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MBM > Proteins > Flashcards

Proteins Flashcards

1
Q

Peptide bond?

A
  • covalent amide bond between carboxyl group of one amino acid and amino group of another
  • not ionizable
  • forms H bonds
  • water soluble
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2
Q

N terminal end has free what? C terminal end?

A

N- free amine group

C- free carboxyl group

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3
Q

What are the 4 interactions between amino acid side chains?

A
  1. Electrostatic interactions (ionic)
  2. Dipole dipole interactions (H bonds)
  3. Hydrophobic interactions
  4. Covalent interactions (disulfide)
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4
Q

What are electrostatic interactions between?

A

oppositely charged hydrophilic amino acid side chains

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5
Q

what are dipole dipole interactions between?

A

hydrogen bonds are formed between two amino acid side chains

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6
Q

Where are hydrophobic interactions found?

A

found in interior of globular proteins where water is excluded

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7
Q

What are covalent interactions between?

A

two non metals such as disulfide bonds between two cysteine side chains

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8
Q

What are the small amino acids? functions?

A

glycine and alanine

-found in places where two polypeptide chains have to come close together

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9
Q

branched amino acids? side chains?

A

valine, leucine, isoleucine

-hydrophobic side chains

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10
Q

hydroxyl amino acids? functions?

A

serine, threonine

  • form H bonds with hydroxyl group
  • forms covalent bonds with carbs in glycoproteins and with phosphate in phosphoproteins
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11
Q

sulfur amino acids? functions?

A

cysteine, methionine

  • hydrophobic
  • cysteine weakly acidic
  • forms disulfide bonds
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12
Q

aromatic amino acids? bonds formed?

A

phenylalanine, tyrosine, tryptophan

  • hydrophobic
  • tyr and trip can form H bonds
  • tyrosine OH group carries covalently bound phosphate group in some phosphoproteins
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13
Q

acidic amino acids? functions?

A

glutamate, aspartate
-negatively charged at pH 7

glutamine, asparagine

  • not acidic but form strong H bonds
  • asp forms strong N glycosidic bond with carbs in some glycoproteins
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14
Q

basic amino acids? function?

A

lysine, arginine, histidine

  • positive charge on side chain
  • pK of His is low
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15
Q

proline? function?

A
  • nitrogen tied into ring structure
  • stiff and angled
  • found at bends in polypeptide
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16
Q

cause of sickle cell anemia?result?

A
  • valine is substituted for glutamic acid at 6th amino acid for both beta chains
  • changes in primary and quaternary structures, hemoglobin shape
  • lowers O2 concentration
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17
Q

7 functions of proteins?

A
  1. binding- antibodies
  2. cell structure- strength, ex. collagen
  3. enzyme catalysis- largest function, lactase
  4. mechanical support- muscle contraction, actin, myosin
  5. regulation- behavior or abundance of enzymes, cell process regulation, insulin
  6. storage- reservoirs for nutrients, store metal ions, ferritin
  7. transport - delivers specific substances, hemoglobin, myoglobin, across ion channels
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18
Q

primary structure of proteins?

A

determine by the DNA of the gene, is the amino acid sequence

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19
Q

secondary structure?

A
  • alpha helix
  • beta pleated sheet
  • combination of the two
  • provides maximal H bonding in interior of polypeptides
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20
Q

silk fibroin?

A

beta pleated sheets alternating glycine and alanine

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21
Q

super secondary structure?

A
  • random or non repetitive sequences
  • organized motifs of secondary structures in a particular geometric arrangement
  • presence of alpha helices and beta sheets in a protein give it flexibility
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22
Q

tertiary structure? interactions?

A
  • folding of secondary structure into 3D shape
  • primary sequence determines tertiary
  • interactions between side chains guide folding

Four interactions for tertiary structures:

  1. electrostatic
  2. H bonds
  3. hydrophobic
  4. disulfide
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23
Q

Quaternary structure? interactions?

A

-arrangement of more than one polypeptide chain

Three non covalent interactions:

  1. electrostatic
  2. H bonds
  3. hydrophobic
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24
Q

homoproteins?

A
  • simple proteins

- contain exclusively amino acids

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25
Q

heteroproteins?

