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M2M - My Cards > Unit 1 > Flashcards

Unit 1 Flashcards

1
Q

Free energy equations?

A

delta G = delta G knot + RT lnKeq

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2
Q

Forward direction when?

A

Keq >1

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3
Q

2 types of high energy bonds? Ex?

A
  1. ) Thioester (C-S) = Acetyl CoA
  2. ) Phosphate bonds
    - Phosphoanhydride = ATP (P-O-P)
    - (P-N) = phosphocreatine
    - (C-O-P) = phosphophenolpyruvate
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4
Q

Diseases related to insoluble purines?

A
  1. ) Gout

2. ) Lesch-Nyhan

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5
Q

Methylation

A

Often happens with C-G, but can be dangerous because it is inversely related to transcription level

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6
Q

Deamination

A

C to U = usually caught

5-methylcytosine to T = not good

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7
Q

Regulatory RNA

A

miRNA

siRNA = down regulate gene expression

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8
Q

Stabilize single single strands of fork during replication?

A
  • SSBP’s - single stranded binding proteins
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9
Q

Diseases from mutations in DNA repair machinery?

A

Cockanyes and XP

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10
Q

What fixes bulky chemical adducts?

A

NER

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11
Q

What fixes uracil in DNA?

A

BER - No distortion of DNA

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12
Q

MMR: Recognized when? By what proteins?

A

Shortly after DNA synthesis; MLH (MutL proteins)

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13
Q

Double breaks fixed by? (2)

A
  • HR (homologous recombination)

- NHEJ (non-homologous end joining)

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14
Q

Last case scenerio if Pol 3 can’t move?

A

Damage bypass/tolerance

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15
Q

TFIID function?

TFIIH function?

A
  • Binds to TATA box

- Facilitates NER repair, adds PO4 to C terminal of Pol II, acts as helicase

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16
Q

Diseases related to mutations of TFIIH?

A

XD, Cockanyes, trycothiodystrophy

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17
Q

Area after 3’ UTR that contains the AAUAAA

A

Consensus sequences

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18
Q

Functions of cap? (4)

A
  1. ) Resistant to exonucleases
  2. ) Cap binding complex helps with splicing
  3. ) eIF4E recognizes it for transport to ribosomes
  4. ) Decapping leads to degradation
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19
Q

Reactions to make cap? (3)

A
  1. ) Cut off PO4
  2. ) Add backwards GTP
  3. ) Methlyate 7 position
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20
Q

Splicing genetic disorders?

A
  1. ) Marfins

2. ) CD44 (cell-surface glycoprotein

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21
Q

Example when alternative poly A sites are used for multiple proteins?

A
  • IgM (membrane bound vs free immunoglobulins)
22
Q

Cis acting elements?

A
  • TATA, promoters, enahncers
23
Q

Diseases that arise from mutations in DNA control elements?

A
  1. ) Thallessemias - b-globin mutation in promoter sequence, Locus control region
  2. ) Hemophelia B- Leyden - Factor IX gene,
  3. ) Fragile X - CGG repeat that is methylated and under transcribed
24
Q

2 classes of activators / repressors?

A
  1. ) Cofactors

2. ) Sequence specific DNA binding proteins

25
Q

4 major families of SSDBP’s?

- Mutations related to each one?

A
  1. ) Homeodomain - Craniosynostosis
  2. ) Zinc Finger - AIS
  3. ) bZIP -
  4. ) HLH - Waardenburg type II
26
Q

2 chromatin remodeling factors?

A
  1. ) ATP dependent SWI/SNF

2. ) Modify Histones via N tails that are rich in Lysine

27
Q

HATS vs. HDACS

A 
HATS = coactivators
HDATS = corepsressors
28
Q

Diseases related to histone acetylation alteration? (2)

A
  1. )Rubenstein-Taybi = Mutation in 1 copy of CREB binding protein
  2. ) Leukemia = Fusion of HATS / HDACS
29
Q

How do activators/repressors modulate transcription?

A
  1. ) Interact with TF’s

2. ) Interact with chromatin that allows accesibilty

30
Q

Ways sequence specific binding proteins are regulated?

A

1.) Binding a ligand: Steroid hormones bind to Zn finger TF’s that recruit HATS; ex = Tamoxifin

2.) Regulate entry: NFkB bound to IkB = no inflamm. response (Aspirin does this)
Calcineurin dephosphorylates NF-ATc which leads to inflammatory response

3.) Regulate amount of TF: WNT activates APC which phosphorylates B-Catenin; No APC = Increased B-Catenin and increased polyps
Increased MDM2 = decreased P53

  1. ) Regulate binding in DNA = E and Id protein home and heterodimers of Basic HLH
  2. ) Phos. of CREB = CREB-P = increased transcription by recruiting HATS (CBP/Pol II)
31
Q

Importance of eIF 4E in translation?

A
  • Binds 7 methyl guanosine of the cap
32
Q

Importance of IRES?

