Biotech Exam 1

Front 1

Adenine & guanine have ___ ring stuctures.
They are found in:

Back 1

Adenine & guanine have purine ring stuctures.
They are found in: both DNA & RNA

Front 2

Name the structures and if they are found in DNA and/or RNA.

Back 2

A. Purine ring
B. Adenine, DNA/RNA
C. Guanine, DNA/RNA

Front 3

Cytosine, Uracil, and Thymine have ___ ring stuctures.
DNA contains:
RNA contains:

Back 3

Cytosine, Uracil, and Thymine have Pyrimidine ring stuctures.
DNA contains: cytosine & thymine
RNA contains: cytosine & uracil

Front 4

Name the structures and if they are found in DNA and/or RNA.

Back 4

A. Pyrimidine ring
B. Cytosine DNA/RNA
C. Uracil RNA
D. Thymine DNA

Front 5

1. ___ are compounds in which purine or pyrimidine base is covalently linked to the sugar at carbon # ___.
2. In RNA the sugar is ___ making ___.
3. In DNA the ___ is ___ at the ___ carbon to afford ___ making ___

Back 5

1. Nucleosides, 1.
2. D-Ribose, ribonucleoside.
3. ribose, reduced, 2, deoxyribose, deoxyribonucleoside.

Front 6

Name these Purine nucleosides:
A.
B.
C.
D.

Back 6

A. Adenosine
B. Guanosine
C. 2'-Deoxyadenosine
D. 2'-Deoxyguanosine

Front 7

Name these Pyrimidine nucleosides:
A.
B.
C.
D.

Back 7

A. Cytidine
B. Uridine
C. 2'-Deoxycytidine
D. thymidine

Front 8

Nucleotide is the ___ ___ of a nucleoside.
Examples are:
AMP: full name
ADP: full name
ATP: full name

Back 8

Nucleotide is the phosphate ester of a nucleoside.
Examples are:
AMP: Adenosine 5'-Monophosphate
ADP: Adenosine 5'-Diphosphate
ATP: Adenosine 5'-Triphosphate

Front 9

Show mechanism of cAMP formation.

Back 9

Front 10

Nucleotides have a wide variety of functions in the body including:
1.
2.
3.
4.
5.

Back 10

1. carry activated groups in synthesis of carbohydrates, lipids, and proteins.
2. Structural comp of coenzymes (FAD, NAD+, NADP+, coenzyme A ect)
3. energy sources (ATP, GTP)
4. precursors for DNA/RNA
5. second messengers

Front 11

Their cellular levels are maintained by both ___ ___ synthesis and by ___ ___. Cellular conc of nucleotides are controlled by ___ regulated enzymes. The nucleotide end products of these pathways serve as effectors for key steps.

Back 11

Their cellular levels are maintained by both de novo synthesis and by salvage pathways. Cellular conc of nucleotides are controlled by allosterically regulated enzymes. The nucleotide end products of these pathways serve as effectors for key steps.

Front 12

Folate Coenzymes are involved in Purine and Pyrimidine Synthesis:
Folic acid must be converted to ___ and then to ___ - which accepts a carbon from serine to become a coenzyme in purine synthesis. The enzyme converting in both steps is ___ and the coenzyme is ___.

Back 12

Folic acid must be converted to dihydrofolic acid and then to tetrahydrofolic acid - which accepts a carbon from serine to become a coenzyme in purine synthesis. The enzyme converting in both steps is dihydrofolate reductase and the coenzyme is NADPH.

Front 13

Methotrexate is a potent inhibitor of ___ ___ in humans.

Back 13

dihydrofoloate reductase

Front 14

Trimethoprim is a potent inhibitor of ___ ___ in bacteria

Back 14

dihydrofoloate reductase

Front 15

Folic acid and its coenzymes are ___ ___ into cells.
Once inside they are ___ by an enzyme known as ___ ___.
___ ___ have greater affinity for the folate-dependent enzymes needed for purine and thymidylate (not needed for cytosine & uracil) synthesis, but NOT for ___ ___.

Back 15

1. actively transported
2. polyglutamylated, folypolyglutamyl synthetase
3. polyglutamylated folates, dihydrofolate reductase.

Front 16

Interconversion of ___ ___ is necessary for synthesis of purines and thymidine monophosphate.

Back 16

FH4 coenzymes

Front 17

___ make up the majority of nucleotides found in cells, with ___ being present in the greatest concentration.

Back 17

5'-Nucleotides, ATP

Front 18

Nucleosides:
In normally functioning cells, ___ ___ predominate. ___ and ___ predominate in hypoxic cells.

Back 18

nucleoside 5'-triphosphates
5'-mono, diphosphates

Front 19

de novo Purine biosynthesis:
___ is the common intermediate ("fork in the road") in the synthesis of the other purines.

Back 19

inosine 5'-monophosphate (IMP)

Front 20

Origin of the atoms in the purine ring.

Back 20

A. Glycine
B. N10-Formyl-
tetrahydrofolate
C. Glutamine
D. N10-Formyl-
tetrahydrofolate
E. Aspartic acid
F. CO2 (HCO3)

Front 21

Ribose 5-phosphate is converted to 5-Phosphoribosyl-1-pyrophosphate (PRPP) by the enzyme ___. This enzyme is activated by ___ and inhibited by ___ ___ ___.
PRPP is also involved in the synthesis of ___ nucleotides and in the ___ ___ rxns in both ___ & ___.

Back 21

1. 5-Phosphoribosyl-1-pyrophosphate synthetase
2. Pi (from ATP), purine nucleotide di/triphosphates.
3. pyrimidine, salvage pathway, purines, pyrimidines

Front 22

PRPP stands for ___, it is formed from ___ catalyzed by ___ ___.

Back 22

5-phosphoribosyl-1pyrophosphate, ribose 5-phosphate, PRPP synthetase

Front 23

From PRPP to IMP (inosine 5'-monophosphate), there are ten steps.
List sites of inhibition here: 3 points of inhibition.

Back 23

1. Glutamine PRPP amidotransferase: inhibited by IMP, AMP, GMP, 6-MPRP (6-mercaptopurine ribose phosphate), 6-TGRP (6-thioguanine ribose phosphate).
2. GAR (Glycinamide ribonucleotide) formyltransferase: inhibited by Methotrexate - reduces coenzyme (N10-formyltetrahydrofolate) that transfers the formyl moiety.
3. AICAR (5-aminoimidazole-4-carboxamide ribonucleotide) formyltransferase: Methotrexate again for same reason.

Front 24

Once IMP is synthesized - list the 2 points of end product inhibition and what pathway they are in. This inhibition allows diversion of IMP to synthesis of the purine present in lowest concentration.

Back 24

1. adenylosuccinate synthetase: inhibited by AMP - in the ADP pathway
2. inosate dehydrogenase: inhibited by GMP plus 6-MPRP and 6-TGRP - in the GDP pathway

Front 25

1. 6-MPRP:
2. 6-TGRP:
3. PRPP
4. GAR

Back 25

1. 6-mercaptopurine ribose phosphate
2. 6-thioguanine ribose phosphate
3. 5-phosphoribosyl-1pyrophosphate
4. Glycinamide ribonucleotide

Front 26

1. Base ___ nucleoside monophosphate kinases convert nucleoside monophosphates to ___. These enzymes do not discriminate between ___ & ___ sugars in the substrate. Name the 2 kinases:
2. Nucleoside diphosphates are converted to triphosphates by the ___ enzyme nucleoside diphosphate kinase.

