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PLE > Biochemistry: Proteins > Flashcards

Biochemistry: Proteins Flashcards

1
Q

How many amino acids are found in mammalian proteins?

A

20

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2
Q

Each amino acid has 3 groups (enumerate) except for (identify)

A

Carboxyl group
Amino group
R group/side chain

Proline
[Amino acids containing a secondary amine group (the only proteinogenic amino acid of this type is proline) are sometimes named imino acids]

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3
Q

Enumerate the non-polar amino acids

A

GAP VW LIMP

Glycine 
Alanine
Phenylalanine
Valine
tWyptophan
Leucine
Isoleucine
Methionine
Proline
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4
Q

Non-polar amino acids
Net charge
Kind of interactions/bonds
Location

A

Zero net charge
Hydrophobic interactions
Interior of the protein

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5
Q

Polar uncharged amino acids
Net charge
Kind of interactions/bonds
Location

A

Zero net charge
Hydrogen bonds
Surface of the protein

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6
Q

Enumerate the uncharged polar amino acids

A

Tired Surgeon Aspirated The Gluteal Cyst, Uncharged

Threonine (-OH)
Serine (-OH)
Asparagine (Amide)
Tyrosine (-OH)
Glutamine (Amide)
Cysteine (-SH)
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7
Q

Charged/Hydrophilic amino acids
Net charge
Kind of interactions/bonds
Location

A

Positive or negative (Acidic or basic)
Forms ionic interactions
Surface of the protein

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8
Q

Enumerate the charged/hydrophilic amino acids

A

The movie Shallow HAL has a POSITIVE message.
Histidine
Arginine
Lysine

Stop being a NEGATIVE ASshole, MATE.
Aspartate
Glutamate

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9
Q

Which AA is this?

Smallest side chain (H)
Synthesis of: heme, purines, creatine,
Conjugated to bile acids, drugs, other metabolites
Major inhibitory neurotransmitter in the spinal cord
No optical isomer
Like alanine, major fraction of AAs in blood

A

Glycine/ Gly/ G

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10
Q

Which AA is this?

Methyl group (CH3)
Carrier of ammonia and carbons of pyruvate from skeletal muscle to liver
Like glycine, major fraction of AAs in blood

A

Alanine/ Ala/ A

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11
Q

Branched-chain AAs whose metabolites accumulate in MSUD

A

Valine/ Val/ V
Leucine/ Leu/ L
Isoleucine/ Ile/ I

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12
Q

Which AA is this?

Accumulates in phenylketonuria
Precursor of tyrosine

A

Phenylalanine/ Phe/ F

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13
Q

Which AA is this?

Largest side chain - indole/bicycle ring
Precursor for niacin, serotonin (5-hydroxytryptamine), melatonin

A

Tryptophan/ Trp/ W

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14
Q

Which AA is this?

Transfer of methyl groups as SAM
Precursor of cysteine and homocysteine (homologues)

A

Methionine/ Met/ M

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15
Q

Which AA is this?

Imino acid
Fibrous structure of collagen
Interrupts alpha helices in globular proteins

A

Proline/ Pro/ P

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16
Q

Which AAs are these?

Have polar hydroxyl group
Site of O-link glycosylation and phosphorylation of proteins
One of them is the precursor of several compounds: Thyroxine, melanin, catecholamines (enumerate pathway)

A

Serine/ Ser/ S
Threonine/ Thr/ T
Tyrosine/ Tyr/ Y

Catecholamine formation:
Pare, True Love Does Not Exist
Phenylalanine –> Tyrosine –> L-Dopa –> Dopamine –> Norepinephrine –> Epinephrine

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17
Q

Which AAs are these?

Have carbonyl group and amide group that can form H bonds
One is the site of N-linked glycosylation of proteins
One is deaminated by glutaminase resulting in ammonia formation, and is a major carrier of N to the liver from peripheral tissues

A

Asparagine/ Asn/ N - N-linked glycosylation

Glutamine/ Gln/ Q - deaminated by glutaminase

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18
Q

Which AA is this?

