Biological Molecules

pH
pH = -log [H+] Kw = [H+].[OH-] = 10-14 M2

Strong acids – nearly completely disassociate in water. Weak Acids – Partially disassociate.

1

opposes change in pH. Amino Acids  Proteins This diagram explains the rigidity and the planar properties of the peptide bond. as electrons are delocalised across it.HA ↔ H+ + A[ [ ][ ] ] In weak acids pH = pKa + log ([A-]/ [HA]). Where pKa of a weak acid is where it is 50% protonated. Titration of a weak acid Buffer – weak acid & conjugate base. It is defined by a solution whose pH remains virtually unchanged by dilution or by the addition of acid or alkali. As it gives the C-N bond double bond type structure. 2 . Chief buffer in blood and extracellular fluids is the bicarbonate (H2CO3/HCO3-) system.

-CH2-CH3) Basic – Arginine. Makes either a α-helix or β-sheet. Phenylalanine. Tertiary structure: The three-dimensional arrangement of all atoms in a single polypeptide chain. Histidine (-CH2CH2NH2+) Acidic – Aspartate.g. Isoleucine. Cysteine (-SH) Cyclic – Proline – side chain joined to both the α carbon and the amino group Enzymes Enzyme assays are laboratory methods for measuring enzymatic activity.    Primary structure: The linear amino acid sequence of the polypeptide chain. Leucine. The primary structure determines all higher order structure. Tryptophan.g. Lysine. Threonine Aromatic – Phenylalanine. Leucine (e. Enzyme activity is expressed in standard units. Histidine. Methionine. Arginine. One unit (U) is the enzyme activity at 25oC which under optimum conditions of pH. Valine. benzene ring) Alipathic – Glycine. Secondary structure: Local structure of linear segments of the polypeptide backbone atoms. Isoleucine. Lysine. substrate and co-factors converts 1 μ mole min-1. Alanine. Quaternary structure: The arrangement of separate polypeptide chains (subunits) in the protein. 3 . Glutamate (-COO-) Sulphurous – Methionine. Tyrosine (e. In the α-helix the backbone –C=O group of one residue is H-bonded to the –NH group of the residue four amino acids away. Valine. Amino Acids Essential – Tryptophan. Β-sheets can be parallel where polypeptide chains are going in the same direction or anti-parallel or mixed.

‘Isoenzymes’ are variant forms of enzymes that catalyse the same reaction but differ slightly in structure and kinetic behaviour. Enzyme Regulatory Strategies There are 4 principal ways of regulating enzyme activity. Molecule added ATP Acetly CoA NAD HCO3Example of enzyme acted on Glycogen phosphorylase Histones RNA polymerase prothrombin  Modification Phosphorylation Acetylation ADP.  Allosteric control. (E. Catalytic properties are changed by the covalent attachment of a modifying group.g. 4 . ATP is the phosphoryl donor and the reactions are catalysed by protein kinases. allows derivation of an equation that relates Vo to [S]. Also active by F2. so it depends on the amount of enzyme present. though Km is unaffected. as follows: Vo = Vmax [S]/(KM + [S]) Inhibition Km is the concentration of substrate where the rate of reaction is half of Vmax. phosphorylase kinase A (PKA) in glycogen breakdown. Binding of a ligand at the regulatory site brings about a conformational change in the enzyme that affects the active site.The Michealis-Menten Equation The model proposes that a specific complex between the enzyme and the substrate is a necessary intermediate in catalysis. Example: Haemoglobin. Vmax affected by non-competitive.ribosylation g-carboxylation Phosphorylation uses kinases to donate phosphate from ATP acts upon Serine (regulating enzyme activity) or Tyrosine (regulating protein activity) i. Reversible covalent modification. Two states R(elaxed) (high aff.) & T(ense). The regulatory site and the active site are different. The phosphate groups can be removed by hydrolysis carried out by phosphatases. and inhibited by H+ (anaerobic respiration)  Multiple forms of enzymes. so no effect on Vmax. Km affected by competitive. Lactate dehydrogenase) – It allows for fine tuning of metabolic processes.e.6bisPi. Assuming steady-state. Vmax is the maximum observable velocity of the reaction. commonly a phosphoryl group. phosphofructokinase (fundamental step in glycolysis) PFK is inhibited by ATP (to T state) and AMP and ADP cause the R state. adding enough substrate will always overcome the effect of the inhibitor. when the rates of formation and breakdown of ES are equal.

