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Biochem > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

Name the aliphatic or hydrocarbon or non- polar amino acids.

A

Gly, Ala, Val, Leu, Ile

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2
Q

Name the sulfur containing amino acids

A

Cys, Met

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3
Q

Name the aromatic amino acids.

A

Phe, Tyr, Trp

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4
Q

Name the imino amino acids.

A

Pro

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5
Q

Name the Neutral amino acids.

A

Ser, Thr, Asn, Gln

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6
Q

Name the acidic amino acids. What charge at neutral pH?

A

Asp, Glu, -

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7
Q

Name the basic amino acids. What charge at neutral pH?

A

His, Lys, Arg, +

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8
Q

What is the three letter abbreviation for Glycine?

A

Gly

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9
Q

What is the three letter abbreviation for Alanine?

A

Ala

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10
Q

What is the three letter abbreviation for Valine?

A

Val

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11
Q

What is the three letter abbreviation for Leucine?

A

Leu

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12
Q

What is the three letter abbreviation for Isoleucine?

A

Ile

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13
Q

What is the three letter abbreviation for Cysteine?

A

Cys

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14
Q

What is the three letter abbreviation for Methionine?

A

Met

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15
Q

What is the three letter abbreviation for Phenylalanine?

A

Phe

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16
Q

What is the three letter abbreviation for Tyrosine?

A

Tyr

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17
Q

What is the three letter abbreviation for Tryptophan?

A

Trp

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18
Q

What is the three letter abbreviation for Proline?

A

Pro

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19
Q

What is the three letter abbreviation for Serine?

A

Ser

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20
Q

What is the three letter abbreviation for Threonine?

A

Thr

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21
Q

What is the three letter abbreviation for Asparagine?

A

Asn

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22
Q

What is the three letter abbreviation for Glutamine?

A

Gln

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23
Q

What is the three letter abbreviation for Aspartic acid?

A

Asp

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24
Q

What is the three letter abbreviation for Glutamic acid?

A

Glu

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25
Q

What is the three letter abbreviation for Histidine?

A

His

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26
Q

What is the three letter abbreviation for Lysine?

A

Lys

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27
Q

What is the three letter abbreviation for Arginine?

A

Arg

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28
Q

What is the side chain for Gly?

A

H

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29
Q

What is the side chain for Ala?

A

CH3

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30
Q

What is the side chain for Cys?

A

CH2-SH

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31
Q

What is the side chain for Ser?

A

CH2-OH

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32
Q

What are the classifications for amino acids?

A

Alaphatic, Sulfur, Imino, Neutral, Acidic, Basic or Amide or Cyclic Amino

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33
Q

Keq=

A

[products]/[reactants]

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34
Q

^G=

A

^H - T^S

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35
Q

if Keq > 1, then…

A

rxn favors products

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36
Q

if Keq<1, then…

A

rxn favors reactants

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37
Q

if Keq = 1

A

equilibrium

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38
Q

pH =

A

log 1/[H+] or -Log [H+]

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39
Q

pH=pKa when?

A

pI

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40
Q

pK +log[base]/[acid] =

A

pH

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41
Q

Buffering zone =

A

pKa +/- 1 pH unit

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42
Q

Carbonic Acid

A

H2CO3

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43
Q

Bicarbonate

A

HCO3-

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44
Q

CO2 + H2O =

A

H+ + HCO3-

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45
Q

What is the intermediate of this rxn? CO2 + H2O = HCO3- + H+

A

H2CO3

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46
Q

if pH > pKa, then

A

unprotonated

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47
Q

if pH < pKa, then

A

protonated

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48
Q

pHs charge is?

A

positive

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49
Q

pH>pI then the protein’s charge is?

A

negative

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50
Q

Which amino acids are strongly polar?

A

Arg, Lys, Asp, Glu

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51
Q

Which amino acids are very hydrophobic?

A

Leu, Ile, Phe, Met, Val, Ala

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52
Q

Which amino acids are diprotic?

A

Ala, Asn, Gln, Gly, Ile, Leu, Met, Phe, Pro, Ser, Thr, Trp, Val

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53
Q

Which amino acids are polyprotic?

