Genomics Exam #2

Front 1

Who is Erwin Chargaff?

Back 1

Discovered that DNA the number of guanine units equals the number of cytosine units, and the number of adenine units equals the number of thymine units.

The ratio of of A & T and G&C is equivalent. I.e. Human Genome A- 29 T-31 and C-18 G-18

Front 2

What are the characteristics of DNA?

Back 2

1. Double stranded molecule

2. DNA alphabet: A,T,C,G

3. Used for longterm information (reference material in a library)

4. Deoxyribose sugar on C2 an H (Hydrogen) is bound.

5. Deox= oxygen missing from the structure on C2

Front 3

What are the characteristics of RNA?

Back 3

1. Single stranded (the molecule can base pair with itself ; like sticky rope)

2. RNA nucleotides: A,U,C,G

3. Used to store short term information

4. Ribose on C2 an OH (hydroxyl group)

5. Has an extra oxygen on the second C.

Front 4

Who are Franklin and Wilikins?

Back 4

use of x-ray crystallography photographs to determine the structure of a molecule. Radar or Sonar technique that aids in trying to discover the approximation of the structure by bouncing "objects" off the desired structures i.e Photo 51

Front 5

What is the structure of DNA backbone?

Back 5

The phosphate group bound to the 5th Carbon of the sugar and a nitrogenous base bound to the 1st Carbon of sugar.

Front 6

What are purines?

Back 6

A and G. Lager nucleotide molecules

Front 7

What are pyrimidines?

Back 7

C, U and T. Smaller nucleotide molecules

Front 8

Back 8

Uracil

Front 9

Back 9

Thymine

Front 10

Back 10

Cytosine

Front 11

Back 11

Adenine

Front 12

Back 12

Guanine

Front 13

What does N mean in a genomic sequence?

Back 13

Any nitrogenous bases (A,T,G,C,U)

Front 14

How does DNA or RNA arranged?

Back 14

5' to 3': phosphate group at the begin attached to the 5' Carbon and the 3' Carbon naked at the end of the molecule.

Front 15

Semi-Conservative

Back 15

produce two copies that each contained one of the original strands and one new strand.

Front 16

Conservative

Back 16

leave the two original template DNA strands together in a double helix and would produce a copy composed of two new strands containing all of the new DNA base pairs.

Front 17

Dispersive

Back 17

produce two copies of the DNA, both containing distinct regions of DNA composed of either both original strands or both new strands.

Front 18

How many Hydrogen bonds are between the nitrogenous bases?

Back 18

3 hydrogen bonds between G and C

2 hydrogen bonds between A and T or U

Front 19

What is the Central Dogma?

Back 19

Front 20

How are the DNA strand arranged?

Back 20

Antiparrell

Front 21

What does PCR stand for?

Back 21

Polymerase Chain Reaction

Front 22

What are the steps for PCR?

Back 22

A. Denaturation at 94 C for 45 seconds: breaks down or separates the hydrogen bonds between nucleotides.

B. Annealing at 60 C for 45 seconds: primers are finding their compliment base pair (18-25 bp) on the DNA strand.

C. Extension at 72 C for 60 seconds: primer extends the desired amplification region. Add nucleotides one at a time.

Front 23

When does elongation stop?

Back 23

The primer knows to stop when the temperature rises up to 94 C (denaturation step). The primer will then bind to a new region of DNA.

Front 24

Where are the new nucleotides added?

Back 24

At the 3' end of the strand.

Front 25

Primer Dimers

Back 25

consists of primer molecules that have attached (hybridized) to each other because of strings of complementary bases in the primers. Typically occur lower than 100 bps.

Front 26

Gradient PCR

Back 26

Varying thermal annealing in order to find the perfect annealing temperature for both primers.

Front 27

What is the Wallace Equation?

Back 27

TM = 4(G+C) + 2(A+T)

Front 28

What process only needs one primer?

Back 28

RT: Reverse Transcription

Front 29

What process uses two primers?

Back 29

PCR: Polymerase Chain Reaction

Front 30

What are the degenerate letters?

Back 30

Y: T or C

R: G or A

N: A, T, U, G, C

Front 31

What does a nucleotide contain?

Back 31

5' carbon sugar or 3' carbon sugar, a phosphate group and one out of the four nitrogen bases.

Front 32

What is the leading strand?

Back 32

3' to 5'. The top strand being replicated.

Front 33

What is the lagging strand?

Back 33

5' to 3'. The bottom strand being replicated.

Front 34

What is the function of the Hhelicase enzyme?

Back 34

Unwinds the DNA structure separating a desired region/section into two halves. Breaking the hydrogen bonds between the nitrogen bases.

Front 35

What is the replication fork?

Back 35

a site on a DNA molecule at which unwinding of the helices and synthesis of daughter molecules are both occurring.

Front 36

How are the primer dimers arranged?

Back 36

Front 37

What would you do if the PCR produced too many bands?

Back 37

increase the annealing temperature and decrease the magnesium concentration.

Front 38

What would you do if the PCR produced no bands?

Back 38

decrease the annealing temperature and increase the magnesium concentration.

Front 39

What does starting material does DNA polymerase need to begin sequence?

Back 39

The polymerase needs DNA as a template.

Front 40

Who is Kary Mullis?

Back 40

Developed the PCR technique in 1983

Front 41

What is the salt adjustment for the %GC Method?

Back 41

usually 0.05 Na+

Front 42

Where does the leading and lagging strand synthesized?

Back 42

These processes occur on both sides of the replication fork.

Front 43

What are the components apart of the replication of DNA?

Back 43

A. DNA Polymerase

B. Topoisomerase

C. DNA Polymerase III & I

D. Ligase

E. Primase

Front 44

What is topoisomerase?

Back 44

An enzyme that regulate the overwinding or underwinding of DNA. regulation of DNA supercoiling is essential to DNA transcription and replication, when the DNA helix must unwind to permit the proper function of the enzymatic machinery involved in these processes. Topoisomerases serve to maintain both the transcription and replication of DNA.

Front 45

What is Helicase?

Back 45

An enzyme used to separate strands of a DNAdouble helix or a self-annealed RNA molecule using the energy from ATP hydrolysis, a process characterized by the breaking of hydrogen bonds between annealed nucleotide bases.

Front 46

What are DNA Polyermerase III & I?

Back 46

III: makes the chain in a 5 to 3 direction and it proofreads with a 3 to 5 exonuclease, so it goes both ways doing something different

I: breaks down the RNA primer with a 5 to 3 exonuclease.

Front 47

What is ligase ?

Back 47

is an enzyme that can catalyze the joining of two large molecules by forming a new chemical bond.

Front 48

What is primase?

Back 48

enzyme that synthesizes short RNA sequences called primers. These primers serve as a starting point for DNA synthesis.

Front 49

Who discovered that eukaryotic genes are composed of intron and exons?

Back 49

Robert and Sharp

Front 50

What provides the primer for the replication?

Back 50

RNA Polymerase; 5' to 3' (leading)

Front 51

What copies a series of segments of the lagging strand?

Back 51

RNA primase starts to encode short RNA segements. DNA Polymerase III works backwards to replicate. And DNA Polymerase I replaces RNA U nucleoides with DNA T nucleotides.

Front 52

What adds complementary nitrogenous bases in replication of DNA?

Back 52

DNA Polymerase III

Front 53

What does the reverse transcriptase?

Back 53

An enzyme used to convert RNA back into DNA

Front 54

What is reverse transcription?

Back 54

used to generate complementary DNA (cDNA) from an RNA template. It is mainly associated with retroviruses.