Has a sulfhydryl group that is an active part of many enzymes
Biosynthesis of coenzyme A
Two cysteines connected by a covalent disulfide bond to form cysteine
Found in keratin (makes hair curly, rebonding breaks cysteine bonds)

A

Cysteine/ Cys/ C

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19
Q

Which AAs are these?

Negatively charged at neutral pH because of the carboxylate group
Participate in ionic interactions
Proton donors
One is the precursor for GABA and glutathione
Magic Sarap granules (umami)

A

Acidic AAs:

Aspartate/ Asp/ D
Glutamate/ Glu/ E

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20
Q

Which AAs are these?

Proton acceptors
At neutral pH, 2 are positively charged, the first is the precursor of creatinine, urea and nitric oxide

The third has no charge since it is a weak base
The last is also the precursor of histamine, used in the diagnosis of folic acid deficiency, concentration in thalamus varies according to circadian rhythm

A

Basic AAs:

Arginine/ Arg/ R
Lysine/ Lys/ K
Histidine/ His/ H

Diagnosis of folic acid deficiency: FIGlu test

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21
Q

Which AA is this?

21st AA
Found in some peroxidases and reductases
Inserted in polypeptides during translation, but has no specific codon

A

Selenocysteine

A selenium atom replaces the sulfur of its structural analog, cysteine

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22
Q

Plant AAs:

Found in Lathyrus sativus (grass pea) seeds
Neurolathyrism - progressive and irreversible spastic paralysis of the lower extremities

A

Homoarginine

B-N-Oxalyldiaminopriopionic acid (B-ODAP)

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23
Q

Plant AAs:

Neurotoxic amino acid in Cycad seeds
Neurodegenerative diseases including amyotrophic lateral sclerosis - Parkinson dementia complex in Guam natives

A

B-methylaminoalanine

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24
Q

All amino acids are chiral except for

A

Glycine/ Gly/ G

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25
Q

Configuration of AAs in:

Proteins
Antibiotics

A

Proteins: L-configuration

Antibiotics and bacterial cell walls: D-configuration

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26
Q

Why can AAs serve as buffers in aqueous solutions?

A

Can accept or donate protons

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27
Q

AA charge depends on

A

pH of aqueous environment

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28
Q

Define “zwitterion”

A

An AA bears no net charge at its isoelectric pH (pI)

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29
Q

What AAs are essential for proper body function since they cannot be synthesized?

A

Essential Amino Acids

PVT TIM HALL Sometimes ARGues, never Completely Tyres

Phenylalanine
Valine
Tryptophan
Threonine
Isoleucine
Methionine
Histidine
Arginine*
Leucine
Lysine

*Considered nutritionally Semi-essential only
Cysteine (from Methionine) and Tyrosine (Phenylalanine) can be synthesized in the body

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30
Q

Primary structure of proteins

Attaches alpha amino group of one AA to the alpha carbonyl group of another

A

Amino acid sequence

Peptide bond

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31
Q

Peptide bond

Partial ____ in character
____ and planar
Generally in ____ configuration
Methods of hydrolysis

A

Peptide bond

Partial DOUBLE-BOND in character
RIGID and planar
Generally in TRANS configuration
Methods of hydrolysis: PROLONGED EXPOSURE TO STRONG ACID OR BASE AT ELEVATED TEMPERATURES

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32
Q

First protein to be sequenced

A

Insulin

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33
Q

Protein sequencing: Attaches to N-terminal AA

A

Sanger’s reagent (1-fluoro-2,4-dinitrobenzene)

Edman’s reagent (Phenylisothiocyanate)

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34
Q

Protein sequencing: Attaches to C-terminal AA

A

Hydrazine

Carboxypeptidase

35
Q

Protein secondary structure and bonding

A

Polypeptides form alpha helix and beta sheets

Hydrogen boding stabilizes configurations

36
Q

Most common protein secondary structure
Keratin
Hemoglobin

A

Alpha helix

37
Q

Parallel or anti-parallel secondary protein structure
Amyloid
Immunoglobulin

A

Beta sheet

38
Q

Supersecondary protein structures such as B-a-B unit, Greek key, B-meander, B-barrel

