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Semester 1 flashcards > Structure of Proteins > Flashcards

Structure of Proteins Flashcards

1
Q

Protein functions x5

A
  • Structure
  • Transport molecules
  • Defence
  • Biological catalysts
  • Regulation of genes
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2
Q

Example - structural protein

  • function
  • where
  • structure
A

Collagen

  • Strength, flexibility
  • Main component of connective tissue
  • Strong fibres in lattice-like structure
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3
Q

Example - transport protein

  • function
  • where
  • structure
A

Haemoglobin

  • Selective delivery of O2 (to areas of low conc.)
  • red blood cells
  • 4 protein subunits –> each has a Haem molecule –> each of these contains an Fe atom
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4
Q

Example - defence protein

  • function
  • where
  • structure
A

Antibody

  • Binds to specific antigens
  • Released into bloodstream
  • Y-shaped, w 2 heart & 2 light chains, liked by disulphide bonds
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5
Q

Example - biological catalyst

  • function
  • where
A

Lysozyme

  • An enzyme –> catalyses cutting of polysaccharide chains
  • In lysosomes
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6
Q

Example - genetic regulator protein

  • function
  • where
A

Lac Repressor Protein

  • Binds to DNA sequences upstream from genes coding for lactose metabolising proteins –> prevents these being expressed in absence of lactose
  • Bacteria
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7
Q

Proteins

A

Large, complex, linear polymers, w a hierarchy of structure

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8
Q

Amino acids

A
  • Central C atom, w amino & carboxylate groups

- R group –> unique to each & defines structure and function

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9
Q

Polypeptides

A

Amino acids are joined by peptide bonds

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10
Q

Position of R groups in polypeptides & 2 effects

A
  • Tend to alternate being on either side
  • Less bulky –> so more stable
  • Can create hydrophilic vs hydrophobic sides (as diff. groups have diff. properties)
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11
Q

Prosthetic group (& example)

A

Non-polypeptide into incorporated into protein structure

- e.g. Haem group in haemoglobin

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12
Q

Amino (N) terminus

A

NH3+

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13
Q

Carboxyl (C) terminus

A

COO-

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14
Q

3 classification groups

A
  • Hydrophilic (polar)
  • Hydrophobic
  • Special
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15
Q

3 groups in the hydrophilic class

A
  • Basic (+ve R)
  • Acidic (-ve R)
  • Polar (uncharged R)
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16
Q

Common properties of hydrophobic class x2

A
  • Long hydrocarbon chains

- Bulky aromatic groups

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17
Q

The 3 special amino acids

A
  • Cysteine
  • Glycine
  • Proline
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18
Q

Cysteine property

A

Forms S-S bonds w other Cys

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19
Q

Glycine property

A

R group = H

- no bulky side chain, so can fit in tight spaces

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20
Q

Proline

A

R group bends back to bond w N atom

- kind in the chain

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21
Q

What is the pKa of an acid?

A

The pH at when 1/2 of the molecules are dissociated

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22
Q

Biological significance of pH and pKa

A
  • Charge of amino acid varies w pH (as different amounts are dissociated)
  • If local environment is close to pKa, small pH changes can cause significant changes in overall charge
23
Q

Example of pH & pKa significance

A

LDL particle uptake

  • Binds to receptor on endoscope surface
  • Endocytosis
  • LDL into cell –> histidine pH = 6.5, BUT in endoscope pH = 5
  • Changes protein structure –> can’t bind anymore –> histidine released
24
Q

Peptide bond

A
  • Covalent

- C from COOH shares e-s w N from NH3

25
Q

Constraints of peptide bond

  • what
  • BUT
  • so
  • advantage
A
  • doesn’t permit rotation
  • BUT rotation can occur on central C
  • Conformation thus determined by one angle per amino acid
  • Limits no. of 3D confirmations
26
Q

Primary structure

A

Sequence of amino acids

27
Q

Secondary structure

A

Initial folding pattern, stabilised by H bonds

28
Q

3 types of secondary structure

A
  • Alpha-helix
  • Beta-sheet
  • Bend/loop
29
Q

Alpha-helix

  • direction
  • no of amino acids
  • H bonds
A
  • R handed (down rotation = clockwise)
  • 3.6 each turn
  • Between every 4th
30
Q

