Biochemistry Test 3

Front 1

Hormone Receptors (or Steroid Receptors)

Back 1

-Hormone Binding
-DNA Binding
-Transcription Activation

Front 2

Tamoxifen and Mifepristone

Back 2

Drugs that control stereoid signaling

Front 3

Stages of the Cell Cycle

Back 3

1) G1 Phase: RNA and protein synthesis. No DNA synthesis.
2) S Phase: DNA, RNA, and protein synthesis.
3) G2 phase: No DNA synthesis. RNA and protein synthesis continue.
4) M Phase: Mitosis and Cytokinesis
G0 Phase: when differentiated cells withdraw from the cell cycle

Front 4

Mechanisms for regulating CDK activities:

Back 4

1)Phosphorylation and desphosphorylation of the CDK
2) Control degradation of cyclins
3) Regulated synthesis of CDKs and cyclins
4) Specific CDK-inhibiting proteins

Front 5

Specific CDK-inhibiting protein

Back 5

p21

Front 6

DBRP

Back 6

Destruction Box Recognizing Protein

Front 7

Regulation of CDK by phosphorylation and desphosphorylation

Back 7

1) CDK is inactive
2) Cyclin synthesis
3) Formation of inactive CDK-cyclin
4) CDK-cyclin is activated by phosphorylation
5) DBRP (Destruction Box Recognizing Protein) triggers addition of ubiquitin to cyclin
6) Cyclin is degraded by proteosome, and CDK is inactivated

Front 8

Important Target Proteins of CDKs:

Back 8

-Laminin
-Myosin
-Retinoblastoma protein (pRb)

Front 9

p53

Back 9

When DNA damage is detected, p53 is activated and stimulates the synthesis of p21. p21 inhibits E-CDK2 and causes pRb-E2F complex to arrest the cell cycle in G1

Front 10

Genes encode regulatory proteins that normally inhibit cell division. Mutations in these genes are genetically recessive

Back 10

Tumor Suppressor

Front 11

Oncogenes

Back 11

v-src
v-erbB
v-ras
v-fas and v-jun

Front 12

v-erbB

Back 12

-Gene that encodes epidermal growth factor (EGF) receptor that lacks the EGF-binding domain, but it retains its transmembrane and tyrosine domain

Front 13

v-ras

Back 13

-Encode v-Ras protein, which is similar to c-Ras protein but v-ras hydrolyzes GTP much more slowly.

Front 14

Tumor Suppressors

Back 14

pRb and p53

Front 15

Apoptosis

Back 15

Programmed cell death

Front 16

Events of Apoptosis

Back 16

-Fas ligand binds its receptor; TNF binds to its receptor
-These activated receptors interact with FADD, and TRADD
-FADD and TRADD activate caspases
-Caspases eventually triggers cell death

Front 17

Receptor Types

Back 17

1) Ion-channel
2) Serpentine receptor (or G Protein Coupled Receptor, GPCR)
3) Receptor enzyme
4) Receptor without intrinsic enzymatic activity
5) Steroid receptor
6) Adhesion receptor

Front 18

Ex. of Ion Channel

Back 18

Acetylcholine receptor

Front 19

Ex. of Receptor Tyrosine Kinase

Back 19

Growth hormone receptor, and insulin receptor

Front 20

Ex. Receptors without enzymatic activity

Back 20

JAK-STAT

Front 21

Ex. of steroid type receptor

Back 21

-Hydrophobic hormones, vitamin D, thyroid hormones

Front 22

What is the target of NO?