Back 26

1. specific, diphosphates, ribose, deoxyribose. Adenylate kinase and Guanylate kinase
2. nonspecific (base)

Front 27

Indirect inhibitors of de novo Purine biosynthesis.
1. sulfonamides act as antibacterial agent by inhibiting ___ ___ which is necessary for bacterial synthesis of ___ ___ preventing them from making ___ coenzymes.

Back 27

1. dihydropteroate synthetase, dihydrofolic acid, folate

Front 28

Indirect inhibitors of de novo Purine biosynthesis cont.
Methotrexate inhibits ___ ___ which in needed for synthesis of folate coenzymes in:

Back 28

dihydrofolate reductase, humans and animals

Front 29

Direct inhibitors of de novo Purine Biosynthesis.
1. 6-Mercaptopurine (6-MP) and 6-Thioguanine (6-TG) are metabolically activated by purine salvage pathways to give the ___ ___ analogues.
2. 6-MPRP inhibits:
3. 6-TGRP inhibits:

Back 29

1. ribose phosphate
2. amidotransferase, adenylosuccinate synthetase, adenylosuccinate lyase, inosate dehydrogenase
3. amidotransferase, inosate dehydrogenase, guanylate kinase

Front 30

Purine salvage pathways.
1. ___ provides the ribose phosphate group for the 2 enzymes involved.
A. ___ catalyzes the rxn with either hypoxanthine or guanine. The products are ___ and ___ respectively.
B. ___ catalyzes the rxn with adenine. The product is ___.

Back 30

1. 5-Phosphoribosyl-1-pyrophosphate (PRPP)
A. Hypoxanthine-guanine phosphoribosyl transferase (HGPRT), IMP, GMP
B. Adenine phosphoribosyl transferase, AMP

Front 31

Purine nucleotide degradation:
1. In humans, the end product of nucleotide degradation is ___.
2. Non-primate mammals oxidize this to ___, which in non-mammal animals is broken further to ___ or ___ in some cases.

Back 31

1. uric acid
2. allantoin, urea, ammonia

Front 32

Formation of uric acid:
1. Removal of the amino group from AMP gives ___, amino removal from adenosine gives ___.
2. IMP and GMP are dphosphorylated by ___ to give ___ and ___ respectively.
3. ___ ___ ___ converts inosine and guanosine to ___ and ___ respectively.
4. Deamination of guanine forms ___.
5. ___ ___ oxidizes hypoxanthine to ___ and again to ___ ___, which is secreted in the urine of humans.

Back 32

1. IMP, inosine (hypoxanthine riboside)
2. 5'-nucleosidase, inosine, guanosine
3. Purine nucleoside phosphorylase, hypoxanthine, guanine
4. xanthine
5. Xanthine oxidase, xanthine, uric acid

Front 33

1. Xanthine oxidase and xanthine dehydrogenase are two ___ forms of the ___ enzyme.
2. In vivo most mammalian forms of the enzyme exist as the ___.
3. Xanthine oxidase transfers electrons to O2 to form ___ - this is a problem in pathophysiological conditions (ischemia or oxidative stress) in which XD is converted to XO.

Back 33

1. interconvertable, same
2. dehydrogenase
3. H2O2

Front 34

Breakdown of dietary nucleic acids:
1. Pancreatic juice contains ___ & ___ which hydrolyze DNA and RNA to ___.
2. ___ ___ further hydrolyzes these to 3'- and 5'-mononucleotides. ___ then remove the phosphate groups and the nucleosides undergo intestinal absorption.

Back 34

1. ribonucleases, deoxyribonucleases, oligonucleotides
2. Pancreatic phosphodiesterase, Nucleotidases

Front 35

Pathology assoc with purine metabolism: Adenosine Deaminase (ADA) Deficiency.
1. ADA catalyzes the rxn of adenosine to ___.
2. Deficiency causes ___ ___ ___. The ___ concentration increases in RBCs, this inhibits ___ ___, thus DNA synthesis is inhibited.
*remember - ___ ___ catalyzes ribonucleotide diphosphates to deoxyribonucleotide diphosphates.

Back 35

1. inosine
2. severe combine immunodeficiency (SCID) impaired B & T-cell function, dATP, ribonucleotide reductase
* ribonucleotide reductase

Front 36

Pathology assoc with purine metabolism: Purine Nucleoside Phosphorylase Deficiency
1. ___ function is impaired, no apparent effect on ___ function.
2. ___ ___ formation is decreased.
3. Purine ___ and ___ concentrations are increased.
4. ___ is the major nucleotide that accumulates in RBCs which stimulates reduction of ADP to dADP which is converted to dATP leading to inhibition of ___ ___. dGTP also inhibits reduction of UDP & CDP.

Back 36

1. T-cell, B-cell
2. uric acid
3. nucleoside, nucleotide
4. dGTP, ribonucleotide reductase

Front 37

Pathology assoc with Purine metabolism: Gout
1. Gout is characterized by increased ___ ___ in the blood and urine - AKA ___ & ___ respectively. This leads to attacks of acute ___ ___ ___ due to deposition of uric acid crystals.
2. Primary gout is due to inborn error of metabolism - ie - overproduction of uric acid.
3. Secondary gout is caused by other diseases such as ___(HGPRT) deficiency.
4. Gout may be treated with the ___ ___ inhibitor, allopurinol.

Back 37

1. uric acid, hyperuricemia, hyperuricuria, arthritic joint inflammation
3. Hypoxanthine-guanine phosphoribosyltransferase (salvage pathway!)
4. xanthine oxidase

Front 38

Pyrimidine Biosynthesis and Metabolism:
1. Unlike the synthesis of purines (built on top of ribose phosphate), the ___ ___ is built first and attached to the ___ ___ to form the nucleotide.
A. ___ (from CO2) and ___ (from hydrolysis of amide of glutamine) plus 2 ATPs give carbamoyl phosphate.
B. ___ provides N1 and C4-C6 of the ring.

Back 38

1. pyrimidine ring, ribose phosphate
A. Bicarbonate, ammonia
B. Aspartate

Front 39

Synthesis of Pyrimidine ring:
1. Carbamoyl phosphate synthetase II is inhibited by ___ and is activated by ___ and ___.
Differences btw CPS I and II (chart)

Back 39

1. UTP, ATP, PRPP.

Front 40

The first 3 steps of pyrimidine biosynthesis ctalyzed by ___, ___ ___, and ___, give dihydroorotic acid. These 3 enzymes are all ___ of the ___ polypeptide chain.

Back 40

CPS II, aspartate carbamoyltransferase, dihydroorotase, domains, same

Front 41

1. Once dihydroorotic acid is formed, it is oxidized to ___ acid by ___ ___.
2. Orotate phosphoribosyltransferase the catalyzes the coupling of PRPP to give orotidine 5'-monophosphate (OMP), decarboxylation by orotate decarboxylase gives UMP.
UMP synthatase is a bifunctional enzyme on which ___ ___ ___ & ___ ___ are separate domains on the same ___ ___.

