Thread of L ife

1. Thread of Life

2. TL1 - The Human Genome Project • A genome is all the genetic material contained in the chromosomes of an organism • The human genome project maps the complete DNA of human beings • DNA carries our genetic code and carries instructions for making proteins • Some of the key goals for the Human Genome Project were; • Identify all the genes in human DNA (about 20000-25000) • Determine the sequences of base pairs (about 3 million) • Store this information on databases • Address ethical, legal and social issues arising from the project

3. TL2 – What are proteins? • Natural polymers with Mr up to 10000 • Play a key role in almost every structure and activity or a living organism… Globular… Muscle Fibres Enzymes Fibrous… Binding proteins (for storing or transporting substances e.g. haemoglobin) Cell Structures (such as membranes) Proteins Hair and nails (and feathers) Hormones(not all are proteins)

4. Amino Acids • All proteins in the living world are made from combinations of 20 α-amino acids • These all have the same general structure • The only difference is the side chain R • TL2.1 • CI13.3, 13.4, 13.8 • CI13.9 • During digestion we break any proteins we eat into amino acids and then reassemble them into the proteins we need • What makes each protein different is the order that the amino acids are joined to each other. • This is called the primary structure Amino group Carboxylic acid group

5. e.g. for the hormone insulin • Each of the letters is the abbreviation for a certain amino acid • Amino acids join together by condensation reactions • They therefore form –CONH- bonds… • …secondary amides or peptide bonds • A dipeptide is two amino acids joined together

6. Representing amino acid Sequences • Abbreviations for each amino acid listed one after another • Read from left to right • Free NH2 group on left • Ass 1,2 • TL2.2 • TL2.3 • CI7.3 (T.L.C.) • CI3.5 (Optical Isomerism) • TL2.4

7. We cannot make amino acids react together directly • The –COOH group is not reactive enough • We need to convert them into acyl chloride groups (-COCl) • We also need to remember that amino acids are 3-D molecules based around a tetrahedral carbon • This means that they all (except for glycine) exist in two forms (D and L) • These are mirror images of one another… • …optical isomers • Proteins are made using only the L enantiomers • TL2.4

8. TL3 Proteins in 3-D • Primary structure (order of amino acids) does not provide enough detail • We need to know the precise shape to understand exactly what it does • This precise shape develops because of… • Secondary structure… • …How the chain folds as a result of hydrogen bonding to form… • … a HELIX (spiral) • or a PLEATED SHEET

9. Tertiary structure… • …How the chains the fold further as a result of the bonds between the R-groups • There are 4 main interactions • Instantaneous dipole-induced dipole attractions • Caused by non polar side chains • Hydrogen bonds • Between peptide groups • Also due to –OH and -NH groups on side chains • Ionic bonds • Ionisable side chains such as –COO- and –NH3+ • Sulphur-sulphur covalent bonds • S-S links form when –SH groups on cysteine residues become oxidised • CI5.3 & 5.4 (Intermolecular forces) • CI13.9 (2º and 3º structures of proteins) • TL3

10. TL4 Enzymes • Enzymes are: • Catalysts • Speed up a reaction but are chemically unchanged at the end of the reaction • Provide an alternative route with a lower activation energy. • Highly specific • Will catalyse one reaction only due to the presence of an active site • pH sensitive • Work best at a particular, optimum, pH • Become inactive at high or low pH • Can affect way active site functions • Temperature sensitive • Work best at a particular, optimum, temperature • Most are denatured above 60ºC • CI10.5 + 10.6

11. Active Sites • The precise tertiary structure leads to a ‘cleft’ in the enzyme surface • This is the active site • R groups from the amino acid residues point into this cleft • Here they form interactions with the molecule that is reacting - the substrate • These are usually H-bonds or ionic attractions • This weakens bonds within the substrate or alters its shape, enabling it to react • The products will have weaker or fewer imfs holding them in the active site and can therefore leave

13. Sometimes different molecules can fit onto the active site but can’t be catalysed • These are called inhibitors • Ass 3 + Activity EP6.3 Factors affecting enzyme function • pH and temperature will both affect the performance of an enzyme • Both will change the tertiary structure of the enzyme • This means the active site is destroyed and the enzyme is said to be denatured

14. Initially increasing temperature increases rate as for any reaction (see collision theory/Maxwell-Boltzmann distribution) • Higher temperatures increase k.e. and cause the imfs to break • Enzyme becomes denatured and so activity falls • Human enzymes have an optimum temperature of between 35 and 40ºC

15. Changing pH will alter ionic groups holding the tertiary structure together • It could also alter the activity of the active site if the substrate is held by any ionic groups • –COO- groups could gain H+ if pH is lowered • –NH3+ groups could lose H+ if pH is raised • Enzymes will have an optimum pH • This is usually around pH7 but will vary depending on the conditions the enzyme has to work in