A

Motifs

39
Q

Less regular protein secondary structure forming loops and bends

A

Non-repetitive secondary structures

40
Q

3D shape of a protein

A

Tertiary structure

41
Q

Examples of tertiary structure:
Globular
Fibrous

A

Globular - hemoglobin, myoglobulin

Fibrous - collagen, elastin

42
Q

Tertiary structure is stabilized by these bonds

A

Disulfide, Hydrophobic interactions, Hydrogen bonds, Ionic interactions

43
Q

Functional and 3D structural units of a polypeptide

A

Domains

44
Q

Quaternary structure of a protein

A

Monomeric vs Dimeric

Homodimers vs Heterodimers

45
Q

Specialized proteins required for proper folding of other proteins
Can “rescue” proteins from misfolding, prevents aggregation

A

Chaperones

46
Q

Denaturation targets which protein structures?

A

Secondary and tertiary protein structures, peptide bonds are not hydrolyzed

Most denaturation is irreversible

Denaturing agents: heat, organic solvents, mechanical mizing, strong acids or bases, detergents, ions of heavy metals such as lead or mercury

47
Q

Examples or protein misfolding disorders

A

Prion diseases

Alzheimers Disease

48
Q

Disease of secondary structure proteins, causes neurologic symptoms

A

Prion diseases
PrPc (alpha-helix, normal) to PrPsc (beta-sheets, pathologic)
Protein alone is transmitted

49
Q

Involves ApoE, most common and important neurodegenerative disease of the brain

A

Alzheimers Disease

50
Q

2 configurations of hemoglobin

A

T (taut form) - low O2 affinity

R (relaxed form) - high O2 affinity (300x)

51
Q

Property of hemoglobin wherein 4 molecules of O2 may bind, with increasing affinity

A

Positive cooperativity

52
Q

Where are hemoglobin and myoglobin found?

A

Hemoglobin - Heme protein only in RBCs

Myoglobin - Heme protein in heart and skeletal muscle

53
Q

Factors that cause a shift to the right in the oxygen dissociation curve

A 
Increase in CO2
Increase in acidity (Decrease in pH)
Increase in 2,3 bisphosphoglycerate
Increase in exercise
Increase in temperature

When you get LEFT behind, you HOLD ON, but LETTING GO is the RIGHT thing to do.

54
Q

What has more affinity for O2 in infants? HbF or HbA?

A

HbF, since 2,3 BPG binds more weakly to it

55
Q

Why does prolonged exposure high altitude lower affinity of HbA for O2?

A

Increased RBC production –> Increased Hgb –> Inc 2,3 BPG

56
Q

What binds to Hgb following:
Bohr effect
Haldane effect

A 
Booohr = Proooton
Haaaldane = Caaarbon (polite, will only bind to Hgb if O2 is not bound)
57
Q

HbA1C

When blood glucose enters RBCs, it glycosylates what?

A

epsilon-amino group of lysine residues

amino terminals of hemoglobin

58
Q

Hgb that consits of 2 alpha and 2 gamma chains, 60% of hemoglobin in fetus, higher affinity for O2 than HbA

A

Fetal hemoglobin (HbF)

59
Q

Hgb that consists of 2 alpha and 2 delta chains, 2% of hemoglobin of adults

A

Hemoglobin A2 (HbA2)

60
Q

Treatment for carbon monoxide poisoning

A

100% oxygen therapy

Carboxyhemoglobin: Hgb bound to CO, since CO has 200x more affinity for Hgb than O2

61
Q

Inherited/intrinsic RBC membrane defect (spheroidal in shape), ankyrin mutation, splenic sequestration, manifest as anemia, jaundice and splenomegaly, Dx: osmotic fragility test, Tx: splenectomy

A

Hereditary spherocytosis

62
Q

Point mutation in both genes coding for beta chain (Glu –> Val), homozygous recessive