Back 41

1. orotic acid, dihydroorotate dehydrogenase
2. orotate phosphoribosyl transferase, orotate decarboxylase, polypeptide chain

Front 42

UMP is changed to UTP using ___ ATP. UTP is used in ___ synthesis.

Back 42

2

Front 43

Synthesis of CTP from UTP is catalyzed by ___ ___ ___ using ___ as a nitrogen source. CTP is used in ___synthesis, or it can be used to synthesize ___ used in DNA synthesis.

Back 43

Cytidine triphosphate synthetase, Gln (glutamine), RNA, dCTP

Front 44

UDP is reduced to dUDP by ___ ___. dUDP is loses a phosphate to form Deoxyuridine monphosphate (dUMP). dUMP is methylated by ___ ___ (one carbon transfer) using coenzyme N5,N10- methylene-tetrahydrofolate (FH4), formation of FH4 from FH2 by ___ ___ can be inhibited by ___.

Back 44

ribonucleotide reductase, Thymidylate synthetase, dihydrofolate reductase, methotrexate

Front 45

Remember, ___ are required for DNA synthesis and are biosynthesized from ribonucleotide diphosphates by the enzyme ___ ___.

Back 45

Deoxyribonucleotides, ribonucleotide reductase

Front 46

1. Nucleotides are phosphate esters of ___ (1, 2, or 3 phosphate groups attached).
2. Nucleosides are a purine or pyrimidine base attached to a ___ (RNA) or ___ (DNA).

Back 46

1. nucleosides
2. D-ribose, D-2'-deoxyribose

Front 47

Give nucleotide functions.
1.
2.
3.
4.

Back 47

1. energy source for cellular processes
2. structural components of coenzymes
3. second messengers in signal transduction
4. precursors for DNA and RNA sythesis

Front 48

*DNA is a nucleic acid linked by ___ bonds. DNA has 2 ___ strands. DNA has a ___ and ___ groove.

Back 48

phosphodiester, anti-parallel, major, minor

Front 49

DNA hydrogen bonds:
1. A purine base pairs with a ___ base.
2. There are ___ H-bonds between adenine and thymine.
3. There are ___ H-bonds between guanine and cytosine

Back 49

1. pyrimidine
2. 2
3. 3

Front 50

The 3D structure of DNA depends mainly on:
1.
2.

Back 50

1. hydrogen bond formation
2. base stacking

Front 51

*DNA conformations:
In ___, a right handed spiral is most common.

Back 51

B-DNA
Other conformations are A-, H-, Z-

Front 52

1. In a normal (relaxed) DNA molecule, the two DNA strands make a full twist every ___ base pairs.
2. If the molecule has more twists, the strands will coil around eachother causing ___ ___.
3. If a molecule has less twists it is considered to be ___ ___.

Back 52

1. 10.4
2. positive supercoiling
3. negatively supercoiled

Front 53

*
___ are enzymes that can monitor and adjust the number of supercoils in DNA

Back 53

Topoisomerases

Front 54

Type ___ topoisomerases can make a break in both DNA strands, ___/___ the DNA, and ___ the breaks.

Back 54

2, wind/unwind, reseal

Front 55

Type ___ topoisomerases make a break in one of the DNA strands, ___/___ the DNA, and ___ the break.

Back 55

1, wind/unwind, reseal

Front 56

Topoismoerases play a role in:
1.
2.
3.

Back 56

1. DNA replication
2. separation of new DNA during cell proliferation
3. RNA transcription

Front 57

Differences btw prokaryotes vs eukaryotes:

Back 57

Prokaryotes have circular DNA and no nuclear membrane.
Eukaryotes have DNA in nucleus inside nuclear membrane.

Front 58

Prokaryotic and eukaryotic DNA is surrounded by structural proteins called ___.

Back 58

chromatin

Front 59

*DNA in prokaryotes:
1. The ___ chromosome contains ___ to ___ base pairs that are compacted into 40 to 50 loops of supercoiled DNA - aka ___.
2. Sometimes prokaryotes have plasmids in addition with ___ to ___ basepairs.

Back 59

1. circular, 600000 to 5000000, nucleoid
2. 1000 to 10000

Front 60

*
1. Eukaryotic DNA is very long, humans 3.2 billion base pairs = ___ meters.
2. Eukaryotic chromosomes consists of ___. The DNA structural proteins are ___.

Back 60

1. 1-2 meters
2. nucleosomes, histones

Front 61

___ base pairs are wrapped around a core of ___ histone proteins. There are ___ to ___ base pairs in linker DNA.

Back 61

146, 8, 20 to 90

Front 62

*
1. Mitochondria have their own ___ DNA.
2. Human mitochondrion DNA consists of ___ base-pairs. Each mitochondrion has ___ to ___ copies of this DNA molecule.
3. About ___% of the mitochondrial proteins are encoded by the mitochondrial DNA.

Back 62

1. circular
2. 16000, 2 to 10
3. 5

Front 63

Baltimore classification of viruses.
I.
II.
II.
IV + V.
VI + VII.

Back 63

I. double stranded DNA viruses
II. single stranded DNA viruses
III. double stranded RNA viruses
IV + V. single stranded RNA viruses
VI + VII. retroviruses

Front 64

*The genome of a DNA virus is a single molecule (___ to ___ base pairs), which is ___ or ___.
I. Double stranded DNA viruses
a.
b.
II. Single stranded DNA viruses
a.
b.

Back 64

The genome of a DNA virus is a single molecule (5000 to 360000 base pairs), which is linear or circular.
I. Double stranded DNA viruses
a. Adenoviruses
b. Herpes viruses
II. Single stranded DNA viruses
a. Adeno-associated viruses
b. Bacteriophages

Front 65

___ (class I) and ___ (adeno-associated) are used in gene therapy. Both are taken up in the cell via ___. The DNA is transferred to the nucleus via ___ ___. The DNA is ___ incorporated in the cellular DNA.

Back 65

ADENOVIRUSES (class I) and ADENO-ASSOCIATED (class II) are used in gene therapy. Both are taken up in the cell via ENDOSOMES. The DNA is transferred to the nucleus via NUCLEAR PORES. The DNA is NOT incorporated in the cellular DNA.

Front 66

DNA has a ___ and a ___ groove.

Back 66

major, minor

Front 67

1. DNA replication is ___, the 2 parental strands are separated and each is used as a template for synthesis of a new strand.
2. The two new DNA molecules each contain one ___ and one ___ strand.

Back 67

1. semiconservative
2. parental, new

Front 68

*Three stages of DNA replication.
1.
2.
3.

Back 68

1. Initiation - DNA helix is opened up and the DNA replication proteins are positioned.
2. Elongation - sythesis of the new DNA strands
3. Termination - DNA sythesis is stopped

Front 69

Replication Initiation:
Replication begins at the ___ ___ ___, from here 2 ___ ___ are formed.

Back 69

origin of replication, replication forks.

Front 70

Replication Initiation:
1. In each replication fork, the 2 DNA strands are separated by ___.
2. ___ ___ ___ ___ (SSB) bind and hold the separated strands apart.

