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POM > week 2 > Flashcards

week 2 Flashcards

1
Q

what genes cause hereditary breast and ovarian cancer?

A

BRCA1 and BRCA2

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2
Q

What is Lynch syndrome? What causes it?

A

early colon, uterine, and other cancers

caused by inherited genes that affect the MMR process (mismatch repair)

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3
Q

immediate precursor of urea and precursor of nitric oxide?

A

arginine

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4
Q

role of aspartate as an effector molecule?

A

excitatory neurotransmitter

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5
Q

role of glycine as an effector molecule?

A

inhibitory neurotransmitter

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6
Q

role of glutamate as an effector molecule?

A

excitatory neurotransmitter

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7
Q

what is glutamate the precursor of?

A

precursor of y-amino butyric acid (GABA), an inhibitory nt

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8
Q

what is histidine the precursor of?

A

histamine, a mediator of inflammation and is a nt

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9
Q

tryptophan us a precursor of what (x2)?

A

serotonin (potent smooth muscle contraction stimulator); melatonin (circadian rhythm regulator)

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10
Q

tyrosine is the precursor of what?

A

hormones and nt catecholamines (dopamine, epinephrine, norepinephrine, and thyroxine)

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11
Q

why do chaperones aid in protein folding?

A

binds the hydrophobic regions of a polypeptide; the chaperones are cage like structures consisting of 2 stacked rings. the partially folded protein enters the central cavity through hydrophobic interactions, is folded, and is released.

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12
Q

what are chaotropic agents?

A

a molecule in water that can disrupt hydrogen bonds between H2O molecules

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13
Q

name 2 chaotropic agents:

A

urea and guanidinium hydrochloride

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14
Q

what 3 diseases are caused by the prion protein (PrP)?

A
  1. Creutzfeldt-Jakob (humans)
  2. scrapie (sheep)
  3. bovine spongiform encephalopathy (mad cow disease)
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15
Q

enzyme that converts dietary protein into polypeptides and amino acids (stomach)?

A

pepsin

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16
Q

enzymes from the pancreas that create oligopeptides and amino acids from polypeptides:

A 
TCEC
Trypsin
Chymotrypsin
Elastase
Carboxypeptidase
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17
Q

enzymes from the small intestine that convert oligopeptides into single amino acids:

A

Amino peptidases

Di and Tri peptidases

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18
Q

where do single amino acids go after being degraded in the digestive organs?

A

liver

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19
Q

what is the categorical name of the pancreas enzymes responsible for digesting AAs?

A

zymogens

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20
Q

what is trypsin’s specificity for protein cleavage?

A

carbonyl must be from an arginine or lysins

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21
Q

what is chymotrypsin’s specificity for protein cleavage?

A

carbonyl must be from a Trp, Tyr, Phe, Met, or Leu

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22
Q

what is elastases’ specificity for protein cleavage?

A

carbonyl must be that of an Ala, Gly, or Ser

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23
Q

what is Carboxypeptidase A/B’s specificity for protein cleavage?

A

A) Ala, Ile, Leu, or Val

B) Arg, Lys

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24
Q

what is the common activator of all of the pancreatic enzymes?

A

trypsin

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25
Q

what are the 2 gluconeogenic organs?

A

liver and kidneys

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26
Q

what are the 2 exclusively ketogenic AAs?

A

lysine and leucine

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27
Q

what mutation causes IVA?

A

mutation in the gene that encodes isovaleryl CoA dehydrogenase (IVD)

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28
Q

what is isovaleric acidemia (IVA)?

A

condition that results in the accumulation of isovaleric acid as a result in mutation for the gene that encodes IVD

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29
Q

what is isovalery-CoA an intermediate of?

A

leucine catabolism

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30
Q

what is IVA known for in infants?

A

sweaty feet w/ a distinct odor

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31
Q

what are the 2 metabolic byproducts of isovalery-CoA that are found in IVA patients?