Effect on RBC:
Distorted RBC membrane
Misshape, rigid RBCs occluding capilaries
Polymerization and decreased solubility of the deoxy form
of Hgb

Manifestation:
Anemia, tissue anoxia, painful crises, protective against malaria

Treatment: Hydration, analgesics, antibiotics if with infection, transfusions, hydroxyurea

A

Sickle Cell Disease

63
Q

(Lys –> Glu) in beta-globin chain, homozygosity: mild hemolytic anemia, no therapy needed

A

Hemoglobin C Disease

64
Q

Inadequate synthesis of alpha globin chains, anemia, accumulated Hgb Bart (gamma 4) and H (B4) and beta chain precipitation

Symptoms appear at birth since alpha chains needed for HbF and HbA synthesis

A

Alpha thalassemia

Silent carrier (1 gene missing)–> Alpha thalassemia trait (2 genes missing)–> Hgb H disease (3 genes missing)–> Hydrops fetalis

65
Q

Inadequate synthesis of beta chain

Anemia, accumulation of Hgb Barts (4 gamma globulins) and alpha chain precipitation

A

Beta thalassemia

B thalassemia minor (one gene affected)–> B thalassemia major (2 genes affected)

66
Q

Most common form of collagen

A

Type I

67
Q

Roles of proline and lysine in collagen formation

A

Proline/X: Kinking

Y: Hydroxyproline or hydroxylysine strengthens

68
Q

Type of collagen found in bone, skin, tendon, dentin, fascia, cornea, late wound repair

A

Type I

tendbONE

69
Q

Type of collagen found in cartilage (including hyaline), vitreous body, nucleus pulposus

A

Type II

carTWOlage

70
Q

Type of collagen found in skin (reticulin), blood vessels, uterus, fetal tissue, granulation tissue

A

Type III

THREEticulin

71
Q

Type of collagen found in basement membrane or basal lamina

A

Type IV

under the FOUR is the basement

72
Q

Type of collagen found beneath stratified squamous epithelium

A

Type VII

73
Q

Manifestation of Classical subtype of Ehlers-Danlos Syndrome

A

Type I and V defect
Joint hypermobility
Skin > Joint

74
Q

Manifestation of Hypermobility subtype of Ehlers-Danlos Syndrome

A 
Type III defect
Joint hypermobility
Skin abnormalities
Osteoarthritis
Severe pain
75
Q

Manifestation of Vascular subtype of Ehlers-Danlos Syndrome

A 
Type III defect
Fragile blood vessels, organs, small stature
Thin and translucent skin, easy bruising
Intracranial aneurysms
Most serious
76
Q

Brittle bone disease, autosomal dominant, multiple fractures, blue sclerae, hearing loss (ossicles, conductive hearing loss), dental imperfection, type I collagen defect

A

Osteogenesis Imperfecta

77
Q 
Type IV collagen defect, basement membrane of renal glomeruli affected
Hematuria
Ocular lesion
Hearing loss (sensorineural)
ESRD
A

Alport Syndrome

alFOUR

78
Q

Epidermolysis bulosa is a defect in what type of collagen?

A

Basal lamina, blistering

Type VII

79
Q

Vitamin C deficiency hampers post-translational modification of collagen (hydroxylation = strengthening), sore gums, loose teeth, poor wound healing, petechiae on skin and mucous membranes

A

Scurvy

80
Q

Kinky hair, growth retardation, copper deficiency (required by lysyl oxidase)

A

Menkes Disease

81
Q

Rich in proline and lysine, but little hydroxyproline and no hydroxylysine

A

Elastin

82
Q

Mutation in fibrillin gene, autosomal dominant
Taller and thinner than family members, aortic dilatation and dissection, ectopia lentis, arachnodactyly, dolichostenomelia

A

Marfan syndrome

83
Q

Prevents proteolytic enzymes in lungs such as elastase from destroying alveolar walls (pan-acinar) which lead to emphysema

A

Alpha-1-antitrypsin deficiency

PLE (14 decks)

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