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Biochemistry 1 > Amino Acids & Protein (midterm) > Flashcards

Amino Acids & Protein (midterm) Flashcards

1
Q

What are amino acids involved in?

A

-cellular metabolism (enzymes)
-precursors of various biologically active compounds like neurotransmitters and hormones

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2
Q

What are zwitterions?

A

amphoteric electrolytes
-its a neutral molecule with a positive and negative electrical charge
-neutral amino acids with 2 charges that cancel each other out

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3
Q

Acids are proton _________

A

donors

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4
Q

Bases are proton __________

A

acceptors

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5
Q

What are the different major categories of R groups?

A

-nonpolar
-polar (neutral, acidic, or basic)

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6
Q

What are characteristics of nonpolar R groups (think definition)?

A

-do not gain or lose protons or form H bonds
-hydrophobic and neutral
-in aqueous solutions, those side chains tend to cluster in the interior (wanted to be buried in the protein)
-CH or CC bonds

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7
Q

What are the 3 types of polar R groups?

A

1) neutral (side chains are hydrophilic but have no charge at physiological pH (7/neutral, pka is 7), participates in hydrogen bonds, ex: R group with OH)
2) acidic (at physiological pH (pka < 7), the side chains are ionized with a negatively charged carboxylate group (COO-))
3) basic (side chains accept protons (H+), at physiological pH (pka > 7) the side chains are ionized and positively charged, ex: side chains with NH2)

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8
Q

Which AA is important for collagen production?

A

glycine

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9
Q

What is the most abundant protein in the body?

A

collagen (glycine is needed to make collagen, and so 1/3 of our AAs in body are glycine)

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10
Q

What are chiral carbons?

A

alpha carbons that have a D and L form, and have 4 different attachments

SO, glycine is the only achiral AA bc it does not have 4 different groups attached, and so it also does not have D and L form bc of this

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11
Q

What does aliphatic mean?

A

linear (only CH bonds)

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12
Q

What are the 3 different nonpolar AAs groups?

A

-aliphatic or branched chain AAs
-aromatic
-sulfur containing AAs

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13
Q

What are the 3 nonpolar aliphatic AAs?

A

-glycine
-alanine
-proline

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14
Q

What is the simplest AA?

A

glycine

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15
Q

What AA is this?

A

glycine/gly

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16
Q

What happens to alanine if the amino group is removed?

A

it becomes an alpha ketoacid and the NH2 will be replaced with H

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17
Q

What is the side chain on alanine?

A

methyl group (CH3)

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18
Q

Which AA is closely linked with pyruvate? Why?

A

alanine

If alanine is broken down, it will make pyruvate

note: pyruvate makes glucose
-this is called gluconeogenisis (making new glucose that is not from carbs, glycogen to glucose is NOT gluconeogenisis)
-glycogen only maintains blood glucose levels for up to 12 hours, usually overnight, after that gluconeogenisis is used

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19
Q

What AA is this?

A

alanine/ala

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20
Q

Is proline aromatic?

A

no, its cyclic

and bc its cyclic it will form a kink when it binds to other AAs in peptide chain

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21
Q

What AA is this?

A

proline/pro

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22
Q

What are the 3 branched chain AAs (BCAAs)?

A

valine, leucine, and isoleucine

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23
Q

What AA is this?

A

valine/ val

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24
Q

What AA is this?

A

leucine/ leu

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25
Q

What AA is this?

A

isoleucine/ ile

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26
Q

What happens to BCAAs if you remove the amino group?

A

it will be converted to a branched chain alpha keto acid, which is good for heart muscle and performance especially in athletes (if theres a deficiency then it can lead to heart failure)

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27
Q

What is maple syrup urine disease?

A

-enzyme deficiency that increases branched chain alpha keto acids
-causes vomiting, brain damage, and eventually death
-high conc. of branched chain alpha keto acids will make urine smell like rotten maple syrup
-treatment is to avoid BCAAs, aka high quality proteins (animal products)
-newborn screening is done to prevent brain damage and death
-this is genetic when found in children, but can also be found in adults and at this point its usually associated with a high protein diet

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28
Q

Are all vitamins essential?

