Understanding Polypeptides and Protein Synthesis

1. Proteins

2. 2.4.1 Amino acids are linked together by condensation to form polypeptides • Polypeptides • are chains of amino acids linked together by condensation reactions • the main, or only, component in proteins • Some proteins are composed of only one polypeptide chain, while others are made of 2 or more

3. Polypeptides can contain any number of amino acids (typically called oligopeptides if less than 20) • Insulin- two polypeptides; one with 21 aa, the other with 30 aa • Titin (a large polypeptide in muscle protein) contains 34,350 aa

4. Polypeptides are formed by condensation reactions • The amine group of one amino acid combines with the carboxyl group of the other amino acid; water is eliminated • The new bond formed between the two amino acids is called a peptide bond

5. S 2.4.1 Drawing molecular diagrams to show the formation of a peptide bond • 2 amino acids are linked by a condensation reaction • Peptide bonds are the same, no matter what the R group is • Show the formation of peptide bonds

6. 2.4.2 There are 20 different amino acids in polypeptides synthesized in ribosomes. • Polypeptides synthesized in ribosomes can be made using 20 different amino acids. • Ribosomes- cell part where RNA codes for proteins…translation • Because of the differences in R groups, the 20 amino acids are chemically diverse • Some proteins contain amino acids that are not the 20 produced on ribosomes. • This is due to an amino acid being modified after the polypeptide has been synthesized. • Example: Collagen • Collagen polypeptides made by ribosomes contain prolineat many positions, but some of these are converted to hydroxyproline, making collagen more stable.

7. Amino acids and origins: patterns, trends, and discrepancies. • Most but not all organisms assemble polypeptides from the same amino acids. • This trend is not due to chance, but why is it? • Several hypotheses: • These 20 aa were produced by chemical processes before the origin of life, so all organisms used them and continue to use them • They are the ideal amino acids for making a wide range of proteins, so natural selection will favor organisms that use them and not others • All life evolved from a single ancestral species, which used all 20 aa. • Some species have been found to use codons that normally signal to stop the amino acid sequence to encode an extra non-standard aa. To learn more, click on the link below: • http://jnci.oxfordjournals.org/content/96/7/504.full

8. 2.4.3 amino acids can be linked together in any sequence giving a huge range of possible polypeptides. • Amino acids can be linked together in any way, peptide bonds can be formed between any two amino acids, so any sequence is possible. • The number of possible amino acid sequences can be calculated: • For a polypeptide with n amino acids, there are 20n possible sequences • Example: • Dipeptides- 2 amino acids (n=2) 202 = 400 possible dipeptides • 3 amino acids (n = 3) 203 = 8,000 possible sequences

9. Complete the following table:

10. The number of aa in a polypeptide can be from 20 to tens of thousands • Of a polypeptide has 400 amino acids, there are 20400 possible aa sequences • Calculator • If we add all of the possible sequences together the number of potential polypeptides is effectively infinite.

11. 2.4.4 The amino acid sequence of polypeptides is coded for by genes. • A cell must have the information to make all of these polypeptides (a typical cell produces thousands of different sequences) • The amino acid sequence is stored in coded form in a gene • A gene is a segment of DNA • Remember, DNA is composed of nucleotides, each of which contain a nitrogen base • 3 nitrogen bases of a gene are needed to code for each amino acid • The sequence of bases that code for a polypeptide- open reading frame • DNA strand is longer than the aa sequence

12. 2.4.5 A protein may consist of a single polypeptide or more than one polypeptide linked together. • Proteins may be • A single polypeptide • Many polypeptides linked together • Examples • Integrin- membrane protein • 2 polypeptides, each having a hydrophobic portion imbedded in the membrane • Collagen- • 3 long polypeptides wound together to form a rope like protein great tensile strength, while allowing it to stretch

13. 2.4.6 The amino acid sequence determines the three-dimensional conformation of a protein. • The conformation of a protein is its 3-D structure, which is determined by the amino acid sequence of a protein and its constituent polypeptides. • Some proteins (fibrous proteins) are elongated with a repeating structure • Some proteins are globular, with an intricate shape, including parts that are helical or sheet like

14. In globular proteins, the polypeptides gradually fold up as they are made to develop the final conformation. This is stabilized by bonds between the R groups of the amino acids that have been brought together by the folding.

