Chapter 6

Question 1

Nucleosides

Answer 1

• Composed of a 5 carbon sugar (pentose) bound to a nitrogenous base
• Formed by covalently linking base to C1 of the sugar

Question 2

Nucleotides

Answer 2

• Formed when one or more phosphate groups are attached to C5 of a nucleoside
• Often named by the number of phosphates bound
• High-energy compounds because of teh energy associated with the repulsion between closely associated negative charges on the phosphate groups
• Nucleotides are the building blocks of DNA

Question 3

Backbone of DNA

Answer 3

• Alternating sugar and phosphate groups
• Always read 5’ to 3’

-Formed as nucleotides are joined by 3’ to 5’ phosphodiester bonds

Question 4

Purines

Answer 4

• Contain two rings

- Adenine and guanine

Question 5

Pyrimidines

Answer 5

• Contain only one ring
• Cytosine, thymine and uracil

-Thymine is only found in DNA and Uracil is only found in RNA

Question 6

Watson-Crick model

Answer 6

• Two strands of DNA are antiparallel (oriented in opposite directions)
• Sugar phosphate backbone is on the outside (hydrophilic) of the helix with nitrogenous bases on the inside (hydrophobic)
• A with T (2 H bonds) and G with C (3 H bonds) thus C/G is a stronger bond

Question 7

Chargaff’s Rules

Answer 7

The total amount of purines will be equal to the total pyrimidines overall

Question 8

B-DNA

Answer 8

• Right-handed helix

- Makes a turn every 3.4 nm and contains 10 bases within that span

Question 9

Denaturation

Answer 9

• Conditions that disrupt h bonds and base-pairing
• “melting” of the double helix into two single strands (none of the nucleotides in the backbone break)

-Heat, alkaline pH and chemicals like formaldehyde/urea are most commonly used

Question 10

Reannealing

Answer 10

• DNA can be brought back together if the denaturing condition is slowly removed
• Important step in laboratory processes like polymerase chain reactions (PCR)

Question 11

DNA Replication- Heterochromatin and euchromatin

Answer 11

• During the S phase of interphase
• Small percentage of chromatin remains compacted during interphase and is referred to as heterochromatin (Transcriptionally silent)

-Dispersed chromatin is euchromatin- contains genetically active DNA

Question 12

Telomere

Answer 12

• Repeating unit TTAGGG at the end of DNA
• Some lost in each round of replication but can be replaced by the enzyme telomerase
• Progressive shortening of telomeres contributes to aging
• High GC content creates strong strand attractions at the end of chromosomes to prevent unraveling
• Think of telomeres as “knotting off” the end of the chromosome

Question 13

Centromeres

Answer 13

• Found at the center of chromosomes
• Composed of heterochromatin- which is composed of tandem repeat sequences that contain high GC content (why microtubules have to separate the chromatids during anaphase)

Question 14

Replisome/Replication Complex

Answer 14

Set of specialized proteins that assist the DNA polymerases

Question 15

Origins of replication

Answer 15

• Where DNA begins unwinding (Where replication begins)

- Generation of new DNA proceeds in both directions- creating replication forks

Question 16

Helicase

Answer 16

-Enzyme responsible for unwinding DNA, generating two single stranded template strands ahead of the polymerase

Question 17

Nucleases

Answer 17

Degrade DNA

Question 18

DNA gyrase/DNA topoisomerase II

Answer 18

introduces negative supercoils by working ahead of helicase, nicking both strands, passing dna through the strands and releasing it

Question 19

DNA polymerase

Answer 19

• Responsible for reading the DNA template (parent strand) and synthesizing the new daughter strand
• Reads template 3’ to 5’ while synthesizing in the 5’ to 3’ direction

Question 20

DNA Ligase

Answer 20

• Closes the gaps between Okazaki fragments

- Lacks proofreading ability so likelihood of mutations in lagging strand is considerably higher

Question 21

Single Stranded DNA binding proteins

Answer 21

Bind to unraveled DNA strands, preventing both the reassociation of the strands and degradation by nucleases

Question 22

Supercoiling

Answer 22

• Wrapping of DNA on itself (as its helical structure is pushed further toward the telomeres during replication
• Picture telephone cord wrapping on itself

Question 23

DNA gyrase/DNA topoisomerase II

Answer 23

introduces negative supercoils to reduce the risk of strand breakage

Question 24

Leading strand

Answer 24

• strand that is copied in a continuous fashion, same direction as the replication fork
• read 3’ to 5’ and replicated 5’ to 3’

Question 25

Primase

Answer 25

- Synthesizes RNA primer that is laid down to start DNA replication - RNA primers are constantly added to lagging strands because each Okazaki fragment must start with a new primer

Question 26

DNA polymerase III (prok) & DNA polymerases alpha and delta (euk)

Answer 26

Synthesize daughter strand in 5' to 3' manner

Question 27

DNA polymerase I (prok) & RNase H (euk)

Answer 27

Remove RNA primer

Question 28

DNA polymerase I (prok) & DNA polymerase delta (euk)

Answer 28

Add DNA nucleotides where RNA primer had been

Question 29

Methylation

Answer 29

Parent strand has been around longer so it is more methylated than the daughter strand. -also plays a role in transcriptional activity of DNA

Question 30

Metastasis

Answer 30

Migration to distant tissues by the bloodstream or lymphatic system

Question 31

Cancer cells

Answer 31

Proliferate excessively b/c they are able to divide without stimulation from other cells -Over time cancer cells tend to accumulate mutations

Question 32

Oncogenes

Answer 32

Mutated genes that cause cancer | -encode cell cycle related proteins

Question 33

Proto-oncogenes

Answer 33

oncogenes that are not yet mutated

Question 34

Tumor suppressor genes

Answer 34

Genes like p53 or Rb -encode proteins that inhibit the cell cycle -normally function to stop tumor progression and can be called antiongogenes

Question 35

Mismatch Repair

Answer 35

-Machinery in the G2 phase (encoded by MSH2 and MLH1 which detect and remove errors introduced in replication that were missed during the S phase)

Question 36

Nucleotide Excision Repair

Answer 36

``` Thymine dimers (induced by ultraviolet light) that interfere with DNA replication are removed from DNA -Recognized by bulge in the strand ``` -Excision endonuclease nicks the phosphodiester backbone of damaged strand and removes defective oligonucleotide

Question 37

Base Excision Repair

Answer 37

- Uracil found in DNA - Affected base is recognized and removed by a glycosylase enzyme- leaving an AP site -AP site recognized by an AP endonuclease that removes damage sequence

Question 38

Palindromic

Answer 38

The 5' to 3' sequence of one strand is identical to the 5' to 3' sequence of the other in antiparallel orientation

Question 39

Restriction enzymes/restriction endonucleases

Answer 39

- Enzymes that recognize specific double stranded DNA sequences - Isolated from bacteria, their natural source -Some produce offset cuts, yielding sticky ends on framents

Question 40

DNA libraries

Answer 40

-Large collections of known DNA sequences- these sequences could equate to the genome of an orangism

Question 41

Hybridization

Answer 41

The joining of complementary base pair sequences -Uses two single stranded sequences and is a vital part of PCR and southern blotting -Can be DNA-DNA recognition or DNA-RNA recognition

Question 42

Southern Blot

Answer 42

Used to detect the presence and quantity of various DNA strands in a sample -DNA cut by restriction enzymes and then separated by gel electrophoresis.