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41 Cards in this Set
- Front
- Back
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c=log(b)a, find a.
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a = b to the power of c
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List some roles of proteins.
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- enzymes-> catalysts
- Movement (across membrane eg proton transport complex)- ions and molecules - structure - immunity Proteins are polypeptide chains of amino acids formed by translation |
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Describe the classification of amino acids.
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Classified by Polarity of R group - tendency to interact with water at pH 7
- non polar- hydrophobic: aromatic (benzene ring- large) eg phenylalanine, tyrosine ( think PKU tyrosine is made from phenylalanine) aliphatic (no benzene ring- small) eg alanine and glycine. valine, ( most are small and hydrophobic to promote alpha helix except for proline - no H on amide - kinks, and glycine -too small and flexible more suited for other 2ndry structures) - polar- uncharged - serine and threonine ( O linked glycosylation), asparagine ( N linked glycosylation), glutamine ( most abundant aa in blood converted from glutatmate and ammonia - glutamine synthase) - polar negatively charged eg glutamate, aspartate ( transamination - aspartate aminotransaminase) - polar positively charged r groups eg arginine and lysine, histidine ( makes chromatin along with DNA - negatively charged) |
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Give examples of amino acids with large hydrophobic aromatic R groups, small hydrophobic aliphatic R groups, polar positively charged R groups and polar negatively charged R groups.
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hydrophobic:
large aromatic: tryptophan small aliphatic: alanine, glycine Hydrophilic: positively charged: lysine, arginine negatively charged: glutamate |
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Draw the basic structure of an amino acid.
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- central carbon atom with 4 covalent bonds leading to: amino group NH3+, carboxyl group COO-, H and R group
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Define stereoisomerism,
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- 2 unique spatial arrangements ( mirror images, non-superimposible)
- D &L forms - L-form of amino acids found naturally - alpha carbon- chiral centre bound to four different groups. - all amino acids have stereoisomers except glycine, R group = H |
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Draw and list the main points about the peptide bond.
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formed during translation by peptidyl transferase,
- elimenation of 1 mole of H2O- condensation reaction - O=C-N-H ( bond between C of carboxyl group and N of amino group) MAIN POINTS: - all atoms of the bond are in the same plane - no rotation around peptide bonds due to double bond attached to C. -carbonyl oxygen and amide hydrogen are in trans orientation - amino acids --> folding and structure of protein - side chains --> charge seen on the protein. |
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What is the isoelectric point (pI)?
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The pH at which protein has no overall net charge.
Acidic proteins- low pI - mainly negatively charged aas Basic proteins- high pI - mainly positively charged aas |
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What does pH > pI and pH < pI indcate.
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pH >pI indicates more DEPROTONATED forms ( because high pH= low [H+] )
pH < pI indicates more PROTONATED forms ( because low pH = high [H+]) |
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Define ionisation of amino acids stating which groups can ionise.
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Ionisation of amino acids is the gaining or lossing of protons. The amino and carboxyl group and some R groups can ionise.
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What is a zwitterion?
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Dipolar form of amino acids which lack an ionisable R group when dissolved in H20. pH determines relative amounts of protonated/ deprotonated forms.
NH2 + H <-> NH3+ COOH <-> COO- + H+ |
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Compare eukaryotes and prokaryotes.
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Eukaryotes: membrane bound organelles, 80s ribosomes, DNA enclosed in nucleus.
Prokaryotes: no membrane bound organells, 70s ribosomes, circular DNA plasmid, chromosomal DNA is naked in cytoplasm, pili( attach to solid surface, DNA exchange) capsule(barrier to phagocytosis), flagella |
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List the bonds found in monomeric units, macromolecules and describe their function.
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monomeric units - covalent bonds, sharing elections.
Macromolecules - non covalent weak interactions which are multiple bonds leading to stability eg hydrogen bonds, van de waals forces, ionic bonds, hydrophobic interactions. Breaking weak interactions- loss of structure and functions. |
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Compare hydrophobic and hydrophilic molecules.
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Hydrophobic molecules cannot form hydrogen bonds with water molecule ( lack H bonded to electronegative atom eg oxygen, chlorine or nitrogen) therefore they don't dissolve in water, instead they cluster with other hydrophobic molecules to form micelles.
Hydrophilic molecules do form hydrogen bonds with water and so can dissolve. Amphipathic - have both hydrophobic and hydrophillic regions eg phospholipid membrane. |
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What is pK?