A

Glu, Arg, Lys, Asp, Cys, His, Tyr

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54
Q

N=

A

equivalents/L

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55
Q

equivalents=

A

wt(g)/EW

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56
Q

EW+

A

MW/n n=# of H or OH per molecule

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57
Q

weight/volume%

A

g/100mL or g/dL

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58
Q

milligram %

A

mg/100mL or mg/dL

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59
Q

log (10^x) =

A

x

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60
Q

10^-x =

A

1/10^x

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61
Q

log 0.1

A

-1

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62
Q

log 0.001

A

-2

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63
Q

log 1

A

0

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64
Q

log 10

A

1

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65
Q

log 100

A

2

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66
Q

if log (x) = y then

A

x = 10^y

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67
Q

Negative regulator of hemoglobin?

A

pH, CO2, BPG

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68
Q

Type 1 collagen is functionally set up how? Where is it found?

A

Fibrillar, Bone, skin, tendon, scar tissue, heart valve, intestinal and uterine wall

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69
Q

Type IV collagen is functionally set up how? Where is it found?

A

Network, Basement membrane, lens capsule

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70
Q

Collagen requires post-translational modification of amino acids by what enzyme and what cofactor? What disease is associated with the lack of the cofactor?

A

prolyl hydroxylase, vitamin C, scurvy

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71
Q

Characterstics of collagen.

A

rigid and strong, glycosylated, sequence repeats every third is Gly, triple helix, individual is left handed helix cord of three is right handed helix

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72
Q

Ehlers-Danlos Syndrome (EDS)

A

disease of collagen struct./strength, hyperextensible skin, poor wound healing, ragged scarring, and joint hypermobility (thumb sign)

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73
Q

Osteogenesis Imperfecta

A

type I collagen disorder, mutation in COL1A1 and COL1A2 gene, “Brittle bone disease”, multiple fractures w/ no apperent trauma, skeletal disformities, blue sclerae, autosomal dominant

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74
Q

Matrix proteins are made by what cells?

A

fibroblasts, osteoblasts, chondroblasts

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75
Q

matrix is mostly what molecules?

A

proteoglycans and fibrous proteins

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76
Q

Ground substance is made up of what?

A

glycosaminoglycans (GAGs)

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77
Q

Name 5 types of GAGs and where they are foudn

A

Chondroitin sulfate in cartilage, tendons, and ligaments; dermatan sulfate in skin, blood vessels, and heart; heparin and heapran sulfate in cell surface of blood vessel walls; keratin sulfate in same as CS; and hyaluronan in synovial fluid and vitreous humor of the eye.

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78
Q

What is the repeating sequence that makes up hyaluronan? whys is it unique from other GAGs?

A

glucuronic acid and N-acetylglucosamine, unique because it is not synthesized on a core protein

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79
Q

Name the functions of proteoglycans.

A

Primarily rigidity in hydrated spaces, bind growth factors ( insulin like, transforming) to serve as a reservoir, bind proteolytic enzymes and inhibitors, degradation is important in regulation of cell migration and tissue remodeling and cancer

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80
Q

What is mucopolysaccharidoses?

A

lysosomal storage disorder due to defective GAG degradation, normal at birth, develop dismorphic features, coarse facial hair hirsutism, macrocephaly, learning disabilities

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81
Q

Hurler Syndrome

A

MPS type I, deficiency of alpha-iduronidase, dermatan sulfate and heparin sulfate, gargoylism, fatal cardiomyopathy

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82
Q

Hunter syndrome

A

MPS type II, x-linked, deficiency of iduronate sulfatase which helps degrade heparin sulfate and dermatan sulfate

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83
Q

Fibronectin

A

ECM, major glycoprotein, bound to integrins on surface of matrix cells

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84
Q

Marfan Syndrome

A

disorder of fibrillin defects, tall stature, skeletal deformities, long thin bones, joint hypermobility, positive wrist and thumb sign, mitral valve prolapse, loss of elasticity in aortic root may lead to aneurysm and potentially aortic dissection

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85
Q

Basal Lamina is what? What are its two layers?

A

mat of extracellular matrix, lamina lucida (mostly laminin) and lamina densa (mostly collagen)

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86
Q

Purines

A

A, G, two rings

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87
Q

Pyrimadines

A

C, T, one ring

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88
Q

Three factors stabilizing DNA

A

H bonds, Base stacking, ions

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89
Q

Helicase

A

enzyme separating DNA during replication

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90
Q

topoisomerase

A

I and II, relax supercoiling, 1- breaks sugar phosphate backbone of one strand then swivels and relegates broken strand, 2 breaks both strands of one loop then passes the other strand through the break and relegates.

