Amino Acids and Proteins: Structure, Function, and Interactions, Exams of Biochemistry

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MODULE 2: Principles of Biochemistry Carbon - - backbone of life - cell = 70-95% water, rest consists mostly of carbon-based components - ability to form 4 bonds - unparalleled ability to form large, complex & diverse molecules - key molecules of life = proteins, DNA, carbohydrates & lipids - all composed of carbon - has 6 electrons, with 2 in first shell & 4 in second shell - 4 valence electrons in shell that holds 8 electrons Hydrocarbons - - organic molecules consisting of only carbon & hydrogen - undergo reactions that release large amount of energy - EXAMPLES: methane, ethane, ethene - atoms of hydrogen attached to the carbon skeleton wherever electrons are available for covalent bonding Isomers - 1. structural isomers - have different covalent arrangements of their atoms - one carbon skeleton is straight whilst other is branched 2. geometric isomers - have same covalent arrangements, but differ in spatial arrangements enantiomers - mirror images of each other, differ in shape due to presence of an asymmetric carbon (attached to 4 different atoms or groups of atoms) Properties of organic molecules - - depend on carbon skeleton & molecular components attached to it 7 functional groups that are most important in chemistry of life - 1. hydroxyl group 2. carbonyl group 3. carboxyl group 4. amino group 5. suplphydryl group 6. phosphate group 7. methyl group Molecules of life - - living things are made up of 4 classes of biological molecules: 1. carbohydrates 2. lipids 3. proteins 4. nucleic acids Macromolecules - - large molecules composed of thousands of covalently connected atoms - polymer, built from monomers - polymers: carbohydrates, proteins, nucleic acids - use ability to form covalent bonds between units to form complex molecules Monomers of RNA - nucleotides Polymers - - long molecule consisting of many similar building blocks Monomers - - repeating units that serve as the building blocks of a polymer Fats - - macromolecules constructed from 2 types of smaller molecules, a single glycerol & 3 fatty acids - larges molecules assembled from smaller molecules by dehydration reactions - glycerol = 3 carbon alcohol with hydroxyl group attached to each carbon - fatty acid = carboxyl group attached to a long carbon skeleton - making a fat = 3 fatty acids each joined to glycerol by an ester linkage (bond between hydroxyl & carbonyl group) - SATURATED fatty acids (butter) = have the maximum number of hydrogen atoms possible & no double bonds - UNSATURATED fatty acids (oil) = have one or more double bonds Hydrogeneration - - process of converting unsaturated fats to saturated fats by adding hydrogen Trans & Cis fats - - trans fats = chains are on opposite sides of the double bond = more healthy - cis fats = chains are on the same side of the double bond, resulting in a kink Phospholipids - - 2 fatty acids & phosphate group (negative electrical charge), attached to a glycerol - 2 fatty acid tails are hydrophobic, but phosphate group & its attachments form a hydrophilic head - make up cell membranes - major component - when added to water - phospholipids self-assemble into a bilayer, with the hydrophobic tails pointing toward the anterior - structure results in bilayer arrangement found in cell membranes DNA -> protein (flow of genetic information) - - DNA (deoxyribonucleic acid) = double stranded providing directions for its own replication - directs synthesis of messenger RNA (mRNA) & this control protein synthesis - protein synthesis occurs in ribosomes (molecular machine) - DNA inherited by parents - each chromosome contains one long DNA molecule - carries several hundred or more genes - cell reproduces itself by dividing - DNA molecules are copied & passed along from one generation of cells to the next DNA > RNA > protein - 1. synthesis of mRNA in the nucleus 2. movement of mRNA into cytoplasm via nuclear pore 3. synthesis of proteins using information carried on mRNA Nucleic Acids - - DNA & RNA - store & transmit hereditary information - amino acid sequence of polypeptide is programmed by a unit of inheritance called a gene - genes found in DNA Components of DNA & RNA - - polynucleotide has a sugar-phosphate backbone with variable appendages, the nitrogenous bases joined by hydrogen bonds - nucleotide monomer includes a nitrogenous base, a sugar & a phosphate group - differences = (1) make up of nitrogenous bases (DNA: thymine, RNA: uracil), (2) sugar structure chemistry (DNA: deoxyribose, RNA: ribose) Structure of nucleic acids - - polymers called polynucleotides - each one made up of monomers called nucleotides - each nucleotide consists of (1) nitrogenous base, (2) a pentose sugar, and (3) a phosphate group - adjacent nucleotides joined by covalent bonds that form between the -OH group on the 3' carbon of one nucleotide, and the phosphate