MGD S1 - Amino Acids, Protein Folding and Function Flashcards
Describe a prokaryotic cell
Bacteria have no separate nucleus, contain a cell wall and a plasma membrane, and lack most organelles
How do antibiotics work?
They exploit the differences between prokaryotes and eukaryotes
Name the Level 1 cell/organelle, Level 2 macromolecular complex, Level 3 macromolecules and Level 4 monomeric units of the nucleus, ER and ER/Golgi/membrane
Nucleus - chromatin - DNA/protein - nucleotides/amino acids ER - ribosome - protein/RNA - amino acids/nucleotides ER/Golgi/membrane - membrane - protein/oligosaccharide - amino acids/sugars
How are monomeric units joined?
By covalent bonds to form macromolecules
How are macromolecules/complexes held together?
By non-covalent interactions
Describe the weak interactions between biomolecules
Formation of macromolecules and complexes requires weak, non-covalent interactions. Multiple weak interactions increases the stability of these complexes. Breaking interactions causes loss of structure and function
What does electrostatic mean?
Involves charges
What does solubility depend on?
The ability to form hydrogen bonds. Polar biomolecules form H bonds and dissolve. Non-polar molecules cannot form H bonds and are insoluble
What happens to amphipathic molecules in aqueous solution?
Hydrophobic regions cluster together. Hydrophilic regions interact with water
What are amphipathic molecules?
They have polar and non-polar regions
Describe a micelle
Hydrophobic groups away from water. Ordered shell of water that interacts with hydrophilic head groups
Describe the fluid mosaic model of a membrane
Lipid bilayer. Proteins embedded in the bilayer
List some of the crucial roles that proteins play in virtually all biological processes
- Catalysts - enzymes - Transporters (e.g. Fe, O2) - Structural support (e.g. collagen in skin and bones) - Machines (e.g. muscular contraction and motion) - Immune protection (e.g. immunoglobulins) - Ion channels - Receptors (for hormones, neurotransmitters etc) - Ligands in cell signalling (growth factors etc) CIRL MIST
Describe the key features of proteins
- Proteins are polypeptides: macromolecules made up of amino acid residues - The amino acid sequence of a protein is encoded by a gene: the nucleotide sequence of a gene determines the amino acid sequence of a protein - The polypeptide chain folds into a complex and highly specific 3D structure, determined by the sequence of amino acids - The folding of proteins depends on the chemical and physical properties of the amino acids - The 3D shape is important for the function of the protein
What are amino acids?
The building blocks of proteins. They consist of a central carbon atom (the alpha carbon) covalently bonded to: - an amino group (-NH2) - a carboxyl group (-COOH) - a hydrogen atom (-H) - a distinctive R group (side chain)
Describe ionisation of an amino acid
Both the carboxyl group (-COOH) and the amino group (-NH2) can ionise Base: NH2 + H+ -> NH3+ Acid: COOH -> COO- + H+
Give the two stereoisomers of amino acids
L isomer = the isomer found in proteins. Non super-imposable and not a mixture. D isomer is not naturally occurring in proteins
How are amino acids classified?
According to the chemical properties of the R groups. Only one alpha-NH3+, at the N terminal end, and one alpha-COO-, at the C terminal end. Acid-base behaviour determined by the R groups
What is an amino acid residue?
The part of the amino acid left after a peptide bond is formed
Give the classifications of amino acids
- Non-polar (hydrophobic) amino acids: glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tryptophan - Polar (hydrophilic) uncharged amino acids: serine, threonine, asparagine, glutamine, tyrosine, cysteine - Polar (hydrophilic) charged amino acids: lysine, arginine, histidine, aspartame, glutamate
What can cause problems with amino acids?
- If a small amino acid is mutated to a big one - Big side chains
Describe the effects of the difference between the pH of the solution and the pK value
- If the pH of the solution is bigger than the pK value then the group will be deprotonated
- If the pH of the solution is smaller than the pK value then the group will be protonated
Describe peptide bond formation
The linking of two amino acids is accompanied by the abstraction of a water molecule
Describe the features of peptide bonds
- They are planar: alpha-carbon, C, O, N, H and alpha-carbon all lie in a plane - C-N has partial double bond characteristics which makes it rigid and planar - It is shorter than expected, so stronger due to delocalised electrons
Describe the difference between cis and trans peptide bonds
- Trans: alpha-carbons on opposite sides of peptide bond. Occurs naturally - Cis: alpha-carbons on same side of peptide bond, leading to steric clashes. Doesn’t occur naturally
Outline the importance of amino acids in proteins
The amino acid sequence of a protein determines: - the way in which the polypeptide chain folds - the physical characteristics of the protein
What is the isoelectric point (pI)?
The isoelectric point, pI, of a protein is the pH at which there is no overall net charge
- Basic proteins, pI greater than 7, contain many positively charged (basic) amino acids
- Acidic proteins, pI less than 7, contain many negatively charge (acidic) amino acids
- pH less than pI, the protein is protonated
- pH greater than pI, the protein is deprotonated
Describe the size of different peptides and proteins
- Peptides/oligopeptides: a few amino acids in length (less than 100)
- Polypeptides/proteins: many amino acids
What are conjugated proteins?
Some proteins contain covalently linked chemical components in addition to amino acids
What are the different levels of protein structure?