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91
Q

RNA primer is made by what?

A

DNA primase

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92
Q

DNA Polymerase

A

elongates synthesis of DNA after RNA primer

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93
Q

Fidelity

A

intrinsic feat. accuracy, proof reading 3’-5’ repair, primase 1 in 10k mistakes= low fidelity

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94
Q

Lagging strand repair

A

RNase H- digests and removes RNA primer, DNAPol fills gap, Ligase joins the ends

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95
Q

Differences between leading and lagging strand

A

discontinuos synthesis (lag), frequent repair (lag), frequent ligation (lag), leading strand extended by telomerase and lagging by DNA primase and DNA Pol, Single strand binding proteins (more important on lag)

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96
Q

DNA repair types

A

Proofreading, Lagging strand repair, Mismatch repair, Nucleotide Excision repair, Base excision repair, strand break repair, transcription coupled repair

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97
Q

What is spontaneous depurination? how is it repaired

A

purine group come off phosphate sugar backbone, repaired via BER

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98
Q

What does radiation do to DNA? How is it repaired?

A

Ionizing- strand breaks- non-homologous end joining

UV- pyr-pyr dimers- NER

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99
Q

How do Xenobiotics effect DNA? Repair?

A

Adducts (covalently modifies base) - direct or NER

100
Q

How can Metabolic Errors effect DNA? repair?

A

replication past a single strand break- homologous recombination or less likely non-homologous end joining

101
Q

How are proofreading errors fixed?

A

mismatch repair, 3’-5’ exonuclease

102
Q

How does deamination effect DNA? repair?

A

spontaneous hydrolysis of NH2 (almost always get an unnatural base except methylated C -> T ok but not a great match), BER

103
Q

What is heritable damage? repair?

A

wrong base but chem. normal, (missense, nonsense, frameshift, silent) or
damaged bases chem and base change or
Insertions and Deletion; BER

104
Q

What is Xeroderma pigmentosum?

A

UV damage not repaired efficiently, mutation in NER, pyrimidine dimers, basal cell cancer, squamous cell cancer, melanoma

105
Q

rRNA types? funct.?

A

28s, 18s, 5.8s, 5s, protein translation machinery, most abundant

106
Q

RNA types?

A

rRNA, mRNA, tRNA, snRNA, snoRNA, miRNA

107
Q

mRNA fact and function?

A

longest, directs synthesis of proteins

108
Q

tRNA fact and function?

A

shortest major, carry amino acid residues

109
Q

snRNA fact and function?

A

uridine rich, mRNA splicing

110
Q

snoRNA fact and function?

A

small nucleolar, rRNA modification

111
Q

microRNA fact and function?

A

in cytoplasm, can be in nucleus, mRNA expression

112
Q

lncRNA fact and function?

A

long non-coding, varied funct. structural, imprinting, etc.

113
Q

Types of RNA Pol? what do they synthesize?

A

Pol I: rRNA 5.8s, 18s, 28s
Pol II: mRNA, snoRNA, miRNA, snRNA
Pol III: tRNA, 5s rRNA, snRNA

114
Q

Regulation of RNA synth.?

A

mostly promoter pol complex, alternative splicing, alternative poly A, altenrative initiation points

115
Q

Steps to mRNA synth.

A

closed complex, open complex, initiation, promoter clearance, elongation, termination, separation of RNA

116
Q

Necessary components of mRNA synth. (pro)

A

DNA dependent RNA pol, DNA template, cis element on DNA to recruit trans acting factors, nucleotides

117
Q

POL II synth:

A

Pol II, template, cis seq, trans factors, and nucleotides, GTF, CTD

118
Q

What is the PIC?

A

preinitiation complex, trans factor, pol II, GTFs, and cis seq.

119
Q

What is the function of CTD?