Back 70

1. helicase
2. single-stranded DNA binding proteins

Front 71

Replication Initiation:
___ ___ unwinds the DNA while it is being separated.

Back 71

Topoisomerase I

Front 72

Replication Initiation:
The anti-cancer drug ___ blocks the action of human ___ ___, inhibiting the unwinding of DNA during replication.

Back 72

topotecan, topoisomerase I

Front 73

*Replication Elongation:
1. ___ ___ follow the nucleotide sequence of the template strand in the ___ to ___ direction and synthesize the new strand ___ to ___.
2. The substrates of DNA polymerases are ___ ___ (dATP, dGTP, dTTP, dCTP)

Back 73

1. DNA polymerases, 3' to 5', 5' to 3'
2. deoxyribonucleoside triphosphates

Front 74

Replication Elongation:
A phosphodiester bond is formed between the ___ OH group of the last deoxynuleotide in the DNA and the innermost ___ atom of the new deoxynucleoside triphosphate.

Back 74

3', phosphor

Front 75

*DNA polymerases make a mistake only once every ___ to ___ deoxynucleotides. If a mismatch does occur, ___ ___ can remove the mispaired deoxynucleotides - AKA ___.

Back 75

10000 to 1000000, DNA polymerases, proofreading

Front 76

DNA polymerase proofreading = ___ to ___ exonuclease activity.

Back 76

3' to 5'

Front 77

1. DNA polymerases can only add deoxynulceotides to an ___ ___ - they need a free ___ group to start adding, this is provided by a primer which is an ___ molecule.
2. The RNA primer is synthesized by ___, which is an ___ ___.

Back 77

1. existing strand, 3'-hydroxy, RNA
2. primase, RNA polymerase

Front 78

*
1. DNA sythesis occurs continuously from 5' to 3' on the ___ ___.
2. DNA sythesis occurs in fragments - AKA - ___ ___ in the ___ ___.

Back 78

1. leading strand
2. Okazaki fragments, lagging strand

Front 79

1. In eukaryotes, Okazaki strands are ___ to ___ nucleotides long.
2. In prokaryotes, Okazaki fragments are ___ to ___ nucleotides long.
3. The reason for the difference is the ___ from ___ in eukaryotes means fragments are smaller.

Back 79

1. 100 to 200
2. 1000 to 2000
3. unbinding, histones

Front 80

Each Okazaki fragment, needed to duplicate the lagging strand of the DNA molecule, starts off with an ___ ___.

Back 80

RNA primer

Front 81

RNA Primer:
1. Once DNA synthesis is completed, the RNA primer is removed by ___ ___.
2. ___ ___ fills in the gap where the RNA primer used to be.
3. ___ ___ seals the last two nucleotides together.

Back 81

1. RNA hybridase
2. DNA polymerase
3. DNA ligase

Front 82

DNA replication summarized:

Back 82

DNA replication summarized:

Front 83

DNA replication in Prokaryotes:
___ ___ unlinks the two new chromosomes.

Back 83

DNA gyrase (topoisomerase II)

Front 84

DNA polymerases in Prokaryotes:
1. Pol I works as ___ ___ and sythesizes DNA within the gap where the ___ ___ used to be.
2. Pol II is a slow working ___ ___ that comes into action when other ___ can no longer work due to ___ ___.
3. Pol III is the ___ polymerase for DNA synthesis.

Back 84

1. RNA hybridase, RNA primer
2. DNA polymerase, polymerases, DNA damage
3. main

Front 85

Some anti-biotics work by inhibition of bacterial DNA synthesis.
1. quinolones inhibit ___ ___.
2. sulfonamides inhibit synthesis of ___, necessary for purine and pyrimidine synthesis.
3. These are both ___ rather than ___.

Back 85

1. DNA gyrase
2. folate
3. bacteriostatic, bactericidal

Front 86

*Eukaryotic DNA has ___ origin(s) of replication - it starts at all ___ at the same time.
Prokaryotes have ___ orgin(s).

Back 86

multiple, origins, one

Front 87

DNA polymerases in Eukaryotes:
Pol alpha and Pol delta are involved in DNA replication.
1. Pol alpha forms a comlex with ___ and elongates the ___ with the first ___ to ___ deoxynucleotides.
2. Pol delta is the ___ polymerase for ___ ___.
3. Pol ___, ___, and ___ are involved in DNA repair.
4. Pol ___ replicates mitochondrial DNA.

Back 87

1. primase, primer, 15 to 30
2. main, DNA synthesis
3. Beta, delta, e (epsi)
4. gamma

4.

Front 88

DNA polymerase in not capable of replicating the DNA all the way to the end of the chromosome. During each round of replication, some DNA is ___.

Back 88

lost

Front 89

*
___ are sequences of DNA at the end of eukaryotic DNA that serve as a ___ to prevent ___ of vital genetic information.

Back 89

Telomeres, buffers, loss

Front 90

___ is an enzyme that adds DNA to the end of telomeres. Uses a small ___ molecule as a template.

Back 90

Telomerase, RNA

Front 91

___ and ___ ___ cells have high telomerase activity. Most cancer cells have ___ telomerase levels.

Back 91

Stem, white blood, high

Front 92

Telomer is not a ___ structure. The overhanging end forms a loop that is stabilized by telomer binding proteins. ___ are formed from guanosines.

Back 92

straight, G-quadruplexes

Front 93

Telomeres with G-quadruplexes are no longer accessible for the enzyme ___. Introducing G-quadruplexes in telomeres may inhibit ___ growth.

Back 93

telomerase, cancer

Front 94

*
1. DNA methylation is found in ___ and ___.
2. It occurs by ___ at the cytosines in CG base-combinations (CpG - side by side, not base pairs), which are often found in clusters (___).
3. ___% of all CpG combinations have a methylated cytosine. In humans this is about ___% of all nucleotides.

Back 94

1. prokaryotes, eukaryotes
2. DNA methyltransferase, CpG islands
3. 70, 1

Front 95

*DNA methylation:
Each cell type in the human body has it's own ___ pattern. This is copied during DNA replication.

Back 95

methylation

Front 96

DNA methylation:
DNA replication is semiconservative.
1. Each ___ strand keeps its methylation pattern.
2. The methylation pattern is copied onto the new DNA strands by ___ ___.

Back 96

1. parental
2. DNA methyltransferase

Front 97

*Functions of DNA methylation:
1. ___ ___ is the silencing of one of two alleles of certain genes throught lifetime.

Back 97

1. Genomic imprinting

Front 98

Functions of DNA methylation:
X-chromosome inactivation in females, one of the x chromosomes is silenced ___.

Back 98

randomly

Front 99

*Functions of DNA methylation:
___ ___ is a specialized form of DNA repair that recognizes wrongly placed nucleotides during DNA replication.The mismatch repair machinery is able to recognize the ___ strand.

Back 99

mismatch repair, unmethylated

Front 100

*DNA recombination:
___ is unwanted DNA recombination.

Back 100

translocation

Front 101

*Homologous recombination is found:
1.
2.