on the 5' carbon on the next - links create backbone of sugar-phosphate units, with nitrogenous bases as appendages Nitrogenous bases & sugars - - 2 families of nitrogenous bases - (1) pyrimidines - cytosine, thymine & uracil - have 6 membered ring, (2) purines - adenine & guanine - have 6 membered ring fused to a 5 membered ring Assembly of DNA - - DNA molecule has 2 polynucleotides, which spiral to form a double helix, the 2 backbones run in opposite 5' to 3' directions from each other, referred to as antiparallel - nitrogenous bases in DNA pair up & form hydrogen bonds - adenine (A) always with thymine (T) & guanine (G) always with cytosine (C) From gene to protein - - flow of information is based on triplet code (codon) - series of non-overlapping, three- nucleotide words - triplets are smallest units of uniform length that can code for all the amino acids - AGT (on DNA template) codes for amino acid sequence Protein functions - 1. Structural support (collagen - strength to skin & bone) 2. Storage (caesin - amino acids in milk) 3. Transport (hemoglobin - transport O2) 4. hormonal regulation (insulin - sugar control) 5. movement (actin/myosin - muscle contraction) 6. defence (immunoglobin - recognise viral & bacterial infections as foreign) 7. enzymes to accelerate chemical reactions Polynucleotides - - polymers built from the same set of 20 amino acids - protein consists of one or more polypeptides - results from non-covalent interactions between amino acids & R groups (side chains) - polypeptide chain folding back on itself = conformation - disulphide bonds - are covalent bonds between 2 sulfur atoms in cysteine residues - proinsulin = inactive form of insulin - connecting piece of peptide, which must be cleaved to become active Quaternary Structure - - assembly structure of individual polypeptide chains - chains can be identical or different - peptide chains are bonded to form the protein - hemoglobin is a tetramer because it has four polypeptide chains in its structure Hemoglobin & Myoglobin - Function: - myoglobin - stores & delivers O2 in muscle cells - hemoglobin - transports & delivers O2 through the veins & arteries Hemoglobin - - major protein of red blood cells - heme group (co-factor) is attached to the polypeptide by non-covalent bonds - Fe2+ ion is "coordinated" to the heme & to a histidine side chain - one site around the Fe2+ is available for O2 binding Myoglobin & Hemoglobin function by reversibly binding O2 - - myoglobin + O2 myoglobin - O2 - hemoglobin + 4O2 hemoglobin - 4O2 - myoglobin is a single polypeptide monomer - hemoglobin is a tetramer allowing "communication" between polypeptides (subunits) Saturation Curves - - tells us the percentage of protein molecules that have oxygen molecules bound at any one time - amount varies depending on the partial pressure exerted by O2 (concentration [partial pressure] of O2) - concentration of O2 [partial pressure] varies depending on body part - partial pressure determines how much oxygen is present Sickle-cell disease - - condition where there are not enough healthy red blood cells to carry oxygen throughout the body - symptoms: fatigue, pain (veins/arteries are blocked) - inherited blood disorder - results from single amino acid substitution in the haemoglobin protein Sickle-cell haemoglobin (molecular basis) - - sickle cell haemoglobin (HbS) has a single amino acid difference compared with normal haemoglobin - occurs in the beta-subunit - non-conservative amino acid substitution where VAL is substituted with GLU - GLU = negatively charged side chain on surface of normal haemoglobin - VAL = non-polar - substitution takes place at hydrophobic residue on the surface of the protein - greatly reduces solubility of deoxygenated form of haemoglobin - VAL beta6 forms hydrophobic patch - beta-chain of deoxyhaemoglobin has another hydrophobic patch formed by Phe 85 & Leu 88 - mutant molecules aggregate to hide the sticky patches Sickle cell disease quaternary structure - - NORMAL haemoglobin = molecules do not associate with one another; each carries oxygen - SICKLE CELL haemoglobin = molecules interact with one another & crystallise into a finer; capacity to carry oxygen is greatly reduced Insulin - - polypeptide hormone that controls blood glucose levels - diabetes = disease where insulin molecules no longer carry out regulation of glucose levels - proinsulin = the active precursor form of insulin - has a connecting piece of peptide which must be cleaved before it can become active Active Insulin - - after proteolytic (enzyme) cleavage insulin becomes active - however, disulphide bonds hold the two separated chains together - insulin can now bind with its receptor on the surface of the cell, regulating glucose/sugar levels What else determines protein structure? - - physical & chemical conditions can affect structure - alteration in pH, salt concentration, temperature, or detergents can cause a protein to unravel - loss