Chapter 6- DNA and Biotechnology

Question 1

nucleoside

Answer 1

pentose (5C sugar) bound to a nitrogenous base formed through a covalent link with C1 of sugar.

Question 2

nucleotides

Answer 2

formed when one or more phosphate groups are attached to C5 of nucleoside. building blocks of DNA

Question 3

5 bases in DNA/RNA

Answer 3

1. adenine
2. guanine
3. cytosine
   4/5. uracil (RNA or DNA)/ thymine (DNA)

Question 4

backbone of DNA

Answer 4

sugar and phosphate- create phosphodiester bonds (phosphate makes DNA negative)
DNA is always read from 5’ to 3’

Question 5

purines

Answer 5

2 ring structure found in both DNA and RNA (PUR As Gold, two gold rings at a wedding)

1. adenine
2. guanine

Question 6

pyrimidines

Answer 6

1 ring structure (CUT PYI, pie crust has one ring)

1. cytosine (DNA and RNA)
2. thymine (DNA only)
3. uracil (RNA only)

Question 7

complementary base pairings in DNA

Answer 7

A-T (2H bonds)

G-C (3H bonds)

Question 8

B-DNA

Answer 8

most DNA is a right-handed helix, turning every 3.4nm (~10 bases between each turn)

Question 9

major and minor grooves in DNA

Answer 9

provide binding sites for regulatory proteins

Question 10

Z-DNA

Answer 10

zigzag appearance. left-handed helix turns every 4.6nm (~12 bases between each turn). this form may occur with a high G-C content or high salt concentration. less stable than B-DNA.

Question 11

commonly used to denature DNA

Answer 11

heat, alkaline pH, chemicals (formaldehyde and urea)

Question 12

denature vs reannealed

Answer 12

denature- 2 strands separated

reannealed- 2 strands brought back together

Question 13

H1

Answer 13

the last histone that seals off the DNA as it enters and leaves the nucleosome, adding stability

Question 14

heterochromatin

Answer 14

dark, dense, and silent DNA, compacted during interphase

Question 15

euchromatin

Answer 15

light, uncondensed, expressed DNA (genetically active), dispersed chromatin

Question 16

telomere

Answer 16

repeating unit at the end of DNA (TTAGGG), some of this is lost every time during replication. telomerase fixes this and is highly expressed in rapidly diving cells.

Question 17

replisome

Answer 17

aka replication complex. specialized proteins to assist DNA polymerases.

Question 18

helicase

Answer 18

responsible for unwinding DNA

Question 19

DNA gyrase (DNA topoisomerase II)

Answer 19

alleviates torsional stress and reduces risk of strand breakage by introducing negative supercoils. works ahead of helicase (prokaryotes)

Question 20

DNA polymerases

Answer 20

reading DNA template (parental strand) and synthesizing the new daughter strand. reads parent in 3 to 5 direction and builds the daughter in 5 to 3 direction.

Question 21

5 classic eukaryotic DNA polymerases

Answer 21

1. alpha- synthesizes leading/lagging strands
2. beta- DNA repair
3. gamma- replicates mitochondrial DNA
4. delta- synthesizes leading/lagging strands, fills in gaps left behind when RNA primers are removed, forms sliding clamp to strengthen interaction b/w DNA polymerase and template strand
5. epsilon- DNA repair, forms sliding clamp to strengthen interaction b/w DNA polymerase and template strand

Question 22

oncogenes

Answer 22

mutated genes that cause cancer

Question 23

proto-oncogenes

Answer 23

before genes are mutated to become oncogenes. they promote rapid cell cycle advancement more than usual.

Question 24

nucleotide excision repair (NER)

Answer 24

eliminates thymine dimers from DNA using a cut and patch process

Question 25

excision endonuclease

Answer 25

makes a nick in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removed the defective oligonucleotide (based on bulge in the strand)

Question 26

what can thermal energy do to DNA

Answer 26

cytosine deamination: los of amino group from cytosine turning it into uracil (which should not even be in DNA)

Question 27

base excision repair

Answer 27

repairs small, non-helix-distorting mutations in other bases as well.

1. affected base is recognized and removed by glycosylase enzyme
2. apurinic/apyrimidinic (AP) site is left open aka: abasic site
3. AP site recognized by AP endonuclease that removes damaged sequence from DNA
4. DNA polymerase and ligase fill and seal the strand

Question 28

exon vs intron of DNA

Answer 28

exon- coding

intron- noncoding

Question 29

hybridization

Answer 29

joining of complementary base pair sequences. can be DNA-DNA or DNA-RNA

Question 30

PCR

Answer 30

automated process that can produce millions of copies of a DNA sequence without amplyfying DNA in bacteria.

• primer prepared with complementary sequence to part of the DNA of interest
• repeated heating and cooling cycles allow the enzymes to act specifically and replaces helicase
• each cycle of PCR reaction doubles the amount of DNA of interest

Question 31

gel electrophoresis

Answer 31

separates macromolecules (ex: DNA) by size and charge

Question 32

southern blot

Answer 32

used to detect the presence and quantity of various DNA strands in a sample. DNA is cut by restriction enzymes and separated by gel electrophoresis. then radioisotopic probes bind to the one youre looking for based on the sequence you want.

Question 33

dideoxyribonucleotide

Answer 33

once incorporated into the chain then nothing else can be added after b/c it has H instead of OH at C3

Question 34

cDNA library

Answer 34

only expressed genes included (complementaryDNA) results from reverse transcription of processed mRNA