Back 101

1. DNA repair, one homologous chromosome used as template to repair double strand break in another
2. crossing over during meiosis

Front 102

*Non-Homologous Recombination = ___ ___, requires enzymes that recognize specific nucleotide sequences.
A. Mobile genetic elements
1. Viruses
2. ___ - small segments of that move around in the genome
B. formation of antibodies
C. Form of DNA damage repair

Back 102

site-specific recombination
2. transposons

Front 103

Transposition is the movement of small segements of DNA (transposons) via non-homologous recombination.
1. ___ ___ - the transposon is moved from one site to another.
2. ___ ___ - the transposon is copied and inserted somewhere else in DNA.
3. ___ ___ - copy themselves via RNA intermediate.

Back 103

1. simple transposition
2. replicative transposition
3. retrotransposons

Front 104

in prokaryotes, transposons may contain genes for ___ ___.
In eularyotes, transposons do not contain ___ genes.

Back 104

antibiotic resistance, functional

Front 105

Hemophilia, Duchene muscular dystrophy, severe combine immunodeficiency are examples of inherited diseases caused by ___.

Back 105

transposons

Front 106

Antibody formation:
1. The human genome is not large enough to contain ___ genes for each antibody that is produced.
2. During B-cell development in the bone marrow, antibody gene segments are ___ into a unique combination by ___ recombination.

Back 106

1. separate
2. rearranged, non-homologous

Front 107

Antibody Formation cont:
End result of non-homologous recombination and somatic hypermutation is > ___ possible antibodies.
Total genes for:
1. Variable chain:
2. Diveristy chain:
3. Joining chain:
4. Constant chain:

Back 107

10^10
1. 150
2. 12
3. 4
4. 8

Front 108

Translocation nomenclature:
In abnormal exchange if genetic material between non-homologous chromosome, t(4;20) signifies:

Back 108

genetic material on chromosomes 4 and 20 have been swapped (abnormal)

Front 109

Chronic myeloid leukemia is caused by a ___ in a hemapoietic stem cellPart of the BCR gene is fused with the ABL gene. The resulting Bcr-Abl protein is a ___ ___ that constantly stimulates cell proliferation.

Back 109

translocation, tyrosine kinase

Front 110

*Spontaneous Hydrolysis:
1. Spontaneous depurination: mammalian cells loses about ___ - ___ purines a day.
2. Spontaneous depyrimidation: a mammalian cell loses about ___ pyrimidines per day.
3. Spontaneous hydrolysis damage is repaired by ___ ___ ___.

Back 110

1. 2000 - 10000
2. 500
3. base excision repair

Front 111

Oxidative stress: Give common reactive species.
1.
2.
3.
4.

Back 111

1. superoxide anion (O2-)
2. hydrogen peroxide (H2O2)
3. hydroxy radical
4. hydroxyl ion

Front 112

Reactive oxygen species can be caused by:
1.
2.
3.

Back 112

1. byproducts of oxidative metabolism (e transport chain leak)
2. Produced by inflammatory response (neutrophils/macrophages)
3. ionizing radiation

Front 113

*DNA damage from reactive oxygen species can be in the form of (show repair mech for each):
1.
2.
3.

Back 113

1. base oxidation - base excision repair
2. single strand breaks - base excision repair
3. double strand breaks - homologous and non-homologous (end joining) recombination

Front 114

Base oxidation (Guanine)

Ex, formation of 8-oxoguanine no longer pairs with cytosine, but mispairs with ___.

Back 114

adenine

Front 115

Many single and double strand breaks are formed by ___ radicals.

Back 115

OH

Front 116

Ultraviolet radiation:
1. ___ - long wave: 320-400 nm
2. ___ - medium wave: 280-320 nm
3. ___ - short wave: < 280
4. UVA, UVB, and UVC can all damage ___ and enhance ___ aging.
5. UVB and UVC have high energy , due to shorter wavelengths, and can cause ___ damage.

Back 116

1. UVA
2. UVB
3. UVC
4. collagen, skin
5. DNA

Front 117

1. Ultraviolet radiation reacts ___ with DNA (unlike ionizing which forms reactive oxygen species).
2. Main DNA damage is ___ formation between nucleotides that distort the DNA ___.

Back 117

1. directly
2. dimer, helix

Front 118

Chemical DNA damage:
1. ___ agents add alkyl groups (methyl or ethyl) to DNA bases. For example, O6 methylated guanine mispairs with ___ during DNA replication
2. ___ agents wedge between bases in the DNA strands. Chemotherapeutic agent cisplatin forms DNA crosslinks that make replication impossible.

Back 118

1. alkylating, thymine
2. intercalating

Front 119

Repair on a single strand:
1. Spontaneous hydrolysis, base oxidation, and single strand breaks can be repair via ___ ___ ___.
2. UV damage, chemical adducts are repairs by ___ ___ ___.

Back 119

1. base excision repair
2. nucleotide excision repair

Front 120

Base excision repair steps:
1.
2.
3.
4.

Back 120

1. DNA glycosylase removes bad base from the ribose backbone.
2. 5' endonuclease cuts at 5' prime end of ribose backbone where base was
3. DNA polymerase Beta replaces with proper base
4. DNA ligase seals the ribose backbone gap

Front 121

Nucleotide Excision repair:
1.
2.
3.

Back 121

1. a series of nucleotides (ribose backbone and all) containing the UV or chemical adduct damaged is removed
2. DNA polymerase delta or epsi synthesizes the gap from 5' - 3'
3. DNA ligase seals the gap

Front 122

Nucleotide excision repair:
1. Transcription coupled repair focuses on genes that are being transcribed. ___ proteins recognize gene expression proteins that are unable to proceed because of DNA damage.
2. Global genome repair covers the whole genome. ___ proteins recognize damage and locally unwind DNA.

Back 122

1. CS (Cockayne Syndrome)
2. XP (Xeroderma Pigmentosum)

Front 123

*Double strand break (from oxidative stress) repair:
1. occurs by ___ ___, two types of this that occur are
___ ___ and ___ ___ ___.

Back 123

1. DNA recombination, homologous recombination, non-homologous end joining

Front 124

Homologous recombination:
1. Mutations in genes coding for proteins that are involved in homologous recombination such as ___, ___, ___ are strongly correlated with ___.

Back 124

ATM, BRCA1, BRCA2, cancer

Front 125

*Repair of UV damage can be repaired two ways.
1.
2.

Back 125

1. nucleotide excision repair
2. Photoreactivation Photolyase - binds to UV damage and reverses bond linking two bases (dimer)

Front 126

*
1. Eukaryotic cell cycle lasts ___ to ___ hours.
2. ___ consists of G1 + S + G2 + G0 phases.
3. ___ cells are in G0 undergoing repair.
4. ___ cells undergo cell death

Back 126

1. 12 to 24
2. Interphase
3. Quiescent
4. Senescent

Front 127

In the G1 phase:
1.
2.

Back 127

1. Preparation for DNA duplication. Cell grows and duplicates important cell organelles.
2. G1 checkpoint will stop progression into S-phase if cell has too much DNA damage

Front 128

In the S-phase:
1.

Back 128

1. Cell duplicates its DNA, each chromosome has 2 identicle chromatids bound by a centromere.

Front 129

In the G2 phase:
1.
2.