of the native protein structure is called DENATURATION - denaturated protein is biologically inactive Denaturation & Renaturation of a protein - - high temperatures or various chemical treatments will denature a protein - causing it to lose its shape & ability to function - denatured protein remains dissolved - can often renature when the chemical & physical aspects of its environment are restored to normal Shapes of proteins - globular - - do not aggregate into microscopic structures - can contain helices and/or sheets - perform wide variety of functions (enzymatic, transport, regulatory, protective) - usually require solubility in blood or other aqueous media of cells & tissues - little repeated primary & secondary structure - protein is shaped roughly spherical Characteristics of globular proteins - - high the number, the better Enzyme inhibition - - normal binding - enzyme can bind normally to active site of an enzyme - competitive inhibition - competitive inhibitor mimics the substrate, competing for the active site - non-competitive inhibition - non competitive inhibitor binds to the enzyme away from the active site, altering the shape of the enzyme so that even if the substrate can bind, the active site functions less effectively Synthetic inhibitors can become therapeutic drugs - - study enzyme & its activities (e.g. importance for virus, bacteria or cancer cells) - determine 3D structure of enzyme - design/find inhibitor molecules that block active site - test inhibitor for biological activity e.g. cancer, AIDS & antibiotics Collagen - - most abundant protein in vertebrates (in ECM) - makes up about 40% of total body protein - provides mechanical strength to connective tissues - skin, bone, tendon, cartilage, blood vessels - is fibrous & not soluble in water 5 types of collagen - - 28 different collagens (amino acid sequences are similar but distinctly different from each other) - 90% of collagen in body is collagen 1 - collagen 1 = skin, tendon, vascular ligature, organs, bone - collagen 2 = cartilage (main component of cartilage) - collagen 3 = connective tissue around the liver Collagen fibrils - - collagen - rod shaped molecule, about 300nM long & only 1.5nM thick - each chain has approx. 1000 amino acids - made from collagen molecules aligned in staggered fashion - cross-linked (covalent bonds) fro strength - specific alignment & degree of cross-linking vary with type of collagen - molecules associate with one another in fibrils - breaks in between gives it its flexibility 3D structure of collagen - (a) single chain of collagen - not helical structure - one polypeptide chain (b) single chain of collagen - atoms drawn as spheres (c) three stranded 'triple-helix' of collagen - each polypeptide chain is coloured differently - atoms are joined to the backbone via covalent bonding 4-hydroxyprolin in collagen - - forces proline ring into more favourable conformation for stabilising the triple helix - offers more hydrogen bonding potential between the three strands of collagen - process is catalysed by propyl hydroxyls in presence of ascorbate (vitamin C) - amino acid side chain links back on to polypeptide - closed ring structure - modified to put hydroxyl on Vitamins - - an organic compound required as a vital nutrient by an organism - cannot be synthesised by organism (e.g. humans) - must therefore be obtained from diet Vitamin C activates propyl 4-hydroxylase - - prolyl-4-hydroxylase is a metalloenzyme & needs Fe2+ to be fully active - vitamin C adds an electron to Fe3+ making it Fe2+, activating propyl 4-hydroxylase - without vitamin C, proline in collagen will have less of a tendency to become hydroxylated - collagen will become weaker Scurvy - - disease now known to be caused by lack of vitamin C - weakening collagen Cross linking of collagen triple-helices - - cross links are covalent bonds formed between the side chains of amino acids in two different triple helices, or within a triple helix Steps in collagen biosynthesis - 1. single strands of polypeptide are made in ribosome 2. hydroxylation of lysine & proline side chains 3. triple helix is formed 4. procollagen is converted to collagen by pro collagen peptidase (type of occurring reaction) 5. bundles form with lyoside oxidise present 6. cross links form Metabolism - - is the totality of chemical reactions within an organism - property of life that arises from interaction between molecules with the cell - potential energy of the food (chemical bonds) is converted into kinetic energy (motion) - heat & small molecules (from complex chemicals in the food) are produced when the cheetah is under exercise Free energy change - Change in free energy ( G) during a process is related to: - change in heat ( H) (enthalpy); (internal energy) - if the system of molecules gives heat to the surrounding H is negative) - change in entropy ( S); (order) - if the system of molecules goes from ordered to disordered, S is positive