A

isovaleryl glycine

3-hydroxy isovaleric acid

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32
Q

what are MMA disorders?

A

(methylmalonic acidemia)

family of disorders that have an elevation of methylmalonic acid in the blood and urine

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33
Q

what is methylmalonic acid an intermediate of? (which metabolic pathways)

A

methionine, isoleucine, valine, threonine
along with fatty acid metabolism that contain an ODD # of carbons

Valine
Odd number of carbons in FAs
Methionine
Isoleucine
Threonine
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34
Q

what are the 3 enzymes used to convert propionyl CoA into succinyl CoA in the TCA cycle?`

A
  1. propionyl CoA carboxylase (uses biotin)
  2. methylmalonyl CoA epimerase
  3. methylmalonyl CoA mutase (uses B12)
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35
Q

what causes PKU, Phenylketonuria?

A

block in the conversion from phenylalanine into tyrosine

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36
Q

What is type 1 PKU?

A

2/3 of PKU patients

phenylalanine hydroxylase is deficient

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37
Q

What is type 2 PKU?

A

1/3 of cases
deficiency of BH4
defect in dihydropteridine reductase or in the conversion of GTP into tetrahydrobiopterin

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38
Q

at what concentration does phenylalanine turn into metabolites in PKU patients? what are the metabolites?

A

1 mmol/L
phenylpyruvate, phenyl-lactate, phenylacetate, phenylacetylgutamine
excreted into urine (gives mousy odor)

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39
Q

what are the characteristics of PKU?

A

elevated phenylalanine and BH2
mousy odored urine
hypopigmentation and albinism (tyrosine produces melanin)
intellectual disability and delayed mental development (

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40
Q

pathway of tyrosine —> melanin

A 
tyrosine 
DOPA 
DOPAquinone
LeucoDOPAchrome
DOPAchrome 
Melanin
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41
Q

what is the 1st step in melanin synthesis from tyrosine?

A

hydroxylation of tyrosine by tyrosinase

tyrosinase inhibited in PKU patients due to the high concentration of phenylalanine

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42
Q

what does the diet of a PKU patient look like?

A 
low phenylalanine diet (kept below 6 mg/dL)
tyrosine supplements (since Phe is being kept low, the body cannot make as much endogenous tyrosine; therefore need supplements)
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43
Q

what are the effects of maternal PKU?

A

mental retardation, microcephaly, congenital heart disease, intrauterine growth retardation

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44
Q

what is the dose response relationship (maternal PKU)?

A

lower frequencies of abnormalities associated with lower Phe levels

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45
Q

what causes tyrosinemia, type I?

A

deficiency of fumarylacetoacetate hydrolase

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46
Q

what are the characteristics associated with tyrosinemia, type I?

A

elevated serum fumarylacetoacetate
cabbage like odor
neurological abnormalities, liver damage, and renal tubular function

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47
Q

what causes tyrosinemia, type II?

A

deficiency of tyrosine transaminase in the liver

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48
Q

what are characteristics of tyrosinemia, type II?

A

elevated serum tyrosine levels
affects eyes and skin
causes keratitis (inflammation of the cornea)

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49
Q

what causes tyrosinemia, type III?

A

deficiency of 4-hydroxyphenylpyruvate DH

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50
Q

what is a characteristic of tyrosinemia, type III?

A

mild mental retardation, seizures

51
Q

what is alkaptonuria?

A

inborn error of tyrosine metabolism
asymptomatic until adulthood
due to absence of homogentisate oxidase
causes an increase of homogentisate (an intermediate of tyrosine metabolism)

52
Q

what are the characteristics of alkaptonuria?

A

urine becomes dark (hemogentisate is excreted via urine and is oxidized by air)
pigmentation of connective tissue (ochronosis)
damage to joint cartilages, arthritis
pigmented spots on the sclera and ears

53
Q

treatment for alkaptonuria:

A

restricted intake of phenylalanine and tyrosine

in an effort to decrease homogentisate and dark pigmentation

54
Q

what causes maple syrup urine disease (MSUD)?

