Structure of Proteins Flashcards
Protein functions x5
- Structure
- Transport molecules
- Defence
- Biological catalysts
- Regulation of genes
Example - structural protein
- function
- where
- structure
Collagen
- Strength, flexibility
- Main component of connective tissue
- Strong fibres in lattice-like structure
Example - transport protein
- function
- where
- structure
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
Example - defence protein
- function
- where
- structure
Antibody
- Binds to specific antigens
- Released into bloodstream
- Y-shaped, w 2 heart & 2 light chains, liked by disulphide bonds
Example - biological catalyst
- function
- where
Lysozyme
- An enzyme –> catalyses cutting of polysaccharide chains
- In lysosomes
Example - genetic regulator protein
- function
- where
Lac Repressor Protein
- Binds to DNA sequences upstream from genes coding for lactose metabolising proteins –> prevents these being expressed in absence of lactose
- Bacteria
Proteins
Large, complex, linear polymers, w a hierarchy of structure
Amino acids
- Central C atom, w amino & carboxylate groups
- R group –> unique to each & defines structure and function
Polypeptides
Amino acids are joined by peptide bonds
Position of R groups in polypeptides & 2 effects
- Tend to alternate being on either side
- Less bulky –> so more stable
- Can create hydrophilic vs hydrophobic sides (as diff. groups have diff. properties)
Prosthetic group (& example)
Non-polypeptide into incorporated into protein structure
- e.g. Haem group in haemoglobin
Amino (N) terminus
NH3+
Carboxyl (C) terminus
COO-
3 classification groups
- Hydrophilic (polar)
- Hydrophobic
- Special
3 groups in the hydrophilic class
- Basic (+ve R)
- Acidic (-ve R)
- Polar (uncharged R)
Common properties of hydrophobic class x2
- Long hydrocarbon chains
- Bulky aromatic groups
The 3 special amino acids
- Cysteine
- Glycine
- Proline
Cysteine property
Forms S-S bonds w other Cys
Glycine property
R group = H
- no bulky side chain, so can fit in tight spaces
Proline
R group bends back to bond w N atom
- kind in the chain
What is the pKa of an acid?
The pH at when 1/2 of the molecules are dissociated
Biological significance of pH and pKa
- 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
Example of pH & pKa significance
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
Peptide bond
- Covalent
- C from COOH shares e-s w N from NH3
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
Primary structure
Sequence of amino acids
Secondary structure
Initial folding pattern, stabilised by H bonds
3 types of secondary structure
- Alpha-helix
- Beta-sheet
- Bend/loop
Alpha-helix
- direction
- no of amino acids
- H bonds
- R handed (down rotation = clockwise)
- 3.6 each turn
- Between every 4th
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
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
Bend/loop
- where
- no. of amino acids
- common amino acid
- Connect helices & sheets
- Normally 4 for a turn
- Proline (as bends back on itself)
Important of H bonds in protein structure
Stabilises secondary structure –> as needed for helices and sheets
Tertiary structure
- Folding due to bends/loops
- Globular structure
- e.g. hydrophobic residues get buried
Interactions that stabilise tertiary structure x4
- Disulphide (between 2 cysteine)
- H bonds
- Ionic
- Hydrophobic interactions
Quaternary structure
> 1 polypeptide –> forms oligomeric functional protein
2 examples of quaternary structure
- Stored insulin
- 70s ribosomes
Stored insulin –> quaternary structure
- 6 identical units
- Bound to Zn
70s ribosomes –> quaternary structure
- ~30 different subunits
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
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
O2 binding affinity
- 1st affinity
- THEN
- 1st O binding = low affinity
- BUT changes shape –> affinity increases
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
Relationship between pH & O2 binding affinity
- SO –> example
Higher pH = higher affinity
- Lungs = high affinity, tissues = lower (so O2 is released)
Oxygen delivery during exercise
- CO2 build-up
- More acidic
- Lower affinity
- Faster O2 delivery
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
Tropocollagen
- structure x2
- strength added by
- 3 polypeptide chains
- Helical w l-handed twist
- Strength added by r-handed supercoil
Tropocollagen: role of glycine
- R-group = H –> so tight turns –> tight packing
Tropocollagen: role of proline x2
- Bends back –> so imposes LH twist = stabilising
- Hydroxylation of proline forms H bonds
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
Osteogenesis imperfecta
- it causes….
- gene mutation
- effect
- Brittle bones
- Cysteine –> glycine
- Kink in tropocollagen chain –> don’t pack properly –> collagen loses structure
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
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
