Learn: UA BSC 315 Exam 2 Study Guide

Describe the four phenotypic classes that occur in the F2 progeny of F1 dihybrids

Two are parental and two are recombinant

Syntenic genes

Genes located on the same chromosomes

When genes on the same chromosome are completely linked, the test cross results in only two possible genotypes in progeny, and these are ___________________ phenotypes

parental

What indicates gene linkage?

Departure from the 1:1:1:1 ratio of F1 gametes in dihybrid cross

Recombinant classes are never over what percent of total F2 progeny?

50%

Recombination

Reciprocal exchange of genetic material as a result of crossing-over during meiosis

How can linkage be detected in autosomal genes?

By generating a double heterozygote (dihybrid) and crossing to a homozygous recessive individual

Dihybrid test cross of independently assorting genes produces what kind of progeny ratio?

1:1:1:1

Dihybrid test cross of completely linked genes produces what kind of progeny ratio?

1:1

Recombination frequencies (RF)

Measures of physical distance between two linked genes. (map units)

% Recombinance (

Two-point crosses

Gene pair recombination frequencies that display relative gene position

Linkage group

Chromosome

What is the purpose of a Chi square test

To evaluate deviation from expected values and the probability that the data fits the expected outcome

What are the steps of a Chi Square Test?

1. Formulate a null hypothesis (observed and expected are the same)

2. Obtain raw observational data

3. Calculate the Chi-Square statistic ∑((O −E)^2)/E

4. Consider degrees of freedom (df = N-1 where N is the number of classes)

5. Determine a p value using chi-square value and df

What is the cutoff p value for chi square tests?

0.05.

95% confidence in rejection of null hypothesis

Can a chi-square test prove linkage?

No.

Phosphodiester bonds

Covalent bonds joining adjacent nucleotides

How many different subunits make up DNA?

4

How many different subunits make up proteins?

20

What is the basic structure of DNA

A phosphate, a Deoxyribose sugar, and one of four nitrogenous bases

What are the four nitrogenous bases of DNA?

Adenine, Guanine, Thymine, and Cytosine

Which nitrogenous bases are Purines?

Adenine and Guanine.

9 Carbon/Nitrogen central ring structure

Which nitrogenous bases are Pyrimidines?

Thymine and Cytosine.

6 Carbon/Nitrogen central ring structure

What is the difference between a nucleoside and a nucleotide?

A nucleotide is the basic unit of DNA: a phosphate, sugar, and a nitrogenous base. A nucleoside is that same basic unit, but without a phosphate

How are nucleotides linked together in a DNA molecule?

In a 5'-3' chain

Where do phosphodiester bonds covalently link in DNA chains?

Between the 3' carbon of one nucleotide and the 5' carbon of the next nucleotide

The ratios of which nitrogenous bases are equal?

A to T and G to C

What does each DNA base pair consist of?

Hydrogen bonds.

3 between G and C

2 between A and T

Describe the double helix structure of DNA.

Strands are antiparallel, one is 5'-3' up-to-down and the other is 3'-5' up-to-down.

The sugar-phosphate backbone is on the outside and the base pairs are in the middle.

What is the accepted model of DNA replication?

Semiconservative model.

Further describe the Semiconservative model of DNA replication

Unwinding of the double helix exposes bases on each strand. Each strand can act as a template for synthesis of new strands. New strand forms by insertion of complementary base pair. Single double helix becomes two identical daughter double helices.

Each new molecule contains 1 parent strand and one newly synthesized strand.

Where does the energy for DNA synthesis come from?

High-energy phosphate bonds associated with dNTPS (deoxynucleotide triphosphates: i.e. dATP, DGTP, DTTP, dCTP)

DNA polymerase

Cellular complex the catalyzes new phosphodiester bonds.

Describe the 2 steps in the mechanism of DNA replication

1. Initiation - proteins open up the double helix and prepare it for complementary base pairing

2. Elongation - proteins connect the correct sequence of nucleotides on newly formed DNA strands

What are the three strict requirements for DNA polymerase action?

1. Template DNA

2. Primer

3. Four dNTPs

Primer

A short segment of DNA that acts as the starting point for a new strand.

Has an exposed 3' hydroxyl

Template DNA

Strand of original DNA that transcription occurs on.

In what direction does DNA synthesis *always* proceed?

5'-3'

Where does initiation of DNA replication begin?

At the origin (Ori) of replication

What proteins bind to Ori?

Initiator proteins

What complex unwinds the DNA double helix?

Helicase

What keeps the DNA helix open?

Single-strand binding proteins

Primase

An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.

What complex catalyzes phosphodiester bond formation between adjacent nucleotides?

DNA polymerase III

What is the function of DNA polymerase III?

