Exam 2 Genetics

CH 14, 15, 16, 17, 18

How do we known proteins are the gene products?

• Early evidence came from mutations in metabolic pathways

• Archibald Garrod’s work: Inborn erros of metabolism

• Attributed a biochemical role to genes

  • Alkaptonuria

    • Garrod provided the first published account of a case of recessive inheritance in humans

  • Phenylketonuria

Beadle and Tatum

George Beadle and Edward Tatum (1941) worked on mutants of fungus Nerospora crassa (a mould), leading to their groundbreaking discovery that genes provide the instructions for making proteins

One Gene: One Enzyme Hypothesis

One Gene: One Enzyme Hypothesis

• Beadle and Tatum (1940s). They proved Garrod’s hypothesis that genes had a biochemical role

• Worked with a bread mold called Neurospora

• Neurospora can synthesize nearly ebery biomolecule it needs

• Used radiation to induce mutations in Neurospora

• Determined which biomolecule the mutant could NO LONGER synthesize

Updated to:

One Gene: One Polypeptide Hypothesis

What follows after translation?

Polypeptides fold up and assume higher order structures, and they may interact with other polypeptides

What are the 4 levels of structures in proteins?

1. Primary

2. Secondary

3. Tertiary

4. Quaternary

What is the protein’s primary structure?

Amino Acid Sequence

How do polypeptide folds?

It folds into a tertiary structure

• the amino acid sequence of the enzyme lysozyme

When does the polypeptide folding begin?

Begins during translation

• within the cell, the protein will not be found in this linear state

• Rather, it will adapt a compact 3-D structure

• folded lysozyme

What dictates the progression from the primary structure ot the 3-D strucutre?

The amino acid sequence within the polypeptide

What are the 2 types of secondary structures?

• A helix

• B sheet

  • certain amino acids are good candidates for each structures

How are secondary structures stabilized?

By the formation of hydrogen bonds between atoms located in the polypeptide backbone

The primary structure of a protein folds regular to form?

Repeating shapes known as secondary structure

• primer structure is the linear

Tertiary structure

The short regions of secondary structure in a protein fold into a three-dimensional (3-D)

What is the final conformation of proteins?

Are composed of a single polypeptide

• tertiary structure

How can you determine the tertiary structure?

By

• hydrophobic ionic interactions

• hydrogen bonds

• Van der Waals interactions

Quaternary structure

Proteins made up of 2 or more polypeptides

When is quaternary structures are formed?

When the various polypeptides associate with one another to make a functional protein

What did the studies of human hemoglobin established?

That one gene encodes 1 polypeptide

• phosphate/backbone has a (-) charge

Hemoglobin

isolated from diseased and normal individuals differ in their rates of electrophoretic migration. This was the result of a single amino acid change: valine was substitute for glutamic acid at the 6th position of the B chain

What can the posttranslational processing can modify?

Polypeptide structure

a. Cleavage may remove an amino acid

• fMET- Enzyme removes fMet - New N terminus

b. Cleavage may split a polyprotien

• multiple smaller polypeptides

c. Chemical constituent addition may modify a protein

• Serine - Kinase add - remove phosphate

What does Protein synthesis require?

The translation of mRNA

Mutations

refers to a heritable change in the genetic material

What do mutations provide?

Allelic variations

• positive side

• negative side

Positive side of mutation

• Mutations are the foundation for evolutionary change

Negative side of mutation

• Mutations are the causes of many disease

• Since mutations can be quite harmful, organisms have developed ways to repair damaged DNA

What are the 3 main types of mutations?

1. Chromosome mutations

2. Genome mutation s

3. Single-gene mutations (focus on)

Chromosome mutations

changes in chromosome structure

Genome mutations

changes in chromosome number

Single-gene mutations

relatively small changes in DNA structure that occur within a particular gene

Point mutation

change in a single base pair

• it involves a base substitution

Transition

change of a pyrimidine (C,T) to another pyrimidine

CT-CT

or

a pruine (A,G) to another purine

AG-AG

• are more common than transversion

same

Transversion

change of a pyrimidine to a purine

• vice versa

pyrimidine - purine

or

purine- pyrimidine

different

Silent mutations

those base substitutions that do not alter the amino acid sequence of the polypeptide

• due to the degeneracy of the genetic code

Missense mutations

those base substitution sin which an amino acid change does occur

Nonsense mutations

base substitutions that change a normal codon to a termination codon

Frameshift mutations

involves the addition or deletion of nucleotides in multiples of 1 or 2

• this shifts the reading frame so that a completely different amino acid sequence occurs downstream from the mutation

Point mutations

base substitutions in which one base pair is altered

What is the most common genotype in a natural population?