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The pH when both forms( deprotonated and protonated) are in equal concentration. [H+] =[A-]
pH> pK - deprotonated form dominates as not many H+ ions pH < pK - protonated form dominates as there are many H+ ions |
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Give 2 forumulas for calculating pH.
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pH= -log(low10)[H+]
pH = pKa + log [A-]/[HA- acid before dissociation] |
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Define a buffer.
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A buffer is a solution of weak acid and its conjugate base that resists change in pH when a small amount of acid or alkali is added.
Biological processes are pH dependant. A change in pH effects charges on molecules and so effects their function. Buffers are important in homeostasis eg bicarbonate buffer. |
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Describe the bicarbonate buffer system in blood.
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CO2+ H20 <> H2CO3 <> HCO3- + H+
[CO2] in lungs is proportional to [CO2] dissolved in blood plasma (pH 7.4). Metabolically active tissues make a lot of co2 that lower the pH of the local blood causing a localised lowered of blood plasma pH.The bicarbonate buffer system quickly restores the pH back to 7.4 by HCO3- (biocarbonate ions) binding with the excess H atoms. Other organs of the body help to control the amounts of HCO3- ions and CO2 in the blood. The lung removes excess CO2 by increasing the rate of removal of CO2- hyperventilation. The kidney removes excess HCO3- ions from the blood. |
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What effect would a pulmonary obstruction have on blood pH?
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Blood pH would decrease because less CO2 is being exhaled by the lungs due to narrowing of the airways. Therefore [CO2] increases which increase [H+] in blood plasma, lowering blood pH.
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What is a hydrogen bond?
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A hydrogen bond is a weal electrostatic interaction formed between a delta negative, electronegative atom eg O,Cl,N and a delta positive H atom bonded to an electronegative atom. Many of these bonds create stability of molecule and maintain its structure and function. water molecules are constantly making and breaking H bonds.
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Given that the pH of the stomach is about 1.5 and the pH of the small intestine is about 6, is more aspirin( weak acid of pKa of 3.5) absorbed from the stomach or the small intestine.
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pH>pKa- deprotonated form dominates as less H+ ions, more are made
pH< pKa - protonated form dominates as more H+ ions present so less are made. In the stomach the carboxyl groups of aspirin will be protonated and so more easily absorbed across the membrane. |
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Why would a deprotonated(ionised) form of aspirin ( weak acid, pKa = 3.5) not pass readily through the plasma membrane?
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The carboxyl group of aspirin is able to ionise. Ionised aspirin will not be able to pass through a memembrane as it is charged and the membrane is hydrophobic. Therefore the uncharged form will more readily pass/
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Histones are proteins abundant in eukaryotic cell nuclei where they form part of chromatin. The pI of histones is very high at 10.8.
What charge will histones have under physiological condition? which type of amino acids must be present in large numbers in these proteins? why do you think histones have this charge? |
Under physiological conditions of pH=7.4, histones will be protonated ( pH< pI) and so have a positive charge (have positve H atoms)
A pI of 10.8 indicates basic amino acids present and they must have high pk values so that histones are positvely charged at physiological pH such as arginine and lysine. Chromatin is macromolecular complex containing DNA and histone proteins. Histones are positviely charged so they can form electrostatic interactions with the negatively charged DNA. |
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Define pH, Ka, acid, amphipathic, base, covalent bond, ionic bond.
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pH - a measurement of the concentration of H+ ions in solution ( pH =-log[H+], pH = pKa + [A-]/[HA]
Ka - acid dissociation constant, the tendency of an acid to dissociate, lose a proton. acid- a chemical that can dissociate to lose a proton ie proton donor base - a chemical that can combine with a hydrogen ion ie proton acceptor amphipathic - a molecule that has both a polar and non-polar end. covalent bond - bond formed between 2 atoms by the sharing of electrons ionic bond - a bond formed between 2 atoms where there is a complete transfer of an electron resulting in the formation of 2 ions (anion (-ve) and cation) |
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Describe what is meant by the primary, secondary, tertiary and quaternary structure of proteins.
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Primary structure- the linear amino acid sequence of the polypeptide chain. Defines overall structure and function of protein. Covalent Peptide bonds.