A

YES

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29
Q

What are the 2 nonpolar neutral aromatic AAs?

A

phenylalanine and tryptophan

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30
Q

What are the 3 aromatic AAs?

A

1) phenylalanine (nonpolar neutral)
2) tryptophan (nonpolar neutral)
3) tyrosine (polar neutral)

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31
Q

Which 2 aromatic AAs are essential?

A

phenylalanine and tryptophan (both are nonpolar neutral as well)

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32
Q

What AA is this?

A

phenylalanine/ phe

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33
Q

What AA is this?

A

tryptophan/ trp

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34
Q

What is the largest AA?

A

tryptophan/ trp

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35
Q

Which AA is a precursor for niacin (vitamin B3)?

A

tryptophan/ trp

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36
Q

Which AA can be used to make serotonin?

A

tryptophan/ trp (so lack of trp can cause depression)

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37
Q

Which AA can synthesize vitamin D from sunlight?

A

tryptophan/ trp

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38
Q

What are the 2 nonpolar neutral AAs with sulfur containing side chains?

A

cysteine and methionine

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39
Q

Which AA has a thiol group attached?

A

cysteine (which also means its an antioxidant)

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40
Q

What AA is this?

A

Cystine/Cys

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41
Q

What 2 AAs provide 100% of the sulfur in our body?

A

cysteine and methionine

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42
Q

Is sulfur abundant in the body?

A

yes, 3rd most abundant (1st is calcium and 2nd is phosphate)

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43
Q

Which AA initiates protein synthesis?

A

methionine

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44
Q

What AA is this?

A

methionine/ met

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45
Q

Which AAs face the water?

A

polar AAs

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46
Q

Which AAs fold/try to hide away inside of the protein?

A

nonpolar AAs

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47
Q

T/F: usually AAs with OH are neutral

A

true

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48
Q

What are the 3 polar neutral AAs with OH in the side chain?

A

serine, threonine and tyrosine (this means phosphate can bind to any of these and make an enzyme easily)

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49
Q

What AA is this?

A

serine/ ser

50
Q

What AA is this?

A

threonine/ thr

51
Q

What AA is this?

A

asparagine/ asn

52
Q

What AA is this?

A

glutamine/ gln

53
Q

What is the most abundant AA in the blood?

A

glutamine

54
Q

What is the difference between tyrosine and phenylalanine?

A

OH group!

phenylalanine can make tyrosine

55
Q

What AA is an important precursor for catecholamines (dopamine, epi, NE)?

A

tyrosine

56
Q

What are the 5 polar neutral AAs?

A

1) serine
2) threonine
3) asparagine
4) glutamine
5) tyrosine

note: they all have a side chain that contains OH bond OR CO-NH2 bond

57
Q

What are the 5 polar charged AAs?

A

1) lysine
2) arginine
3) histidine
4) aspartate (aspartic acid)
5) glutamate (glutamic acid)

58
Q

What are the 3 basic/positively charged (protonated) polar AAs?

A

1) lysine
2) arginine
3) histidine

59
Q

Which enzyme is used to add OH to make tyrosine?

A

phenylalanine hydroxylase

60
Q

Which AA helps with oxidative stress?

A

cysteine bc its an antioxidant bc of the thiol group in side chain

61
Q

Which AA is this?

A

tyrosine/ tyr

62
Q

What AA is this?

A

lysine/ lys

63
Q

Which AA is a precursor for NO?

A

arginine

64
Q

Which AA is a precursor for urea?

A

arginine

65
Q

Which AA is a precursor for histamine/inflammation?

A

histidine

66
Q

Which AA is this?

A

arginine, arg

67
Q

Which AA is this?

A

histidine/ his

68
Q

Histones are basic. Why?