Back 129

1. Preparation for mitosis - cell also continues to grow
2. G2 checkpoint will prevent progression into M-phase if too much DNA damage

Front 130

*In the M-phase:
1.

Back 130

1. The cell separates its chromosomes (mitosis) and its cytoplasm (cytokinesis) to form 2 daughter cells.

Front 131

*The stages of mitosis are:
1.
2.
3.
4.

Back 131

1. prophase - chromosomes condense (topoisomerases involed)
2. Metaphase - chromosomes line up at the metaphase plate
3. Anaphase - chromosomes are pulled towards poles of cell
4. Telophase - new nuclear membrane formed for each daughter cell

Front 132

Prophase:
Chromosomes condense.
1. The ___ start to form ___ ___ made from protein ___.
2. The cetrosomes move to ___ ___ of the cell

Back 132

1. centrosomes, mitotic spindles, tubulin
2. opposite sides

Front 133

Prometaphase:
The centrosomes arrive at opposite sides of the cell.
1. Mitotic spindles now cover the nucleus and connect to the ___ of the chromosomes.
2. The nuclear membrane ___.

Back 133

1. centromeres
2. disappears

Front 134

*Metaphase:
Chromosomes line up at the metaphase plate.
1. Metaphase cells are used to prepare a ___.
2. Humans have ___ chromosomes - ___ pairs.

Back 134

1. karyotype
2. 46, 23 (diploid)

Front 135

Anaphase:
1. Sister chromatids ___.
2. Mitotic spindles ___ and pull the chromosomes towards the ___.

Back 135

1. break
2. shorten, centrosomes

Front 136

Telophase:
1.

Back 136

1. A new nuclear envelope forms around the 2 new nuclei and the chromosomes unfold.

Front 137

*Cell cycle regulation:
1. Occurs by ___ ___.
2. A Cdk is active when it is bound to its specific ___.
3. An activated Cdk activates other proteins that promote the ___ ___.
4. Each phase of the cell cycle has its own ___ and ___.

Back 137

1. cyclin-dependent kinases (Cdk)
2. cyclin
3. cell cycle
4. cyclins, Cdk's

Front 138

Cell cycle regulation:
The G1 and G2 checkpoints can inhibit ___, preventing progression into next phase.

Back 138

cdk's

Front 139

*___ ___ are proteins located in the extracellular space that determine cell survival and cell proliferation after binding to their receptor on the surface of a target cell.

Back 139

Growth factors

Front 140

The effects of growth factors depend on their ___ in the extracellular space.
1. ___ = cell death
2. ___ = cell survival
3. ___ = promotion of cell cycle (S-phase)

Back 140

Concentration
1. no growth factor
2. low concentration
3. high concentration

Front 141

1. Vascular endothelial growth factor:
- produced by many cell types
- induces proliferation of endothelial cells and formation of ___ ___ ___.
2. Platelet derived growth factor
- produced in many cell types and in platelets
- induces proliferation of many cell types including ___ cells (wound healing)

Back 141

1. new blood vessels
2. epithelial

Front 142

Meiosis:
Normal tissue cells are ___. Gametes are ___ and are formed by meiosis.

Back 142

diploid (2n), haploid (n)

Front 143

*Meiosis stages:
1.
2.
3.

Back 143

1. replication of homologous pairs of chromosomes
2. meiosis I - replicated homologous pairs separated, these daughter cells are 1n (sister chromatids remain intact)
3. meiosis II - sister chromatids split and haploid gametes formed

Front 144

DNA recombination: crossing over occurs in ___, when homologous chromosomes start to form pairs.

Back 144

prophase I (in meiosis I)

Front 145

Properties of cancer cells:
Normal skin:
- organized tissue
- cells communicate
Skin carcinoma:
- cells divide ___
- no ___

Back 145

uncontrollably, organization/communication

Front 146

Mutations are caused by:
1.
2.
3.

Back 146

1. Viral DNA that becomes incorporated in the genome can act as an oncogene
- Epstein-Barr virus (Burkitt's Lymphoma)
- Hepatitis B virus (liver cancer)
2. inherited mutations
3. incomplete/incorrect DNA damage repair

Front 147

*Cancer genes are genes involved in normal cellular processes such as ___ ___ and ___ ___, which upon mutation contribute to cancer formation.
2 types:
1.
2.

Back 147

cell cycle, cell death
1. tumor suppressor genes
2. proto-oncogenes

Front 148

Tumor Suppressor Genes:
1. Normal genes that suppress cell ___ or promote ___.
2. A mutation in a tumor suppressor gene may lead to ___ of this gene, which ___ tumor formation.

Back 148

1. division, apoptosis
2. inactivation, promotes

Front 149

*Functions of P53:
1. Normal conditions, p53 is ___
2. DNA damage will lead to ___ and ___ of p53.
a. This inhibits ___ ___ ___ leading to ___ ___ ___.
b. it also causes release of ___ from ___ leading to ___.

Back 149

Functions of P53:
1. Normal conditions, p53 is degraded
2. DNA damage will lead to phosphorylation and activation of p53.
a. This inhibits cyclin dependent kinases leading to cell cycle arrest.
b. it also causes release of cytochrome-C from mitochondria leading to apoptosis.

Front 150

1. Normal active p53 holds the cell cycle at ___ or induces ___.
2. > ___% of human tumors have a mutation that leads to the ___ or ___ of p53.

Back 150

1. G1/S, apoptosis
2. 50, loss, inactivation

Front 151

Functions of the Retinoblastoma Protein (Rb):
1. Regulates the cell cycle by inhibiting a transcription factor that induces ___ ___ progression.
2. Cyclin-dependent kinases 2 and 4 ___ Rb by phosphorylation.

Back 151

1. cell cycle
2. inactivate

Front 152

*
1. The Retinoblastoma (Rb) gene is a common ___ ___ gene.
2. The normal Rb protein inhibits the ___ ___.
3. >___% of human tumors have a mutation that leads to the ___ or ___ of Rb.
4. Rb gets its name from ___, a cancer caused by loss of the Rb gene.

Back 152

1. tumor suppressor
2. cell cycle
3. 70, loss, inactivation
4. retinoblastoma

Front 153

Human Papillomavirus (HPV) is a ___ stranded virus.
1. To replicate it needs ___ cells.
2. HPV proteins inhibit ___ and ___ protein to induce ___ ___.

Back 153

double stranded
1. proliferating
2. p53, Rb, cell proliferation - both p53 and Rb are tumor suppressor genes.

Front 154

Proto-oncogenes are normal genes that often regulate division or apoptosis, but over-promote division or inhibit apoptosis upon mutation.
1. After mutation, proto-oncogenes become ___.

Back 154

1. oncogenes

Front 155

*
1. Ras is a common ___.
2. Growth factors act on surface of cell on ___ ___ ___ which in turn activate Ras which then activates a ___ ___ ___ that activates a transciption factor to cause synthesis of ___ ___.

Back 155

1. proto-oncogene
2. receptor tyrosine kinase, protein kinase cascade, cyclin D1 (this leads to cell cycle progression)

Front 156

Ras is a common Proto-oncogene.
About ___% of human cancers have a mutation in the Ras gene that leads to activation of Ras.