A
  • conjugated proteins

- prosthetic group - non protein part

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26
Q

Two classes of proteins?

A
  1. Fibrous

2. Globular

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27
Q

3 examples of fibrous proteins?

A
  1. keratin
  2. collagen
  3. elastin
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28
Q

Fibrous proteins properties? amino acids? structure?

A
  • water insoluble
  • Ala, Val, Leu, Lle, Met, Phe
  • single repeating elements of secondary structure
  • rope like proteins
  • contractile properties
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29
Q

2 examples of globular proteins?

A
  • heme

- myoglobin

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30
Q

Globular proteins properties?

A
  • water soluble
  • hyrdophilic
  • stable structures (3D), complex interactions
  • variety of globular protein structures
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31
Q

Keratin? properties?

A
  • fibrous
  • main constituent of structures that grow from skin
  • mechanically durable
  • chemically unreactive
  • occurs in all higher vertebrates
  • glycine and alanine
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32
Q

Keratin deficiencies?

A

-loss of skin integrity, loss of hair, brittle nails

Epidermolysis Bullosa Simplex

  • blister formation in epidermis caused by defects in keratin filaments
  • Mutations in KRT5 or KRT14 gene

Monilethix
-autosomal dominant hair disease, beaded hair

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33
Q

Collagen? where found? properties?

A
  • fibrous
  • found in extracellular matrix (ECM)- gives support to cells, cell attachments, strength
  • cartilage, tendons, bones, teeth, skin, blood vessels
  • vitreous humor of eye, cornea
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34
Q

What other ECM proteins does collagen interact with?

A
  • proteoglycans- sugar chain around protein core

- integrin- bound in cell membrane

35
Q

nascent peptide?

A
  • collagen

- high glycine and proline/hydroxyproline content

36
Q

pro collagen?

A
  • cells secrete collagen as this precursor form

- processed by proteolysis of staggered ends leading to cleavage of pro collagen to form Tropocollagen

37
Q

Tropocollagen?

A
  • triple helix is basic unit of collagen

- formed be cleavage of staggered ends, assembly, and cross linking out of cell

38
Q

what is cross linking important for with collagen?

A
  • achieves tonsil strength necessary for function of connective tissue
  • stability
39
Q

How are collagen fibrils formed?

A

by covalently cross linked via Lysyl Oxidase

40
Q

What leads to further strengthening of collagen?

A

extensive H bonds using carbonyl and amine of Gly

41
Q

What vitamin is needed for proper collagen formation?

A

C (ascorbic acid)

42
Q

Collagen diseases?

A

Scurvy

  • ascorbic deficiency, lack of hydroxylation
  • collagen not cross linked, decreased strength
  • capillary insufficiency
  • bruises on limbs and swollen gums, bleed, teeth fall out

Ehlers-Dalos Syndrome

  • Cutis hyperelastica
  • inherited defects of synthesis of types 1, 3, 5 collagens
  • deficiency in collagen processing enzyme
  • reduced tensile strength of skin, very stretchy
  • loos joints, bruise easily, fragile

Osteogenesis Imperfecta (OI)

  • brittle bone syndrome
  • can be mild, severe, extremely severe, undefined
  • autosomal dominant disease
  • glycine is replaced by other amino acids in gene of type 1 of pro collagen, impaired formation of triple helix in ER
43
Q

clinical symptoms of OI?

A
  • blue tint to whites of eyes
  • early hearing loss
  • weak bones susceptible to fractures
  • loose joints (hyper mobility) and flat feet
  • some have poor teeth
  • bowed legs and arms
  • kyphosis
  • scoliosis
  • humped back
  • retarded wound healing
44
Q

Elastin? where found?

A
  • fibrous, elastic
  • protein located in connective tissue
  • rubber band like, not high tensile strength
  • lungs, ligaments, arteries, tendons
  • stretch and recoil
  • insoluble
  • irregular amino acid structure (Gly, Ala, Val, with some Lys, Pro)
  • random coil structure
  • demosine- unique crosslinks (4 Lys connected at side chains)
45
Q

Disorders of Elastin degradation?