A

c-terminus domain,recruits modifying proteins cap mRNa 5’-5’ bond (cotranscriptional),
poly A Pol, post-transcriptional, poly

120
Q

2 methods of splicing mRNA

A 
invariant A (2'-5' bond, release lariat)
snRNA splicisome U1,2,4,5,6
121
Q

rRNA synthesis

A

Pol I same as Pol II minus CTD ( no capping, splicing, or polyadenylation), synth in cluster (18s, 5.8s, 28s) 45s precursor, in nucleolus genes transcribed, rRNA processed by snoRNA (telomerase) snoRNP (splicisome RNA and protein), and rRNA and ribosomal proteins assembled

122
Q

rRNA modification

A

chem modified to include pseudouridine or modified 2’Omethyl ribose, each repeated ~100x

123
Q

rRNA cleavage

A

endonuclease hydrolyzes into 3 fragments, directed by snoRNA (U3)

124
Q

5s RNA synth.

A

Pol III, separate gene, not processed from precursor

125
Q

tRNA maturation

A

Pol III, modified bases: pseudouridine, dihydrouridine, and thymidine, 3’ terminal CCA = charging

126
Q

miRNA synth/cleavage

A

Pol II, capped, spliced, polyadenylated, clustered stem loops ( can be from host gene intron), RNase Drosha separate stem loops from sequence, Dicer cuts loop off stem, stem = miRNA

127
Q

Notable structures on tRNA

A

acceptor stem ( site of CCA tail), D arm, Anticodon arm, anticodon, variable arm, TPsiC arm, methylated bases, irreg. bases inosine and pseudouridine

128
Q

Aminoacyl-tRNA formation

A

catalyzed by aa tRNA synthetases, 2 step, very important because codon and anticodon rxn independent of AA attached to tRNA

129
Q

3 phases of protein synth.

A

chain initiation, elongation, termination

130
Q

Chain initiation req.

A

regulated not ongoing, 1st AA Met, mRNA, GTP, Mg2+, ribosomal subunit, eukaryotic initiation factors, cap binding protein

131
Q

summary of Chain initiation

A

ribosome dissociation-> 40s and 60s
40s + Tert. complex -> 43s preinitiation comp.
43s PIC + mRNA -> 48s PIC
48s PIC + 60s subunit -> 80s initiation comp.

132
Q

Peptide elongation req.

A

active 80s initiation comp., aa-tRNA specified by next codon (n+1), 2GTP, Mg2+, Peptidyl transferase, 2 elongation factors (EF-1, EF-2)

133
Q

Peptide elongation summary

A

For each peptide elongation cycle 2 GTPs hydrolyzed forming a peptide bond, followed by movement by ribosome to next available codon on mRNA

134
Q

Polypeptide termination req.

A

Active 80s, Termination codon on mRNA, GTP, Peptidyl transferase, release factors (RF-1, RF-3), Mg2+

135
Q

Summary of Polypeptide chain termination

A

3 termination codons (UAA, UAG, UGA), no known tRNA’s w/ comp., codon at A site will cause bindng of RF-1 and RF-3 to catalyze termination

136
Q

Fidelity of Protein Synth. (quality control)

A

P (processing) bodies, selectively degrade nonsense sequences of mRNA; ubiquitin-proteasome system (UPS) degradation of misfolded protein

137
Q

Regulation of Translation?

A

miRNA and RNAis bind by base pairing to 3’UTR on specific mRNA prevent translation/trigger destruction, RNP complex known as RISC (RNA-initiated silencing complex) sequester RNA; Riboswitches & gene specific proteins, control specific mRNA by specific metabolites, translation prod, or related protein, ex. IRF ( Iron responsive Factor control of ferritin mRNA)

138
Q

silent mutation

A

change of a base but codon still codes same amino acid

139
Q

missense mutation

A

change in base change amino acid coded for, sometimes see phenotypic change ex sickle cell

140
Q

non-sense mutation

A

base change code for stop instead of a AA

141
Q

deletion/insertion

A

frame shift mutation, changes entire sequence

142
Q

splice site mutations

A

consensus sequences if mutated cause in correct splicing ex B-thallasemia

143
Q

trinucleotide repeat expansions

A

slipping during replication, trinucleotides repeated cause protein aggregates, ex huntingtons

144
Q

How does tetracycline work?

A

binds to 30s, inhibits binding of aminoacyl-tRNA (pro)

145
Q

How does chloramphenicol work?

A

inhibits peptidyl transferase of 50s, not used, liver failure, mitochondria

146
Q

How does puromycin work?

A

premature chain termination, analog of aminoacyl tRNA (pro and eu) not clinically used

147
Q

How does streptomycin work?