Catalyzes polymerization of new strands of complementary DNA

Leading strand

DNA strand being replicated by continuous polymerization at the 3′ growing tip.

Lagging strand

DNA synthesized away from the replication fork

Okazaki fragments

the DNA fragments that are synthesized in short stretches on the lagging strand

What is the function of DNA polymerase I?

It replaces RNA primer with DNA sequence. Fills in gaps between Okazaki segments

What is the function of DNA ligase?

It covalently joins successive Okazaki fragments together

Unwinding of DNA creates _____________ DNA ahead of replication fork

supercoiled

What is the function of DNA topoisomerase

it relaxes supercoils by cutting the sugar phosphate backbone bonds of strands of DNA.

What is true of DNA polymerase after the removal of the last RNA primer?

DNA polymerase cannot replicate some of the sequences at the 5' end

Telomeres

DNA caps that protect the ends of eukaryotic chromosomes and that require special mechanisms for replication

Telomerase

A ribonucleoprotein that extends telomeres

What are the 3 ways to ensure fidelity of DNA information

1. Redundancy - either strand of the double helix can specify the sequence of the other strand

2. Precision: of cellular replication machinery (DNA polymerase I and III have proofreading ability

3. DNA repair enzymes

DNA synthesis always proceeds in what direction?

5' to 3'

Mutations

heritable changes in DNA base sequences

Gene

A specific protein encoding segment of DNA

Forward mutation

mutations that changes wild-type allele to a different (non-wild type) allele

Reverse mutation (reversion)

Mutation that changes a mutatnt allele back to wild type

Substitution

Replacement of a base by another base

Transition

Substitution of a purine in place of another purine or of a pyrimidine in place of another pyrimidine

Transversion

Substitution of a purine in place of a pyrimidine or of a pyrimidine in place of a purine

Deletions

Block of 1 or more base pairs lost from DNA

Insertions

block of 1 or more base pairs added to DNA

Inversion

180° rotation of a segment of DNA

Reciprocal transloaction

Parts of two nonhomologous chromosomes change places

Germ-line mutations

Mutations that occur in gametes or in gamete precursor cells

Somatic mutations

Mutations that occur in non-germ cells

Mispaired base is recognized and excised by __________________ portion of DNA polymerase

3'-to-5' exonuclease

__________________ is used to determine if a particular recessive phenotype arises from mutations in the same or separate genes

Complementation testing

Complementation group

A collection of mutations that do not complement each other

R group

The side chain that is unique to each amino acid

What is the generic amino acid structure?

Amino group-Central Carbon-Craboxyl group

(NH2)-(CHR)-(COOH)

Proteins

Chains of amino acids linked by peptide bonds

How many levels of polypeptide structure are there?

4

Primary structure (1°)

The amino acid sequence

Secondary structure (2°)

The characteristic geometry of localized regions

(alpha helix or Beta pleated sheet)

Tertiary structure (3°)

The complete three-dimensional arrangement of a polypeptide.

The natural folding of a polypeptide under typical physiological conditions

Quarternary structure (4°)

The overall protein structure that results from the aggregation of two or more polypeptide subunits.

Missence mutation

When a point mutation results in substituting one amino acid for another

What does one gene equiate to?

One polypeptide

What are the three aspects of protein recognition of DNA?

1. Particular structure

2. Specific DNA shapes

3. Specific nucleotide sequences

What is the function of RNA polymerase?

It transcribes DNA to produce an RNA transcript

What is the function of ribosomes?

They translate mRNA sequences to synthesize polypeptides

The is the sequential pathway for the transfer of genetic information?

DNA -> RNA -> Protein

What is the key to the transfer of information from DNA to RNA and from RNA to protein?

The pairing of complementary bases

What helps guide the mechanisms of gene expression?

Polarities of DNA, RNA, and polypeptides

Template strand

DNA strand that is being used to synthesize RNA strand

Sense strand

strand that has the same base sequence as the mRNA

Antisense strand

Template strand

What are three major chemical differences between RNA and DNA?

Ribose sugar instead of deoxyribose

Uracil (U) instead of Thymine (T)

Most RNAs are single stranded

Transcription generates a _____________ polarity RNA chain using DNA as a template

5'-to-3'

What enzyme catalyzes transcription?

RNA polymerase

Promoters

DNA sequences that provide the signal to RNA polymerase for starting transcription

Terminators

RNA sequences that provide the signal to RNA polymerase for stopping transcription

What are the two kinds of terminators in bacteria?

Extrinsic - requires rho factor

Intrinsic - doesn't require additional factors, forms a hairpin loop

Sigma factor

Bacterial transcription protein that increases RNA polymerase affinity to promoter but at the same time decreases its affinity for the DNA

Core enzyme

RNA polymerase with detached sigma factor