Wild-type

Forward mutation

changes the wild-type genotype into some new variation (the mutant allele)

wild-type → new variation

Reverse mutation aka (reversion)

the opposite effect of forward mutation

• it reverts the mutant allele back to the wild-type

mutant allele → back to wild-type

Variant

When a mutation alters an organim’’s phenotypic characteristics

How are Variants characterized?

By their differential ability to survive

Deleterious mutations

Decrease the chances of survival

Lethal mutations

the most extreme deleterious mutation

• they interrupt an essential process and result in death

Beneficial mutations

enhance the survival or reproductive success of an organism

Conditional mutants

Affect the phenotype only under a defined set of conditions. The expression of conditional mutations depends on the environment in which the organism finds itself.

• ex: temperature-sensitive mutation

  • Siamese cate - tyosinase gene

What is the Metabolic pathway involving?

Phenylalanine and tyrosine

How can a mutation alter the sequence?

Within a promoter

Up promoter mutations

make the promoter more like the consensus sequence

• they may increase the rate of transcription

Down promoter mutations

make the promoter less like the consensus sequence

• they may decrease the rate of transcription

What does a mutations affect or alter the ability of pre-mRNA?

Affects a splice recognition sequence

- to be properly spliced

What can the sites of mutations outside the coding sequence do?

Can disrupt gene expression

Neutral mutations

don’t have a positive or negative effect

ex:

• In humans the vast majority of all mutations occur in the large portions of the genome that do not contain genes and therefore have no effect on gene products

silent mutations

• aka classified as neutral mutations

How are protein function changed?

By a mutation

Phenotype depends on what?

On how proteins function is changed

changed by mutation

Null mutation

no gene no function (no gene product or non-functional product)

• usually recessive but can be dominant

Hypomorphic mutation

reduce gene function (protein retains part of its activity)

• usually recessive but can be dominant

less

Hypermorphic mutation

enhance gene function (protein functions more effcientyl)

• extremely rare

• usually dominany

more

Neomorphic mutation

novel gene function (proteins have novel properties or is expressed ectopically, at the wrong place or the wrong time)

• dominant

Loss-of-function mutations

Null and Hypomorphic (less)

Gain-of-function mutations

Hypermorphic (more), neomorphic

How can mutations occur?

Spontaneously or be induced

Spontaneous mutations

Result from abnormalities in cellular/biological processes

• errors in DNA replication, for example

• underlying cause originates within the cell

Induced mutations

• caused by environmental agents

• arise from DNA damage

  • caused by chemical or Radiation

Mutagens

agents that are known to alter DNA structure

• these can be chemical or physical agents (radiation)

How frequent are gene mutations?

Very rare! In part due to mechanisms that protect against or repair mutations

What does the frequencies show on gene mutations?

Show great variation depending on gene and organisms

Range of gene mutations

1 mutation in a gene in 10^4 to 10^8 gametes

• Mutation rates for 2 different genes can differ 10.000-fold

  • due to differences in gene size, in nucleotide sequence, and others

Are mutations spontaneous occurrences or causally related to environmental conditions?