A
  1. alpha-1 antitrypsin antitrypsin deficiency
  2. Marfan syndrome
  3. Cutis Laxa
46
Q

alpha-1 antitrypsin deficiency? symptoms?

A
  • this protein normally inhibits proteolytic enzymes that degrade elastin in lungs and other tissues (elastase)
  • deficiency leads to degradation of elastin
  • emphysema
  • cirrhosis in liver
  • smokers are at risk
47
Q

Marfan syndrome? symptoms?

A
  • autosomal dominant
  • degenerative disorder of connective tissue
  • tall, long limbs, long fingers
  • affects eyes, heart, blood vessels, skeletal system
  • defects of heart valves and aorta
  • no strenuous activity allowed
48
Q

Cutis Laxa (CL)? symptoms?

A
  • rare, inherited connective tissue disorder
  • skin becomes inelastic and hangs loose, internal organs frequently involved
  • heterogeneity (autosomal dominant, recessive, X linked)
  • serine to proline amino acid substitute
49
Q

what are the proteins in cell membranes?

A

Globular proteins:

  1. integral membrane proteins
  2. peripheral membrane proteins
  3. glycoproteins
50
Q

Functions of cell membrane proteins?

A
  • constitute about 25% of all proteins
  • cell communication to outside world
  • transport molecules in or out of cells
  • cell recognition, receptors, cell to cell communication
  • energy metabolism
  • amino acid side chains are non polar
  • Ala, Val, Leu, Lle, Phe
51
Q

Function of integrins?

A
  • penetrate hydrophobic regions of bilayer

- transport

52
Q

Examples of integral membrane proteins?

A
  1. hormone receptors (N linked oligosacc)
  2. membrane transporters (Na-K ATPase, ABC transporter, Glucose transporters)
  3. ion channels and gates
  4. histocompatibility antigens
  5. certain enzymes of electron transport chain
  6. Gap junction proteins
53
Q

What do all membrane transporters contain?

A

transmembrane domain which consists of hydrophobic (within membrane) amino acids and hydrophilic amino acids

54
Q

Function of Na-K ATPase?

A
  • some cells use gradient to facilitate transport of glucose and amino acids
  • nerve cell electrical impulsion
55
Q

ABC transporters function?

A
  • nutrient uptake
  • protein, drug and antibiotic excretion
  • osmo regulation
  • antigen presentation
  • signal transduction

-use energy of ATP hydrolysis to transport across cell membranes

56
Q

Common features of ABC transporters?

A
  • consensus ATP binding domain
  • transmembrane domain
  • or integral membrane consists of alpha helices, embedded in bilayer
57
Q

Examples of ABC transporters?

A
  1. ion transporters (CFTR)
  2. cholesterol transporters (ABCA1)
  3. transporters of bile acids
  4. transporters of drugs
58
Q

Peripheral membrane proteins? attached? example?

A
  • more loosely associated with membrane
  • attached noncovalently to protruding integral proteins
  • restricted in their movements
  • some tethered to cytoskeletal elements like actin microfilaments
  • some anchored to collagen
  • Cytochrome C in electron transport chain
59
Q

Glycoproteins?

A
  • covalently attached to oligosaccharides
  • glycosylated extracellular segments
  • often integral membrane proteins (cell-cell)
  • contain N terminal signal sequence- direct growing polypeptide chain to ER, Golgi where carb is added to protein
60
Q

Functions of glycoproteins?

A
  • cell surface recognition (other cells, hormones, viruses)
  • cell surface antigenicity (blood group antigens)
  • membrane receptors (ligand receptor function)
  • component of extracellular matrix and mucins (human gastric glycoproteins)
61
Q

Oxidoreductases?

A

transfer electrons from a donor (reducing agent) to acceptor (oxidizing agent)

62
Q

transferases?

A

transfer functional group (amino, phosphate) between molecules

63
Q

isomerases?

A

rearrange/isomerize molecules

64
Q

lyases?

A
  • synthases

- add or remove atoms to or form double bond

65
Q

ligases?

A
  • synthetases

- form bonds with hydrolysis of ATP

66
Q

hydrolases?