A

disorder of the branched chain amino acids (leucine isoleucine, and valine)
absent or deficient branched chain a-ketoacid dehydrogenase (BCKAD)
leads to accumulation and urine excretion of branched chain AAs

55
Q

characteristics of MSUD:

A

within 1 week of birth: lethargy, vomiting, aversion to food

followed by severe brain damage and ultimately death

56
Q

treatment for MSUD:

A

exclusion of branch chained AAs from diet followed by a restricted diet
some patients are responsive to thiamine (B1) along with the restricted diet

57
Q

what is the milder variant of MSUD?

A

intermittent branch chain ketonuria
decrease in the BCKAD enzyme is only moderate
symptoms are milder and occur much later
the excretion of branch chained AAs is increased intermittently

58
Q

what causes homocystinuria?

A

occurs in the metabolism of methionine into cysteine
methionine —> homocysteine —-> cysteine
severely deficient in cystathionine synthetase

59
Q

what are the effects of homocystinuria?

A

urinary excretion of homocysteine is increased
plasma methionine and homocysteine are increased

clinical features:
thrombotic phenomena, osteoporosis, dislocation of lenses, mental retardation, ischemic vascular disease

accumulation of homocysteine causes:
abnormal cross linking of collagen (causes ocular lens dislocation, osteoporosis)
abnormalities in the ground substance of blood vessel walls
increased platelet adhesiveness

60
Q

what does thrombotic phenomena (in homocystinuria) lead to?

A

abnormalities in the blood vessel walls and increased platelet adhesiveness:

ischemic heart disease
cerebral thrombosis
peripheral vascular disease

61
Q

what is the treatment for homocystinuria?

A

low methionine, high cysteine diet

pyroxidine (Vit B6) supplements –> helps activate the residual cystathionine synthetase

62
Q

what vitamin deficiencies can lead to hyperhomocysteinemia?

A

folic acid
B12

treatment: supplements of these vitamins

**betadine and vitamin B12 promote the conversion of homocysteine back to methionine

63
Q

what causes cystathioninuria?

A

deficiency of cystathionase

converts cystathionine —-> cysteine

64
Q

what are the effects of cystathioninuria?

A

none, it is a benign condition

65
Q

what is the cause of histidinemia?

A

inborn error of histidine metabolism

histidase is deficient (histidine —> urocanic acid/urocanate)

66
Q

what are the effects of histidinemia?

A

increased histidine concentration in the plasma and increased metabolite excretion

most patients do not have symptoms
1% exhibit behavioral problems, learning disabilities, and intellectual disabilities (usually happens when the babies are exposed to perinatal hypoxia)

67
Q

what are the differences of prokaryotic and eukaryotic mRNA?

A

prokaryotes: polycistronic (mRNA can encode for multiple genes), non compartmentalized, naked 3’ and 5’ ends
eukaryotes: monocistronic (mRNA encodes for one gene), transcription (nucleus) and translation (cytoplasm) are compartmentalized, have a 5’ cap and a polyA 3’ end

both are processed differently

68
Q

in what direction does RNA read the template strand?

in what direction does the RNA synthesize the complimentary RNA strand?

A

reads 3’ to 5’

synthesizes 5’ to 3’

69
Q

what are the main, 4 consensus sequences of RNA splice sites?

A
  1. 5’ splice site donor (GU)
  2. 3’ splice site acceptor (AG)
  3. branch point A
  4. polypyridine stretch
70
Q

what are the steps of mRNA splicing?

A
  1. 5’ splice site is broken off of the exon and connects with the branch point A, forming an intron lariat
  2. the 3’ splice site end breaks off of its exon
  3. the intron piece is discarded and the exons are ligated together
71
Q

where does RNA splicing occur?

