Intro Gen 3

What was the conclusion of Griffith's experiment?

Heat killed S cells (virulent) combined with R cells (avirulent) resulted in the transformation of R cells -> virulent S Cells; this is due to some sort of transforming material \[genetic material\]

What did Avery, MacLeod, and McCarty find?

When destorying DNA via DNase, there was no transformation of R cells, meaning that DNA is the transforming material turning R cells into S cells. 

What did Hershey and Chase find?

Using T2 bacteriphage, they found that protein was not genetic material (left in phage ghosts) but DNA is (recovered in host and passed on to the phage progeny).; DNA is the genetic material, not protein. 

What are the 3 parts of a nucleotide (molecule of DNA)?

Deoxyribose Sugar  \n Phosphate Group  \n 1/4 Nitrogenous bases 

On deoxyribose, which carbon has the Hydroxyl group?

Carbon 3

What carbon is hydroxyl found on in Ribose?

Carbon 2

What are the 2 purines?

Adenine and Guanine 

How many rings do purines have?

2

What are the 2 pyrimidines?

Thymine and Cytosine 

How many rings do pyrimidines have?

1

What is the DNA backbone made up of?

Alternating sugars and phosphates

The 5' end of DNA is known as the _______?

Phosphate group

The 3' end of DNA is known as the ______?

Hydroxyl Group 

To what carbon does phosphate attach to in DNA?

C #5

How are nucleotides connected in a single strand (carbon/chemical level)?

C #3 attaches (w/ Hydroxyl) attaches to the phosphate of the next nucleotide

What is a phosphodiester bond?

Links two adjacent nucleotides in a single strand of DNA

What did Rosalind Franklin and Maurice Wilkins find?

THey used X-Ray diffraction patterns to find that DNA forms a regular helix.

How many hydrogen bonds are between G and C?

3

How many hydrogen bonds are between A and T?

2

How does DNA maintain it's 20 Angstrom diameter?

By pairing purines (A and G) and pyrimidines (C and T)

What did Chargaff find? Why is this the case?

He found that the ratios of Adenine to Thymine, and Guanine to Cytosine are equal. This is due to base pairing. 

What is the purpose of major and minor grooves?

Sites for protein binding 

How are DNA strands formed in relation to each other?

They are anti-parallel with a sugar phosphate backbone on the outside, and pairs of nitrogenous bases in the middle 

How do the two strands of DNA wrap around each other? (How many base pairs?)

They complete a 360° turn once every 10 base pairs (30 Angstroms)

How are the two strands of DNA held together? 

Hydrogen bonds  \n (A-T = 2) \n (C-G = 3)

Use the ladder analogy to describe the structure of DNA:

The sugar phosphate backbone are the sides of the ladder while the nitrogenous base pairs in the middle are the ladder rungs.

Is RNA single or double stranded?

RNA is a single strand of ribonucleotides 

What are the four bases of RNA?

Adenine \n Guanine  \n Cytosine  \n Uracil

Prior to experiments done by Avery, MacLeod + McCarty, and Hershey + Chase, what was thought to be the genetic material?

Protein 

How many amino acids make up protein?

20

What happened to the mice when Griffith injected them with heat killed S cells, mixed with R cells?

They died b/c the R cells were transformed into S cells

Who figured out the structure of DNA?

Watson and Crick 

Are the 5' and 3' ends of DNA the same or different?

They are chemically different

What is the B form of DNA (most common form)?

It is right handed and has a smooth backbone 

What is the Z form of DNA (less common)?

Forms left handed helix and irregular backbone 

What do both strands acts as during DNA rep?

Templates

Steps of DNA Rep (Unw, Rep Temp, DNAP-S, BP, + DAU):

1\. DNA helix unwinds and strands separate  \n 2. Both strands act as replication templates  \n 3. DNA Polymerase synthesizes two new strands of DNA via semiconservative rep \n 4. Complementary base pairing (A + T, C + G) \n 5. Two daughter helices are produces and each is half original DNA and have newly synthesized DNA.

What is the genetic makeup of the two daughter helices formed after DNA replication?

They have half of the original DNA (template strand) and half newly synthesized DNA.

What are the three models for DNA replication? (SCD)

Semiconservative  \n Conservative  \n Dispersive 

SCD

The three possible models for DNA replication: \n Semiconservative  \n Conservative  \n Dispersive 

What is Semiconservative replication? 

Watson-Crick Model; Two strands of DNA unwind and each strand acts as a template for a new DNA strand. 

What is conservative replication?

The parental double helix remains intact and both daughter helices are made up of newly synthesized DNA.

What is dispersive replication?

 both strands of both daughter helices contain a combination of original and newly synthesized DNA

What was the conclusion of the Meselson-Stahl experiments?

DNA is replicated in a semiconservative fashion 

What does it mean that DNA replication is bidirectional?

It goes from the origin of replication in both directions, resulting in a leading and lagging strand 

What are the steps of DNA rep?

1\. Initiator Protein binds to the origin of replication  \n 2. Helicase unwinds the helix and opens the strand \n 3. Single-strand binding proteins keep the helix open  \n 4. Primase synthesizes RNA primers that are complimentary and anti-parallel to the template strand.  \n 5. DNA Polymerase starts the new strand from the RNA Primer \n 6. Ligase seals the gap

In what direction is DNA always synthesized in?

5 - 3’

What is the leading strand?

The strand that is synthesized continually in the 5' to 3' direction towards the replication fork.

What is the leading strand going towards?

The replication fork 

What is the lagging strand?