(e. Since the proteins may be enzymes. A single activated kinase can phosphorylate hundreds of target proteins in a few seconds. Many enzymes are activated by cleavage of one or more peptide bonds in inactive precursors called zymogens or proenzymes. insulin. by covalent binding of a phosphate group. partial digestion of a protein. 2. Phosphorylation is a very effective means of controlling the activity of proteins: 2. 4. 5. digestive enzymes) Phosphorylation in depth 1. Phosphorylation often generates high amplification. Proteolysis is the cascade activation mechanism responsible for the blood clotting mechanism.Acetylation acts upon Lysine changing the charge of the residue. changing the potential for electrostatic interactions. the use of this compound as the phosphoryl donor links the energy status of the cell to the regulation of metabolism. 3. 104) to the conformational equilibrium between different functional states of the protein. Synthesis: Glycogenn + UDP-glucose  glycogenn+1 + UDP Degradation: Glycogenn+1 + Pi  glycogenn + glucose-1-phosphate Enzyme Cascades They involve a series of enzymes. This type of covalent modification is irreversible. Phosphorylation of protein/enzyme components of a cascade. there is the potential for amplification via a cascade of successive events. Phosphorylation alters the thermodynamics of the protein and can make a large change (ca. may be the activating factor. The phosphoryl group adds two negative charges to a modified protein. This type of activation can be simply revered by phosphatase-catalysed removal of the phosphate group. extrinsic and final common pathways. Cascade activation mechanisms can work in two ways: 1. Example: Glycogen metabolism. A phosphate group can form three or more hydrogen bonds. This type of modification is irreversible and the system remains permanently activated. Limited proteolysis. 7. Since ATP is the cellular energy currency. 6. one activating the next progressively in a sequence so that an initial small response is amplified into a very large change at the end of the cascade. Alters the binding properties of Histone H4 to DNA  Proteolytic activation. The blood clotting cascade A fibrin clot is formed by the interplay of the intrinsic. Phosphorylation and dephosphorylation can take place in less than a second or over several hours.g. The intrinsic pathway begins with the activation of factor XII by contact with abnormal surfaces produced 5 . The kinetics can be adjusted to meet the timing of a physiological process.

Phosphorylase Kinase I. a proteolytic enzyme. and most of these act in a sequential manner leading to the conversion of prothrombin to thrombin. More than a dozen proteins found in plasma are required to bring about the clotting of blood. As the action progresses more and more fibrinogen molecules interact to form a network of insoluble fibrin and so initiate clot formation. from blood vessels.by injury. tissue factor. and acts at various points in contact pathway Control of Glycogen Metabolism Glycogen phosphorylase catalyses the sequential removal of glycosyl residues from the non-reducing ends of glycogen. Glycogen ↔ glucose 1-pi + glycogen Glucose-1-pi  glucose 6-phosphate phophoglucomutase G-6-Pi  glycolysis Glycogen phosphorylase is controlled by phosphorylation. Thus the activity of phosphorylase is controlled by the energy charge of the muscle cell. Vitamin K is essential for the carboxylation of specific glutamine residues of prothrombin. Phosphorylase a (active) and phosphorylase b (inactive) Phosphorylase b + ATP  phosphorylase a + ADP.e in other words it goes from R state  T state when ATP is high. Warfarin competes with Vitamin K preventing its activation and subsequent g-carboxylation Heparin prevents thrombin activation. acts of fibrinogen. As synthesis and degradation of glycogen are separate pathways there is greater metabolic control. The extrinsic pathway is triggered by trauma. Blood clotting is a function of the blood platelets. which activates factor VII and releases the lipoprotein. A notable feature of the process is that the signal is progressively amplified at each step. 6 . so that small amounts of the initial factors are sufficient to trigger the cascade and ensure a rapid response to trauma. Thrombin.

