Proteins and Amino acids

What is an amino acid?
Building block of protein, 20 different amino acids commonly found in proteins, contain C, H, O, N and occasionally S
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Describe the structure of an amino acid
Central carbon atom, carboxylic acid group, amino group, hydrogen atom, R-group (Differ between amino acids)
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Non-polar side chain
Hydrocarbon chains or rings (Alanine and phenylalanine)
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Polar but uncharged side chain
Contain hydroxyl or amide groups (Serine and tyrosine)
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Polar - acidic side chains
Contain carboxylic acid groups (Negatively charged at physiological pH) - Aspartic acid
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Polar - basic groups
Contain basic groups which are positively charged at physiological pH (Lysine)
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Special side chains
None of the above (Cysteine and glycine)
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What is a condensation reaction?
Where a new covalent bond is formed between 2 atoms with the release of a molecule of water
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What is a hydrolysis reaction?
A covalent bond is split by the addition of water
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What type of bond is formed between two amino acids?
Peptide bond
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What is formed when 2 amino acids are joined?
An amide
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Primary structure of proteins
The sequence of amino acids in a polypeptide, the primary structure is determined by the code on the DNA
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What bonds are in the primary structure?
Peptide bonds
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Secondary structure
Due to the formations of the hydrogen bonds (conformations that can be adopted by different parts of the polypeptide chain), forms a-Helix or B-pleated sheet
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What bonds are in the secondary structure?
Hydrogen bonds
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a-Helix
3.6 amino acids per turn, side chains (R-grous) face outside the helix, the C=O of one amino acid is hydrogen bonded to the N-H of the 4th amino acid away
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B-pleated sheet
Hydrogen bonds form between the C=O of an amino acid in one part of a protein chain with the N-H group of another amino acid elsewhere in the chain, can be parallel or anti-parallel depending on the relative directions of the protein chain
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Where are the side chains in the B-sheet?
Alternate above and below the strand
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What types of B-sheets can you get?
Parallel or anti parallel
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Tertiary structure
The overall 3D configuration of a protein, bending and folding of the secondary structure, shape held by interactions between amino acid side chains (R-groups)
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What bonds are in the tertiary structure?
Hydrogen bonding, electrostatic bonding, disulphide bridges and hydrophobic interactions
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Hydrophobic interactions
Non-polar chains are hydrophobic, associate together and repel/ are repelled by water, often found in the middle of the 3D structure
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Quaternary structure
The association between different polypeptides to form multi-subunit proteins, 2 or more individual polypeptides aggregate to form larger protein molecules
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What bonds are involved in the quaternary structure?
The same as those involved in tertiary structure
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Fibrous proteins
A protein that is not folded into a tertiary structure, usually have a quaternary structure, large proportions are in sheet or helical conformations, low water solubility, structural function, strong and/ or flexible
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Globular proteins
May have quaternary structure, complex tertiary structure, fold into compact specific forms, highly specific shape, structural diversity allows large number of functions, soluble, shape allows recognition of and binding to other molecules
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What are some functions of globular proteins?
Catalysis, transport, defence, regulation
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Fibroin (B-keratin)
Protein in silk, molecules pack alongside and above and below each other, anti parallel B-sheets, long regions where glycine alternates with alanine or serine, R-groups of alternate amino acids project on opposite sides of protein backbone
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a-keratin
Contains about 300 amino acids in a-helix form, non-helical regions at either end of helix, helical portion has repeating sequence of 7 amino acids w/ non-polar, hydrophobic residues at 1 and 4, side chains project outwards along an axis
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Collagen
Most abundant protein in mammals, structural, in extracellular matrix of connective tissue, 3 helical polypeptides a-chains, each chain 1000 residues long, every 3rd is glycine, high no. of proline and hydroxyproline
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What are the 2 main proteins in muscles?
Actin and myosin
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Actin
Globular protein, thin filaments, monomeric actin (G actin) is a globular protein which then polymerises to form long strands which then form a 2-stranded helical filament (F actin)
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Myosin
Fibrous protein with globular heads (which bind to actin), made from 6 different protein molecules, 2 identical heavy chains, 4 light chains
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Describe how the final structure of myosin is formed
tail regions of heavy chains coil around each other with heads bending away from each other at the neck, myosin molecules aggregate to form thick filament w/ heads at either end and a bare zone with no heads in the middle
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Myoglobin
