Structure of Proteins Flashcards
1
Q
Protein functions x5
A
- Structure
- Transport molecules
- Defence
- Biological catalysts
- Regulation of genes
2
Q
Example - structural protein
- function
- where
- structure
A
Collagen
- Strength, flexibility
- Main component of connective tissue
- Strong fibres in lattice-like structure
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
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
5
Q
Example - biological catalyst
- function
- where
A
Lysozyme
- An enzyme –> catalyses cutting of polysaccharide chains
- In lysosomes
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
7
Q
Proteins
A
Large, complex, linear polymers, w a hierarchy of structure
8
Q
Amino acids
A
- Central C atom, w amino & carboxylate groups
- R group –> unique to each & defines structure and function
9
Q
Polypeptides
A
Amino acids are joined by peptide bonds
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)
11
Q
Prosthetic group (& example)
A
Non-polypeptide into incorporated into protein structure
- e.g. Haem group in haemoglobin
12
Q
Amino (N) terminus
A
NH3+
13
Q
Carboxyl (C) terminus
A
COO-
14
Q
3 classification groups
A
- Hydrophilic (polar)
- Hydrophobic
- Special
15
Q
3 groups in the hydrophilic class
A
- Basic (+ve R)
- Acidic (-ve R)
- Polar (uncharged R)
16
Q
Common properties of hydrophobic class x2
A
- Long hydrocarbon chains
- Bulky aromatic groups
17
Q
The 3 special amino acids
A
- Cysteine
- Glycine
- Proline
18
Q
Cysteine property
A
Forms S-S bonds w other Cys
19
Q
Glycine property
A
R group = H
- no bulky side chain, so can fit in tight spaces
20
Q
Proline
A
R group bends back to bond w N atom
- kind in the chain
21
Q
What is the pKa of an acid?
A
The pH at when 1/2 of the molecules are dissociated
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
Constraints of peptide bond
- what
- BUT
- so
- advantage
- 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
Primary structure
Sequence of amino acids
27
Secondary structure
Initial folding pattern, stabilised by H bonds
28
3 types of secondary structure
- Alpha-helix
- Beta-sheet
- Bend/loop
29
Alpha-helix
- direction
- no of amino acids
- H bonds
- R handed (down rotation = clockwise)
- 3.6 each turn
- Between every 4th
30
Beta-sheet
- structure
- H bonds
- 2 types
- At least 5 amino acids = beta-strand --> organised next to each other = sheets
- Pattern depends on sheet
- Parallel & anti-parallel
31
Anti-parallel beta-sheet
- structure
- stability (& why)
- Adjacent strands are orientated in SAME direction (N-end to C-end)
- Often more stable --> as H bonds align more squarely
32
Bend/loop
- where
- no. of amino acids
- common amino acid
- Connect helices & sheets
- Normally 4 for a turn
- Proline (as bends back on itself)
33
Important of H bonds in protein structure
Stabilises secondary structure --> as needed for helices and sheets
34
Tertiary structure
- Folding due to bends/loops
- Globular structure
- e.g. hydrophobic residues get buried
35
Interactions that stabilise tertiary structure x4
- Disulphide (between 2 cysteine)
- H bonds
- Ionic
- Hydrophobic interactions
36
Quaternary structure
> 1 polypeptide --> forms oligomeric functional protein
37
2 examples of quaternary structure
- Stored insulin
| - 70s ribosomes
38
Stored insulin --> quaternary structure
- 6 identical units
| - Bound to Zn
39
70s ribosomes --> quaternary structure
- ~30 different subunits
40
Haemoglobin structure x3
- 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
Effect of O2 binding on Haem structure
- 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
O2 binding affinity
- 1st affinity
- THEN
- 1st O binding = low affinity
| - BUT changes shape --> affinity increases
43
Sickle cell anaemia
- gene mutation
- change in structure
- effect
- glutamic acid --> valine
- beta-subunit w a hydrophobic region
- molecules react differently to bury hydrophobic surface --> fibres
44
Relationship between pH & O2 binding affinity
| - SO --> example
Higher pH = higher affinity
| - Lungs = high affinity, tissues = lower (so O2 is released)
45
Oxygen delivery during exercise
- CO2 build-up
- More acidic
- Lower affinity
- Faster O2 delivery
46
Foetal haemoglobin
- structure
- effect of difference
- why difference needed
- 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
Tropocollagen
- structure x2
- strength added by
- 3 polypeptide chains
- Helical w l-handed twist
- Strength added by r-handed supercoil
48
Tropocollagen: role of glycine
- R-group = H --> so tight turns --> tight packing
49
Tropocollagen: role of proline x2
- Bends back --> so imposes LH twist = stabilising
| - Hydroxylation of proline forms H bonds
50
Formation of collagen
| - 3 steps involving 2 enzymes
- 3 strands of procollagen
- Procollagen peptidase cleaves off ends --> tropocollagen
- These subunits assemble --> Lysyl oxidase joins them by forming covalent crosslinks
51
Osteogenesis imperfecta
- it causes....
- gene mutation
- effect
- Brittle bones
- Cysteine --> glycine
- Kink in tropocollagen chain --> don't pack properly --> collagen loses structure
52
Scurvy
- it causes...
- it is due to...
- effect of this
- Dry skin, gum disorders
- Lack of vitamin CC
- Lack of proline hydroxylation --> no H bonds
53
Ehlers-Danloss Syndrome
- it causes...
- it is due to...
- effect of this
- Loose skin, hypermobile joints
- Lack of procollagen peptidase & Lysyl oxidase
- Cross links can't form between tropocollagen fibres
