**** I Forget In Biochem

Front 1

What does Hsp 70 do?

Back 1

prevents aggregations of unfolded protein

Front 2

What does Hsp 60 do?

Back 2

allows proteins to fold inside it's "barrel"

Front 3

What is TSE (transmissible spongiform encephalopathy?)

Back 3

Mad cow disease, where the brain develops holes leading to dementia

Front 4

Proline is grouped as an amino acid, but is actually a what?

Back 4

Imino group

Front 5

T/F: Humans have mainly D amino acids

Back 5

False (L-form!)

Front 6

What biologically active compound is formed from [hydroxy-] tryptophan?

Back 6

Serotonin

Front 7

What biologically active compound is formed from [dihydroxy-] phenylalanine (L-Dopa)?

Back 7

Dopamine

Front 8

What biologically active compound is produced from L-Arginine?

Back 8

Nitric oxide

Front 9

The cell requires the presence of ribosomes and translation to create peptide bonds. What is the only exception?

Back 9

Glutathione

Front 10

Approximately how many amino acids are present in an oligopeptide?

Back 10

Up to 20

Front 11

Approximately how many amino acids are present in a peptide?

Back 11

20-50

Front 12

Approximately how many amino acids are present in a polypeptide?

Back 12

More than 50

Front 13

Which terminal (C or N) is considered the first amino acid?

Back 13

N-terminal

Front 14

How many peptides does aspartame possess?

Back 14

Two (dipeptide)

Front 15

How many peptides does glutathione possess?

Back 15

Three (tripeptide)

Front 16

T/F: A motif is a repetitive supersecondary structure

Back 16

True

Front 17

Heat, 5-10 M urea, salt

Back 17

break hydrogen bonds

Front 18

Strong acids or bases

Back 18

break ionic bonds

Front 19

1-2% SDS (detergent)

Back 19

break hydrophobic interactions

Front 20

Thiolcontaining compounds (β-mercaptoethanol or
2-mercaptoethanol)

Back 20

reduce disulfide bonds

Front 21

Proteins that are misfolded

Back 21

tagged by the protein ubiquitinand degraded in a complex called the proteasome (diffiency=alzheimers)

Front 22

Prion diseases- (PrPsc, prionprotein)

Back 22

Creutzfeld-Jacob disease, Transmissible Spongiform Encephalopathy (mad cow), The diseased brain develops holes (resembles sponge)

Front 23

What conformational change does oxygen binding cause in Hb

Back 23

Causes Fe to move back into plane making the bonds between dimers stronger

Front 24

Which type of Hb maintains a high O2 affinity and a cherry red appearance?

Back 24

Carboxyhemoglobin

Front 25

What disorder is carboxyhemoglobin associated with

Back 25

CO poisening

Front 26

Describe the mutation in the DNA that causes sickle cell

Back 26

Position 6- Glutamic acid - valine

Front 27

Which collagens are network forming?

Back 27

4 and 7

Front 28

Which collagens are fibril forming

Back 28

1-3

Front 29

Which collagens are fibril associated

Back 29

9 and 12

Front 30

What types of bonds are used to link the chains in collagen?

Back 30

disulfide bonds

Front 31

What causes Ehlers Danols Syndrome

Back 31

mutation of the gene required for the pro alpha chains of collagen. Deficiency of enzymes in the synthesis of collagen (hydroxy-lusine/proline, lysl oxidase)

Front 32

Describe the AA composition of Elastin

Back 32

Alternating domains of (hydrophillic- lysine and alanine) and (hydrophobic- glycine valine and proline)

Front 33

Describe the structure of elastin

Back 33

3 allysine and one lysine residue

Front 34

What enzyme forms allysine?

Back 34

Lysyl oxidase

Front 35

What is a elastic fiber composed of?

Back 35

microfibril (glycoproteins, fibrillin)
and amorphous elastin inside it

Front 36

What does Marfans syndrome result from?

Back 36

Autosomal dominant defect in the FIBRILLIN gene

Front 37

Describe the general structure of GAG's

Back 37

composed of repeating disaccharide units - generally contain - repeated units of glucuronic acid and an amino sugar, and the amino sugars can be sulfated or acetylated - bottle brush appearance, highly negative - slippery mucous, compressibility of cartilage, synovial fluid

Front 38

Describe the general structure of proteoglycans

Back 38

contain mainly GAGs and some protein - are extracellular, contain long unbranched chains of negatively charged sugars - major component of ECM, bind large amounts of water and form a gel-like matrix that embeds collagen

Front 39

OI type IV (most common)

Back 39

deforming but with normal sclerae

Front 40

Fibrillin?

