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BIOL200 > 3. Protein Structure > Flashcards

3. Protein Structure Flashcards

1
Q

polypeptides

A

linear polymers of amino acids joined by peptide bonds

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2
Q

the hydrophobic effect

A

water molecules surrounding hydrophobic molecules adopt a constrained organisation that has low entropy

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3
Q

oil drop model of protein folding

A

protein conformation where hydrophobic amino acid side chains are embedded within the protein’s core while hydrophilic side chains are exposed in the surface

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4
Q

primary structure of proteins

A

amino acid sequence

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5
Q

secondary structure of proteins

A

alpha helix or B sheets: local conformations of peptide chain backbone

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6
Q

tertiary structure of proteins

A

interactions between secondary structures, overall polypeptide conformations

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7
Q

functions of a protein determined by

A
  • its overall shape
  • distribution of amino acid side chains
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8
Q

amino acid sequence is determined by

A

DNA

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8
Q

beta sheets properties

A
  • can create large surfaces
  • H-bonds link 2 adjacent B-strands
  • sheets may be parallel or antiparallel
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8
Q

alpha helix properties

A
  • straight rod
  • amino acid (n) H-bonds with other amino acid at n+4
    –> tilts axis of helix, driving periodicity of 3.6 residues/turn
  • surface properties exclusively dependent on side chains
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9
Q

quaternary structure of proteins

A

different tertiary structures come together

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9
Q

amino acid sequence determines

A
  • protein structure
  • protein function
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9
Q

secondary structure is based on

A

Hydrogen bonding between peptide bond between carbonyl oxygen and amino group hydrogen on a different amino acid residue

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9
Q

amino acid side chains protrude above and below B-sheet plane, determining…

A

interactions of B-sheets with other parts of the protein + its propensity to form

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10
Q

amino acid side chains mediate interactions between… (2)

A
  • different parts of the protein
  • the protein and its ligand GDP
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11
Q

most structure-driving interactions among amino acids are…

A

non-covalent bonds

11
Q

disulfide bond

A
  • type of covalent bond
  • side chain of cysteine contains sulfhydryl group, forming S-S bonds with other cysteine side chains
  • can be intrachain: contribute to tertiary structure
  • can be interchain: contribute to quaternary structure
11
Q

motifs of protein structure

A

combinations of secondary structures forming distinct local 3D structures

12
Q

are motifs independent?

A

motifs are not structurally independent entities: too small, insufficient bonds

12
Q

domains

A

40 amino acid long region, tertiary structures that are compactly folded
–> can be made of various motifs

13
Q

are domains independent?

A

domains are structurally independent entities

13
Q

motifs and domains are both…

A

local structures

14
Q

motif examples

A
  • coiled-coil motif: 2 long alpha helices joined together, involved in protein-protein interactions
  • EFhand/helix-loop-helix motif: Ca2+ binding motif
  • Zinc-finger motif: common in transcriptions factors -> binds to DNA/RNA
15
Q

similar domains can be found in diverse proteins example

A

Epidermal Growth Factor (EGF) found in Neu oncogene protein and TPA tissue plasminogen activator

15
Q

domain example

A

influenza virus hemagglutinin HA2 subunit contains globular and fibrous domains
–> HA2 fibrous domain interacts with HA1 subunit

15
Q

4 major structural classes of proteins

A
  • fibrous
  • globular
  • integral membrane
  • intrinsically disordered
16
Q

multimeric proteins

A

can contain any number of identical or different polypeptides

17
Q

example of heterodimer

A

hemagglutinin subunit: formed by 2 different proteins: HA1 + HA2

17
Q

protein tertiary structure can reveal…

A

ancient evolutionary relationships

17
Q

evolutionary patterns

A

different amino acid sequences may still lead to very similar structures

BIOL200 (6 decks)

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