1. ADVANCED HIGHER CELLS AND PROTEINS DNA, PROTEINS AND BINDING TO LIGANDS

2. THINK What proteins are associated with DNA? How are proteins involved in transcription? How is protein production controlled? Why is it important that protein production is controlled? Why is protein structure important in relation to its function?

3. DNA AND PROTEINS This lesson will cover DNA and its associated proteins Other proteins involved with transcription

4. DNA AND PROTEIN ASSOCIATION

5. DNA binds to a number of proteins. Positively charged histone proteins bind to the negatively charged sugar-phosphate backbone of DNA in eukaryotes. DNA is wrapped around histones to form nucleosomes packing the DNA in chromosomes.

6. DNA AND PROTEIN ASSOCIATION Animation

7. HISTONE PROTEINS AND NUCLEOSOME

8. OTHER DNA PROTEINS AND LIGAND BINDING Other proteins have binding sites that are specific to particular sequences of double stranded DNA. When this happens they can stimulate or inhibit the initiation of transcription. Animation

9. DNA AND PROTEIN COMPLEX IN TRANSCRIPTION

10. TRANSCRIPTION FACTORS Transcription factors (TFs) are molecules involved in regulating gene expression. They are usually proteins, (they can be short, non-coding RNA). TFs are also usually found working in groups or complexes, forming multiple interactions that allow for varying degrees of control over rates of transcription.

11. TRANSCRIPTION FACTORS In people (and other eukaryotes), genes are usually in a default "off" state, so TFs serve mainly to turn gene expression "on". TFs work by recognizing certain nucleotide sequences (motifs) before or after the gene on the chromosome. The TFs bind, attract other TFs and create a complex that eventually facilitates binding by RNA polymerase, thus beginning the process of transcription.

12. BINDING CHANGES THE CONFORMATION OF A PROTEIN Proteins including enzymes are three-dimensional and have a specific shape or conformation. As a ligand binds to a protein binding site, or a substrate binds to an enzyme’s active site, the conformation of the protein changes. This change in conformation causes a functional change in the protein and may activate or deactivate it.

13. BINDING TO LIGANDS A ligand is a substance that can bind to a protein. R groups not involved in protein folding can allow binding to these other molecules. Binding sites will have complementary shape and chemistry to the ligand. The ligand can either be a substrate or a molecule that affects the activity of the protein.

14. All chemical reactions require energy to enable them, this is the activation energy. Enzymes lower the activation energy. 2 types of reaction are: Anabolic (synthesis) a dehydration synthesis reaction. Catabolic (degradation) a hydrolysis reaction. Enzymes

15. Anabolic Reactions Uses energy to SYNTHESISE large molecules from smaller ones e.g. Amino AcidsProteins Also known as endothermic reactions ENDOTHERMIC REACTION

16. Catabolic Reactions These release energy through the BREAKDOWN of large molecules into smaller units e.g. Cellular Respiration: ATP ADP + Pi Also known as exothermic reactions EXOTHERMIC REACTION

17. Enzyme types Proteases - break down proteins into amino acids by breaking peptide bonds (hydrolysis). Nucleases - break down nucleic acids into nucleotides (hydrolysis). ATPases - hydrolysis of ATP. Kinases - add phosphate groups to molecule. Phosphatases – remove phosphate groups

18. Control of Enzyme activity Control of enzyme activity occurs in these ways number of enzyme molecules present compartmentalisation change of enzyme shape by competitive inhibitors, non-competitive inhibitors, enzyme modulators, covalent modification end product inhibition

19. How do enzymes work?

20. Induced fit and enzymes Enzymes are not necessarily a perfect sit to substrate The enzyme changes shape in response to close association with the substrate. This the Induced fit theory

21. A molecule close to shape of substrate competes directly for active site so reducing the concentration of available enzyme. This can be reversed by increasing the concentration of the correct substrate unless the binding of competitor is irreversible. Competitive inhibition

22. Succinate dehydrogenase catalyses the oxidation of succinate to fumarate (respiration) Malonate is the competitive inhibitor Malonate example

24. An inhibitor binds to the enzyme molecule at a different area and changes the shape of the enzyme including the active site. This may be a permanent alteration or may not. Non-competitive inhibition

26. Inhibition can either be reversible or non-reversible Some inhibitors bind irreversibly with the enzyme molecules. The enzymatic reactions will stop sooner or later and are not affected by an increase in substrate concentration. Irreversible inhibitors include heavy metal ions such as silver, mercury and lead ions.

