Biochemistry: Exam 2

Front 1

describe purines and pyrimidines

Back 1

heterocyclic
weakly basic
relatively insoluble in water (nucleotides are soluble)
unsat w/ conjugated dbl bonds

Front 2

glycosidic bond

Back 2

links the base to the sugar

Front 3

importance of negativity of phosphate

Back 3

makes nucleic acid polyanions. crucial to function

Front 4

A DNA

Back 4

more tightly wound, has grooves of equal width. predominates in DNA-RNA hybrids. Forms when DNA is dehydrated

Front 5

Z DNA

Back 5

has no grooves and bases positioned towards periphery of left handed helix

Front 6

prok vs euk genome size

Back 6

euk is 1000 times bigger

Front 7

packing of prok DNA

Back 7

supercoiled and attached to an RNA-protein core in large loops
-called the nucleoid structure

Front 8

chromatin

Back 8

euk DNA plus various proteins
beads on a string look

Front 9

nucleosomes

Back 9

histones plus DNA

Front 10

histones

Back 10

small basic proteins containing lots of lysine and arginine (+)
-euk have five classes
-positive histones attracted to neg sugar-phosphates on backbone

Front 11

nucleosome core

Back 11

histone octamer of two of each histones with about 140 bp wrapped around it

Front 12

linker DNA

Back 12

part of it complexed with H1 that locks the coiled DNA in place on the histone octamer

Front 13

solenoid structures

Back 13

further compaction of the DNA
-helical structures
-associate through weak interactions between H1 molecules

Front 14

heterochromatin

Back 14

densely packed DNA-seen in interphase

Front 15

euchromatin

Back 15

loosely packed DNA-in interphase

Front 16

importance of mtDNA mutations

Back 16

OXPHOS diseases-associated with brain and muscle, where large amts of ATP are formed

Front 17

rRNA

Back 17

accounts for 80% of RNA in cells
-very stable, integral part of RNA
-contain stem loop structures

Front 18

tRNA

Back 18

carries activated amino acids to ribosomes for polypeptide synthesis
-smallest RNA

Front 19

mRNA

Back 19

Carry sequence information from DNA to ribosomes
-translated by ribosomes/tRNA to form proteins
-rapidly degraded by nucleases

Front 20

erythromycin

Back 20

used as an antibiotic
-inhibits protein synthesis by binding the 50S ribosomal unit in prok.

Front 21

modified nucleotides in tRNA

Back 21

ribothymadine
dihydrouridine
pseudouridine

Front 22

structure of tRNA

Back 22

all have three arms:
1. D arm, contains dihydrouridine
2. anticodon arm
3. TC arm, contains ribothymadine and pseudouridine
4. some contain variable arm as well

Front 23

role of snRNA

Back 23

recognize key RNA sequence elements at splice sites
-allow spliceosome to correctly cut out introns
-allow for alternative splicing

Front 24

ribozyme

Back 24

enzymes whose catalytic sites contain RNA

Front 25

4 other types of RNA

Back 25

1. sn ribonuclear proteins
2. ribozymes
3. RNA "primers" for DNA synthesis
4.RNA genome of retroviruses

Front 26

5-fluorouracil

Back 26

cancer chemotherapeutic agent. Inhibits synthesis of thymine. Used for colon cancer treatment.

Front 27

Doxorubicin

Back 27

slips b/w stacked base pairs of DNA
-DNA cannot act as template for transcription/translation
-used in treatment of solid malignancies (ex: breast cancer)

Front 28

AZT

Back 28

blocks viral DNA polymerase (reverse transcriptase) activity

Front 29

3 R's of DNA

Back 29

1. Replication
2. Repair
3.Recombination

Front 30

requirements of DNA replication

Back 30

1.template
2. primer
3. precursors
4.enzymes

Front 31

helicase

Back 31

unwinds the DNA

Front 32

topoisomerase

Back 32

breaks and rejoins the dbl helix. prevents knot formation

Front 33

single stranded DNA

Back 33

prevents the single strand of DNA from recombining

Front 34

RNA primase

Back 34

initiates the first nucleotides of the leading strand and the okazaki fragments

Front 35

DNA polymerase III

Back 35

elongation of new strands. goes in 3'->5' direction

Front 36

RNAase H, FENI

Back 36

removes primers

Front 37

DNA pol I

Back 37

replaces RNA primer

Front 38

DNA ligase

Back 38

connects the okazaki fragments and other loose DNA fragments

Front 39

Tsu

Back 39

a bacteria that blocks helicase activity

Front 40

DNA gyrase

Back 40

induces or removes supercoiling of DNA
-absent in euk cells

Front 41

telomerase

Back 41

prevents chromosomes fusing

Front 42

DNA replication in prokaryotes

Back 42

bidirectional until meet at termination point
-primase forms RNA primer
-girase unwinds the DNA
-single stranded DNA proteins bind
-

Front 43

replisome

Back 43

protein machinery that carries out the polymerization reaction

Front 44

steps of e.coli replication

Back 44

1. primase lays primer
2. DNA Pol III lays down the DNA
3.DNA Pol I removes the primer
4. Pol I fills in the gaps

Front 45

DNA pol I

Back 45

repairs DNA and participates in DNA synthesis of one strand

Front 46

DNA pol II

Back 46

role in DNA repair

Front 47

DNA pol III

Back 47

major role in DNA replication enzyme. responsible for chain elongation

Front 48

eukaryotic DNA polymerases

Back 48

at least 15
very low error rate

Front 49

okazaki fragments

Back 49

DNA pol cannot initiate!
-RNA polymeraes (primase) initiates oligonucleotide primer
-DNA pol III uses primer to start lagging strand DNA synthesis

Front 50

Proofreading tools

Back 50

1. DNA pol III has 3' to 5' proofreading
2.pol III can catalyze chain elongation and degradation
3.exonuclease activity
4. post-replication mismatch repair

Front 51

what happens in gap 1 of cell cycle

Back 51

cells increase in size, produce RNA and synthesize proteins
-G1 checkpoint

Front 52

what is G0

Back 52

cells may leave cell cycle and quits dividing. may be temporary or more permanent

Front 53

synthesis phase of cell cycle

Back 53

DNA replication takes place

Front 54

what is G2 of cell cycle

Back 54

cell continues to grow and produce new proteins.
-G2 checkpoint for entering mitosis

Front 55

three possible fates of DNA damage

Back 55

1. cancer
2. senesence
3.apoptosis

Front 56

4 types of DNA repair

Back 56

1. base excision repair
2. nucleotide excision repair
3. mismatch repair
4. transcription coupled repair

Front 57

translocation

Back 57

exchange of chromosome segments b/w two usually nohomologous chromosomes
-cause of Burkitt's lymphoma

Front 58

transposons

Back 58

jumping genes
mobile DNA sequences that may encode transposase
-found in the junk DNA

Front 59

what do transposons code for?

Back 59

1. may have regulatory function and code for RNA
2.code for drug resistant markers
3. enzymes degrading toxic and carcinogenic compounds

Front 60

telemorases

Back 60

act to maintain the length of the telomeres
-are ribonucleoprotein complexes containing a small RNA molecule that serves as a template