Back 22

GC (guanylate cyclase)
GC catalyzes the rxn from GTP to cGMP. cGMP PDE catalyzes the reverse rxn. Viagra inhibits cGMP PDE causing a increase of cGMP, which causes vasodilatation
viagra + organic nitrate is not good... because the blood pressure drops dramatically

Front 23

Types of DNA:

Back 23

A---ex.RNA-DNA, or RNA-RNA
B---ex. hydrated DNA
Z

Front 24

Helical Sense

Back 24

A and B are right handed
Z is left handed

Front 25

Major Groove

Back 25

A DNA: narrow and deep (ND)
B DNA: wide and deep (WD)
Z DNA: flat (FF)

Front 26

Minor Groove

Back 26

A DNA: wide and shallow (WS)
B DNA: narrow and deep (ND)
Z DNA: narrow and deep (ND)

Front 27

Code
DNAType+major groove+minor groove

Back 27

ANDWS
BWDND
ZFFND

Front 28

Sugar Pucker

Back 28

A DNA: C3'-endo
B DNA:C2'-endo
Z DNA: C2'-endo pyri... and C3'-endo purine

Front 29

Glycosidic Bond Formation:

Back 29

A DNA: anti
B DNA: anti
Z-DNA: anti for pyrimidine, and syn for purine

Front 30

Superhelix Topology

Back 30

L = T + W

Front 31

L

Back 31

Linking Number
# that one strand of the duplex passes the other

Front 32

T

Back 32

Twist
# of revolutions that one strand makes around the duplex axis

Front 33

W

Back 33

Writhing number
# of supercoils present
-right handed supercoil is negative
left handed is positive

Front 34

Topoisomerases

Back 34

Control of topological state (linking number) of DNA

Front 35

Classification of Topoisomerases

Back 35

-Type I: single strand cleavage
(L=+/- 1)
-Type II: double strand cleavage
(L = +/- 2)

Front 36

Type I Topoisomerase

Back 36

Type IA: strand passage mechanism with 3'-phosphotyrosine enzyme-DNA intermediate
Type IB: controlled rotation mechanism with 3'-phosphotyrosine enzyme-DNA intermediate
Type IB:

Front 37

For what inhibitors of topoisomerases?

Back 37

Inhibitors of topoisomerases as antibiotics and anticancer agents

Front 38

Non-Watson Crick base pairs:

Back 38

A-A pair
A-T Hoogsteen pair
Hypothetical T-C pair
G-U Wooble pair in RNA structures

Front 39

How are nucleic acids stabilized?

Back 39

Nucleic acids are stabilized by base stacking and hydrophobic interactions

Front 40

Enzymes required for DNA replication:

Back 40

-DNA gyrase: topoisomerase
-Helicase: for unzipping
-SSB proteins for stabilization of single strands of DNA
-Primase for making primers
-DNA Polymerase III for adding nucleotides
-DNA Polymerase I: for removal of primers and replace them with DNA nucleotides
-Ligase: seals nick

Front 41

Why do DNA Polymerase I can remove primers?

Back 41

Because DNA Polymerase I has 5'-->3' activity

Front 42

Requirements for High Fidelity of DNA replication:

Back 42

-Equal ratio of dNTPs
-Base pairing (A-T, and G-C)
-Proofreading (3'-->5')
-RNA primers
-Mismatch repair

Front 43

E. coli DNA Polymerase I

Back 43

-Polymerase activity, 3'-->5' activity (proofreading), 5'-->3' activity
-Recognizes the shape of the base pair
-Repair of damaged DNA
-Nick translation
-Removal of RNA primer

Front 44

E. coli DNA Polymerase III

Back 44

-DNA replicase
-Many subunits: sliding clamp (beta clamp)

Front 45

E. coli DNA Polymerase II

Back 45

Repairing DNA via SOS response

Front 46

Reverse Transcription:

Back 46

(cap) eukaryotic mRNA (polyA tail) ---> RNA-DNA hybrid --> single stranded DNA --> double stranded DNA

Front 47

Telomers

Back 47

Telomers consists of 1000 or more tandem repeats of a short guanine sequence

Front 48

Telomerases

Back 48

Telomerases synthesize and maintain telomeric DNA. They are ribonucleotides.

Front 49

DNA damage:

Back 49

-Dimerization by UV radiation
-Methylation
-Deamination
-Intercalation

Front 50

Nitrogen mustard and ethylnitrosourea

Back 50

They are alkylating agents

Front 51

Ethidium, Proflavin, and Acridine Orange

Back 51

They are intercalating agents that can cause insertion or deletion mutations