A

binds 30s, inhibition by codon misread

148
Q

How does erythromycin work?

A

blocks translocation, binds to a protein on 50s, (pro)

149
Q

How does cycloheximide work?

A

inhibits peptidyl transferase of 60s (eu)

150
Q

How does rifamycin/rifampicin work?

A

blocks intiation of bacterial RNA synth (transcript.)

151
Q

How does diphtheria toxin (natural) work?

A

inactivates EF-2, inhibits translocation

152
Q

How does miRNA or RNAi work?

A

inhibit mRNA translation, cause degradation

153
Q

What role does EF1a and EF2 a play and in what pathway?

A

protein chain elongation 1a brings a new aatRNA to the a site and takes the tRNA off the e site, 2 helps translocase move the tRNA from a to p site

154
Q

How do mitochondrial protein synthesized in the cytoplasm get into the mitochondria?

A

have a amphipathic leader sequence, recognized by cytosolic chaperonins, chaperonins direct proteins to outer mitochondrial membrane

155
Q

Secretory proteins/lysosomal proteins synth.

A

leader sequence recognized once it exits ribosome, elongation halted with binding of SRP, SRP binds to its receptor on ER surface next to ribosome receptor, SRP dissociates, ribosome continues elongation of protein thru receptor into ER lumen

156
Q

Why does glycosylation happen? Types of bonds?

A

maintain stability, increase solubility, occurs in ER and Golgi, N link oligosaccharide (complex or manose) to Asn, O link oligosaccharide to OH of Ser Thr, now glycoproteins

157
Q

synthesis of o linked glycoproteins

A

transfer of sugars as nucleoside derivatives to seryl and threonyl residues. enz: glycosyltransferase

158
Q

synthesis of n linked glycoproteins

A

added en bloc (presynth oligo assembled on dolichopyrophosphate) enz: glycosyltransferase, attach in ER, trim in ER, transport via vesicle to Golgi, trimmed again or monosaccharides added in Golgi, released as secretory protein in secretory granule or phosphorylated attached to manose-6-phosphate receptor and transported w/receptor in vesicle to acidified compartment, separated from receptor, protein cleaved to catalytically activate and transferred to lysosome.

159
Q

Alpha-1-antitrypsin deficiency?

A

inability to secrete a-1AT into circulationdue to polypeptide mut., emphysema, cirrhosis, hepatocellular carcinoma, unable to degrade, just builds up in cell.

160
Q

I-cell disease (mucolipidosis II)?

A

defective phosphotransferase activity to mannose, lysosomal enzyme secretion instead of transfer to lysosome, cong. heart fail, pneumonia susceptible

161
Q

Protein phosphorylation

A

rapidly raise or lower protein activity, depending on target protein and phosphorylation site

162
Q

Proteolytic modification (trimming)

A

in ER and Golgi, removal of NH2 terminal sequences, stepwise protein maturation

163
Q

Ubiquitylation of protein

A

degradation by proteasome or signaling (alter function)

164
Q

Acetylation of protein

A

mech. for enhancement of protein stability, activity, and gene expression

165
Q

hydroxylation of protein

A

protein cross-linking ex collagen

166
Q

Methylation of protein

A

regulate protein function and structure

167
Q

Sulfation of protein

A

amino acid modification and signaling

168
Q

lipid binding to protein

A

localize proteins in lipid bilayer of membranes

169
Q

Functions of epithelia

A

selective barrier, protective function, sensory surfaces

170
Q

Epithelial tissue derived from what germ layers. be specific.

A

Ecto-epidermis, gland of breast, cornea, part of oral and anus
Endo, alimentary canal and glands, most respiratory, distal urogenital
Meso- mesothelium-internal cavities, endothelium- BV and LV lining, epithelia-prox urinary and genital

171
Q

Characteristics of epithelia

A

cellular( little ECM), Polarized, Numerous CJ, Polygonal, Avascular, Can be removed surgically with underlying CT, Basal surface in contact with Bsal Lamina,

172
Q

What makes up the basal lamina? Describe each.

A

lamina densa: filametous network of laminins bound by integrins, come collagens type IV, proteoglycans, and glycoproteins
Lamina lucida: CAMs (cell adhesion molecules), fibronectin, laminin receptors

173
Q

What makes up the basement membrane? Describe each layer.