A

in the splicesome (in the nucleus)

72
Q

what are the functions of poly A tail binding to poly A binding protein?

A
  1. mRNA stability
  2. neucleosytoplasmic transport
  3. translational efficiency
73
Q

what are the 2 possibilities for RNA editing?

A

cytosine to uridine

adenosine to inosine

74
Q

what structural components of the mRNA is important in nucleocytoplasmic transport?

A

cap
poly A tail
hnRNP proteins

75
Q

what are the 3 types of mRNA decay?

A
  1. deadenylation dependent: remove poly A tail, degrades from 3’ end
  2. deadenylation independent: remove 5’ cap, degrades from 5’ end
  3. endonuclese mediated: cut and degrade from middle of the strand
76
Q

list some naturally intronless genes:

A

herpes simplex virus thymidine kinase (TK)
human c-jun
histone genes

77
Q

what are the steps of RNA interference (RNAi) or post-transcriptional gene silencing?

A
  1. dsRNA (common to viruses) is recognized and “diced” up by DICER
  2. the dsRNA is now a bunch of small pieces, or small interfering RNAs (siRNA)
  3. siRNA is recognized by the RISC complex and the siRNA fragment associates with argonaute
  4. then that same exact sequence is found in the host genome and is degraded
  5. in the case of a virus, the RNA viral genome is degraded and infection is stopped
78
Q

what is an snRNP?

A

small nuclear ribonucleoprotein

combine with pre-modified RNA in the splicesome and facilitates splicing

79
Q

what is the role of hnRNP in alternative splicing?

A

binds to ISS and ESS (intron and exon suppressor sequence)

blocks snRNPs from facilitating splicing

80
Q

what is the role of SR in alternative splicing?

A
  • binds to ISE and ESE (enhancer regions)

- increases snRNP activity, increases splicing

81
Q

smooth ER is extensively developed in which tissue types?

A 
skeletal muscle 
liver hepatocytes 
renal tubules 
testes
ovaries
82
Q

what types of proteins are synthesized by membrane-bound ribosomes?

A

secreted proteins
lysosomal proteins
integral membrane proteins

83
Q

what type of proteins are synthesized by free ribosomes (in the cytosol)?

A

proteins destined for the cytosol: glycolytic enzymes, cytoskeletal proteins
peripheral proteins in the inner plasma membrane surface (spectrins, ankyrins)
nuclear proteins *
proteins incorporated into peroxisomes and mitochondria *

*imported post-translationally across the organelle membrane

84
Q

what is N-glycosylation?

A

a process that most proteins produced from membrane-bound ribosomes undergo
addition of a 14 carbon sugar to the nascent peptide
occurs co-translationally (occurs simultaneously with translation)

85
Q

what is the purpose/effects of N-glycosylation in glycoproteins?

A
  • serve as binding sites in interactions with other macromolecules
  • aid in proper protein folding
86
Q

what is the 2-3 consensus sequences needed for N-glycosylation?

A

Asn-X-Ser
Asn-X-Thr

but X CANNOT = Proline

87
Q

what is the name of the enzyme that transfer the 14C sugar onto the nascent polypeptide chain (N-glycosylation)?

A

oligosaccharyltransferase

88
Q

what is the name of the lipid carrier embedded in the rough ER membrane that is required for glycosylation? (flips the sugars over the membrane so that they can be added)

A

dilochol phosphate

89
Q

what sugars comprise the 14C sugar that is added in N-glycosylation?

A

3 glucose
9 mannose
2 N-Acetylglucosamine (NAG)

90
Q

what is O-glyosylation?

A

the 14C sugars that are attached to proteins during N-glycosylation are modified, made more complex

removal of 3 glucose and various mannose molecules

new sugars are added via glycosyltransferases (in the golgi)

91
Q

oligosaccharides are attached to what amino acids and what function group?