- Primary structure: the linear amino acid sequence of the polypeptide chain - Secondary structure: local spatial arrangement of polypeptide backbone - Tertiary structure: 3D arrangement of all atoms in a polypeptide - Quaternary structure: 3D arrangement of protein subunits
Describe protein conformation
Covalent (peptide) bonds hold primary structure together. Angles determine the conformation of peptide backbone and hence the “fold” of the protein
Describe the structure of an alpha helix (secondary structure)
- 3.6 amino acids per turn - 0.54nm pitch (5.4Å) - Right-handed helix - R groups play no part in formation of the helix - 1.5nm between each residue - The backbone -C=O group of one residue is H bonded to the -NH group of the residue four amino acids away
How does sequence affect alpha helix stability?
- Not all polypeptide sequences adopt alpha-helical structures - Small hydrophobic residues such as Ala and Leu are strong helix formers - Pro acts as a helix breaker because the rotation around the N-alpha carbon bond is impossible - Gly acts as a helix breaker because the tiny R-group supports other conformations
Describe the structure of a beta strand
- Fully extended conformation - 0.35nm between adjacent amino acids - R groups alternate between opposite sides of chain
Describe the structure of an antiparallel beta sheet
Adjacent beta strands run in opposite directions, with multiple inter-strand H bonds stabilising the structure
Describe the bonds of a parallel beta sheet
H bonds at more of an angle Also get mixed beta sheets
Describe the structure of ferritin and fatty acid binding protein
- Iron storage protein ferritin - largely alpha helix - Fatty acid binding protein - largely beta sheet
What is tertiary structure?
The spatial arrangement of amino acids far apart in the protein sequence
Compare globular and fibrous proteins
- Fibrous: role is support, shape, protection. Long strands or sheets. Single type of repeating secondary structure. For example collagen - Globular: role is catalysis and regulation. Compact shape. Several types of secondary structure. For example haemolytic
What are the different specialised cell types?
- Epithelial cells - Nerve cells - Adipocytes - Muscle cells - Red blood cells DNA same, differences due to proteins expressed
Describe collagen
Triple helical arrangement of collagen chains. Contain Gly-X-Y repeating structure. Hydrogen bonds stabilise interactions between chains. Collagen fibrils formed from covalently cross-linked collagen molecules
Describe the variety of tertiary structures of globular proteins
- Motifs: folding patterns containing 1 or more elements of secondary structure. E.g. beta-alpha-beta loop, beta-barrel - Domains: part of a polypeptide chain that fold into a distinct shape. Often have a specific functional role. E.g. calcium-binding domains of troponin C
Describe the folding of water-soluble proteins
Polypeptide chains fold so that the hydrophobic side chains are buried and polar, charged chains are on the surface e.g. myoglobin
Describe the folding of membrane proteins
Membrane proteins often show “inside-out” distribution of amino acids e.g. porins: water-filled hydrophilic channel and largely hydrophobic exterior
Describe the quaternary structure of haemoglobin and a ribosome
- Haemoglobin - 2 alpha and 2 beta subunits - Ribosome - 55 protein subunits and 3 RNA molecules
What are the forces involved in maintaining protein structure at the different levels?
- Primary: covalent (peptide) - Secondary: H-bonds - Tertiary: covalent (disulphide), ionic, H-bonds, Van der Waals, hydrophobic - Quaternary: covalent (disulphide), ionic, H-bonds, Van der Waals, hydrophobic
Describe covalent (disulphide) bonds
- Formed between Cys residues - 214 kJ/mol - Can be broken by reducing agents e.g. beta-mercaptoethanol - Work for longer - strong bonds - Most proteins with disulphide bonds are secreted e.g. ribonuclease - Proteins are quite fragile
Describe electrostatic interactions
- Formed between charged groups e.g. Glu-, Asp- and Arg+, Lys+, His+ - 10-30 kJ/mol - Salt bridge
Describe hydrogen bonds
- Formed between electronegative atom and a hydrogen bound to another electronegative atom - 10-30 kJ/mol
Describe the hydrophobic effect
- Interactions between hydrophobic side chains - Due to displacement of water - ~10 kJ/mol - Not bonds
Describe Van der Waals forces
- Dipole-dipole interactions - 4 kJ/mol - Important when surfaces of 2 large molecules come together
Describe protein denaturation
- Proteins are not very stable - Disruption of protein structure is known as denaturation - Caused by breaking of forces that hold proteins together: - Heat increases vibrational energy - pH alters ionisation states of amino acids and changes ionic/H bonds - Detergents / organic solvents disrupt hydrophobic interactions
How do proteins fold?
- All the information needed for folding is contained in the primary sequence - Folding is not a random process but may proceed through localised folding - Some proteins need chaperones to assist in folding: stop a protein mis-folding by holding onto it
What is the problem with protein mis-folding?
- Can cause disease - Transmissible spongiform encephalopathies e.g. BSE, kuru, CJD - Altered conformation of a normal human protein promotes the conversion of the existing protein into a diseased state - e.g. PrPc -> PrPSc causes the formation of big aggregates
What are amyloidoses?
Big clusters of mis-folded proteins
Describe the formation of amyloid fibres
- They are a mis-folded, insoluble form of a normally soluble protein that cause disease - Highly ordered with a high degree of beta-sheet - Core beta-sheet forms before the rest of the protein - late-onset diseases - Interchain assembly stabilised by hydrophobic interactions between aromatic amino acids
When are amino acids aromatic and when are they aliphatic? Give examples of each
Aromatic when they contain a benzene ring, aliphatic when straight chain
- Aromatic R groups: phenylalanine, tyrosine, tryptophan
- Polar, uncharged R groups: serine, threonine, cysteine, asparagine, glutamine
- Non-polar, aliphatic R groups: glycine, alanine, proline, valine, leucine, isoleucine, methionine
- Negatively charged R groups: aspartate, glutamate
- Positively charged R groups: lysine, arginine, histidine