A

rich in lysine and arginine

69
Q

Is DNA basic or acidic?

A

acidic bc of the phosphate backbone

70
Q

What are the 2 acidic/ negatively charged (deprotonated) polar AAs?

A

1) aspartate (aspartic acid)
2) glutamate (glutamic acid)

71
Q

Aspartate can make asparagine. How?

A

add an amino group to aspartate

72
Q

What AA is this?

A

aspartate/ asp

73
Q

Glutamate can make glutamine. How?

A

add an amino group to glutamate

74
Q

Which AA is a neurotransmitter activator/stimulatory neurotransmitter?

A

glutamate

75
Q

What happens if glutamate is decarboxylated?

A

will become GABA, which is an inhibitory neurotransmitter

76
Q

What AA is this?

A

glutamate/ glu

77
Q

Which 2 AAs are ketogenic (cannot make glucose)?

A

lysine and leucine

ALL OTHER AAs ARE GLUCOGENIC, NOT KETOGENIC

78
Q

What are the 10 essential AAs?

A

-phenylalanine
-valine
-threonine
-tryptophan
-isoleucine
-methionine
-histidine
-arginine
-leucine
-lysine

PVT TIM HALL

79
Q

Which 8 AAs are essential all the time?

A

-phenylalanine
-valine
-threonine
-tryptophan
-isoleucine
-methionine
-leucine
-lysine

80
Q

Which 2 AAs are conditionally essential, only during positive nitrogen balance?

A

histidine and arginine

81
Q

Which 3 amino acids do kinase modification (addition of phosphate group)?

A

serine, tyrosine, and threonine

82
Q

define nitrogen balance

A

the normal condition in which the amount of nitrogen entering the body everyday equals the amount excreted

83
Q

Define negative nitrogen balance

A

occurs when nitrogen loss exceeds nitrogen intake (less N in, more N out) and is associated with the following:
-protein malnutrition (kwashiorkor)
-dietary deficiency of 1+ essential AA (body will breakdown existing proteins to try to find essential AAs it needs)
-starvation (maramus, no carbs, lipids, or proteins in food, body eats itself, body muscles are breaking down)
-uncontrolled diabetes (insulin is low in diabetes and the body thinks you’re not eating so it will make more glucose even if you have a bunch, so insulin injections are needed to stabilize)
-infections

84
Q

define positive nitrogen balance

A

occurs when the amount of nitrogen intake exceeds the amount excreted (more N in, less N out) and is associated with the following:
-growth (usually in children, kids create more proteins for growth)
-pregnancy
-recovery phase of injury or surgery (regain muscles, muscles increase because the change of AAs into protein through DNA replication, transcription, and translation)
-recovery from any negative nitrogen balance

85
Q

What is the cause of pellagra?

A

niacin (vitamin B3) or tryptophan deficiency

86
Q

Who commonly has pellagra?

A

people who obtain most of their food energy from maize, usually in rural parts of South America

87
Q

What are the 4 Ds of pellagra?

A

-diarrhea
-dermatitis
-dementia
-death

88
Q

Is pellagra easy to treat?

A

yes

89
Q

What is the treatment for pellagra?

A

-tryptophan rich foods like meat, fish, and eggs
-take nicotinamide (a type of vitamin B3)

90
Q

Wheat and rice are low in which AAs?

A

lysine and isoleucine

91
Q

Maize is low in which AAs?

A

tryptophan and lysine

92
Q

Vegetables, pulses, and legumes are low in which AAs?

A

methionine and tryptophan

93
Q

What are the 2 types of protein?

A

high quality protein
-contains all/is an abudnance of all essential AAs
-animal proteins like eggs, meat, fish

low quality protein
-lacking some essential AAs
-plant based proteins

94
Q

Grains are low in which AAs?

A

lysine and isoleucine

95
Q

T/F: Peanuts are considered legumes, so a PB&J sandwich will give you all the essential AAs

A

true!

legumes are low in met and trp
grains are low in lys and ile

so together, you get the essentials you need

96
Q

Nuts are low in which AAs?

