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#‼️BIOCHEMISTRY - PLE TOPNOTCH 2020 > PROTEINS > Flashcards

PROTEINS Flashcards

1
Q

Contains an INDOLE RING

A

Tryptophan (W)

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2
Q
  • The skin breaks and blisters as a result of minor trauma
  • Dystrophic form is due to mutations affecting the structure of type VII collagen, which anchors the basal lamina to collagen fibrils in the dermis
A

EPIDERMOLYSIS BULLOSA

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3
Q

Contains Guanidino Group

A

Arginine (R)

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4
Q
  • Disorder characterized by an inherited (intrinsic) defect in the RBC membrane that renders the erythrocytes spheroidal, less deformable, and vulnerable to splenic sequestration and destruction
  • Multiple mutations have been described: ankyrin (most common), spectrin, band 4.1 and band 3​
A

HEREDITARY SPHEROCYTOSIS

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5
Q
  • Hemoglobin variant that has a single amino acid substitution in the 6 th position of the β-globin chain, in which lysine is substituted for glutamate
  • Patients homozygous for hemoglobin C present with mild hemolytic anemia
A

HEMOGLOBIN C DISEASE

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6
Q
  • Partial double-bond character
  • Rigid and planar
  • Generally in the trans configuration
  • Disrupted by hydrolysis through prolonged exposure to a strong acid or base at elevated temperatures
A

Peptide Bonds

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7
Q

• Brittle bone syndrome

  • Mutation in collagen genes result to bones that easily bend and fracture
  • Most common form is autosomal dominant with abnormal collagen type I
A

OSTEOGENESIS IMPERFECTA

  • Multiple fractures (need to rule out child abuse)
  • Blue sclerae
  • Hearing loss
  • Dental imperfections
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8
Q

Uncharged POLAR AA

A

STCY QN

Serine (S), (Threonine (T), Cysteine (C), Tyrosine (Y), Glutamine (Q), Asparagine (N)

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9
Q

secondary structure is stabilized by what bond?

A

hydrogen bonding

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10
Q

attach the α-amino group of one amino to the α carbonyl group of another

A

Peptide bonds

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11
Q

z 2 ε 2 Hb

A

Embryonal hemoglobin (Hb Gower 1)

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12
Q

refers to carbon monoxide bound to hemoglobin

A

carbohyxhemoglobin

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13
Q
  • Present in Lathyrus seeds
  • Implicated in neurolathyrism, characterized by progressive and irreversible spastic paralysis of the lower extremities
A

Homoarginine and β-N-Oxalyldiaminopriopionic acid (β-ODAP)​

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14
Q

Basic AA

  • Proton acceptors
A

“BASIC HKR”

Histidine (H)

Lysine (K)

Arginine (R)

  • At neutral pH:
    • Arginine and lysine are positively charged
    • Histidine, being a weak base, has no charge
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15
Q

• Genetic disorders affecting the structure of type IV collagen fibers, the major collagen found in the basement membranes of the renal glomeruli

A

ALPORT SYNDROME

  • Hematuria (main presenting sign)
  • Ocular lesions
  • Hearing loss
  • Patients may eventually develop end-stage renal disease
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16
Q

Collagen is rich in what AAs?

A

glycine and proline

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17
Q

Precursor of carnitine

A

LYSINE​

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18
Q

NON POLAR AA

A

“GAVIL Pro MidWiFe”

  • Glycine (G)
  • Alanine (A)
  • Valine (V)
  • Isoleucine (I)
  • Leucine (L)
  • Proline (P)
  • Methionine (M)
  • Tryptophan (W)
  • Phenylalanine (F)
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19
Q
  • Autosomal dominant connective tissue disorder
  • Mutation in the fibrillin gene
A

MARFAN SYNDROME

  • Usually taller and thinner than family members
  • Dolichostenomelia
  • Arachnodactyly
  • Aortic dilatation (70 to 80%) and dissection
  • Upward dislocation of the lens (ectopia lentis)
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20
Q

Heme protein present in heart and skeletal muscle

A

MYOGLOBIN

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21
Q
  • Not an amino, but an imino acid
  • Contributes to the fibrous structure of collagen and interrupts αhelices in globular proteins
A

PROLINE​

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22
Q

Types of Collagen

A
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23
Q
  • Most common type of secondary structure
  • Spiral structure with polypeptide backbone core, with side chains extending outward
  • 3.6 AA per turn
  • Disrupted by proline, AAs with large or charged R-groups
A

Alpha Helix

• Examples:

o Keratin (100% α-helix)

o Hemoglobin (80% α-helix)

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24
Q

PHENYLALANINE / TYROSINE DERIVATIVES​

A

Pare, True Love Does Not Exist To Me

Phenylalanine →Tyrosine → L-dopa → Dopamine → Norepinephrine → Epinephrine

Tyroxine, Melanin

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25
Q

R (relaxed) form: ____ oxygen affinity (300x)

A

high

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26
Q

The set of all the proteins expressed by an individual cell at a particular time

A

PROTEOME

*Unlike your genome which remains the same throughout life, your proteome changes all the time.