Strand that is synthesized discontinually in the 5' to 3' direction, __opposite__ of the fork; it is synthesized in short fragments called okazaki fragments.

What does DNA Polymerase I do?

Replaces the RNA primer (from primase) with a DNA sequence 

What is the function of DNA ligase?

Covalently joins successive Okazaki fragments together

What is required for DNA polymerase to bind?

A free 3' hydroxyl group to accept the first nucleotide 

What is the main function of DNA Polymerase III?

Does the bulk of DNA synthesis 

What is the main function of DNA Polymerase I?

Removes RNA primers and replaces them with DNA

Which strand is continuosly synthesized and which is discontinuosly synthesized?

Continuously = Leading Strand  \n Discontinuosly = Lagging Strand 

How are new combinations of alleles created?

Two events in meiosis:  \n 1. Independent Assortment  \n 2. Crossing Over 

What is independent assortment?

Each pair of homologous chromosomes segregate freely from each other, creating new allele combinations for unlinked genes 

What is crossing over?

Two homologous chromosomes exchange portions of DNA, creaing new allele combinations for linked genes. Also ensures proper chromosomal segregation during meiosis 

What process creates new allele combinations for unlinked genes?

Independent Assortment 

What process creates new allele combinations for linked genes?

Crossing over 

What is a mutation?

Heritable changes in DNA base sequences that modify the information content of DNA 

What is a germline mutation?

Mutation found in gametes and passed onto the next generation 

What is a somatic mutation?

Affects specific person and the mutation is not passed onto the next generation

What is a forward mutation?

Wild-type changed to a different allele (i.e. T --> t)

What is a reverse mutation?

A new mutation that results in a reversion to the wild-type phenotype (t --> T)

Which mutation (forward or reverse) is most common/higher?

Forward mutation happens at a higher rate (always) over reverse mutation 

Which scientist conducted an experiment with mice, R cells, and S cells?

Griffith 

Which scientist(s) did the experiment where it was determined that DNA was the genetic transfroming material?

Avery, MacLeod, and McCarty 

Which scientist(s) did the experiment with bacteriophage and determined that DNA was the genetic material, not protein?

Hershey and Chase 

Which scientist(s) determined that DNA is replicated in a semiconservative fashion?

Meselson-Stahl

What does DNA polymerase require for DNA Replication? (3 - TPN)

Template  \n Primer w/ exposed 3' OH \n Nitrogenous Bases 

What are the three stages of the mechanism of DNA replication?

Initiation, Elongation, and Termination 

What is an initiator protein?

Binds to the origin of replication 

What is the function of helicase?

Unwinds the helix

What is the function of single-strand binding proteins?

Keep the DNA helix open 

What is the function of primase?

Synthesizes RNA primers that are complementary and antiparalell to the template strand 

What is the function of DNA Polymerase?

Synthesizes new proteins in the 5' --> 3' direction 

What is the function of ligase?

Seals the nicks or gaps that are left behind after DNA polymerase synthesizes a new strand 

What is the function of DNA Polymerase III? In regards to nucelotide bonds?

Does the bulk of DNA synth. and catalyzes phosphodiester bond formation between adjacent nucleotides on the new strand.

Unw, Rep Temp, DNAP-S, BP, + DAU)

Steps of DNA Rep \n 1. Double Helix Unwinds  \n 2. Both Strands act as replication templates  \n 3. DNA Polymerase synthesizes 2 new strands via semiconservative replication  \n 4. Base pairing occurs  \n 5. 2 daughter helices form; 1 with the original DNA, and the other being newly synthesized DNA

What is the function of DNA Polymerase I?

Replaces the RNA primer with DNA sequence

What is the function of DNA Ligase?

Covalently joins successive Okazaki fragments together via phosphodiester bonds

How are Okazaki fragments joined together?

Phosphodiester Bonds

What happens to the functionality of DNA Polymerase if Hydroxyl is missing?

DNA Polymerase won't bind and no new DNA is made 

In what direction is the lagging strand synthesized?

The direction opposite of the fork, in the 5' - 3' direction 

What is the Central Dogma of Molecular Biology?

DNA --(transcription)--> RNA --(translation)--> Protein 

What do genes specify?

The identity and order of amino acids in a \[linear\] polypeptide chain 

How is the lagging strand synthesized?

In fragments called okazaki fragments

Which human gamete has a higher mutation rate? Why?

Human sperm; due to older males having gone through multiple mitotic divisions 

What are the three types of point mutations? (SDI)

Substitution  \n Deletion  \n Insertion 

What is a substitution mutation?

A base is replaced by one of the other three bases 

What is a transition mutation?

Purine switched for purine; Pyrimidine switched for pyrimidine 

What is a transversion mutation?

Purine for pyrimidine; pyrimidine for purine 

What happens if a mutation isn't repaired?

There's a possibility that it will cause permanent damage and be passed to future generations

What impact do X-Rays have on DNA? What can this lead to?

They create double stranded breaks in the DNA backbone, leading to deletions 

What impact can UV Light have on DNA? What can occur?

They can produce pyrimidine (thymine) dimers that if not repaired, they can interfere with DNA replication (Ex: TT to CC Substitution)

What can a mutagen lead to or cause in regards to a nitrogenous base?

It can alter the structure of the nitrogenous base, leading to a mutation.

Mutagens that alter the structure of a nitrogenous base can lead to ______?

New (and incorrect) base pairing, causing propogation of the mutation 

Mutagen: Active Oxygen Species 

Free Radical