Secondary structure - the local spatial arrangement of the polypeptide back bone (c-n). Rigid peptide bonds, bonds either side of peptide bond are not rigid -> freely rotate. Regular secondary structure adopted when angles remain the same throughout a segment of polypeptide. Alpha or beta pleated sheet. Tertiary structure: 3D arangement of all atoms in the polypeptide. Folding up of the secondary structure (AAs far apart in primary structure can interact). Domains- regions of polypeptide that have distinct structures and particular roles eg substrate binding. H bonds, di- sulphide bonds, ionic and hydrophobic interactions and van der waals.( same as quaternary) Quaternary structure: 3D arrangement of the multi subunits within protein eg haemoglobin- 4 subunits. Homomeric- identical polypeptide chains Heteromeric- different polypeptide chains. |
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Explain the key features in the major secondary structures.
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Alpha - helix:
- right handed helix - 3.6 amino acids per turn - 0.54nm pitch ( distance of 1 turn - vertical distance between 2 consequtive turns on a helix) - hydrogen bonds form between N-H group and the C=O group. - small hydrophobic AAs are strong helix formers eg alanine and leucine. - proline - kinks or breaks helix as can't form hydrogen bond, no amide hydrogen. - glycine - Tiny R group supports other conformations- very flexible. Beta pleated sheet - extended conformation: parallel or antiparallel - parallel - more bent H bonds-> less stable - Antiparallel sheets -> strong ordered H bonds -> stable - mixture of both possible - R groups alternate between opp. sides of chain |
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Compare fibrous and globular proteins.
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Fibrous:
- usually insoluble, - long strands or sheets, - little or no tertiary structure - single type of repeated secondary structure - structural role usually eg collagen Globular - Usually soluble - compact - complex tertiary structure - several types of secondary structure - many roles including catalysis and regulation eg enzymes |
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Describe the types of bonds and forces involved in proein structure.
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1- Covalent peptide bonds - sharing electrons
2- Covalent disulphide bridges - s-s in cysteine residues - very strong - broken with reducing agents eg NADPH - most common in secreted proteins. 3- Electrostatic attractions/ ionic interactions - formed between charged atoms - salt bridges - 5-10% strength of covalent bond 4- Hydrogen bonds - a weak electrostatic interaction formed between an electronegative atom (O,N,Cl) and a H atom which is attached to an electronegative atom. - same strengh electrostatic interaction 5- Hydrophobic interactions - grouping of hydrophobic side chains -> displace water - weak, broken up by detergents and organic solvents 6- Van der waals - weak dipole-diplole attraction - important when surfaces of 2 large molecules come together |
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How do proteins fold?
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Information to fold is within primary sequence -> fold spontaneously
Molecular chaperones assist some proteins eg in mitochondrial targeting proteins - peptides fold in matrix with help of ATP and molecular chaperones. Amyloidoses - misfolds -associated with alzeihmers |
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How does a protein become denatured.
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Denaturation is the breaking of forces which hold the protein together.
1- heat -> increase in vibrational energy 2- pH - alters ionisation states of amino acids, changes charges so changes bond formation eg ionic and hydrogen bonds do or don't form. 3- detergents and organic solvents disrupt hydrophobic interactions. |
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Explain the phsiological roles of myoglobin and haemoglobin.
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myoglobin is found in skeletal muscle as an oxygen store - pink pigment.
Haemoglobin is found in the bloodstream: To transport oxygen in the bloodstream from lungs to tissues - oxygen is non polar so doesn't dissolve in blood but must be transported - Also transports CO2 and H+ ions to meet oxygen demands |
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Explain the importance of haem in oxygen transport carriers.
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- porphyrin ring derivative
- central iron atom is the site of reversible oxygen binding - one molecule of O2 binds to it |
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In oxygen transport carriers, how does the binding of O2 change the conformation of protein from tense to relaxed?
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O2 binds to the Fe atom in the porphyrin ring, which causes movement of Fe from slighly below the plane of the ring, to into the plane of the ring.This causes a change in overall protein conformation and so the following oxygens bind more easily to the 3 other subunits.
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Contrast the oxygen binding properties of myoglobin and haemoglobin and explain why haemoglobin is most suited to its role as an oxygen transporter.