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27
Q

contains IMIDAZOLE RING

A

Histidine (H)

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28
Q
  • Connective tissue protein with rubber-like properties, responsible for extensibility and elastic recoil in tissues
  • Found in tissues where elastic recoil is needed
    • lungs, large arteries, elastic ligaments, vocal cords, ligamentum flavum
  • Rich in proline and lysine, but contains little hydroxyproline and no hydroxylysine
  • Precursor tropoelastin is deposited into an irregular fibrillin scaffold cross-linked by desmosine
A

ELASTIN

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29
Q
  • Source of methyl groups in metabolism
    • Involved in transfer of methyl groups as S-adenosylmethionine (SAM)
  • Precursor of homocysteine and cysteine
A

METHIONINE

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30
Q
  • Precursor of histamine
  • Also used in the diagnosis of folic acid deficiency (FIGLU excretion test)
  • Concentration in the brain hypothalamus varies in accordance with the circadian rhythm
A

Histidine

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31
Q

Contains a BENZENE RING

A

Phenylalanine (F)

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32
Q

α 2 β 2 Hb

A

Hemoglobin A (HbA)

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33
Q

21st AMINO ACID

A

SELENOCYSTEINE

  • Found in a handful of proteins, including certain peroxidases and reductases, where it participates in the catalysis of electron transfer reactions
  • A selenium atom replaces the sulfur of its structural analog, cysteine
  • Inserted into polypeptides during translation but is not specified by a simple three-letter codon
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34
Q
  • When blood glucose enters the erythrocytes, it glycates the ε amino group of lysine residues and the amino terminals of hemoglobin
  • ↑ glycation of hemoglobin noted in patients with diabetes mellitus due to ↑ glucose in blood
A

GLYCATED HEMOGLOBIN (HbA1C)

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35
Q

• The folding of short (3–30 residue) contiguous segments of polypeptide into geometrically ordered units

A

SECONDARY STRUCTURE

36
Q
  • Contains a sulfhydryl group that is an active part of many enzymes
  • Participates in the biosynthesis of coenzyme A
  • Two cysteines can be connected by a covalent disulfide bond to form cystine
A

CYSTEINE

37
Q
  • Inadequate synthesis of α-chains
  • Leads to anemia, accumulation of Hb Bart (γ4 )and Hb H (β4 ), and β-chain precipitation
    • Silent Carrier → α-thalassemia Trait → Hb H Disease → Hydrops Fetalis
  • Symptoms appear at birth because α-chains are needed for HbF and HbA
A

ALPHA THALASSEMIA

38
Q

• Branched-chain amino acids whose metabolites accumulate in maple syrup urine disease

A

VALINE, LEUCINE, ISOLEUCINE

39
Q
  • Neurotoxic amino acid in Cycad seeds
  • Implicated in neurodegenerative diseases, including amyotropic lateral sclerosis-Parkinson dementia complex in natives of Guam
A

β-Methylaminoalanine​

40
Q

Myoglobin vs Hemoglobin

A
41
Q

Precursor of creatinine, urea and nitric oxide

A

ARGININE​

42
Q

T (taut) form: ____ oxygen affinity

A

low

43
Q
  • Accumulates in phenylketonuria
  • Precursor of tyrosine
A

PHENYLALANINE​

44
Q

Acidic AA

  • Negatively charged at neutral pH because of the carboxylate group
  • Participate in ionic interactions
  • Serve as proton donors
A

Aspartate (D)

Glutamate (E)

45
Q
  • Carrier of ammonia and of the carbons of pyruvate from skeletal muscle to liver
  • Together with glycine, constitutes a major fraction of free amino acids in the blood
A

ALANINE

46
Q

AA with sulfhydril (-SH)

A

Cysteine

47
Q

Except for______, all amino acids are chiral

A

glycine

48
Q
  • Characterized by kinky hair and growth retardation
  • Reflects a dietary deficiency of the copper required by lysyl oxidase
    • Catalyzes a key step in formation of the covalent cross-links that strengthen collagen fibers
A

