GN 311 Module 2

First to isolate DNA

Meischer

Transformation - Genetic material can move. Did not identify the transforming principle.

Griffith

Discovered DNA is the transforming principle

Avery, MacLeod, and McCarty

Identified DNA as the genetic material in bacteriophages

Hershey and Chase

Discovered colinearity between DNA and proteins

Yanofsky

Discovered the helical structure of DNA using X-ray crystallography

Franklin and Wilkins

Base composition - Determined that DNA for yeast consisted of equal amounts of purines and pyrimidines.

Chargaff

Determined that DNA replication is semi-conservative

Meselson and Stahl

Double crossover (DCO) will be the ___________ group in a testcross for a genetic map

Smallest

No crossover (NCO) will be the _____________ group in a testcross for a genetic map

Largest

The closer two genes are on a chromosome, the ________ likely a crossover event is to occur. On the other hand, the farther apart two genes are on a chromosome, the ________ likely a crossover event is to occur.

Less; More

GWAS uses _____ variations at a single _____ base to look for associations between _____s and a trait.

SNP; DNA; SNP

GWAS is used to study what?

Populations

Linked alleles are _______ likely to be in the same gamete.

More

Recombination frequency is __________ to the distance between genes

Proportional

If there is a 6% recombination frequency, what is the distance (in centimorgans) between locus one and locus two?

6cM

The ________ of the F2 tells you the _________ of the F1 gamete in the testcross.

penotype; genotype

True or False: To find the number of centimorgans in map distance, you must divide the number of recombinant progeny by the total progeny and multiply by 100

True

For a two-point mapping Chi-Square test for independent assortment, you should test a ____________ (correct/incorrect) hypothesis.

Incorrect

True or False: Linkage and Random Segregation are related

False. Linkage has nothing to do with Random Segregation

Is DNA negatively or positively charged? Why?

Negatively charged because of the phosphate group attached

Purines are bases ___ and ____. Pyrimidines are based ___, ___, and ___.

A, G; C, T, U

What is a nucleotide composed of?

Sugar + Base + Phosphate

A pairs with T using ___ hydrogen bonds

2

G pairs with C using ___ hydrogen bonds

3

True or False: Hydrogen Bonds are the main force joining two strands of DNA

False

_____________ bonds connect the sugar-phosphate backbone of DNA

Phosphodiester

The __’ end of one nucleotide bonds to the __’ end of the next one

3; 5

DNA has _________ bases in the center and a ________ backbone on the outside

Hydrophobic; Hydrophilic

A ____________ cannot be pulled apart

Plectonic coil

Major grooves are ____nm while minor grooves are _____nm

3.4; 0.34

_________ interactions are the main force in stabilizing the double helix

Hydrophobic

If a DNA molecule consists of 15% Adenine, what is the percent of each of the other bases?

A: 15%

T: 15%

G: 35%

C: 35%

How do you determine if DNA is left-handed or right-handed?

Follow the front strand of DNA to the top where it will be directed either left or right

In electrophoresis, DNA fragments migrate from _______ to _______

Negative; positive

Denaturing the DNA means breaking down ________ bonds and ________ interactions with heat or chemicals that allows the two strands to __________.

Hydrogen; Hydrophobic; Separate

Hyperchromic effect is an _________ in UV absorption due to denaturation

Increase

What is Tm on a DNA melting curve?

Midpoint of Thermal Denaturation (50% of DNA is denatured)

A higher content of __s and __s results in a higher Tm

G;C

The formula for Tm is:

Tm = 69 +(.41)(%GC)

You discovered that the base composition of a species of bacteria was 20% A. What do you predict the Tm to be for this species?

First find the % composition for the bases: A = 20%, T - 20%, C = 30%, G = 30%

Then use the percentages of GC to calculate Tm. 

Tm = 69 + (0.41)(60) = 93.6 (Degrees celsius)

If one strand of a double-stranded DNA molecule has the sequence below, what is the sequence of the complementary strand? Label the ends.

5’ - GTACCAGTTACTAGCCTGA - 3’

3’ - CATGGTCAATGATCGGACT - 5’

________ is the complex of DNA, chromosomal proteins and RNA within the nucleus

Chromatin

___________ is the lighter staining parts of the chromosome during interphase. 

Euchromatin

______ contains actively transcribed genes and is MOST commonly used

Euchromatin

True or False: Heterochromatin condenses and relaxes (stretches out)

False - EUchromatin condenses and relaxes. Heterochromatin is usually condensed

__________ is the darker staining parts of the chromosome. There are fewer genes, and it’s usually not involved in crossing over.

