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FOM: Nutrition > Proteins > Flashcards

Proteins Flashcards

1
Q

How do amino acids/ proteins assist with homeostasis?

A

they have pH and osmotic affects that assist with homeostasis

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2
Q

structural proteins

A

form scaffolds of the extracellular matrix and of chromatin

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3
Q

Membrane Proteins

A

play critical roles in cell signaling

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4
Q

Protein Enzymes

A

foundation of anabolic and catabolic metabolism

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5
Q

Aberrant Proteins

A

are at the heart of multiple diseases

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6
Q

enzyme vs protein malfunction

A

enzyme malfunction = inborn or acquired errors of metabolism

protein malfunction = neurodegenerative conditions and cognitive decline

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7
Q

Name the monomer + examples of:

– proteins

– carbohydrates

– lipids

– nucleic acids

A
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8
Q

amino acids basic structure

A

central alpha carbon

carboxylate

amino group

hydrogen

side chain R

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9
Q

Henderson-Hasselbach equation

A

pH = pKa + log[conjugate base/ conjugate acid]

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10
Q

pI of a protein depends on

A

the distribution of R groups

– this is because amide bonds between NH3 and COOH groups eliminate their ability to ionize

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11
Q

PI Equation

A

pI = [pKa (COOH) + pKa (NH3)]/2

– this is for a non-ionizable group R

– about 5.5 for a non-ionizable group R

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12
Q

buffering capacity of amino acids and proteins

A

+/- 1

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13
Q

protein charge based on pH and PI

A

pH > pI = protein charge negative

pH < pI = protein charge positive

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14
Q

CO2/ Bicarbonate balance

A

blood pH is determined by the henderson-hasselbach equation and CO2/ bicarbonate play an important role in buffering capacity

– dissolved CO2 = conjugate acid & dissolved HCO3 = conjugate base

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15
Q

Electrophoresis

A

done at a pH of 8.6

major plasma proteins separated based on charge differences → migrate towards anode

alterations in normal electrophoretic pattern = stress, trauma, infection, or autoimmune disorder

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16
Q

acidosis and alkylosis

A

blood levels of CO2 and bicarbonate = critical factors in maintaining normal blood pH (normal = 7.4)

acidosis and alkylosis = serious complications of metabolic or respiratory imbalance → can cause decrease or increase in blood bicarbonate

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17
Q

ionization of drugs affect

A

it’s oral ability, ability to cross placenta/ blood, and ability to cross the blood brain barrier

drug in a unionized (neutral state) is membrane permeable, but a charged drug is not

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18
Q

neutral form of weak acidic/ basic drug

A

neutral form of weak acidic drug = conjugate acid

neutral form of weak basic drug = conjugate base

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19
Q

what is critical for protein folding

A

the side chains R of amino acids that form a protein

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20
Q

hydrophobic vs hydrophilic protein formation

A

hydrophobic proteins = interior of globular proteins while hydrophilic proteins = exterior because they can form intramolecular hydrogen bonds and have interactions with water molecules

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21
Q

R groups determine what for an enzyme

A

dictates the specificity of enzyme active sites for the substrate

ex: cysteine = disulfide bonds and proline = break up helix

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22
Q

hierarchy of protein formation

A

primary structure - amino acid sequence

secondary structure = polypeptide chain interactions (alpha/Beta sheets)

tertiary structure = side chain interactions

quaternary = higher order structures → association of proteins into multimers or fibrils

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23
Q

neurodegenerative diseases occur when

A

a normally globular protein misfolds = exposes hydrophobic residues that cause aggregation and formation of amyloid fibrils or neurofibrillary tangles

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24
Q

Alzheimers

A

globular proteins misfolded

AB-42 peptide

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25
Q

Frontotemporal dementias

A

globular protein misfold

tau protein

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26
Q

transmissible spongiform encephalopathies

A

globular protein misfold

– prion protein (PrP)

normal functioning PrP = alpha helix; an increase in B-sheet content occurs because of either a mutation in PrP = less stable alpha helix or because of propagation through an infectious B-sheet rich Prp (prion)

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27
Q

reasons for an increase in beta sheets in transmissible spongiform encephalopathies