Back 40

scaffold for tropoelastin

Front 41

How ATP energy is harnessed

Back 41

phosphoryl group transfer and nucleotidyl group transfer.

Front 42

Phosphoryl group transfer

Back 42

donating a phosphate group to a substrate. typically irreversible. ex. Glucose kinase phosphorylates ATP to ADP. Kinases transfer the gamma P of ATP to the substrate

Front 43

what is ATPs phosphoric group transfer potential?

Back 43

same number as for ATP hydrolysis -35, but sign is changed. So here it is +35.

Front 44

Nucleotidyl group transfer

Back 44

transfer of a nucleotidyl group from a nucleotide triphosphate. typically the AMP part. Activation of sugars for other rxns.

Front 45

phosphagens

Back 45

High energy phosphoamide compounds. Creatine phosphate becomes creatine by enzyme creatine kinase. Anhydride bond is P-N i the creatine phosphate. Direction of the rxn depends on prevailing ATP. During exertion, direction favors forming ATP. At rest, direction favors formation of creatine-phosphate by using ATP.

Front 46

Thioesters

Back 46

energy rich compounds. Acetyl CoA, Succinyl Coa, Acyl CoA. SH is the thiol part. ex: makes a thioester bond to pyruvate to make acetyl coA by way of the enzyme pyruvate dehydrogenase.

Front 47

adenylate kinase

Back 47

ATP goes to AMP and PPi. AMP must reenter the ATP/ADP cycle. ex: AMP+ATP goes to (via enzyme adenylate kinase)=2ADP.

Front 48

What are the Purines?

Back 48

Adenine, Guanine,

Front 49

What are the pyrimidines?

Back 49

Uracil, Thymine, cytosine

Front 50

what is the purpose of miRNA?

Back 50

what is the purpose of miRNA?

Front 51

What is the analog of DDL?

Back 51

deoxyadenosine

Front 52

What is the analog for acyclovir?

Back 52

Deoxyguanosine

Front 53

What is the mechanism for Acyclovir and how does it affect specificity?

Back 53

Missing the 3' end (pentose sugar) required for nucleic acid polymerization. Acyclovir enters the host cell and is converted to acyclovir-triphosphate via VIRAL kinase, thus it is very specific to infected cells.

Front 54

What is the analog for Tenefovir?

Back 54

Deoxyadenosine monophosphate

Front 55

What is the mechanism for Tenefovir

Back 55

Missing 3' OH. Upon entry into cell converted into Teneforvir diphosphate.

Front 56

What nucleotide does tenefovir compete with for incorporation into host DNA?

Back 56

Deoxyadenoside triphosphate

Front 57

What is the mechanism for cytosine arabinoside?

Back 57

Converted into araC-triphosphate. But has an extra OH at pos2 which sterically hinders the next base from being added causing termination

Front 58

What is the mechanism for araA

Back 58

converted into araA triphosphate. 3'OH is present but planar configuration prevents elongation of DNA

Front 59

What is the analog for Decitabine and 5-azacytidine?

Back 59

Cytidine

Front 60

What is the use of Decitabine and 5-azacytidine?

Back 60

Anti-cancer drugs. Myelodysplastic syndrome and acute myeloid leukemia

Front 61

What occurs during Prokaryotic DNA Replication Initiation?

Back 61

DNAa recognizes and binds 9bp, then at the 3AT rich sequence Gyrase seperates the two strands to form bubble

Front 62

What signals termination?

Back 62

Ter sequence which bind the Tus protein

Front 63

What protein is required for the seperation of the daughter chromosomes?

Back 63

Prokaryotic Gyrase

Front 64

What is the main replicative enzyme in Eukaryotic Replication

Back 64

Polymerase delta

Front 65

Trypanosomes and Leishmania

Back 65

RNA editing is more extensive and involved the editing of multiple bases. Typically the editing comes in the form of inserting of a number of uracil bases. Involves the complimentary binding of a guide RNA and the action of a large enzyme complex that possesses endonuclease (cleavage) activity, a terminal uridyltransferase and a RNA ligase.