A

lysine and isoleucine

97
Q

Do fruits have AAs?

A

no

98
Q

Does maize/corn have AAs?

A

no

99
Q

Which AA is toxic to PKU patients?

A

phenylalanine

100
Q

Which AA is non-essential but becomes essential for PKU patients?

A

tyrosine

101
Q

What causes phenylketonuria (PKU)? What is it?

A

-genetic mutation that causes a deficiency in phenylalanine hydroxylase (PAH), which is the enzyme that converts phenylalanine to tyrosine
-phenylalanine builds up in the brain which causes mental retardation, seizures, and death
-newborn screening is done to avoid death

102
Q

What should PKU patients avoid?

A

artificial sweetener like aspartame bc it contains phe+asp

so PKU patients should avoid anything sugar free

103
Q

What is the tx for PKU?

A

low phe diet with some tyr intake

104
Q

Which AA is a precursor for thyroid hormones T3 and T4?

A

tyrosine

105
Q

Which AA is a precursor for melanin?

A

tyrosine

106
Q

What is kwashiorkor? What is it caused by?

A

-due to negative nitrogen balance
-pt eats lots of carbs and lipids, but none, or not enough protein
-common in developing countries
-will result in low albumin (which is a protein in blood that keeps osmotic pressure), and causes big belly because of fluid in abdominal cavity (fluid will go to all the tissues and cause edema because of lack of albumin)
-will also result in low lipoprotein which causes fatty liver

107
Q

What is thyroxine?

A

thyroid hormone T4

108
Q

T/F: thyroid hormones are protein hormones

A

true, bc they’re made from AAs

109
Q

The thyroid gland produces thyroxine (T4). How?

A

by attaching iodine atoms to the ring structure of tyrosine molecules

thyroxine contains 4 iodine atoms (note: triodothyronine T3 is identical to thyroxine but has only 3 iodine atoms per molecule)

110
Q

What foods have high iodine?

A

seafood and salt

111
Q

Glutathione (GSH) is an important antioxidant created by the body. What does it do?

A

GSH is a tripeptide that is biosynthesized in the body from cysteine, L-glutamic acid, and glycine

the sulfhydroyl group SH of cysteine serves as a proton donor and is responsible for it biological activity

2 GSH molecules will react with hydrogen peroxide and make water and GSSG which is the antioxidant

GSSG is made when S-S bond forms called a disulfide bond between 2 cysteines, which is now called a cystine

GSSG prevents damage to important cellular components caused by reactive oxygen species such as free radicals, hydrogen peroxide, lipid peroxides, or heavy metals

112
Q

All AAs in animals are ____ form

A

L

113
Q

What is taurine? Where is it found?

A

-nonstandard AA
-found in bile salts

114
Q

What is hydroxyproline? Where is it found?

A

-nonstandard AA
-hydroxylated proline
-found in collagen

115
Q

What is desmosine? Where is it found?

A

-nonstandard AA
-lysine crosslinked polypeptide (4 lysines linked together)
-found in elastin

116
Q

What is the structure of an AA?

A

an amino group, carboxyl group, hydrogen atom, and an R group

117
Q

AAs are linked together to form peptides with which types of bonds?

A

peptide bonds

118
Q

The amino acids leucine, valine, and phenylalanine would best be described as….
A) polar and uncharged
B) polar and positively charged
C) nonpolar AAs
D) polar and negatively charged

A

C) nonpolar AAs

119
Q

AAs can be described as
A) polar
B) hydrophobic
C) charged
D) uncharged
E) all of the above

A

E) all of the above

120
Q

Of the common AAs, how many as considered essential?
A) 4
B) 8
C) 12
D) 20

A

B) 8

121
Q

A polypeptide chain is polymerized in which direction?

A

amino to carboxyl (N to C terminal)

Biochemistry 1 (12 decks)

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