A
  1. mutation in PrP creating a less stable alpha helix
  2. self propagation through an infectious Beta-sheet rich PrP → known as a prion
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28
Q

stabilization of B-sheets in prion

A

interlocking hydrogen bonds help stabilization the propagation of B-sheet structure

prions = oligomers

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29
Q

misfolded proteins depending on they type

A
  1. amyloid plaques
  2. neurobirillary tangles
  3. intraceullalar inclusions (Lewy or pick bodies)
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30
Q

triple helix in collagen distorted by

A

mutations in glycine →leads to osteogenesis imprefecta

– need glycine for most defining feature of collagen, which is the triple helix

normal sequence: Gly-Pro-Pro/HyP

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31
Q

(severe) anemia genomic cause

A

a single glutamate to valine mutation at position 6 on the Beta-globin chain renders homoglobin less soluble

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32
Q

(mild) sickle cell anemia genomic causes

A

glutatmate to lysine mutation at position 6

– lysine chain does not affect aggregation (like Valine does)

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33
Q

cystic fibrosis genomic causse

A

F508 mutation = mutant of cystic fibrosis transmembrane receptor

CFTR is misfolded and directed towards proteosomes instead of the cell membrane = cyststic fibrosis

– many examples of specific point mutations + examples of heterogenous mutations in protein sequences that give rise to the disease

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34
Q

allostery

A

small molecule modulators binding to one subunit of a multimer = can trigger a conformational change in other subunits

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35
Q

taut vs relaxed

A

allosteric proteins and enzymes can adopt a relaxed form = high affinity for substrate

taut form = low affinity for substrate

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36
Q

hemoglobin

A

a2B2

– four highly helical subunits and 4 heme groups

– binding of one O2 molecule induces a structural change in neighboring subunits that increases their oxygen affinity

– leads to a sigmoidal O2 binding curve

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37
Q

allosteric affectors of hemoglobin

A

CO2, H+, 2-3-BPG allosteric effectors that stabilize the taut (low) affinity conformer = causes oxygen release

CO binding to the O2 binding site stabilizes the relaxed conformation = prevents oxygen release

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38
Q

heterotropic vs homotropic effectors

A

heterotropic: bind at a different site from substrate
ex: CO2, H+, and 2,3 BPG bind a different site than O2 in hemoglobin
homotropic: bind at the same site as the substrate
ex: CO binds at the same site as O2 in hemoglobin

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39
Q

model of hemoglobin binding

A

hemoglobin is allosterically affected = higher affinity with more oxygen binding

relaxed form = when CO2, H+ or 2,3-BPG bind → leads to release of oxygen

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40
Q

sigmoidal O2 curve - hemoglobin

A

binding of one O2 molecule = structural change in neighboring subunits and increases their oxygen affinity

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41
Q

Bohr equations for hemoglobin

A

HbO2 + H2 ←→ HbH O2

HbO2 + 2,3-BPG ←→ Hb-2,3-BPG + O2

Hb-NH2 + CO2 ←→ Hb-NH-COO + H+

more acidic = release more O2

more CO2 = release O2 (makes sense as hemoglobin goes through tissue = want to release O2)

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42
Q

hypoxia effects on hemoglobin

A
  1. hypoxia will cause increased levels of 2-3-BPG to compensate for oxygen deficiency
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43
Q

hyperventilation effect on hemoglobin

A

hyperventilation causes alkylosis (body not able to get out enough CO2) this raises the pH of the blood

as a result, this will decrease the release of oxygen in the tissues

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44
Q

Carbon monoxide effect on hemoglobin

A

O2 starvation due to tight binding of CO at the oxygen binding site and stabilization of the relaxed conformer

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45
Q

Hemoglobinopathies

A

ex: B-thalassemia and sickle cell disease

these are typically autosomal recessive because one good allele = can make enough protein for normal function

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46
Q

Collagen

A

most abundant protein in the human body (45 collagen genes)

fibrous protein

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47
Q

types of fibrous proteins

A

collegen

elastic

fibrillin

alpha-keratin

tropomyosin

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48
Q

Type I - Type IV collagen

– component of

A
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49
Q

Collagen abnormalities can cause?