Front 66

Systemic lupus erthematosis

Back 66

Autoimmune disease whereby Lupus patients possess auto-antibodies that cross react with the UI RNA component of the spliceosome. This may prevent the normal splicing of the mRNA of some genes.

Front 67

beta-thalasemmia and Limb girdle muscular dystrophy

Back 67

Clinical conditions associated with mutations in genes that destroy spice donor/acceptor sites or that generate new splice sites.

Front 68

Transcription initiation proteins- TATA box binding protein

Back 68

protein causes distortion in the DNA helix allowing recruitment of other transcription

Front 69

Transcription initiation proteins- TFIID

Back 69

protein causes distortion in the DNA helix allowing recruitment of other transcription factors

Front 70

Transcription initiation proteins- TFIIB

Back 70

involved in RNA polymerase interactions and start site recognition

Front 71

Transcription initiation proteins- TFIIH

Back 71

contains a DNA helicase to unwind DNA and actives RNA polymerase by phosphorylation

Front 72

Transcription initiation proteins- TFIIE

Back 72

invovled in positioning of RNA polymerase

Front 73

Cytadine deaminase enzyme

Back 73

selective editing changes CAA to UAA (stop codon) to prematurely end apolipoprotein B protein synthesis in the intestine over the liver.

Front 74

Glutamate receptor in brain- adenosine deaminase

Back 74

selectively edits codon for glutamine into arginine, so that glutamate only conducts in response to Na instead of Na and Ca. Important for normal brain function

Front 75

Shine Delgarno

Back 75

purine rich sequence indicating that the start codon is near (prokaryotes)

Front 76

Diphtheria toxin

Back 76

inactivates EF-2 in eukaryotes, (ADP-ribosylation) results in lack of translocation of tRNA

Front 77

Puromycin blocks...

Back 77

elongation; causes peptide to fall out of ribosome P-site and causes premature termination of translation

Front 78

promoter

Back 78

- part of a prokaryotic gene located upstream of the RNA coding sequence

- ensures proper location of transcription initiation (at +1 site)

-35 consensus sequence: 5'-TTGACA-3'

-10 consensus sequence: 5'-TATAAT-3' (Pribnow box)

Front 79

eukaryotic promoters

Back 79

- consist of a collection of conserved short sequence elements located near the transcription start site:

(1) GC box
(2) TATA box
(3) CAAT box

- variation allows for different rates of transcription and control of it

Front 80

GC box

Back 80

DNA sequence: GGGCGG - approx position at -70 to -200

Front 81

TATA box

Back 81

DNA sequence: TATAAA - approx position at -20 to -35

Front 82

CAAT box

Back 82

DNA sequence: CCAAT - approx position at -80

Front 83

courmarins

Back 83

Novobiocin - antibiotics that inhibit the function of bacterial gyrase and topoisomerases that relieve positive supercoiling

Front 84

quinolones

Back 84

Nalidixic acid, Ciprofloxacin - antibiotics that inhibit the function of bacterial gyrase and topoisomerases

Front 85

What is the difference between induction and repression of enzyme synthesis

Back 85

Induction is slow as it makes another enzyme.
Repression is fast as it interefers with transcription

Front 86

homotropic effector

Back 86

The binding of substrates to one subunit can lead to a conformational shift which enhances the binding of the substrates to the other subunits (cooperative substrate binding).

Front 87

Heterotropiceffectors

Back 87

bind
non-covalently to a specific binding site
other than the substrates, coenzymes or products
The heterotropic effector can change the activity of the enzyme.This is often used for feedback inhibition and sometimes for feed-forward activation of pathways.

Front 88

How does DFP block Acetylcholinesterase?

Back 88

DFP binds covalently to the serine in the active site and blocks its catalytic action

Front 89

What is the name of the molecule that stimulates blood thinning?

Back 89

Prostacyclin

Front 90

What is the name of the molecule that stimulates blood clotting

Back 90

Thromboxane

Front 91

Examples of Paracrine Signal Molecules

Back 91

Growth factors, eiconosoids, nitric oxide

Front 92

CREB (desc)

Back 92

cAMP Response Element Binding Protein, phosphorylated by PKA to transcribe specific CRE/cAMP-related genes

Front 93

What are zinc fingers required for?

Back 93

for the steroid hormone complex to bind to DNA to stimulate transcription

Front 94

In the NO pathway, what neurotransmitter and what G protein are used?

Back 94

ACh and Gq