Stores oxygen in muscle, monomer
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Haemoglobin
Transports oxygen in blood, tetramer (Polymer with 4 monomer units)
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Describe myoglobin affinity for oxygen
It has high saturation at normal tissue concentration, however when oxygen levels fall and the supply is low in the tissues, it has low saturation so releases oxygen
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Describe haemoglobin's affinity for oxygen
It has high saturation in lungs, low saturation in the tissues
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Insulin
Small polypeptide, hormone, glucose metabolism, transported readily in blood, only some tissues respond, protein receptor specific to insulin, binding initiates specific actions within cell
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Casein
Mammal milk. mixture of different proteins, a B k caseins, some phosphorylated, form sub-micelles by interacting through hydrophobic regions, form micelles through interactions between phosphate and calcium, highly polar chains on surface with water
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What are the 3 major proteins in eggs?
Ovalbumin, ovomucoid and conalbumin
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Ovalbumin
~60%, major source of amino acids for the growing chick
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Ovomucoid
~10%, Forms mucus-like gel by binding large numbers of water molecules (important allergen)
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Conalbumin
~10%, Protective effect by binding potentially dangerous heavy metals
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Antibodies
An immunoglobulin protein that binds to an antigen, produced by lymphocytes, bind to target molecule by 2 flexible arms, once antibodies have bound, special cells engulf and destroy antigen (Look at structure of antibody)
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Describe the solubility of protein
Held in suspension with water bonds as hydrogen bonds form between the polar groups of water and protein
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What can disturb the solubility of a protein?
Disrupting the hydrogen bonds (interactions)
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What is the iso-electric point (PI) of a protein?
The pH at which the net charge is 0
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When is a protein least soluble?
When the pH of a solution = the PI of the protein
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What can break the protein-water interactions?
A high concentration of ions (salts) as they interact more strongly with water
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What happens when proteins are in a alkaline solution with heavy metal ions?
In alkaline pH, proteins tend to have a negative charge on the surface so they react to the positively charged heavy metal ions, which can form larger complexes between proteins
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What happens in an acidic solution?
The positive charges on the protein surface increase and react with the negative charge on the complex anion, can form larger complexes between proteins
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What is the dielectric constant?
A measure of a substances ability to insulate charges from each other (Taken as a measure of solvent polarity)
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What does a high dielectric constant mean?
Higher polarity and greater ability to stabilise charges
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What is protein denaturing?
Disruption of protein structure resulting in unfolding of the protein, often exposure of hydrophobic groups which then aggregate causing precipitation
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Which structures are usually affected in protein denaturing?
Secondary and quaternary
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What can cause protein denaturing?
Detergents, heat, pH
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How do detergents denature proteins?
Disrupts hydrophobic interactions by having a higher affinity for non-polar side chains, resulting in exposure of hydrophobic residues, disrupting protein structure
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How does heat denature proteins?
Gives energy to the system so the atoms vibrate within the structure
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How does pH denature proteins?
pH depends on presence of H ions, when pH changes, the ionisation of some amino acid side chains also change, therefore changing electrostatic bonding, can result in tertiary unfolding
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What do buffers do?
Minimises the change in pH when there is an increase or decrease in H ions in a solution
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What are the 2 biological buffers?
Phosphate buffers and bicarbonate buffers
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Phosphate buffer
Based on the weak acid phosphoric acid, H3PO4, has 3 H atoms which can be replaced so it dissociates in 3 stages
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Bicarbonate buffer
Formed by CO2 dissolving in water to give H2CO3 which acts as a weak acid, under close control with CO2 controlled by respiration and HCO3- controlled by kidneys
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Exergonic reaction
A reaction that releases energy (Energy required to start the reaction is less than the energy released at the end of the reaction)
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Endogonic reaction
A reaction that requires energy (energy required to start the reaction is greater than the energy released at the end of the reaction)
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Activation energy
The energy required to make the reaction happen, e.g. heat
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Other cards in this set

Card 2

Front

Describe the structure of an amino acid

Back

Central carbon atom, carboxylic acid group, amino group, hydrogen atom, R-group (Differ between amino acids)

Card 3

Front

Non-polar side chain

Back

Preview of the front of card 3

Card 4

Front

Polar but uncharged side chain

Back

Preview of the front of card 4

Card 5

Front

Polar - acidic side chains

Back

Preview of the front of card 5
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