27. Some enzymes change their shape in response to a regulating molecule. These are called allosteric enzymes Positive modulators (activators) stabilise enzyme in the active form. Negative modulators (inhibitors) stabilise enzyme in the inactive form. Enzyme modulators

28. Allosteric Enzymes

29. Involves the addition, modification or removal of a variety of chemical groups to or from an enzyme (often phosphate.) These result in a change in the shape of the enzyme and so its activity. These include phosphorylation by kinases and dephosphorylation by phosphatases. Conversion of inactive forms to active forms e.g. trypsinogen and trypsin Covalent modifications

30. An example of activation is trypsinogen to trypsin trypsinogen activated by enterokinase in duodenum

31. Trypsin is synthesised in the pancreas, but not in its active form as it would digest the pancreatic tissue Therefore it is synthesised as a slightly longer protein called TRYPSINOGEN Activation occurs when trypsinogen is cleaved by a protease in the duodenum Once active, trypsin can activate more trypsinogen molecules

32. Often seen in pathways that involve a series of enzyme controlled reactions. The end product once produced has an inhibiting affect on an enzyme in the reaction. Example: Bacterial production of amino acid isoleucine from threonine. 5 stages enzyme controlled ThreonineIsoleucine End product Inhibition

33. To summarise As a ligand binds to a protein or a substrate binds to an enzyme’s active site, the conformation of the protein changes, This change in conformation causes a functional change in the protein.

34. To summarise In enzymes, specificity between the active site and substrate is related to induced fit. When the correct substrate starts to bind, a temporary change in shape of the active site occurs increasing the binding and interaction with the substrate. The chemical environment produced lowers the activation energy required for the reaction. Once catalysis takes place, the original enzyme conformation is resumed and products are released from the active site.

35. To summarise In allosteric enzymes, modulators bind at secondary binding sites. The conformation of the enzyme changes and this alters the affinity of the active site for the substrate. Positive modulators increase the enzyme affinity whereas negative modulators reduce the enzymes affinity for the substrate.

36. Haemoglobin and Oxygen

37. COOPERATIVITY IN HEMOGLOBIN Deoxyhaemoglobin has a relatively low affinity for oxygen. As one molecule of oxygen binds to one of the four haem groups in a hemoglobin molecule it increases the affinity of the remaining three haem groups to bind oxygen. Conversely, oxyhaemoglobin increases its ability to loose oxygen as oxygen is released by each successive haem group. This creates the classic sigmoid shape of the oxygen dissociation curve.

38. DISSOCIATION CURVE OF HAEMOGLOBIN

39. Deoxyhaemoglobin Oxyhaemoglobin Disassociation releasing oxygen to tissues Association binding oxygen in lungs

40. EFFECTS OF TEMPERATURE AND PH Low pH = low affinity. High temperature = low affinity. Exercise increases body temperature and produces more CO 2, acidifying the blood. This has a corresponding effect on the oxyhaemoglobin dissociation curve.

42. Sickle Cell Anaemia Low oxygen levels cause change in haemoglobin structure. Strands cause cells to take on bent sickle shape blocking capillaries.

43. HIGH ALTITUDE AND OXYGEN The concentration of oxygen (O2) in sea-level air is 20.9%, so the partial pressure of O2 (pO2) is 21.136 kPa. Atmospheric pressure decreases exponentially with altitude while the O2 fraction remains constant to about 100 km, so pO2 decreases exponentially with altitude as well. It is about half of its sea-level value at 5,000 m (16,000 ft), the altitude of the Everest Base Camp, and only a third at 8,848 m (29,029 ft), the summit of Mount Everest. When pO2 drops, the body responds with altitude acclimatization. BBC Horizon How to kill a Human Being

44. To summarise Some proteins with quaternary structure show cooperativity in which changes in binding alter the affinity of the remaining subunits. Cooperativity exists in the binding and release of oxygen in Haemoglobin. Temperature and pH influence oxygen association.