Back 156

30

Front 157

Growth factors and their receptors can be ___.
Both ___ ___ and ___ of growth factors and their receptors are found in tumors.
- Vascular endothelial growth factor (VEGF)
- Platelet derived growth factor (PDGF)
- Fibroblast growth factor (FGF)

Back 157

proto-oncogenes, activating mutations, overexpression

Front 158

*Summary of common cancer genes:
Tumor suppressor genes:
1.
2.
Proto-oncogenes:
3.
4.
5.

Back 158

Tumor suppressor genes
1. p53
2. Retinoblastoma (Rb)
Proto-oncogenes
3. Ras
4. growth factors
5. growth factor receptors.

Front 159

Chronic Myeloid Leukemia:
___ is a molecule that binds to Bcr-Abl in its kinase domain and blocks its activity. It is the first drug that directly blocks a protein known to cause cancer.

Back 159

Gleevec

Front 160

Characteristics of RNA
1. contains these ribonucleotides:
2. the sugar in the backbone is ___ instead of ___ (DNA)
3. Contains ___ instead of ___ (DNA)
4. Cellular RNA is usually ___ ___.
5. Viral DNA can be ___ and ___.
6. RNA has complex and diverse 3D structures.

Back 160

1. contains these ribonucleotides: Cytidine, Adenine, Uracil, Guanine
2. the sugar in the backbone is ribose instead of deoxyribose (DNA)
3. Contains uracil instead of thymine (DNA)
4. Cellular RNA is usually single stranded.
5. Viral RNA can be single-stranded and double-stranded.
6. RNA has complex and diverse 3D structures.

Front 161

Ribonucleases (RNases)
Enzymes that degrade RNA
1. ___ cleave phosphodiester bond within an RNA molecule.
2. ___ cleave nucleotide from the end of an RNA molecule.

Back 161

1. endoribonucleases
2. exoribonucleases

Front 162

Roles of ribonucleases:
1. Regulation of intracellular levels of ___.
2. ___ of RNA molecules
3. Protection against RNA ___.

*RNA molecules have ___ stability

Back 162

1. RNA
2. Processing
3. viruses
* low - unlike DNA which is stable

Front 163

Coding or non-coding RNA:
1. mRNA
2. rRNA
3. tRNA
4. catalytic RNA

Back 163

1. mRNA = coding
2. rRNA = non-coding
3. tRNA = non-coding
4. catalytic RNA = non-coding

Front 164

___% of cellular RNA is mRNA

Back 164

5

Front 165

Eukaryotic mRNA has:
1. 5' cap: a modified ___ nucleotide that helps the initiation of protein sythesis from the mRNA molecule.
2. 3' poly-A tail: up to ___ ___ nucleotides that protects the mRNA from degradation and helps its transport out of the nucleus.

Back 165

1. guanine
2. 200 adenine

Front 166

5' cap on mRNA is made from a guanosine methylated at the ___ position which is then attached to the mRNA ___ by a ___ link.

Back 166

N7, backwards (5' to 5'), triphosphate

Front 167

tRNA = ___% of cellular RNA

Back 167

10

Front 168

1. Transfer RNA is ___ to ___ nucleotides long.
2. The amino acid is bound to the ___ end of tRNA by ___ ___.
3. ___ is a tRNA molecule with it's amino acid bound to it.

Back 168

1. 65-110
2. 3', aminoacyl-tRNA synthetases
3. aminoacyl-tRNA

Front 169

Eukaryotic rRNA molecules are synthesized in 4 sizes:
1.
2.
3.
4.

Back 169

1. 28S
2. 18S
3. 5.8S
4. 5S

Front 170

1. About ___% of the mitochondrial proteins are prodiced by the mitchondira itself.
2. Mitochondrial RNA = about ___% of total RNA in the cell.

Back 170

1. 5
2. 5

Front 171

1. Catalytic RNA can be an ___ (catalytic or ribozyme)
2. Ribosomal RNA catalyzes the sythesis of ___.
3. Ribonuclease P is an RNA molecule that cleaves precursor RNA to form ___ tRNA.

Back 171

1. enzyme
2. proteins
3. mature

Front 172

RNA primer for DNA synthesis is synthesized by ___.

Back 172

primase.

Front 173

RNA-induced silencing complex is activated by ___ in order to regulate levels of mRNA in cells.

Back 173

MicroRNA

Front 174

1. silencing RNA or Small interfering RNA (siRNA) is similar to ___ but only found in ___ and lower ___.
2. When introduced to cells can block and break down mRNAs by binding to the ___ complex - making it useful for research and clinical use.

Back 174

1. MicroRNA, plants, eukaryotes
2. RISC (RNA induced silencing complex)

Front 175

RNA molecules in the clinic:
1. ribozymes and siRNA will bind specific mRNA molecules --> inhibit mRNA translation and induce mRNA degradation.
Problems with this approach are:
1.
2.
3.

Back 175

1. toxicity
2. low stability
3. do not naturally enter cell

Front 176

RNA molecules in the clinic:
Stability can be improved with chemical modifications.
1. methyl groups on the 2' oxygen of ribose protect against ___.
2. sulfur replacement of the 3' oxygen protects against ___.

Back 176

1. endonucleases
2. exonucleases

Front 177

RNA molecules in the Clinic:
1. ___ can be used to carry the siRNA and fuse with the cell membrane.
2. A ___ ___ can be used to inject the siRNA into the cell.

Back 177

1. liposome
2. viral vector

Front 178

Common viral vectors:
1. ___ - replicate their genome via a DNA intermediate (reverse transcription). The DNA gets incorporated into the cellular DNA.
2. ___ - double-stranded DNA viruses. The DNA does not get incorporated into the cellular DNA. Daughter cells will not carry the new gene.
3. ___ - single-stranded DNA virus, not know to cause disease.

Back 178

1. Retroviruses
2. Adenoviruses
3. Adeno-associated viruses

Front 179

Small interfering RNA (siRNA) is similar to microRNA but:

Back 179

siRNA is found in plants and lower eukaryotes and is sythesized in the lab for research and clinical use. Both bind to mRNA molecules and lead to cleavage (degradation).

Front 180

Transcription in eukaryotes:
1. ___ - DNA that is actively transcribed is found in a loose form of chromatin
2. ___ - inactive parts of DNA (highly condensed)
3. ___ - DNA that is used to synthesize rRNA (ribosomes) molecules

Back 180

1. euchromatin
2. heterochromatin
3. nucleolus

Front 181

RNA polymerases: enzymes that sythesize RNA
1. RNA polymerase I ---> ___
2. RNA polymerase II ---> ___
3. RNA polymerase III ---> ___
* most regulation of expression occurs at ___

Back 181

1. RNA polymerase I ---> rRNA
2. RNA polymerase II ---> mRNA
3. RNA polymerase III ---> tRNA
* RNA polymerase II

Front 182

Transcription of RNA from DNA:
The template strand is used as a template to synthesize the RNA.
1. The other strand in the DNA is the ___ strand. It has the same sequence as the ___ molecule. It is used to report the sequence of a gene

Back 182

1. coding, RNA

Front 183

1. Initiation: ___ ___ is properly positioned on the DNA of the gene that needs to be transcribed.
2. Elongation - ___ ___ transcribes the DNA sequence of the gene into an RNA molecule.
3. Termination - ___ ___ is released from the DNA

Back 183

1. RNA polymerase
2. RNA polymerase
3. RNA polymerase

Front 184

Transcription initiation:
1. The ___ ___ factors bind to consensus sequences in the ___.
2. consensus sequences are located ___ of the gene. They are not translated into RNA
3. Consensus sequences are ___ ___, ___ ___ and ___ ___.