The Luria-Delbruck fluctuation test demonstrated that mutations are not adaptive but occur spontaneously

The spontaneous mutation theory

Predicts that the number of tonr bacterial will fluctuate in different bacterial population

The physiological adaption theory

Predicts that the number of tonr bacteria is essentially constant in different bacterial populations

WAS NOT THE IT FOR THE EXPERIMENT

What did Salvador Luria and Max Delbruck studied?

the resistance of E. coli to bacteriophage T1

tonr

T one resistance

The Luria-Delbruck fluctuation test

• Several independent tonr mutations occurred during different stages

  • are mixed together in a big flask to give an average value of tonr cells

• no tonr bacteria spontaneous mutation did not occur

• many tonr bacteria mutation occurred at an early stage of population growth, before T1 exposure

Spontaneous mutations

Can arise from chemical changes

• Spontaneous lesions on the DNA molecule

1. Depurination (the most common)

2. Deamination

3. Oxidation

4. Tautomeric shift

Which level of protein structure is represented by alpha-helices and beta-pleated sheets?

A. Primary

B. Secondary

C. Tertiary

D. Quaternary

E. None of the above

B. Secondary

The corepressor's ability to bind to the operator only after being bound by tryptophan is an example of:

A. catabolite repression

B. cAMP/CAP activation

C. allosteric behavior of proteins

D. positive regulation

E. the activation domain of a transcription factor

C. allosteric behavior of proteins

A common DNA structural feature involved in gene regulatory systems is:

A. supercoiling of DNA

B. looping of the DNA

C. unwinding of the double helix

D. coiling into Z-DNA

E. denaturing of the DNA

B. looping of the DNA

What term describes a mutation that changes the codon UUU (Phe) to GUU (Val)?

A. transversion mutation

B. missense mutation

C. silent mutation

D. A and B are correct

E. A and C are correct

D. A and B are correct

A. transversion mutation

B. missense mutation

A mutation that renders the Trp repressor unable to bind tryptophan will result in

A. Constitutive expression of the Trp operon

B. The repressor not being able to undergo an allosteric change

C. Repression of the Trp operon in the absence of tryptophan

D. A and B are correct

E. A, B, and C are correct

D. A and B are correct

A. Constitutive expression of the Trp operon

B. The repressor not being able to undergo an allosteric change

6. Translational inhibition by miRNAs requires

A. Dicer

B. RISC

C. RNA pol II

D. A) and B)

E. A), B), and C)

E. A), B), and C)

A. Dicer

B. RISC

C. RNA pol II

7. Deamination of cytosine…

A. Can be caused by spontaneous mutations

B. Converts cytosine to uracil

C. Can be repaired by the nucleotide excision repair system

D. A) and B) are correct

E. B) and C) are correct

D. A) and B) are correct

A. Can be caused by spontaneous mutations

B. Converts cytosine to uracil

8. The human genome contains approximately 20,000 protein-coding genes, yet has the capacity to produce several hundred thousand gene products. What can account for the vast difference in gene number and product number?

A. A large number of human genes produce more than one protein by alternative splicing.

B. There are more introns than exons.

C. There are more exons than introns.

D. Much of the DNA is in the form of trinucleotide repeats, thus allowing multiple start sites for different genes.

E. Every gene can be read in both directions, and each gene can have inversions and translocations.

A. A large number of human genes produce more than one protein by alternative splicing.

9. The lac repressor is capable of:

A. Undergoing an allosteric change

B. Binding to the operator

C. Binding to the inducer D. A and B

E. All are correct

E. All are correct

A. Undergoing an allosteric change

B. Binding to the operator

C. Binding to the inducer D. A and B

When bacterial cells are exposed to low glucose and high lactose, the lac operon

A. will be transcribed at high levels

B. will be transcribed at low levels

C. will be expressed constitutively

D. will be completely turned off

E. none of the above

A. will be transcribed at high levels

TBP is a ; ______the TATA box is a ______.

A. cis acting element; cis and trans acting element B. cis acting protein; trans acting element

C. cis acting element, trans acting protein

D. trans acting protein, cis acting element

E. trans acting protein; trans acting element

D. trans acting protein, cis acting element

12. Chromatin remodeling complexes can affect gene expression by:

A. increasing the accessibility of transcription factors to promoters

B. removing or displacing nucleosomes

C. altering chromatin condensation by repressing expression of the linker histone H1

D. A) and B)

E. A), B), and C)

D. A) and B)

A. increasing the accessibility of transcription factors to promoters

B. removing or displacing nucleosomes

13. A class of mutations that results in multiple contiguous amino acid changes in proteins is likely to be the following:

A. base analog

B. transversion

C. transition

D. frameshift

E. recombinant

D. frameshift

14. Which type of DNA repair removes pyrimidine dimers?

A. nucleotide excision repair

B. base excision repair

C. mismatch repair

D. double-strand breakage repair

E. all of the above

A. nucleotide excision repair

Which of the following cluster of terms applies when addressing enhancers or silencers as elements associated with eukaryotic genetic regulation?