The histone proteins are the most abundant of all nuclear proteins and are responsible for the first level of DNA packing in chromatin. Nucleosomes are small particles contain DNA wrapped twice around a protein core of 8 histone protein molecules. (naked) Eukaryotic DNA is condensed into chromosomes in order to manipulate them during mitosis. package DNA into nucleosomes. Target Bacteria Human Gene Expression One RNA polymerase Three RNA polymerases Direct translation of mRNA Translation in cytoplasm NO mRNA processing Capping. Prokaryotic DNA is not. Chain has polarity 5'  3' Base + sugar = Nucleoside Base + sugar + phosphate = Nucleotide Eukaryotic DNA is covered in proteins.Nucleotides and Nuclei Acid Structure DNA Double stranded helix T Deoxyribose Promoters RNA Single stranded U Ribose Primers Purines (2 rings)– Adenine and Guanine Pyrimidines (1 ring) – Tyrosine and Cytosine Binding – A  (2H bonds) T G  (3H bonds) C also Note: Both purines and pyrimidines are planar. the histones. Condensed DNA is called “heterochromatin” Non-condensed (actively transcribing) DNA is called “euchromatin” Comparison of nucleic acid synthesis between human and bacteria. 7 . tailing and splicing of mRNA No splicing DNA replication Single origin Multiple origins Occurs continuously Occurs only during S phase No organised nucleoprotein DNA occurs in nucleosomes A group of basic proteins. and they are arranged along the chromosomal DNA rather like beads on a string. by forming nucleosomes.

This packing on its own effectively shortens the length of the chromosome over 5-fold. (ATP required)  Primase (a special RNA polymerase) is required to initiate new polynucleotide synthesis because DNA polymerase cannot start the reaction (it can only extend existing polynucleotide ‘primers’ in the 3’ direction)  DNA ligase is required to join together the 3’ ends of the new fragments with the 5’ ends of previously formed fragments. 8 .  Helicase is required to unwind the parental strands. and further condensation is achieved by organising the nucleosomes together in tight arrangements to form shorter but fatter fibres. Replication DNA replication requires many proteins and enzymes in addition to DNA polymerase. (ATP required) (dNMP)n + dNTP  (dNMP)n +1 + PPi ( 2Pi) The reaction is driven by the hydrolysis of pyrophosphate.

Processes – capping. RNA polymerase then binds to the factor and begins transcription roughly 20 bases upstream. slicing and poly A tail.Transcription mRNA readout 5’  3’ relates to the direction of protein synthesis N  C Promoters – sections of the DNA in which transcription initiation factors bind. The top strand of DNA is the coding strand as this carries the protein coding sequence. The bottom strand is the template strand and this is complementary to the RNA sequence. Capping and polyadenylation of pre-mRNA protects against degradation by 5’ exonucleases and 3’ exonucleases respectively and so increases the half-life of the mRNA. 9 .

than smaller things. Of kinds Few Copies of each Many Percentage of total RNA 80 RNA polymerase 1 Gene Very many copies in tandem repeated and expressed together mRNA 100. Obviously big things will sediment faster and therefore have higher S values. tRNA Wobble position allows tRNA to pick up more than 1 different amino acid tRNA all about the same structure and 80ish bases long 10 .Making rRNA.000s Few 2 2 Single copy sometimes coordinately expressed tRNA ≈100 Very many 15 3 Often multi-copy clusters expressed together Ribosomes are made up of small subunits and large subunits. Each subunit has a macromolecular assembly of a set of specific RNA and protein molecules. which refer to how fast the particles move (‘sediment’) in a under centrifugal (g) forces. These are known according to their ‘S values’. ribosomes and tRNA Type of RNA rRNA No. The RNA molecules are known as ribosomal RNA or rRNA. Prokaryotes have smaller ribosomal sub-units (50S and 30S) combining to form 70S ribosomes Eukaryotes larger (60S and 40S) forming 80S ribosomes.