A

basal lamina: btwn basal surface of epithelium and underlying CT, lamina lucida touching basal side of cells then lamina densa; reticular lamina: reticular fibers (type III collagen), produced by cells in underlying CT

174
Q

what makes up the terminal bar? What makes up that?

A

multiple junctional complexes, zonula occludens (preserve polarity, separate apical and basal, inhibit protein migration), Zonula adherens, and macula adherens

175
Q

describe simple sqaumous. Where is it found?

A

single layer, flat cell, endothelium, mesothelium, kidney, lungs

176
Q

describe simple cuboidal. Where is it found?

A

tall=wide, one layer, nucleus centered, exocrine ducts, ovary, kidney tubule

177
Q

describe simple columnar. Where is it found?

A

taller than wide, one layer, SI, Colon, Stomach lining, gastric glands, gallbladder

178
Q

describe pseudostratified. Where is it found?

A

all cell reach BM, nuclei on different levels, trachea, bronchial tree, ductus deferns, efferent ductules and epididymis

179
Q

describe stratified cells?

A

squamous, cuboidal or columnar, named for cell on the surface

180
Q

Where is stratified squamous?

A

epidermis, oral cavity, esophagu, vagina

181
Q

Where is stratified cuboidal?

A

sweat gland ducts, large ducts of exo, anorectal junct.

182
Q

where is stratified columnar?

A

anorectal junction, largest exo duct

183
Q

Describe transitional epitlium. Where is it?

A

between cuboidal and squamous, allows distension, squamous when stretched and less layers, more cuboidal when relaxed and more layers, renal calyces, ureters, bladder, urethra

184
Q

What is metaplasia?

A

change in cell type

185
Q

Name the apical surface specializaions of epithelium.

A

cilium w/ microtubules, stereo cilium with microfilaments (elongated w/ branched end), microvilli (extension of membrane with actin core) with glycocalyx. microfilaments

186
Q

Name lateral surface specializations of epithelium. describe them.

A

zonula occludens, zonula adherens (w/actin projection connecting to actin terminal web), macula adherens (w/ tonofilaments connect to actin filaments), lateral interdigitation(inc. plasma membrane surface=more Na/K pumps, rapi H2) transport), gap junction (ions and small molecules), intercellular cannuliculus (liver-bile secretion, specialized membrane around and tight junct.)

187
Q

Name Basal membrane specializations.

A

basal lamina, reticular lamina, basal unfoldings (present w/ lots of active transport, house mitochondria btwn, kidney tubules

188
Q

what is liable epithelial tissue?

A

continuously renewed cells by mitotic activity, rates vary ( stomach)

189
Q

what is stable epithelium?

A

multiply around puberty and in special circumstances, injury, liver, pancreas, thyroid, kidney

190
Q

what is permanent epithelium?

A

cease multiplication at birth, lens of eye

191
Q

Name the different endocrine gland types.

A

cord shape or follicle shape, empties into BV nearby no duct

192
Q

Name and describe the exocrine gland types.

A

Merocrine- secretory vesicle fusses w/ membrane relasing contents
Apocrine- membrane pinches off containing secretory product.
Holocrine- cell dies and product is relased

193
Q

Describe a paracrine gland.

A

product emptied into ECF to act on target cells locally

194
Q

Where can myoepithelial cells be found?

A

btwn secretory cell and basement membrane of exocrine glands, assists expression of secretory product into duct

195
Q

Name the reasons for protein synthesis and degradation.

A

normal protein turnover, gene expression, quality control and peotection (damaged, misfolded, aggregated), cell division, immune response, energy maintainence

196
Q

What are the two proteolytic systems?

A

UPS, lysosomal system

197
Q

What are lysosomes?

A

organelle digestion system, membrane enclosed acid hydrolases,

198
Q

list the lysomsomal membrane proteins and their function.

A

LAMP 1 &2: marker protein; Endolyn: glycoprotein marker, RAB-7: autophagy, CD68: LDL, Cystinosin: transport cysteine, Vacuolar H+ ATPase: allows lysosome to maintain pH 4.7

199
Q

What are the major pathways of lysosomal proteolysis?

A

Endocytosis, Phoagocytosis, Autophagy (macro, micro, and Chaperone mediated)

200
Q

What is endocytosis for in LP path?