A. cis-acting, variable orientation, variable position B. trans-acting, fixed position, fixed orientation

C. cis-acting, fixed position, fixed orientation

D. cis-acting, variable position, fixed orientation

E. trans- and cis-acting, variable position

A. cis-acting, variable orientation, variable position

A mutation is induced in Neurospora that causes the loss of function of an enzyme essential to the biosynthesis of the amino acid lysine. On which medium will such organisms not grow?

A. Complete

B. Minimal + all amino acids

C. Minimal + lysine

D. Minimal + leucine and lysine

E. Minimal + tryptophan

E. Minimal + tryptophan

17. Which of the following is not a posttranslational modification

A. Acetylation of histones

B. Removal of N-terminus amino acid

C. Addition of phosphate groups

D. DNA methylation

E. Polypeptide cleavage

D. DNA methylation

Which of the following statements about base excision repair is true?

A. repair requires visible light.

B. occurs for all types of mutations.

C. requires AP endonuclease.

D. requires DNA polymerase alpha/primase.

E. requires UV light.

C. requires AP endonuclease.

. What is the term for mutations that show a phenotype depending on environmental conditions? A. nutritional mutations

B. conditional mutations

C. induced mutations

D. biochemical mutations

E. spontaneous mutations

B. conditional mutations

Which processes are examples of posttranscriptional regulation of gene expression in eukaryotes?

A. addition of polyA tail, and alternative splicing

B. coupled transcription and translation and alternative splicing

C. alternative splicing of single mRNA transcripts to give rise to multiple mRNAs, and increased stability of the mRNA

D. addition of a cap at the 5' end, and alternative splicing

E. TFIID binding to the TATA sequence, and RNA silencing

C. alternative splicing of single mRNA transcripts to give rise to multiple mRNAs, and increased stability of the mRNA

General transcription factors

A. Are part of the enhanceosome

B. Recruit RNA pol II to the promoter

C. Bind to enhancer regions of the promoter

D. A) and B)

E. A), B) and C)

D. A) and B)

A. Are part of the enhanceosome

B. Recruit RNA pol II to the promoter

22. DNA methylation may be a significant mode of genetic regulation in eukaryotes. DNA methylation refers to

A. altering RNA polymerase activity by methylation. B. changes in DNA-DNA hydrogen binding.

C. altering translational activity especially of highly methylated tRNAs.

D. alteration of DNA polymerase activity by addition of methyl groups to glycine residues.

E. addition of methyl groups to the cytosine of CG doublets

E. addition of methyl groups to the cytosine of CG doublets

Which one of the following mutagenic events can be induced by external factors?

A. pyrimidine dimers

B. alkylation of nucleotides

C. deamination of cytosine

D. A) and B)

E. all of the above

E. all of the above

24. Which of the following elements function specifically in eukaryotic transcription and gene expression?

A. -10 AND -35 boxes and enhancers

B. Origin DNA and promoters

C. Promoters and enhancers

D. Shine-Dalgarno sequences and sigma factors

E. Silencers and operators

C. Promoters and enhancers

25. A short segment of an mRNA molecule is shown below. The polypeptide it codes for is also shown: 5’-AUGGUGCUGAAG : methionine-valine-leucine-lysine Assume that a mutation in the DNA that encodes that mRNA occurs, so that the fourth base (counting from the 5’ end) undergoes a transition. What sequence of amino acids will the mRNA now code for? (You do not need a copy of the genetic code to answer the question.)

A. methionine-valine-leucine-lysine

B. methionine-lysine-leucine-lysine

C. methionine-leucine-leucine-lysine

D. methionine-valine-methionine-lysine

E. methionine-methionine-leucine-lysine

E. methionine-methionine-leucine-lysine