Secretory pathways The initial signal for secretion is the ‘secretory signal’ which will be at the N-terminal end of proteins destined for entry to the secretory pathway. The complex dissociates. The receptor is SRP (signal recognition particle). Translation Peptidyl transferase causes the peptide bond formation. 11 .Amino acid binding to tRNA requires an acyl-tRNA synthetase A single tRNA species can recognise more than one codon specifying the same amino acid due to wobble. Binding halts translation and allows the complex to diffuse to the ER membrane where it binds to ‘docking protein’ (the SRP receptor). translation elongation starts up again and the growing polypeptide is fed through a pore that opens in the membrane. Processing proteins in cells Proteins are targeted to cellular destinations by specific structural signals within the protein or the absence of a specific signal to a default destination. The secretory signal is removed by a specific protease (‘signal peptidase’) that is sitting on the lumenal side of the ER membrane.

nuclear localisation sequence is a cluster of basic residues on the external surface of the protein recognised by receptors on the nucleus. 12 . This bind to a receptor in the trans-golgi.A specialised process whereby contents of secretory granules are exocytosed only when required. Lysosomal targeting – mannose-6-phosphate added post-transitionally in cis-golgi. Nucleus targeting . ER: signal cleavage.amphipathic signal on N-terminus. chaperones aid transport and keep it unfolded. which directs the proteins to acidic sorting vesicles . n-linked glycosylation Golgi: o-linked glycosylation. Extracellular matrix proteins and protein components of the plasma membrane use the constitutive pathway. nuclear pore complex recognises and selectively takes proteins up by active transport. disulphide bond formation. modification of n-linked oligosaccharides & more proteolysis Constitutive pathway – Non-clathrin-coated vesicles bud-off continuously from the trans-Golgi network and migrate to the cytoplasmic face of the plasma membrane. The budding off of vesicles from the trans-Golgi is driven by the formation of a clathrin coat and vesicles are then transferred towards the site of release along micro-tubular fibres. which go to the lysosome. Regulated pathway . Signal is cleaved after entry by TIM and TOM channel complex.Proteins that remain in the ER membrane have a C-terminal amino acid sequence of KDEL. Mitochondria targeting .

For O2 – adaptation to altitude. Foetal Hb higher aff. 13 . binding of oxygen pulls Fe into plane. Haem consists of protoporphyrin ring which binds to Fe. Sigmoidal binding curve (co-operativity) Oxygen binds causing transition from T (deoxy) to R (oxy) state.Myoglobin and Haemoglobin Myoglobin is found in the muscles and acts as an oxygen store there. charge carbamates participate in salt bridge interactions stabilising t state [CO2] increase – Decrease affinity [BPG] increase – reduced affinity Increased pH – increases affinity Graph – increase affinity shift to left. Fe2+ binds Oxygen. changes at a1b1-a2b2 interface. neg. Because it has a gamma instead of Beta with His  Ser substitution Low pH favours protonation and formation of salt bridge to stabilise the t state CO2 reacts with alpha terminus N. 2. Decrease affinity shift to right. Fe lies slightly out of plane towards HisF8.3-BPG reduces Hb aff. (Hyperbolic relationship) Haemoglobin is found in rbcs and acts as the oxygen carrier in the blood.

albumin taken up by cells is source of amino acids Coagulation and fibrinolysis The humoral immune system . leading to anaemia. Prolyl hydroxylase in ER –requires vitamin C and Fe++ ions for activity allows increased H-bonding to stabilise triple helix.regulation of intravascular pH Nutrition . The affected red cells cannot function normally. Other symptoms include enlargement of the spleen and abnormalities of the bone marrow. Glycine present as it is the only amino acid small enough to be accommodated at the centre of the triple-stranded helix.Thalassaemia – A genetic blood disease. triple helix formed by disulphide bond formation in carboxy-terminal extensions Procollagen is secreted and pro segments are cleaved. Plasma Proteins Functions       Transport of many substances Maintenance of intravascular oncotic pressure Buffer . Scurvy is due to weak tropocollagen triple helices Lysyl Oxidase – requires vitamin B6 for making covalent cross-links between adjacent tropocollagen units. in which there is an abnormality in the protein part of the Hb. Collagen Gly – X – Y X and Y are usually proline and hydroxyproline. Triple helix H-bonds between a chains stabilise structure RER: synthesis of preprocollagen Lumen of ER: Hydroxylation of proline and lysine residues Golgi: self-assembly of tropocollagen molecule. Proline and hydroxyproline allow for the H-bonding and increased rigidity of the helix.immunoglobulin and complement components Albumin Maintains colloid osmotic pressure & transports hormones and other things 35-50 g/L 14 .