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Myoglobin is a single subunit and so can only bind one molecule of O2 at a time. Haemoglobin however is tetrameric - 4 subunits and so can bind 4 O2 molecules at a time. Therefore myoglobin exhibits hyperbolic binding as it has no co-operativity but as haemoglobin is an allosteric protein it has co-operative binding where the binding of the first oxygen molecule changes the conformation of the protein from tense to relax state allowing the following oxygens to bind more easily. Hence haemoglobin shows sigmoidal oxygen binding. The oxygen binding in haemoglobin makes it a much better oxygen transporter as it means more oxygen is released at low partial pressures of oxygen eg tissues and more oxygen is picked up at high PO2 eg lungs.
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Describe the major structural differences between oxygenated and deoxygenated haemoglobin and the molecular basis of cooperativity.
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Low affinity for oxygen Tense state= deoxygenated
High affinity for oxygen Relaxed state = oxygenated - oxygen molecule bound to Fe in haem and risen Fe into the same plane as the porphyrin ring, changing conformation of haemoglobin. This change in conformation to R state makes the following oxygen molecules bind more easily to the subunits, cooperativity - sigmoidal oxygen binding. It also makes haemoglobin more sensitive to small changes in [O2] - A Little change in O2 can cause readily binding of O2 are fast dissociation of O2. |
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Describe the effects of carbon monoxide on the binding of oxygen by haemoglobin, and the physiological significance of these effects.
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Carbon monoxide poisoning. CO binds irreversibly with haemoglobin and myoglobin and so blocks O2 transport. It increases the affinity for O2 of other subunits so no o2 is released. Fatal when COHb > 50% - blood transfusion needed or fatal.
CO binds 250 times more readily than O2. |
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Explain how oxygen binding by haemoglobin is regulatated in the body?
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2,3-bisphosphoglycerate(made from 3C during glycolysis) (BPG) is present in RBCs
- 1 BPG molecule binds per tetramer to DECREASE the affinity of haemoglobin fo oxygen. The dissociation curve shifts to the right so that higher PO2 are needed for the same saturation. BPG therefore promotes release of O2 to tissues and [BPG] increases at high altitudes. BPG affects HbA more than HbF so foetus stays alive. BFG concentration is increased in blood by training, so more oxygen is delivered to tissues and exercise can go on for longer. The bohr effect: CO2 and H+ ions binds to Hb lowering its affinity for oxygen, favouring T state. These acidic components are produced by metabolically active tissue and so cause more O2 to be released to the tissues for respiration, ensuring O2 delievery is coupled by demand. |
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Why are peptide bonds important for the secondary structure of proteins.
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Peptide bonds are rigid and so form the structured backbone of the secondary structure, with the other groups rotating to form the shape. Hydrogen bonds form between , the N-H group of one amino acid and the C=O group of another.
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Proteins that span biological membranes often contain alpha helices. Given that the inside of the membranes are hydrophobic in nature and that they are approximately 3nm in width, what types of amino acids would exist in such a helix? what would be the minumum number of amino acids needed to pan such a membrane?
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Small hydrophobic aliphatic amino acids eg leucine and alanine. Not proline - kinks/ breaks helix, can't form hydrogen bonds, not glycine - too flexible, promotes other forms of folding.
pitch = 0.54nm, 3.6 aa per turn, membrane = 3nm 3/0.54 =0.056 0.056* 3.6 = 20 aa |
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Describe some mutations in globin genes that give rise to diseases.
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Sickle cell anaemia: - base mutation leading to acid mutation of polar negative GLU -> small aliphatic hydrophobic VAL in beta chains.
- hydrophobin molecules polymerise by forming interactions during T state of Hb - Polymerisation distorts RBC - sickled - transition from distorted deoxygenated T state to released from distortion, oxygenated R state causes stress on RBC membrane and eventually it becomes stiff and remains in sickled form. - Sickled form more prone to lysis, causes anaemia and blocks vessels - Vessels blocked during sickle crisis due to increased polymerisation because of: cold, dehydration, acidosis, infection, hypoxia. Thalasaemia: Sympton = anaemia alpha - alpha chains decreased or absent, varying levels of severity, stable tetramers formed but reduced affinity for O2, onset before birth Beta - beta chains decreased or absent, unstable tetramers, symptoms appear after birth. |
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Explain how foetal haemoglobin is different to maternal haemoglobin.
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HbF has 2 gamma subunits instead of 2 beta subunits. This gives fetal haemoglobin a higher affinity fo oxygen and so allows the transfer of oxygen from maternal blood to fetal blood.
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