Beta-sheet

  • structure
  • H bonds
  • 2 types
A
  • At least 5 amino acids = beta-strand –> organised next to each other = sheets
  • Pattern depends on sheet
  • Parallel & anti-parallel
31
Q

Anti-parallel beta-sheet

  • structure
  • stability (& why)
A
  • Adjacent strands are orientated in SAME direction (N-end to C-end)
  • Often more stable –> as H bonds align more squarely
32
Q

Bend/loop

  • where
  • no. of amino acids
  • common amino acid
A
  • Connect helices & sheets
  • Normally 4 for a turn
  • Proline (as bends back on itself)
33
Q

Important of H bonds in protein structure

A

Stabilises secondary structure –> as needed for helices and sheets

34
Q

Tertiary structure

A
  • Folding due to bends/loops
  • Globular structure
  • e.g. hydrophobic residues get buried
35
Q

Interactions that stabilise tertiary structure x4

A
  • Disulphide (between 2 cysteine)
  • H bonds
  • Ionic
  • Hydrophobic interactions
36
Q

Quaternary structure

A

> 1 polypeptide –> forms oligomeric functional protein

37
Q

2 examples of quaternary structure

A
  • Stored insulin

- 70s ribosomes

38
Q

Stored insulin –> quaternary structure

A
  • 6 identical units

- Bound to Zn

39
Q

70s ribosomes –> quaternary structure

A
  • ~30 different subunits
40
Q

Haemoglobin structure x3

A
  • 2 alpha-globin & 2 beta-globing chains
  • Each contains a Haem molecule (= porphyrin ring w Fe atom)
  • Haem held in place by H bonds from His F8
41
Q

Effect of O2 binding on Haem structure

A
  • His F8 changes position (= the H bond that holds Haem in place)
  • Ring becomes more balances –> planar
  • Aids O binding to other Haems in the protein
42
Q

O2 binding affinity

  • 1st affinity
  • THEN
A
  • 1st O binding = low affinity

- BUT changes shape –> affinity increases

43
Q

Sickle cell anaemia

  • gene mutation
  • change in structure
  • effect
A
  • glutamic acid –> valine
  • beta-subunit w a hydrophobic region
  • molecules react differently to bury hydrophobic surface –> fibres
44
Q

Relationship between pH & O2 binding affinity

- SO –> example

A

Higher pH = higher affinity

- Lungs = high affinity, tissues = lower (so O2 is released)

45
Q

Oxygen delivery during exercise

A
  • CO2 build-up
  • More acidic
  • Lower affinity
  • Faster O2 delivery
46
Q

Foetal haemoglobin

  • structure
  • effect of difference
  • why difference needed
A
  • 2 alpha & 2 gamma subunits
  • gamma binds O2 at higher affinity (than beta)
  • low O2 when blood reaches placenta –> so needs to bind w greater affinity
47
Q

Tropocollagen

  • structure x2
  • strength added by
A
  • 3 polypeptide chains
  • Helical w l-handed twist
  • Strength added by r-handed supercoil
48
Q

Tropocollagen: role of glycine

A
  • R-group = H –> so tight turns –> tight packing
49
Q

Tropocollagen: role of proline x2

A
  • Bends back –> so imposes LH twist = stabilising

- Hydroxylation of proline forms H bonds

50
Q

Formation of collagen

- 3 steps involving 2 enzymes

A
  • 3 strands of procollagen
  • Procollagen peptidase cleaves off ends –> tropocollagen
  • These subunits assemble –> Lysyl oxidase joins them by forming covalent crosslinks
51
Q

Osteogenesis imperfecta

  • it causes….
  • gene mutation
  • effect
A
  • Brittle bones
  • Cysteine –> glycine
  • Kink in tropocollagen chain –> don’t pack properly –> collagen loses structure
52
Q

Scurvy

  • it causes…
  • it is due to…
  • effect of this
A
  • Dry skin, gum disorders
  • Lack of vitamin CC
  • Lack of proline hydroxylation –> no H bonds
53
Q

Ehlers-Danloss Syndrome

  • it causes…
  • it is due to…
  • effect of this
A
  • Loose skin, hypermobile joints
  • Lack of procollagen peptidase & Lysyl oxidase
  • Cross links can’t form between tropocollagen fibres

Semester 1 flashcards (33 decks)

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