Heterochromatin

A nucleosome core contains __ histone molecules

8

________ is the DNA that is wrapped around histones

Chromatin

DNA has a _______ charge and is attracted to ___________ charged histones

Negative; Positively

Histones and DNA is bound ________________

Electrostatically

________ are basic proteins and have lots of positively charged amino acids.

Histones

Histones are _______ _________ proteins, especially ___ and ____

Highly conserved; H3; H4

A nucleosome is a _______ and ____ together

Histone; DNA

A nucleosome CORE includes core _______ and _____ bp of DNA

Histones; 147 bp DNA

True or False: The core histones include TWO H2A, H2B, H3, and H4

True

A ____ fiber is tandem nucleosomes; often referred to as “beads on a string”

11nm

Chromatin strands are __-__nm, ______, which is smaller than the proposed 30nm in situ model

5-24; in vivo

Chromatin strands are closer together in _______ (mitotic/meiotic) cells

Mitotic (Because it condenses and becomes tightly packed to ensure that chromosomes are properly separated into two new daughter cells).

The _________ ________ is a fibrous network throughout the nucleus that anchors a series of DNA loops

Nuclear Matrix

________ occurs when DNA coils back on itself when it is overwound or underwound

Supercoiling

______ supercoiling occurs when DNA is over-rotated in the same direction as the DNA coil so a left-handed supercoil compensates

Positive

_______ supercoiling occurs when DNA is underwound so a right-handed supercoil compensates

Negative

___________ alters torsional stress in DNA by cutting the DNA backbone

Topoisomerase

_____ are characteristic for a strain of organism and can be used to identify specific chromosomes

Bands

Several rounds of DNA replication without separation of replicated chromosomes is referred to as ____________.

Endopolyploidy

_____ are areas where the DNA is loosely coiled so that transcription can occur

Puffs

______ has a conserved DNA sequence at the centromere, but most organisms do not

Yeast

True or False: There is a specific DNA sequence that identifies centromeres

False: There is no specific sequence found in all centromeres

Stability at the ends of chromosomes, ensuring they are not degraded by exonuclease, is provided by __________.

Telomeres

True or False: Telomeres also prevent chromosomes from joining with each other at the ends due to ligase activity and provide proper replication for the ends of chromosomes

True

Telomeres use a _______ to protect the ends of a chromosome.

T-loop

DNA replicates in a _____________ fashion

Semiconservative

In semiconservative replication, the first replication produces what?

2 helixes with one strand parental DNA and one strand new DNA

In semiconservative replication, the second replication produces what?

2 helixes with one strand parental DNA and one strand new DNA, and 2 helixes with new DNA

All replication starts at an _____ __ __________ and proceeds until the entire _______ (unit replicated together) is replicated.

Origin of Replication; replicon

Theta replication is common in ________ and other circular DNA molecules

Bacteria

Replication for eukaryotic chromosomes, which have multiple origins of replication along their length is known as _____________________.

Linear Eukaryotic Replication

Replication proceeds in both directions from the origin, which is known as _________________.

Bidirectional Replication

Theta replication results in ___ circular molecules

2

In bidirectional replication, there are ___ replication forks

2

What is DNA polymerase 3 responsible for?

Most DNA synthesis and proofreading 3’-5’ exonuclease activity

True or False: DNA polymerase 3 elongates DNA

True

What is DNA polymerase 1 responsible for?

5’-3’ exonuclease activity to remove RNA primers and proofreads with 3’-5’ exonuclease activity

Which was discovered first, DNA polymerase 1 or 3?

1

The _______ strand adds new DNA from the 3’ end in the same direction as the replication fork.

Leading

DNA polymerase can ONLY add nucleotides __’ to __’

5’ to 3’

Replication occurs __’  to __’

5’ to 3’

The _____ strand is created by continuous replication

Leading

The _____ strand is created by discontinuous replication

Lagging

Parental DNA that is used as the template for the leading strand is referred to as what?

Leading strand template

Parental DNA that is used as the template for the ladding strand is referred to as what?

Lagging strand template

__________ ___________ are small pieces of DNA created by discontinuous replication

Okazaki fragments

Relieves tension due to supercoils caused by strand separation

Gyrase

Unwinds the DNA double helix

Helicase

Lays down the RNA primer since DNA polymerase requires a free 3’ OH

RNA primase

Small piece of RNA needed for DNA polymerase to begin replication

Primer

Binds to the strands of DNA to keep them separated

Single stranded binding protein

Attaches to the primer and adds nucleotides

DNA polymerase 3

Removes RNA primer and replaces it with DNA

DNA polymerase 1