16. Rate of enzyme reactions • CI10.3 • Enzyme concs are usually very low • This could have a variety of effects on the rate of the reaction; • Reaction should always be first order wrt [enzyme] (except in very extreme circumstances) • If substrate conc is low… • Not all active sites will be filled at any time • Doubling conc of substrate will double rate • Reaction will be first order wrt [substrate] • RDS will be E + S  ES • If substrate conc is high… • All active sites will have a substrate molecule bound to them • Doubling conc of substrate will have no effect on rate • Reaction will be zero order wrt [substrate] • RDS will be EP  E + P

17. Enzymes at work • Used in diabetes test strips to detect glucose in urine • Huge quantities also used in foods and washing powders • Commonly hydrolases to break down foods… • Amylase : starch  glucose syrup (as a food sweetener) • Rennet : casein  curds + whey (making cheese) • Protease : proteins  amino acids/short polypeptides (in washing powders to remove food, blood, etc) • Lipases : fats  fatty acids + glycerol (in washing powders) • Now also used to: • Destroy cyanide ions left from the extraction of gold • Break up oil spillages • Enzymes allow reactions to occur at lower temperatures • This conserves energy and often reduces the number of steps needed to make a product • This increases the atom economy of the process • CI15.9 “Atom economy”

18. TL5 DNA for life • We need to understand how cells make proteins • As a chemist in a lab we would need three things; • Set of instructions with the primary structure • Supplies of pure amino acids • A way of joining –COOH and –NH2 groups • Our cells are no different • Details of the primary structure of all our proteins is carried by molecules called deoxyribonucleic acid (DNA) • Each strand of DNA consists of alternating deoxyribose (sugar) and phosphate • These form a long chain called a sugar-phosphate backbone • Each deoxyribose group then has one of four bases joined to it: • Adenine (A) • Cytosine (C) • Guanine (G) • Thymine (T)

19. Deoxyribose molecule base Each sugar-phosphate-base group is called a nucleotide Phosphate group

21. It is the order of these bases that determines the ‘function’ of a particular part of the DNA molecule • DNA consists of two strands twisted in a helical form - a double helix • The two strands are held together by hydrogen bonding between pairs of bases…

22. Adenine always pairs with Thymine • Cytosine always pairs with Guanine • Ass 4 • Ass 5 • TL5

23. The base pairing enables DNA to do two things; • One strand can synthesise a copy of its complementary strand (i.e. the strand with which it is normally paired) e.g. • TCGAT would make a new strand with the bases… • …AGCTA • This replication happens prior to cell division • One strand can make a complementary copy of another nucleic acid called messenger RNA • It does this by transcription • mRNA is used to synthesise specific proteins

24. RNA • Very similar to DNA except: • Ribose sugar instead of deoxyribose… • Has the base uracil (U) instead of thymine (T) • Exists in single strands; it does not pair up

25. Transcription • The section of DNA for a specific protein unzips (this is a gene) • The RNA nucleotides join together • The order for this is decided by the order of the bases on the DNA • DNA section zips up again • Newly formed mRNA passes out of the cell nucleus

26. mRNA carries the information for the order of the amino acids in the protein • The code for a particular amino acid is a set of three bases (a triplet code) • Each group of three bases is called a codon e.g. • A codon of GUG codes for valine • There is more than one codon for most amino acids • There is also a codon (AUG) to start chain building and three codons to stop • Ass 6

27. Translation • Protein synthesis occurs in ribosomes (which are in cells) • Once mRNA is made in the nucleus (by transcription) it passes to ribosomes • Protein synthesis needs amino acids to be joined together in the correct order • mRNA provides the ‘information’ to do this • The required amino acids are taken to the mRNA by small pieces of RNA called transfer RNA (tRNA) • The tRNA binds to the mRNA because it has the complementary bases to those on mRNA • The triplet on mRNA is called the codon so the complementary bases on tRNA form an anti-codon

28. The tRNA molecules are each carrying different amino acids • As the ribosome moves along the mRNA chain… • …the correct one binds to the mRNA… • …the amino acid joins to the neighbouring one… • …the tRNA leaves

29. Overall… • DNA provides the codes for each RNA (transcription) • Each RNA provides the code for a protein (translation) • Ass 7, 8

30. TL6 Making use of DNA • DNA fingerprinting uses the fact that no two people have the same DNA (except for identical twins) • Any trace of blood, hair or semen can be used • This is therefore regularly used to help to solve crimes and also paternity disputes, medical analysis and identifying body remains • An enzyme cuts the DNA into a specific pattern of fragments • The areas of ‘junk’ DNA are used as these are different for different families • This solution is applied to a gel which is then put in an electric field • The fragments are –ve due to phosphate groups • Different sized fragments travel at different speeds • This process is called gel electrophoresis • Radioactive tracers are then added which bind to the fragments • The gel plate is then exposed to photographic film • The end result is a series of bands which are compared to a suspect’s • Ass 9