MENKES DISEASE

49
Q
  • Has the smallest side chain
  • Used in the first step of heme synthesis: Glycine + Succinyl CoA to δ-ALA
  • Used in synthesis of purines and creatine
  • Conjugated to bile acids, drugs, and other metabolites
  • Major inhibitory neurotransmitter in the spinal cord
A

Glycine

50
Q

Fatal neurodenegerative diseases characterized by spongiform changes, astrocytic gliomas, and neuronal loss resulting from the deposition of insoluble protein aggregates in neural cells

A

PRION DISEASES

51
Q
  • Inadequate synthesis of β-chains
  • Leads to anemia, accumulation of Hb Barts and α-chain precipitation
    • β-thalassemia Minor → β-thalassemia Major
A

BETA THALASSEMIA

52
Q
  • Consists of 2 α-chains and 2 γ-chains
  • Major hemoglobin found in the fetus (~60%)
  • Normally less than 0.6% in adults
  • Has ↑ affinity for O 2 than HbA
A

FETAL HEMOGLOBIN (HbF)

53
Q
  • Supersecondary structures produced by packing side chains from adjacent secondary structural elements close to each other
  • Examples are β-α-β unit, Greek key, β-meander, β-barrel
A

Motifs

54
Q
  • Hydroxylation of collagen is a post-translational modification requiring ascorbic acid
  • Vitamin C deficiency causes ↓ cross-linking of collagen fibers
A

Scurvy

o Sore spongy gums

o Loose teeth

o Poor wound healing

o Petechiae on skin and mucous membranes

55
Q

An amino acid bears no net charge (zwitterion) at its ____

A

isoelectric pH (pI)​

56
Q

Most common type of collagen

A

Type I

57
Q
A
58
Q

Collagen structure

A
  • Rich in glycine and proline
    • X: proline (facilitates kinking)
    • Y: hydroxyproline or hydroxylysine
59
Q

Factors that cause a shift to the RIGHT:​

A

o ↑ CO 2

o ↑ Acidity (↓pH)

o ↑ 2,3 BPG

o ↑ Exercise

o ↑ Temperature

60
Q

carbon dioxide bound to hemoglobin

A

carbaminohemoglobin

61
Q
  • Aims to identify the entire complement of proteins elaborated by a cell under diverse conditions
  • A major goal is the identification of proteins and of their posttranslational modifications whose appearance or disappearance correlates with physiologic phenomena, aging, or specific diseases
A

PROTEOMICS

62
Q
  • Has the largest side chain
  • Precursor for niacin, serotonin, and melatonin
A

TRYPTOPHAN​

63
Q

• Stepwise process of identifying the specific amino acid at each position in the peptide chain

A

Sequencing

64
Q
  • The release of oxygen from hemoglobin is enhanced when the pH is lowered or when the hemoglobin is in the presence of an increased pCO2
    • Both result in a decreased oxygen affinity of hemoglobin
    • The deoxy form of hemoglobin has a greater affinity for protons than does oxyhemoglobin
A

BOHR EFFECT

65
Q

EHLERS-DANLOS SYNDROME SUBTYPES

  • Group of inherited disorders characterized by:
    • Hyperextensibility of the skin
    • Abnormal tissue fragility
    • Increased joint mobility
A
66
Q

precursor for GABA and glutathione

A

Glutamate

*Recall that GABA is the major inhibitory NT in the brain; Glutamate is excitatory (meron din sa MSG). Glu → GABA is catalyzed by Glu- decarboxylase

67
Q

α 2 δ 2 Hb

A

Hemoglobin A2 (HbA2)

68
Q
  • α-1 antitrypsin inhibits proteolytic enzymes from hydrolyzing and destroying proteins
  • If there is ↓ α-1 antitrypsin in the lungs, elastase destroys the alveolar walls, resulting to emphysema
  • Patients can also manifest with liver disease (eg, cirrhosis and hepatocellular carcinoma)
A

α-1 ANTITRYPSIN DEFICIENCY

*Imagine elastase as if it were scissors that keep on cutting elastin. α-1 antitrypsin prevents it from doing so.