A

O linked = OH (hydroxyl groups)

added to the hydroxyl grounds of serine and threonine
Asn X Ser
Asn X Thr

92
Q

what is the name of the enzyme that phosphorylates the mannose of lysosome destined proteins?

A

N-acetylglucosamine-1-phosphotransferase (GlcNAc-1PT)

  • phosphorylates the mannose
  • yields mannose-6-phosphate
  • which is recognized by M6P receptors
93
Q

what causes I cell disease?

A

autosomal recessive lysosomal storage disorder
defect in the N-acetylglucosamine-1-phosphotransferase (GlcNAc)
therefore, lysosomal enzymes do not acquire the mannose-6-phosphate signal (not recognized by M6P receptors)

result: lysosomal proteins are excreted extracellularly rather than being sent to the lysosome

94
Q

characteristics of I-cell disease:

A

coarse facial features, clouded corneas restricted joint movements, high plasma levels of lysosomal enzymes

often fatal in childhood because as these inclusion bodies accumulate, they compromise the cell’s functions

95
Q

list the steps of nuclear localization of proteins?

A
  1. protein contains a nuclear localization signal (NLS), often times involves one or more short sequences of positively charged arginine or lysine on protein surface
  2. NLS recognized by Importin
  3. binds to a receptor on the nuclear envelop and allows them to move through via nuclear pore
  4. Importin dissociates from the protein cargo via a GTP dependent process
96
Q

what is an NLS?

A 
nuclear localization signal 
many types (e.g. short sequence of positively charged arginines or lysines on protein's surface)
recognized by importin (carries protein cargo into nucleus through nuclear pore)
97
Q

what is the process for importing mitochondria-destined proteins inside the mitochondria?

A
  1. proteins have an N-terminal mitochondrial import sequence
  2. proteins remains in a folded conformation as it binds to a chaperone protein
  3. chaperone brings it to the TOM (translocase of outer mitochondrial membrane)
  4. TOM transports it across the outer membrane where they come in contact with TIM
  5. cross over via TIM’s help and move into the matrix
98
Q

what is the signaling sequence that allows proteins that are destined to be peroxisomal proteins to move into the peroxisome?

A

C-terminal tripeptide

99
Q

what are the 3 protein quality control mechanisms?

A
  1. chaperone system
  2. ubiquitin-proteasome system
  3. autophagy-lysosomal pathway
100
Q

what are heat shock proteins?

A

molecular chaperones whose synthesis increases dramatically in response to stress (e.g. increasing temp, increased number of misfolded proteins)

101
Q

what is common for all chaperone proteins?

A

operate in the cytosol of eukaryotic cells
recognize exposed hydrophobic patches or incompletely folded proteins
hydrolyze ATP

102
Q

summarize function of Hsp70 family of chaperones

A

act before the protein leaves the ribosome
aided by smaller Hsp40 co-chaperone proteins
promote protein refolding using a series of ATP dependent “hold” and “fold” cycles

103
Q

summarize hsp60 family of chaperones (chaperonin)

A

act after a protein has been fully synthesized
form a large barrel shaped structure with hydrophobic binding sites
-prevents protein aggregation
-isolates protein in an enclosed space where it can fold
has a GroES cap
ATP + GroES cap increase barrel diameter, allowing the protein to fit
after ~15s, ATP is needed to release the now folded protein

104
Q

what are the diseases caused by protein misfolding?

A

Amyotrophic Lateral Sclerosis (ALS) – SOD1 mutant aggregates

Creutzfeld-Jakob (CJD) – prion protein aggregates

Alzheimer’s – extracellular amyloid-B peptide

Parkinson’s – alpha-synuclein intracellular aggregates

Huntington’s – expansion of huntingtin polyQ domain prone to aggregation

105
Q

if a protein cannot be repaired by the chaperone systems, it can be degraded via…

A

cytosolic ATP dependent pathway (proteosome/ubiquitin)

  • short half lives
  • defective proteins
  • damaged proteins
  • metabolic enzymes

lysosomal pathway

  • long half lives
  • membrane proteins
  • extracellular proteins
106
Q

what are the 3 pathways to degradation via lysosomes?