A

aortic and arterial aneurisms

heart valve malfunction

bone fragility

skin distensibility

poor wound healing

joint problems

dislocation of the lens

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50
Q

hallmark of collagen

A

is a triple helix formed by association of 3 polyproline helices (alpha chains)

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51
Q

polyproline helices of collagen

A

alpha chains; these give collagen it’s tensile strength

may be homotrimers of same gene product or heterotrimers formed by association of different gene products

(Gly-X-Y)n

(X= Proline, Y= Hydroxyproline)

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52
Q

role of glycine in collagen

A

glycine only has H as it’ R group = allows the central core of the helix to be tightly wound

– glycine makes up the central core of the helix

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53
Q

Proline and Lysine contribution to collagen

A

Hydroxylated Proline (Hyp) and Hydroxylated Lysine (Hyl) = hydroxylate version of Pro and Lys

they contribute toward teh triple helix strength through hydrogen bonds on the outside of the polyproline helices

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54
Q

prolyl hydroxylsae

A

proline → hydroxyproline

cofactors: vitamin C & Fe2+

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55
Q

lysyl hydroxylase

A

lysine → hydroxylysine

cofactors: vitamin C & Fe2+

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56
Q

lysyl oxidase

A

collagen microbrils formed by 5 interlaced tripe helices that are stabilized by covalent crosslinks synthesized by lysyl oxidase

cofactors: vitamin B6 & Cu2+

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57
Q

collagen disorders are ___

A

autosomal dominant

due to dominant negative effect

– mutated alpha chains distort the triple helix and higher order structure even if two of three alpha chains are normal

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58
Q

2 types of autosomal collagen disorders

A
  1. dominant negative effect
  2. null mutation (no collagen produced from that gene)
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59
Q

tropocollagen molecules

A

arranged in sets of five staggered helices

– supported by covalent crosslinking → known as collagen microfibril

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60
Q

collagen microfibril

A

5 staggered helices supported by covalent cross linking

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61
Q

collagen fibril

A

interleaved and interwound collagen microfibrils

collagen fibrils = transversely striated

typically aggregate into collagen fibers = then form bundles and sheaths

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62
Q

which type of collagen is the most vs lease heavily glycosylated

A

type I = least

type IV = most

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63
Q

vitamin C deficiency

A

causes scurvy (lysyl hydroxylase and prolyl hydroxylase of collagen synthesis need vitamin C)

Scurvy = accompanied by bleeding gums and poor wound healing

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64
Q

Menkes disease

A

copper deficiency (lysyl oxidase of collagen synthesis uses this)

manifests as bone and joint deformities

65
Q

what happens with age and collagen

A

increased cross-linking which reduces elasticity and remodeling

66
Q

Osteogenesis Imperfect

A

due to mutations in glycine = critical for tight packing of collagen triple helix

accompanied by brittle bones

67
Q

Ehlers- Danlos syndrome

A

defect in collagen processing enzymes (ex: N/C procollagen peptidase)

mutations in the sequence of collagen genes can also cause this condition

classic form = EDS hyperextensible skin and joints

68
Q

N/C procollagen peptidase

A

cleave of procollagen extensions to form tropcollagen

69
Q

enzymes

A

influence rate of reaction by lower activation energy barrier

sequester substrates into active site

do not alter substrate/ product equilibrium

catalyze reaction in both directions + are regenerated at the end of the rxn

highly specific for substrate

70
Q

clinical significance of enzymes

A

important drug targets

drugs can act as competitive inhibitors

71
Q

cofactors

A

small organic molecules that assist with the chemical reaction catalyzed by the enzyme

72
Q

prosthetic groups

A

may be covalently bound to enzymes and coenzymes = loosly linked

73
Q

substrate vs coenzymes

A

substrate only binds to a specific enzyme but a coenzyme can bind multiple enzymes

– many coenzymes derived from water-soluble vitamins

74
Q

Thiamine

coenzyme, typical reaction, clinical consequence of def

A
75
Q

riboflavin

A
76
Q

Pridyoxine

A
77
Q

Nicotinic Acid

A
78
Q

Pantothenic Acid

A
79
Q

Folic Acid

A
80
Q

Biotin

A
81
Q

Cobalamin

A

(B12)

82
Q

ascorbic acid

A
83
Q

apo vs holo form

A

enzymes that require a cofactor = apo/ holo form

apo = when cofactor not bound

holo = when cofactor bound

84
Q

zymogen

A

inactive precursor of an enzyme

ex: proteases often stored as zymogens as a way to prevent proteolytic cleave of tissues

85
Q

iosenzymes

A

enzymes with equivalent enzymatic function but variations in primary structure and different kinetic parameters