or more enzymes produced. UTIs. DHFR is used in the metabolic synthesis of folic acid. The hydrolytic action of this enzyme breaks the essential β-lactam ring in the penicillin which essentially inactivates the drug. Inhibits protein synthesis by competing with tRNA for the A site during translation. Thus. Resistance due to mutation of DHFR enzyme. Resistance – B-lactamases inactivate penicillin. Tetracycline Resistance mechanism is to reduce the uptake of drug by the bacteria. pneumonia. It is used to treat bacterial meningitis. Rifampicin Binds to and inhibits DNA-dependent RNA polymerase. prevents production of mRNA stopping protein synthesis. 15 . Clinical uses chemotherapy and Crohn’s disease. Wide ranges of uses but lots are now resistant. used against Chlamydia and cholera. bronchitis. A mutation causing a change in the binding site protein is mechanism for resistance and resistance is very easy to acquire. Methotrexate It competitively inhibits the enzyme dihydrofolate reductase (DHFR). It stops crosslinking of the wall and osmotic lysis subsequently occurs. It is used against TB and others.Antibiotics Penicillin It inhibits the transpeptidases in the peptidoglycan cell wall of gram positive bacteria.

immunoglobulin and complement components 16 . Triple helix H-bonds between a chains stabilise structure RER: synthesis of preprocollagen Lumen of ER: Hydroxylation of proline and lysine residues Golgi: self-assembly of tropocollagen molecule. Prolyl hydroxylase in ER –requires vitamin C and Fe++ ions for activity allows increased H-bonding to stabilise triple helix. Glycine present as it is the only amino acid small enough to be accommodated at the centre of the triple-stranded helix. in which there is an abnormality in the protein part of the Hb.Thalassaemia – A genetic blood disease. Scurvy is due to weak tropocollagen triple helices Lysyl Oxidase – requires vitamin B6 for making covalent cross-links between adjacent tropocollagen units. Plasma Proteins Functions • • • • • • Transport of many substances Maintenance of intravascular oncotic pressure Buffer .regulation of intravascular pH Nutrition . Collagen Gly – X – Y X and Y are usually proline and hydroxyproline. Other symptoms include enlargement of the spleen and abnormalities of the bone marrow. triple helix formed by disulphide bond formation in carboxy-terminal extensions Procollagen is secreted and pro segments are cleaved. The affected red cells cannot function normally. Proline and hydroxyproline allow for the H-bonding and increased rigidity of the helix. leading to anaemia.albumin taken up by cells is source of amino acids Coagulation and fibrinolysis The humoral immune system .

used against Chlamydia and cholera. Wide ranges of uses but lots are now resistant. DHFR is used in the metabolic synthesis of folic acid. prevents production of mRNA stopping protein synthesis. UTIs.Albumin Maintains colloid osmotic pressure & transports hormones and other things 35-50 g/L Antibiotics Penicillin It inhibits the transpeptidases in the peptidoglycan cell wall of gram positive bacteria. The hydrolytic action of this enzyme breaks the essential β-lactam ring in the penicillin which essentially inactivates the drug. It is used against TB and others. Resistance – B-lactamases inactivate penicillin. It stops cross-linking of the wall and osmotic lysis subsequently occurs. A mutation causing a change in the binding site protein is mechanism for resistance and resistance is very easy to acquire. Methotrexate It competitively inhibits the enzyme dihydrofolate reductase (DHFR). Rifampicin Binds to and inhibits DNA-dependent RNA polymerase. pneumonia. bronchitis. or more enzymes produced. Clinical uses chemotherapy and Crohn’s disease. Resistance due to mutation of DHFR enzyme. 17 . It is used to treat bacterial meningitis. Tetracycline Resistance mechanism is to reduce the uptake of drug by the bacteria. Thus. Inhibits protein synthesis by competing with tRNA for the A site during translation.

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