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BIOCHEMISTRY 1 > Amino acids, peptides, proteins and enzymes > Flashcards

Amino acids, peptides, proteins and enzymes Flashcards

1
Q

Optical activity of AAs

A
  • at least 1 chiral center ⇒ can have enantiomers/ diastereoisomers
  • enantiomeres can be L or D
  • almost all proteins ⇒ L configuration (except glycine)
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2
Q

Hydropathy index

A
  • represents hydrophobic or hydrophilic properties of the side chain of AA
  • hydrophibic ⇒ +
  • hydrophilic ⇒ -
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3
Q

Isoelectric point

A
  • no net charge
  • isoelectric species: zwitterions
  • isoelectric pH is the pH midway between the pKA values on either side of the point
    pH= pI= (pKa1+pKa2)/2
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4
Q

Configuration

A

geometric relationship between given set of atoms

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5
Q

Conformation

A
  • spatial arrangement of proteins
  • achieved without breaking covalent bonds
  • due to rotation of single bonds
  • the chosen conformation usually ⇒ lowest Gibbs free energy⇒ most thermodynamically stable
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6
Q

Primary protein stucture

A
  • genetically determined
  • stabilizing forces: covalent bod, peptide bond
  • sequence of amino acids in polypeptide chain
  • determines its function
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7
Q

Ramachandran Plot

A
  • helps predict secondary structure of protein

- shows possible rotations of alpha1 and alpha2 carbons

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8
Q

Secondary protein structure

A
  • alpha helix
  • beta sheet
  • beta turn
  • stabilizing forces: H bonds between peptide groups
  • stability base on: minimized steric repulsion between side chains, maximized H-bonds between peptide groups
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9
Q

Alpha helix

A
  • spiral structure consisting of coiled polypeptide backbone core with side chains oriented outwards and hydrophilic elements inward
  • completer turn: 3,6A
  • stability: H bonds between peptide bond carbonyl oxygens and amide hydrogens
  • van der Waals interactions in core of helix
  • right handed or left handed
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10
Q

Decrease of Stability of proteins structure

A
  • electrostatic interactions of side chains
  • bulkiness of side chains
  • positive or negative charged AAs at C- or N-terminal
  • proline
  • interaction between AA residues at end of helical segment and electric dipole inherent to helix
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11
Q

Beta Sheet

A
  • all peptide bonds involved in H-bonding
  • consist of 2 or more polypeptide chains
  • parallel sheets
  • antiparallel sheets
  • right handed twist
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12
Q

Beta turn

A
  • reverses direction of polypeptide chain ⇒ compact globular shape
  • H-bond between 1st and 4th AA
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13
Q

Tertiary protein structure

A
  • Interactions: disulfide bridges, hydrophobic, polar, H-bonds, salt bridges, electrostatic
  • Hydrophobic pocket
  • Domains: structural and functional units of the polypeptides
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14
Q

Quaternary protein structure

A
  • proteins consisting of 2 or more polypeptide chains

- Interactions: hydrophobic, polar, ionic, H-bond

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15
Q

Proteins assisting in proteins folding

A
  • Chaperons: during protein synthesis, help move hydrophobic inside. Heat shock proteins
  • Proteins disulphide isomerase: catalyze formation and breakage of disulphide bonds
  • Proline-cis, trans- isomerase: cis-trans isomerization of peptidyl-prolyl bond
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16
Q

Alpha keratin

A
  • location: hair, nails, horns, hooves, quills etc
  • intermediate filaments
  • right handed alpha helix
  • regular inter-chain H-bonds
17
Q

Silk Fibroin

A
  • protein of silk
  • produced by insects and spiders
  • mainly beta-sheets
  • not stretch
18
Q

Collagen

A
  • location: tendons, cartilage, bone, skin etc
  • fibrous protein
  • provides structural function to the body
  • Primary structure: Gly, Pro, hydroxyproline
  • Post translational modification: proline/lysine ⇒ hydroxyproline or hydroxylysine
  • Secondary structure: collagen helix
19
Q

Procollagen and tropocollagen

A
  • 3 collagen helices ⇒ triple helix with globular part ⇒ Procollagen
  • stabilizing forces: H-bonds
  • function of globular part: promote folding + inhibit fiber formation
  • procollagen peptidase: remove globular part ⇒ Tropocollagen ⇒ can polymerize ⇒ fiber
20
Q

Alpha Keratin

A
  • location: hair, nails, claws, hooves etc.
  • intermediate filaments
  • right handed alpha helix
21
Q

Silk fibroin

A
  • produced by insects and spiders
  • beta sheet ⇒ polypeptide chain
  • highly flexible
22
Q

Myoglobin

A
  • monomer
  • compact
  • 75% alpha helices
  • non-polar side chains inside, polar side chains outside
  • contains a heme
23
Q

DIPF

A

irreversible inhibitor of Ser-proteases

24
Q

Specific inhibitors

A

SH-enzymes: monoiodoacetate

OH-enzymes: DIPF

25
Q

Non-specific inhibitors

A

denaturation of enzymes
heavy metal ions
heat

BIOCHEMISTRY 1 (9 decks)

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