A
  • Allows transcription without a CAP
33
Q

Importance of eIF2 alpha?

A

When phosphorylated it can block translation which is often accomplished using interferons

34
Q

Rapamycin does what?

A

Cancer treatment drug that phospohorylates 4E-BP down regulating translation

35
Q
  • Ferretin vs. transferrin?
A

Ferretin binds iron and transferrin sequesters iron

36
Q

Common post translational covalent modifications? (6)

A

1.) Hydroxyl group to proline
2.) Carboxylation of glutamate
3.) Glycosylation: O = Ser, Thr
N = Asparagine
- CDG-a1 if this doesn’t happen
4.) Acetylation and methylation of of lysine and argenine for DNA-histone interactions
5.) Reverse phosphorylation/dephosphorylation of hydroxyl groups on Ser, Thr, and Tyr which are important for signal transduction pathways
6.) Ubiquitization - add AA to Lyseine to be degraded by proteosomes

37
Q

Most frequently found AA’s in turns and loops?

A
  • Glycine and proline
38
Q

Two major classes of chaperones?

A
  1. ) HSP 70 = Binds to hydrophobic areas to allow folding

2. ) GroEl - same but don’t need heat shcok

39
Q

Approaches to purifying a protein (7)

A
  1. ) Gel filtration chromotography –> Seperated based on size
  2. ) Ion exchange chromotography –> based on charge
  3. ) Affinity chromotography –> based on ligand interactions
  4. ) SDS Page –> purity
  5. ) Mass spec –> mass of the protein
  6. ) N-terminal sequence –> Edmans degradation
  7. ) Western –> identified using antibodies
40
Q

Alzheimers:

  • Progression of disease?
  • AB42 coded on what gene?
  • Problem arrises when?
  • How can genetics play a role?
  • Best treatment option?
  • Current drug used? Does what?
A
  • Plaque - tangles
  • Comes from chromosome 21
  • B secretase followed by gamma secreatase that cleaves two units longer
  • ApoE e4 = increase risk of disease
  • Decrease Beta secratase
  • Donepezil = compensates for neuronal disfunction
41
Q

Types of Prion disease?

A
  • Infection –> vCFJ and canabilism
  • Sporadic –> Alpha helices - beta sheets
  • Inheritied –> Mutation in prion gene
42
Q
  • Restriction endonucleases are often what?
A
  • Palindromic
43
Q
  • PCR amplifiactions often used for what?
A
  • Diagnosing genetic alterations
44
Q

Compare and contrast DNA sequencing with PCR amplification? Goal of each?

A

Similarities: Both use primer sequences to initiate replication of genes

Differences: PCR uses double stranded DNA and sequencing uses single. Sequencing uses ddNTP’s so there isn’t a 3’hydroxyl

Goals: PCR = Amplify a given DNA fragment
Sequencing = Determine sequence of fragment

45
Q
  • What are enzymes? What do they do?
A

Protein catalysts –> increase rate of a reaction by decreasing the activation energy

46
Q
  • Chemistry that helps enzymes work? (3)
A
  1. ) Covalent chemistry
  2. ) Metal ion –> ions position the substrate
  3. ) General acid-base –> Amino acid side chains donate or accept protons
47
Q
  • Km
  • Kcat
  • Enzyme efficiency
A
  • Substrate necessary to reach 1/2 vmax
  • Turnover number when the enzyme is saturated
  • Kcat (speed) / Km (how much is needed)
48
Q
  • Types of inhibition and their effects?
A
  1. ) Competitive = Binds to E and increases Km
  2. ) Uncompetitive = Binds to ES and decrease Vmax and changes apparent Km
  3. ) Mixed = binds outside of active site to either ES or E; both Vmax and Km affected
  4. ) Noncompetitive (mixed) = reduces activity but don’t effect substrate binding
49
Q

Enzyme regulation mechanisms: (4)

A
  1. ) Allosteric = binding of 1 molecule changes conformation
  2. ) Covalent = Phophorylation type deals
  3. ) Binding of a regulatory protein = Similar to allosteric but with peptide
  4. ) Proteolytic cleavage = Cleavge makes them active
50
Q

Inflammatory Bowel Disease:

  • Smokers at greater risk of?
  • Former and nonsmokers at greater risk of?
  • IBD’s extraintestinal manifestations?
  • Rising prevalence related to?

Crohns vs. Ulcerative Colitis:

  • Area affacted?
  • Continuity?
  • Type of inflammation?
  • Bloody stool (hematochezia)?
  • Fistula’s?
  • Upper GI?
A
  • Crohns
  • Ulcerative Colitis
  • Lots of itis stuff
  • Diet, antibiotics, tobacco

Crohns:

  • Ileum
  • Discontinuous
  • Transmural
  • Rare
  • Common
  • Often affected

Crohns:

  • Rectum
  • Continuous
  • Mucosal
  • Common
  • Rare
  • Not affected

M2M - My Cards (1 decks)

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