epigenetics is best described as:

additions to changes in a sequence, like "tags" that sit on the main nucleotide sequence

amino and imino

adenine and cytosine

In lactose metabolism, the enzyme that cleaves the galactosidase linkage between glucose and galactose is:

beta galactosidase

What does DNA polymerase I do?

binds to a single stranded gap and uses two activities to complete replication

In the reproductive cloning of an animal the genome of the cloned individual comes from

body cell

In what cells do you expect to see telomerase activity?

cancer cells, adult B lymphocytes, pluripotent stem cells

topoisomerases

catalyze controlled cleavage and rejoining of DNA that prevents overwinding

nonsense mutation

change a normal coon to a stop codon

Silent Mutation

change a single nucleotide but translates to same amino acid

transversion

change purine (A or G) to pyrimidine

The PCR step where the double strands separate into single strands.

denaturation

Which of the following is the type of DNA repair in which thymine dimers are directly broken down by the enzyme photolyase?

direct repair

DNA polymerase

elongates DNA

In blue-white screening, the blue cells contain?

empty plasmid vectors

Which factors influence epigenetics?

environmental and genetics

You are going to amplify a gene by PCR. If you already have a PCR tube, your DNA sample, water, and Taq polymerase, which of the following components are you still missing? Select all that apply,

forward primer, buffer, reverse primer, nucleotides (dNTPs)

What type of mutations can intercalating agents lead to?

frameshift mutations

When both glucose and lactose are present in the media in which E. coli is growing, which is the preferred carbon source?

glucose

For reverse primer binding to coding strand, what do you do?

go to the 3 prime end, reverser the nucleotide, find the complimentary bases and then insert 5' to 3'

Epigenetics creates noticeable effects by _________________.

histone modifications that alter gene expression

Insulin produced by molecular cloning:

is a recombinant protein

ligase

join okazaki fragments

In the lac operon, when glucose and lactose are both absent in the growth medium for E. coli, ______ is bound to the operator.

lac repressor

Lac operon has the strongest transcription when

lactose is present and glucose is absent

The goal of PCR is to:

make many copies of a region of DNA

Personal genomics is relatively __________.

new, as recent discoveries and genome mapping efforts have made genetic information more readily available.

Operator constitutive mutation

operator site mutation prevents repressor protein binding

The lac operon is what type of regulated?

positively and negatively regulated

SSB protein

prevents reannealing

Repressor mutation

prevents repressor binding to the operator

Lactose (actually allolactose) binds to the lacI protein and regulates its ability to bind to the operator. Lactose binding to lacI protein:

prevents the lacI protein from binding to the operator (acts as an inducer)

Operons are located in what cells:

prokaryotes

Operons like the lac and trp operon are used to control _____ gene expression

prokaryotic

3' to 5' exonuclease activity

proofreading

What does 5'-3' exonuclease do?

removes ribonucleotides from the RNA primer

telomerase

repairs end of chromosome

telomeres

repetitive sequence at the end of chromosome

An operon of genes encoding enzymes in a biosynthetic pathway is likely to be which of the following?

repressible

Wild type lac operon

repressor binds to operator when the inducer is absent and forms an inducer-repressor complex when inducer is present

super repressor mutation

repressor protein mutation blocks binding to the inducer

In negative control, a _____________ binds to DNA to _____ gene transcription.

repressor, prevent

missense mutation

results in a different amino acid

Where is the 3' UTR?

right after stop codon

Which strand of DNA sample do forward primers bind to?

template strand

All of the following are processes used to introduce DNA molecules into bacterial cells except:

transcription

heicase

unwind helix

What kind of traits does epigenetics effect?

widespread, multi-cellular traits like cancer and inherited disorders