A
  1. endocytosis
  2. autophagy
  3. phagocytosis
107
Q

which proteins are targeted for autophagy during periods of starvation?

A

Phe, Lys, Glu, Arg, Gln

“Please let’s get apples, girl.”

108
Q

what are the 2 components of the proteasome?

A
  1. 20 S catalytic core

2. 19 S regulatory particles

109
Q

what is the name of the chaperone required for the assembly of the proteasome 20S catalytic unit?

A

Ump1

110
Q

functions of the 19S regulatory particle?

A

multi Ub binding and disassembly
substrate unfolding / binds regulatory proteins (unfoldases)
regulates axial channel

111
Q

describe lysosome structure:

A

highly compact
7 lysine resides on the surface (for ligating to other Ubs)
highly reactive, carboxy terminus ARG- GLY -GLY (Gly 76)
small hydrophobic patches on the surface

112
Q

what are the 3 key enzymes that promote covalent attachment of Ub to proteolytic substrates?

A

E1: Ub activating enzyme
E2: Ub conjugating enzyme
E3: Ub protein ligase

113
Q

how many ubiquitins are needed in a chain to promote substrate degradation?

A

4 or more

114
Q

which lysine is involved in Ub-Ub linkages?

A

lysine 48 (K48)

115
Q

what part of the polyubiquitin chain is the primary determinant for promoting interaction with the proteasome?

A

hydrophobic stripe

116
Q

What are the PEST proteins, dictated by the N-end rule?

A

Pro (P), Glu (E), Ser (S), Thr (T)

117
Q

senescent vs. quiescence

A

senescent cells permanently cease dividing due to DNA damage or age

quiescent cells temporarily stop dividing and enter G0

118
Q

what is the restriction checkpoint? where is it located in the cell cycle?

A

in the G1 phase
relies on external stimuli and growth factors
determines if the cell should enter cell cycle
cannot turn back once it passes this point

119
Q

what is the normal function of a tumor suppressor gene?

A

normally function to halt cells from continuing past the restriction point if growth is not needed or if the DNA is damaged

mutated tumor suppressor genes – allow cells to continue past checkpoint when it is not appropriate (e.g. cancer cells)

120
Q

what is retinoblastoma protein (RB)?

A

tumor supressor gene

mutated version – leads to eye malignancy called hereditary RB, unable to halt cell cycle in G1

121
Q

how does RB prevent cell cycle progression from G1 into S?

A

in resting cells, RB typically contains very few phosphorylated AA residues
binds transcription factor E2F and its binding partner DP1/2 (they are critical for the G1/S transition)

RB can be hyper-phosphorylated by cyclin D - CDK 4/6 (and further by cyclin E - CDK 2) in which it dissociates from the DNA and promotes cell progression into the S phase

122
Q

cyclin dependent kinase inhibitors (CDK inhibitors)

A

INK4A – inhibit D type cyclins (prevent CD4/6 activation)

CIP/KIP – inhibit CDK2 kinases (includes p21)

123
Q

function of CDK1

A

CDK1 controls entry into mitosis

phosphorylated (inactive)

phosphate removed by cdc25c, allowing it to bind to cyclin B

CDK1-cyclin B moves into the nucleus and activates mitosis by phosphorylating key components of sub-cellular structures (e.g. microtubules)

cell cycle must be suspended? cdc25c can be inactivated via tumor supressors, ATM and ATR

124
Q

what are ATM and ATR?

A

tumor suppressors that inactivate cdc25c (removes phosphate from CDK1, rendering it active)

ATR - responds to double strand DNA breaks (ionizing radiation)
ATM - mediating UV induced DNA damage, secondary role in response to double strand breaks

POM (6 decks)

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