A

remove and degrade obsolete or damaged serum proteins, brought into cell via receptors or pinocytosis, EE->LE->Lysosome, pH drop whole way in

201
Q

What is phagocytosis for in LP path?

A

extracellular particles (bacteria or macrophages), purpose is immunity

202
Q

What is autophagy?

A

destruction of large amounts of intracellular proteins, cellular digestion and quality control

203
Q

What is macroautophagy?

A

digestion of vaccoules and contents, trafficked to lysosome

204
Q

What is microautophagy?

A

small particles taken into Lysosome from cytosol vie invagination

205
Q

What is chaperone mediated autophagy?

A

HSP chaperone recognizes marked protein and attaches, takes it to lysosome (slows with age)

206
Q

How is Macroautophagy affected in post absorptive state

A

nutrients and insulin upregulate mTOR which suppresses macro autophagy. by suppressing the complex that makes both the phagophore and the marker protein

207
Q

How is macro autophagy affa]ected in fasting state?

A

starvation or rapamycin suppress mTOR which then does not suppress the complex which makes the phagophore and the marker protein which make up the autophagosome

208
Q

What is a phagophore?

A

precursor to the autophagosome

209
Q

List the steps and intermediates for the autophagosome marker protein synthesis

A

Pro-LC3 hydrolyzed by Atg4 to LC3-I which goes through lipidation via Atg7 and addition of phosphotidyl ethanolamine via Atg3 to become LC3-II and incorporate with phagophore to make autophagosome

210
Q

What is the importance of Autophagy?

A

macromolecular disposal of waste, removal of defective organelles, removal of aggregates, back up to UPS, responsive to cellular stress

211
Q

What are some clinical disorders associated with autophagy suppression?

A

neoplasia esp in liver, neurodegenerative ex parkinsons, responses to toxins ex alcohol and acetaminophen)

212
Q

Where does UPS take place?

A

cytososl

213
Q

What enzyme ubiquitylates a protein marking it for degradation?

A

E1: activating, E2 conjugating, E3 Ligase

214
Q

What protein recognizes ubiquityn on protein and pulls it in for degradation and removes the ubiquitin?

A

19s regulatory complex on 26s proteasome

215
Q

What part of and what enzyme degrade a ubiquitylated protein?

A

20s catalytic core or 20s proteasome of the 26s proteasome

216
Q

Name the protein substrates degraded by the UPS.

A

regulatory proteins, transcription factors, damaged proteins, metabolic enzymes, antigens (75-80% intracellular proteins)

217
Q

What things regulate the UPS and how?

A

cytokines up, sepsis up, trauma up, Alzheimer’s and ND diseases fails or down, enhanced level of altered proteins up or down

218
Q

How can UPS be targeted therapeutically?

A

anticancer drugs, anti-inflammatory compounds

219
Q

What enzyme and where is the first metabolic step of ethanol ?

A

gastric lining, Gastric Alcohol dehydrogenase (ADH) ethanol-> acetaldehyde, men more than women,

220
Q

What hepatic enzyme metabolizes ethanol in cytosol?

A

cytosolic ADH, reduce NAD to NADH to get acetaldehyde

221
Q

What hepatic enzyme metabolizes ethanol in microsome (R)

A

microsomal cytochrome P450 2E1 (CYP2E1), oxidizes NADPH to NADP and H2O to intermediate the hydrolysis to acetaldehyde (big in brain)

222
Q

What hepatic enzyme metabolizes ethanol in peroxisomes?

A

Peroxisomal Catalase H2O2 to H2O to get acetaldehyde

223
Q

What hepatic enzyme metabolizes acetaldehyde in the mitochondria?

A

Mitochondrial aldehyde dehydrogenase (ALDH) reduce NAD to NADH to get acetic acid, some Asians are deficient in this.

224
Q

what are some consequences of chronic ethanol metabolism?

A

altered redox (increased NADH/NAD), metabolic acidosis (lactate production increase due to NADH increase), enhanced lipogenesis (higher levels of NADH increase NADPH which participates in fatty acid synth.), mitochondrial dysfunction (NADH enhances ETS, elevates leakage of reactive O2-, cause lipid eroxide formationas MDA and 4-HNE), Inhibition of mitochondrial fatty acid oxidation (FA accum, esterifies to TriG), Metabolically derived acetaldehyde forms covalent adducts to protein lipids and DNA, or MDA->MAA)

225
Q

Name 2 major non-oxidative metabolism paths for ethanol.