69
Q
  • Number and types of polypeptide units of oligomeric proteins and their spatial arrangement
    • Monomeric vs Dimeric proteins
    • Homodimers vs Heterodimers
A

QUATERNARY STRUCTURE

70
Q

Fundamental functional and three-dimensional structural units of polypeptide

A

Domains

71
Q

Contains an IMINO ACID

A

Proline (P)

72
Q

AA with polar Hydroxyl (-OH) group

A

Threonine (T), Tyrosine (Y), Serine (S)

73
Q

ESSENTIAL AMINO ACIDS

Amino acids whose intake is essential for proper body function since they cannot be synthesized

A

PVT TIM HALL, always ARGues, never TYRes. A is always ARGinine. T is never TYRosine.​

Phenylalanine

Valine

Threonine

Tryptophan

Isoleucine

Methionine

Histidine

Arginine

Leucine

Lysine

74
Q

• Have a carbonyl group and an amide group that can also form hydrogen bonds

A

Asparagine (N), Glutamine (Q)

  • Asparagine is the site for N-linked glycosylation of proteins
  • Glutamine is deaminated by glutaminase resulting in the formation of ammonia, and is a major carrier of nitrogen to the liver from peripheral tissues
75
Q

Sequencing from the C-terminal amino acid:

A

§ Hydrazine

§ Carboxypeptidase

76
Q

TRYPTOPHAN DERIVATIVES

A

TRYp Mo Siya, ‘No?

TRYptophan Melatonin Serotonin Niacin​

77
Q

Sequencing from the N-terminal amino acid:

A

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

§ Edman’s reagent (Phenylisothiocyanate)

78
Q

• Specialized group of proteins required for the proper folding of many species of proteins

• Prevent aggregation, thus providing an opportunity for the formation of appropriate secondary structural elements and their subsequent coalescence into a molten globule

• Can also “rescue” proteins that have become thermodynamically trapped in a misfolded dead end by unfolding hydrophobic regions

A

CHAPERONES

79
Q
  • Results in the unfolding and disorganization of the protein’s secondary and tertiary structures
  • Not accompanied by hydrolysis of peptide bonds
  • Results from denaturing agents:

o Heat, organic solvents, mechanical mixing, strong acids or bases, detergents, ions of heavy metals (e.g., lead, mercury)

• May be reversible, but most proteins remain permanently disordered

A

DENATURATION

80
Q
  • Amino acid residues form a zigzag or pleated pattern
  • R groups of adjacent residues project in opposite directions
  • Sheets can be parallel or antiparallel
A

Beta Sheet​

  • Examples:
    • Amyloid
    • Immunoglobulin
81
Q
  • Results from a missense point mutation in both genes coding for the β chain that results in a valine rather than a glutamate
  • Homozygous recessive disorder
A

SICKLE CELL DISEASE

* Missense point mutation ito. E6V (glutamic E naging Val V sa 6th position sa β-chain). Di ba nonpolar ang Val, polar (-) charged ang Glu. Nonpolar areas can attract one another forming a hydrophobic patch which can bara in some blood vessels resulting to painful crisis. This happens under deoxygenated states (if ↓ Oxygen kasi mas exposed si Val so mas magform ng patch).

82
Q
  • Overall 3-dimensional shape of the protein
    • Globular proteins vs Fibrous proteins
  • The assembly of secondary structural units into larger functional units such as the mature polypeptide and its component domains
  • Stabilized by disulfide bonds, hydrophobic interactions, hydrogen bonds, and ionic interactions
A

TERTIARY STRUCTURE

83
Q
  • The effect of changes in oxyhemoglobin saturation on the relationship of CO2 content to pCO2
  • O2 bound to hemoglobin changes its affinity for CO2 , such that when less O2 is bound, the affinity of hemoglobin for CO2 increases
A

HALDANE EFFECT

84
Q

Determined by a protein’s amino acid sequence

A

PRIMARY STRUCTURE

85
Q
  • Most common and most important degenerative disease of the brain, presenting with diffuse cerebral atrophy with dementia
  • The characteristic senile plaques and neurofibrillary bundles contain aggregates of the protein β-amyloid
    • β-amyloid becomes elevated, and this protein undergoes a conformational transformation from a soluble α-helix rich state to a state rich in β sheet and prone to self-aggregation
  • Apolipoprotein E has been implicated as a potential mediator of this conformational transformation
A

ALZHEIMER DISEASE

86
Q
  • Most abundant protein in the body
  • A long stiff extracellular structure in which 3 polypeptides (αchains) each 1000 AA in length are wound around one another in a triple helix
  • Stabilized by hydrogen bonds
  • At least 28 distinct types made up of over 30 distinct polypeptide chains have been identified in human tissues
A

COLLAGEN

#‼️BIOCHEMISTRY - PLE TOPNOTCH 2020 (13 decks)

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