15. Protein structure • Primary structure- the linear sequence of amino acids in a polypeptide chain.

16. Protein structure • Secondary structure- 3D structure of regions of a protein chain • alpha-helixes • beta-pleated sheets. • These are stabilized by hydrogen bonds between backbone atoms

17. Alpha-helixes- secondary structure in which proteins are coiled like a loose spring.

18. Beta-pleated sheets- individual protein chains are folded so that they lie along side each other. Every other protein chain is aligned in an opposite direction.

19. Tertiary Structure • Geometric shape of a single polypeptide, consisting of one or more secondary structures • Stabilized by non-covalent interactions between side chains (R groups) • Low energy state

20. Quarternary Structure • The clustering of several polypeptide chains to fit a final specific shape. • Not every protein has quaternary structure.

21. A2.4.1 Denaturation of proteins by heat or by deviation from pH from the optimum. • The 3-D structure of proteins is stabilized by bonds or interactions between R groups of amino acids within the molecule. • These bonds are relatively weak and can be broken, resulting in a change in conformation of protein  denaturation Bonding interactions within tertiary structure of a protein

22. Heat causes denaturation • Heat causes molecule to vibrate, breaking bonds (hydrogen bonds and non-polar hydrophobic interactions), allowing the proteins to unravel or change shape • http://www.sumanasinc.com/webcontent/animations/content/proteinstructure.html • Different proteins tolerate different temperatures

23. Extremes of pH can cause denaturation • Acids and bases can disrupt intermolecular bonds between side chains in a protein, changing the 3-D conformation • Milk in stomach acids? • Hair straighteners? • Cheese production? • Heat sanitation? • how are these things affected by denaturation of proteins? • http://highered.mheducation.com/sites/0072943696/student_view0/chapter2/animation__protein_denaturation.html

24. 2.4.7 Living organisms synthesize many different proteins with a wide range of functions

25. 2.4.7 Living organisms synthesize many different proteins with a wide range of functions

26. 2.4.7 Living organisms synthesize many different proteins with a wide range of functions

27. A2.4.2 Rubisco, insulin, immunoglobins, rhodopsin, collagen, and spider silk as examples of the range of protein functions Rubisco • Ribulose biphosphate carboxylase • Enzyme that catalyses the reaction that fixes carbon dioxide from the atmosphere • Provides the source of carbon from which all carbon compounds required by living organisms are produced • Found in high concentrations in leaves and algal cells

28. Insulin • Hormone- signals cells to absorb glucose and help reduce glucose concentration of the blood • These cells have receptor proteins on their surface to which insulin can (reversibly) bind to • Secreted by  (beta) cells in the pancreas and transported by the blood

29. Immunoglobulin • Antibodies • 2 arms, with sites at the tips that bind to antigens (a molecule on a pathogen which provides an immune response) on bacteria or other pathogen • The other parts of the immunoglobulin cause a response (such as acting as a marker to macrophages to engulf a pathogen) • The body can produce a huge range of immunoglobulins, each with a different type of binding site, which is the basis of specific immunity to disease

30. Rhodopsin- • Pigment that absorbs light • Membrane protein of rod cells of the retina (the light sensitive region in the back of the eye) • Rhodopsin consists of the opsin polypeptide surrounding the light sensitive retinal molecule • When the retinal molecule absorbs a single photon of light it changes shape, which causes the opsin to change causing the rod cell to send nerve impulses to the brain

31. Collagen • Many different forms, all are ropelike made of 3 polypeptides wound together • About 25% of all proteins in human body. • Forms mesh of fibers in skin and blood vessel walls that resist tearing • Provides strength to tendons, ligaments, skin, and blood vessel walls • Forms parts of teeth and bones, helps to prevent cracks and fractures

32. Spider silk • There are many different types of silk with different functions • Dragline silk is stronger than steel and tougher than Kevlar, used to make spokes of spider web and lifelines from which spiders hang • When first made, it contains regions where the polypeptide forms parallel arrays • Other regions form a disordered tangle, but when stretched the polypeptide gradually extends, making the silk extensible and very resistant to breaking

33. 2.4.8 Every individual has a unique proteome Genome • all of the genes of a cell, a tissue, or an organism • Determines what proteins an organism can produce Environmental factors • Environment influences what proteins an organism needs to produce and in what quanitity Proteome- • all of the proteins produced by a cell, tissue, or an organism • A function of both the genome and the environment to which the organism is exposed- variable (over time) and unique to every individual