86
Q

creatine kinase

A

2 unit subenzyme with 3 isoforms:

BB (brain)

MB (heart)

MM (heart, skeletal muscle)

87
Q

alcoholics suffer from

A

maladsorption of water soluble vitamins (especially B1, B6, and folic acid)

88
Q

zymogens and anti-proteases critical for

A

regulation of proteolytic cascade in blood clotting and digestion

89
Q

myocardial infarction markers

A

detected by CK and LDH isoenzymes detected by serum electrophoresis

enzymes associated with specific tissues or organs are released into blood plasma following cell death

90
Q

oxidoreductase

A

utilize NAD or FAD electron pool coenzymes = responsible for oxidation and reduction of substrates

91
Q

transferases

A

transfer a chemical group

ex: kinases phosphorylate proteins

92
Q

hydrolases

A

cleave bonds by addition of water

ex: proteases which cleave peptide groups or bonds in a substrate

93
Q

lyases

A

remove water, ammonia, or CO2

94
Q

isomerases

A

rearrange groups or bonds in a substrate

95
Q

ligases

A

use the energy from ATP to join two molecules together

ex: synthases

96
Q

Bcr-Abl tyrosine kinase

A

kinases = important in signal transduction

aberrant Bcr-Abl tyrosine kinase = causes chronic myelogenous leukemia and cyclin-dependent Serine and Threonine kinases which regulate cell cycle check points

97
Q

emphysema due to what imbalance

A

hydrolases in lysosomes break down unwanted cell products = missing or mutated in lysosomal storage disorders

imbalance between proteases and antiproteases in the lungs causes emphysema

98
Q

cirrhosis

A

oxidoreductase alcohol dehydrogenase (ADH) converts ethanol to acetaldehyde which causes cirrhosis of the liver in high quantities

99
Q

allosteric enzymes

A

enzymes that demonstrate cooperative substrate binding

rate-determining steps of allosteric enzymes = sensitive to the concentration of substrates and products

100
Q

drugs using allosteric mechanism

A

finer control over enzyme activity vs competitive inhibitor

101
Q

valium

A

positive allosteric activator of GABA-A receptor

102
Q

mavaricoc

A

CCR5 inhibitor of HIV entry

103
Q

enzyme regulation

A

affected by

  1. compartmentalization
  2. substrate concentration (M-M kinetics)
  3. allosteric regulation
  4. transcriptional regulation of enzyme levels (slow)
  5. hormonal regulation (signal transduction cascade)
  6. covalent regulation (typically phospho/dephosphorylation)
  7. activation of proenzymes (typically requires cleavage of N terminal)
104
Q

competitive inhibition

A

increase of Km

Km = lower enzyme affinity

105
Q

non-competitive inhibition

A

reduces total amount of enzyme available = decrease Vmax

106
Q

uncompetitive inhibition

A

parallel lines on linear-weaver plot

inhibitor binds to enzyme-substrate complex rather than unoccupied enzyme

107
Q

irreversible inhibition

A

enzyme completely inactivated = cannot be recovered

108
Q

nerve gas biochemistry rx

A

irreversible inhibition

organophosphate (nerve gas binds to acteylcholinesterase

109
Q

water-soluble vitamins

A

typically B vitamins

typically precursors of metabolic pathways

easily excreted in urine (not very toxic in high quantities)

110
Q

fat soluble vitamins

A

(vitamin A, D, K, E)

absorbed and transported with dietary fat

not readily excreted

build up in liver and adipose tissue and can be toxic in large quantities

111
Q

minerals

A

classified as electrolytes

large quantities of inorganic ions = dissolved in fluid compartments of the body

112
Q

trace minerals

A

required for specific enzymes and proteins

113
Q

Vitamin C

UL?, common food sources, consequences of deficiency

A
114
Q

Vitamin B1

UL?, common food sources, consequences of deficiency

A
115
Q

Vitamin B2

UL?, common food sources, consequences of deficiency

A
116
Q

Vitamin B3

UL?, common food sources, consequences of deficiency

A
117
Q

Vitamin B6

UL?, common food sources, consequences of deficiency

A
118
Q

Vitamin B9

UL?, common food sources, consequences of deficiency

A
119
Q

Vitamin B12

UL?, common food sources, consequences of deficiency

A
120
Q

Biotin

UL?, common food sources, consequences of deficiency

A
121
Q

Pantothenic acid

UL?, common food sources, consequences of deficiency

A
122
Q

Choline

A
123
Q

water soluble vitamins with an upper limit

A

vitamin C

vitamin b6

vitamin b9

choline

124
Q

vitamin b12 sources only in

A

animal products

125
Q

high doses of vitamin c result in

A

diarrhea and gastroinstestinal problems

126
Q

choline - clinical consideration

A

plays a role in phospholipid structure, neurotransmission (acetylcholine), and methylation