A

FAEE synthase to fatty acid ethyl ester (disrupts mitochondrial funct.), Phospholipase D to phosphotidylethanol (interferes w/ PLD dependent signaling)

226
Q

How is acetaminophen metabolized?

A

conjugated to either glucuronide or sulfide= nontoxic or if overdosed metabolized with P450 2E1 to NAPQI which is toxic

227
Q

what do you give to counteract acetaminophen overdose? how does it work?

A

NAC which is changed to GSH (depleted antioxidant) which helps change NAPQI to cysteine and mercapturic acid conjugate

228
Q

why is ethanol excess bad with Tylenol ingestion?

A

ethanol increases the rate at which acetaminophen is metabolized by CYP2E1 by inducing it in the first place, forms NAPQI causes 70% depletion of GSH and forms adducts = cell death

229
Q

Ethylene glycol is metabolized how?

A

ADH to glycoaldehyde ALDH to Glycolic acid –> oxalic acid

230
Q

What blocks metabolism of ethylene glycol at what step and why?

A

ethanol, ADH, 100X higher affinity

231
Q

How does methanol metabolize?

A

ADH to fomaldehyde, ALDH to formic acid folate to CO2 H2O

232
Q

What does formic acid damage? What do you give to prevent formic acid from forming?

A

optic nerve, bicarbonate offset acidosis, or ethanol or fomepizole to compete with ADH

233
Q

what are chaperones?

A

assist or mediate folding and assembly of prtoeins, anneal un/misfolded proteins and allow them to find their naitive state

234
Q

Name some examples of chaperones.

A

HSP, GroEL &GroES, Protein disulfide isomerases, peptidylprolyl cis/trans isomerase

235
Q

Alzheimer’shas what types of protein misfolding and why?

A

B-amyloid plaques, cleavage by gama-secretase within membrane spaning domain creates B-amyloid fragment, hydrophobic regions seek each other and form a plaque also form salt bridge

236
Q

How do plaques effect brain in Alzheimer’s?

A

build up in mitochondria and inhibit enzyme funct. and block utilization of glucose, fibrils dirupt Ca2+ homeostasis = apoptosis

237
Q

What protein problem occurs in Huntingtons and why?

A

trinucleotide repeat, CAG, codon for glutamine (Q), poly Q region, amount of repeat effects classification of disease, destroys parts of brain controlling movement, emotion, and cognitive ability

238
Q

what causes CAG repeats?

A

repair strand breaks and remove mispaired bases, often ubiquilated forming aggregates but not degrading suggests problem with proteasome, cross link or polar zipper formation

239
Q

What is Parkinsons?

A

progressive degenerative dopaminergic projection from substantia nigra pars compacta (SNpc) to striatum

240
Q

Pheotype of Parkinson’s is…

A

motor dysfunctions resting tremors, postural instability, bradykinesia

241
Q

What are factors that appear to play a role in Parkinsons

A

lack of dopamine, low norepinephrine, environmental triggers (toxins or viruses), genes LRRK-2 or a-synuclein or presence of lewy bodies

242
Q

What role might a-synuclein play in parkinsons?

A

block ER-Golgi transport, ER stress and Golgi fragmentation, decrease synaptic vesicle relase, impaired energy production-> apoptosis induction, accumulation of CMA substrates -> proteasome impairment

243
Q

How do prions infect and spread?

A

prion protein (PrPc) is affected by infectious isoform PrPsc changing PrPc to PrPsc with interaction. chain reaction, aggregation of isoform form amyloid fibers which form plaques

244
Q

How does sickle cell anemia work?

A

mutant for of hemoglobin when deoxygenated can polymerize in to elongated rope like fiber connection hydrophobic btwn B subunits

245
Q

What happens in Cystic fibrosis?

A

most common mutation of single codon 3nt deletion, phenylalanine deleted, protein fails to fold properly in ER, degraded before reaching surface, upsets NaCl balance needed to maintain normal mucus layer. mucus thick so bacteria and virus stick.

246
Q

What receptor mutation causes immunity to m-tropic HIV if homozygous?

A

CCR5

Biochem (3 decks)

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