A

cleave bonds via the addition of water

67
Q

examples of oxidoreductase reactions?

A
  1. lactate dehydrogenase (NADH and NAD)

2. cytochrome P450

68
Q

Lactate dehydrogenase reaction? cofactors? reducing equivalents?

A
  • simple direct oxidation reduction
    cofactors: NAD+ as acceptor, NADH as donor, NADP,+ FAD+

reducing eq:
-electrons may be transferred as hydrogen proton with its electron (H- atom) or hydride ion (H with extra electron)

69
Q

Cytochrome P450 reaction?

A

-complex and indirect series of oxidation reductions

P450:

  • absorbance of proteins at 450nm when bound to CO
  • CYP family- heme containing
  • acts with other enzymes such as cytochrome P450 reductase, cofactors NADPH as electron donor, flavoprotein

-genetics of P450 enzymes have wide spread implications for drug reactions, CYPs are responsible for metabolizing 1/3 to 1/2 of drugs today

70
Q

What is the overall enzymatic chemical transformation of P450?

A

hydroxylation where the substrate may be a steroid, fatty acid, drug, or other chemical with a site of oxygenation

71
Q

Where are cytochromes found?

A

found embedded in the membranes of the smooth ER, microsome, and mitochondria

72
Q

What are some examples of transferases and hydrolases? why are they important? common amino acid targets?

A
  • kinases (transferase) and phosphatases (hydrolase)
  • important regulating enzymes
  • covalent modifications
  • most common targets are serine, threonine, tyrosine
  • phosphorylation targets amino acids located distant from catalytic site
73
Q

What is Glutathione? functions?

A
  • important tripeptide in metabolism
  • contains glutamic acid, cysteine, glycine
  • carboxyl side chain is part of backbone peptide structure
  • protect cells from oxidizing agents which react with SH of Cys of glutathione
  • antioxidant defense, reduces H2O2
  • assists in transport of certain amino acids across membranes
74
Q

Where is the information required for proper protein folding located?

A

primary structure of peptide

75
Q

What interactions determine how a protein folds?

A

interactions between side chains of amino acids

76
Q

What agents denature proteins?

A
  • change in pH
  • heat
  • organic solvents (urea)
  • mechanical mixing
  • strong acids or bases
  • detergents
  • ions of heavy metals
77
Q

What could denaturation cause?

A

causes permanent unfolding and disruption of protein structure

78
Q

Protein chaperones?

A
  • heat shock proteins
  • required for proper folding of many proteins
  • keep proteins unfolded until biosynthesis is complete
  • act as catalysts in folding process, increasing rate
  • others protect against tangling
79
Q

What characterizes proteins misfolding?

A
  1. many protein misfolding diseases are characterized by absence of a key protein because it has been eliminated by cell machinery
  2. many protein misfolding diseases characterized by its deposition in insoluble aggregates within the cell
80
Q

What diseases are caused by a lack of particular functioning protein due to degradation?

A
  • cystic fibrosis (misfolded CFTR)
  • marfan syndrome (misfolded fibrillin)
  • Fabry disease (misfolded alpha galactosidase)
  • Gauchers disease (misfolded beta glucocerebrosidase)
  • retinitis pigmentosa 3 (misfolded rhodopsin)
  • some cancers (inactive tumor suppressor)
  • Marfan Syndrome (misfolded fibrillin)
  • Osteogenesis Imperfecta (misfolded procollagen)
81
Q

What diseases are caused by protein aggregation?

A
  • alzheimers (deposits of amyloid beta and tau)
  • type 2 diabetes (deposits of amylin)
  • parkinsons (deposits of alpha synuclein)
  • creutzfeldt-jakob (deposits of prions)
  • hereditary transthyretin amyloidosis (heart failure)
82
Q

What is amyloidoses?

A
  • formation of abnormal long fibrillar protein with mainly beta pleated sheets called amyloid, insoluble aggregates form
  • alzheimers
83
Q

Cause of prion disease?

A
  • infectious prion proteins form insoluble aggregates of fibrils
  • TSE
  • creutsfeldt-jakob disease in humans
  • scrapie in sheeps
  • mad cow disease in bovine

MBM (24 decks)

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