Back 184

1. general transcription, promoter (region containing CAAT, GC, and TATA boxes_
2. upstream
3. CAAT box, GC box, TATA box

Front 185

Transcription initiation:
A. The transcription complex is formed. The general transcription factor TFIID binds to the ___ ___ in the promoter region.
B. Then other general transcription factors attach.

Back 185

A. TATA box

Front 186

Transcription initiation:
C. The general transcription factors form a complex with ___ ___ called the ___ ___ ___.
D. RNA polymerase is now ready to leave the initiation complex and start RNA sythesis.

Back 186

C. RNA polymerase, transcription initiation complex

Front 187

Transcription elongation:
1. RNA polymerase locally separates the 2 strands of DNA to form an opening +- 10 mucleotides long.
2. DNA unwinding is facilitated by ____
3. RNA polymerase transcribes the template strand of the DNA into an RNA molecule.
4. The RNA molecule is synthesized from ___ to ___.

Back 187

2. topoisomerases
4. 5' to 3'

Front 188

Transcription termination:
1. not well understood in eukaryotes
2. RNA polymerase can continue for ___ to ___ nucleotides beyond the end of the gene before it releases from the mRNA
3. The ___ RNA is the processed to give correct length.

Back 188

2. 1000 to 2000
3. precursor

Front 189

All mRNA processing occurs in:

Back 189

the nucleus

Front 190

Adding the mRNA 5' cap:
Give enzymes and process:
1.
2.
3.
4.

Back 190

1. phosphatase cleave the 5' terminal end's outer most phosphate
2. Guanylyl transferase attaches a GTP's 5' end inner most phosphate to the 2 phosphates on the 5' end of the mRNA - forming a triphosphate 5' to 5' bond.
3. Methyl transferase methylates N7 on the former GTP
4. methyl transferase methylates 2' oxygen on last couple of nucleotides

Front 191

Adding the Poly(A) tail:
Occurs at the ___ ___ (AAUAAA) in the mRNA.
Hundreds of adenosines can be added

Back 191

polyadenylation signal

Front 192

Splicing:
Genes contain ___ (coding sequences) and ___ (intervening sequences).

Back 192

exons, introns

Front 193

Alternative splicing:
1. The human genome has +-___ protein-coding genes.
2. ___ to ___ different proteins are produced.
* This can be explained by ___ ___.

Back 193

1. 36,000
2. 80,000 to 100,000
* alternative splicing

Front 194

List the 4 difference between DNA and RNA sythesis:
1.
2.
3.
4.

Back 194

1. one makes DNA, the other RNA
2. RNA uses RNA polymerase, DNA uses ....duh!
3. DNA needs primer, RNA synth does not.
4. DNA is proofread, RNA is not
4.

Front 195

___ ___ - process by which DNA molecule is formed from an RNA molecule. Performed by ___ ___.
*example: ___

Back 195

Reverse transcription, reverse transcriptases
* Telomerase

Front 196

The genome of RNA viruses is an ___ molecule.
1. most have ___ stranded RNA
2. Some have double stranded RNA such as ___.
3. They repliate their genome by using a viral ___ ___.

Back 196

RNA
1. single
2. reoviruses
3. RNA polymerase

Front 197

Retroviruses:
1. RNA viruses that replicate their genome via a ___ intermediate formed via viral ___ ___.
2. The viral DNA is incorporated into the cellular DNA via non-homologous recombination
3. Lack of proof reading in reverse transcriptases leads to rapid changes in viral genome.

Back 197

1. DNA, reverse transcriptase

Front 198

Regulation of gene expression:
1. ___ ___ are always expressed at a constant level. Most are involved in maintenance of the cell.
Ex: ___ ___
2. Most genes are expressed only when needed.
3. Some are cell specific.
Ex: insulin gene only expresed in beta cells of pancrease

Back 198

1. housekeeping genes, ribosome genes

Front 199

1. Regulation of mRNA sythesis is about ___% of all gene expression regulation.
2. Regulation of mRNA stability is ___% of all gene expression regulation.

Back 199

1. 60%
2. 40%

Front 200

1. Nuclear receptors are a class of transcription factors that are activated by ___ and ___ ___.
2. These then bind to ___ ___ ___ in the DNA to induce gene transcription.
3. INactive nuclear receptors can be located in the ___ or the ___ of the cell.

Back 200

1. steroid, thyroid hormones
2. hormone response elements
3. cytoplasm, nucleus

Front 201

1. Activators are proteins that enhance gene expression but do not ___ gene expression by themselves.
2. They bind to an ___ ___ in the DNA.
3. These can be close to or far away (___ of base pairs away) from the promoter.
4. They can be ___ or ___ from the promoter.
5. May interact with transcription factors and RNA polymerase by ___ the DNA

Back 201

1. induce
2. enhancer element
3. 1000's
4. upstream, downstream
5. bending

Front 202

1. Repressor are ___ of activators
2. they bind to a ___ in the DNA, which can overlap with:
a.
b.

Back 202

1. counterparts
2. silencer
a. activator binding site
b. transcription start site

Front 203

Repressors in disease:
A double mutation in the Wilms Tumor (WT1) gene leads to kidney tumors at an early age.
1. The WT1 protein is a ___ ___ that inhibits the expression of EGR-1 (early growth response factor-1).
2. Lack of inhibition of EGR-1 leads to ___ ___.
*WT1 is considered a ___ ___ gene.

Back 203

1. transcription repressor
2. uncontrolled growth
*tumor suppressor

Front 204

DNA methylation occurs at ___ in ___ ___. Then ___ ___ bind to these sites (gene inactivation) and the transcription initiation complex can no longer be formed.

Back 204

cytosines, CpG islands, Methyl-CpG-binding proteins

Front 205

DNA methylation in cancer
Hypermethylation of ___ regions of genes is common in cancer cells.

Back 205

promoter

Front 206

Histone acetylation:
___ ___ adds acetyl groups to ___ amino acids in the histone protein, which takes away their net ___ ___. This ___ the interaction btw histones and the DNA.

Back 206

Histone acetyltransferase, lysine, positive charge, losens

Front 207

Acetylation of histones in cancer:
1. ___ of histone acetylation is found in many tumors.
2. This leads to ___ ___ and reduced ___ ___.

Back 207

1. loss
2. gene silencing, DNA repair

Front 208

___ ___ contain proteins that degrade mRNA when a cell is under stress.

Back 208

stress granules

Front 209

P-bodies are similar to stress granules but contain ___. The ___ ___ is thought to bring the mRNA into the P-bodies

Back 209

microRNA, RISC complex (RNA induced silencing)