– provides methyl-groups in the form of trimethylglycine (betaine)

127
Q

Vitamin A

UL?, common food sources, consequences of deficiency

A
128
Q

Vitamin K

UL?, common food sources, consequences of deficiency

A
129
Q

Vitamin D

UL?, common food sources, consequences of deficiency

A
130
Q

Vitamin E

UL?, common food sources, consequences of deficiency

A
131
Q

vitamin A oxides to

A

retinoic acid = causes transcriptional activation of specific genes via the retinoic acid receptor → binds to DNA

132
Q

retinoic acid leads to gene expression of

A

keratin and growth and differentiation of epithelial cells

133
Q

retinal and retinol critical for

A

vision cycle

normal reproduction

(retinoic acid cannot carry out functions of retinol and retinal)

134
Q

y-carboxyglutamate

A

good chelators of Ca2+

prothrombin-calcium complexes bind to membrane of damaged endothelium and platelets in the initiation of clotting cascade

135
Q

vitamin D group of __ that acts as:

A

group of sterols that act as hormones by binding to intracellular DNA binding receptors = trigger transcription of genes for regulating plasma levels of Ca2+ and phosphorus

136
Q

excess Vitamin A

A

dry prurotic skin

enlarged liver

137
Q

all-trans retinoic acid can be used for

A

topical agent to treat acne and psoriasis

138
Q

12-cis retinoic acid

A

can be used to treat severe forms of acne

139
Q

Vitamin K made by

A

gut bacteria

140
Q

dose of vitamin k recommended for

excess causes

A

recommended for infants (whose gut is sterile)

prolonged administration of vitamin K (menadione) results in damage to RBC’s

141
Q

excess vitamin D

A

deposition of calcium in organs, especially kidneys and arteries

142
Q

excess vitamin E

A

increase risk of bleeding problems

143
Q

water-soluble vitamins absorbed through

what can affect this?

A

endothelial cells lining the small and large intestine

– intestinal diseases, resection, or chronic alcohol use can effect their absorption and lead to vitamin deficiencies

144
Q

absorption of fat soluble vitamins

A

incorporation into mixed micelles with other lipids and bile acids in the lumen of the small intestine and enter enterocytes through diffusion

– pancreatic insufficiency may be accompanied by a deficit of fat soluble vitamins

145
Q

main electrolytes in the body

A

sodium

potassium

chloride

146
Q

function of main electrolytes in the body

A

sodium, potassium, chloride

– establish gradients across membranes

– maintain water balance

– neutralize charges on proteins and other biomolecules

147
Q

calcium + phosphorous

A

structural components of bones and teeth

calcium also involved in hormone action and blood clotting

148
Q

calcium binding/ regulating enzymes include

A

calmodulin

calbindin

troponin C

calcineurin

149
Q

phosphorus

A

required for production of ATP

phosphorylation important mechanism of enzyme regulation

important buffer

150
Q

magnesium

A

activates many enzymes (including all that use ATP as a substrate)

required for DNA polymerase, many DNA repair enzymes, and stabilization of DNA structure

151
Q

sulfur

A

primary role = amino acid metabolism

ingested in form of cysteine and methionine

152
Q

iron

A

trace mineral

– most abundant trace metal

– important in O2 transport and redox enzymes

153
Q

zinc

A

– second most important trace metal

– reacts with insulin

– cofactor in many enzymes

154
Q

copper

A

essential for processing of connective tissue proteins (collage and elastin) by lysyl oxidase

155
Q

manganese

A
156
Q

manganese

A

involved in enzymes of gluconeogensis

plus protein/ fat metabolism

157
Q

iodine

A

required for synthesis of thyroid hormones

158
Q

molybenum

A

cofactor in xanthine oxidase

159
Q

selenium

A

critical in reduction of oxidized glutathione

FOM: Nutrition (3 decks)

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