Lecture - 4

1. Lecture - 4 Biological Macromolecules – Proteins

2. Answers – High Fructose Corn Syrup • https://www.sciencenews.org/article/sweet-confusion

3. Answers – Trans fats • Most naturally occurring fats have their hydrogen atoms arrainged in a cis configuration. • Some debate as to whether or not they are any worse than naturally occurring saturated fats • Un-saturated fats are easier to breakdown and metabolize. (the double bonds help facilitate oxidization) • Trans fat synthesis requires extremely high heat and high temperatures that can not be replicated in a home kitchen

4. Outline • Nucleic Acids Cont. • Form follows function • Amino Acids • Protein Structure • Protein Folding

5. #3 Nucleic Acid - refresh • Polymers called polynucleotides • A single nucleotide consists of: • Nitrogenous base • Apentose sugar • One or more phosphate groups

6. Figure 5.26ab Sugar-phosphate backbone 5 end 5C 3C Nucleoside Nitrogenousbase 5C 1C Phosphategroup 3C Sugar(pentose) 5C 3C (b) Nucleotide 3 end (a) Polynucleotide, or nucleic acid

7. #3 Nucleic Acids • There are two families of nitrogenous bases • Pyrimidines(cytosine, thymine, and uracil)have a single six-membered ring • Purines (adenine and guanine) have a six-membered ring fused to a five-membered ring • In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose • Nucleotide = nucleoside + phosphate group

8. Figure 5.26c Pyrimidines Purines Nitrogenous bases Cytosine (C) Uracil (U, in RNA) Thymine (T, in DNA) Sugars Deoxyribose (in DNA) Ribose (in RNA) Adenine (A) Guanine (G) (c) Nucleoside components

9. #3 Nucleic Acids • Nucleotides are 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

10. #3 Nucleic Acids • These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages

11. #3 Nucleic Acids • The sequence of bases along a DNA or mRNA polymer is unique for each gene

12. #3 Nucleic Acids • RNA -single polypeptide chains • DNA - double helix • Two backbones run in opposite 5→ 3direction - antiparallel

13. #3 Nucleic Acids • Complementary base pairing

14. #3 Nucleic Acids • Can also occur between two RNA molecules or between parts of the same molecule • In RNA, thymine is replaced by uracil (U) so A and U pair

15. #3 Nucleic Acids • One DNA molecule includes many genes • ~40,000 genes in the human genome • 23 chromosome pairs • Each chromosome is a DNA polypeptide • 60 – 150 million base pairs per chromosome.

16. Figure 5.27 5 3 Sugar-phosphatebackbones Hydrogen bonds Base pair joinedby hydrogenbonding Base pair joinedby hydrogen bonding 5 3 (b) Transfer RNA (a) DNA

17. Review - Macromolecules • Nucleic Acids • DNA & RNA • Lipids • Fatty Acids • Phospholipids • Steroids • Carbohydrates • Monosaccharides and Disaccharides • Starch/Glycogen • Cellulose/chitin

18. Proteins • Account for more than 50% of the dry mass of most cells • Functions include: • Enzymes • Structural support • Storage • Hormones • Transport • Cellular communications • Movement • Defense against foreign substances

19. Proteins - Enzymes • Enzymes- a type of protein that acts as a catalyst to speed up chemical reactions • Can perform their functions repeatedly. • They carry out the processes of life.

20. Proteins - Enzymes Enzymatic proteins Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysisof bonds in food molecules. Enzyme Figure 5.15a

21. Figure 5.15c Proteins - Hormones Hormonal proteins Function: Coordination of an organism’s activities Example: Insulin, a hormone secreted by thepancreas, causes other tissues to take up glucose,thus regulating blood sugar concentration Insulinsecreted Highblood sugar Normalblood sugar

22. Figure 5.15h Proteins - Structural Structural proteins Function: Support Examples: Keratin is the protein of hair, horns,feathers, and other skin appendages. Insects andspiders use silk fibers to make their cocoons and webs,respectively. Collagen and elastin proteins provide afibrous framework in animal connective tissues. Collagen Connectivetissue 60 m

23. Figure 5.15b Proteins – Storage Storage proteins Function: Storage of amino acids Examples: Casein, the protein of milk, is the majorsource of amino acids for baby mammals. Plants havestorage proteins in their seeds. Ovalbumin is theprotein of egg white, used as an amino acid sourcefor the developing embryo. Amino acidsfor embryo Ovalbumin

24. Figure 5.15f Proteins – Transport/Cell communicaton Transport proteins Function: Transport of substances Examples: Hemoglobin, the iron-containing protein ofvertebrate blood, transports oxygen from the lungs toother parts of the body. Other proteins transportmolecules across cell membranes. Transportprotein Cell membrane

25. Figure 5.15g Proteins – Cell/Cell communication Receptor proteins Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of anerve cell detect signaling molecules released byother nerve cells. Receptorprotein Signalingmolecules

26. Figure 5.15d Proteins - Movement Contractile and motor proteins Function: Movement Examples: Motor proteins are responsible for theundulations of cilia and flagella. Actin and myosinproteins are responsible for the contraction ofmuscles. Actin Myosin Muscle tissue 100 m

27. Figure 5.15e Proteins - Defense Defensive proteins Function: Protection against disease Example: Antibodies inactivate and help destroyviruses and bacteria. Antibodies Virus Bacterium

28. Proteins - Polypeptides • Proteins are Polypeptides (biologically functional) • Polypeptides: unbranched polymers built from the same set of 20 amino acids(Amino acids are linked by peptide bonds) • Range in length from a few to more than a thousand monomers • Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)

29. Amino acids Side chain (R group) • Organic molecules with carboxyl and amino groups • Amino acids differ in their properties due to differing side chains, called R groups  carbon Aminogroup Carboxylgroup

30. Figure 5.16a Nonpolar side chains; hydrophobic Side chain Isoleucine(Ile or I) Valine(Val or V) Alanine(Ala or A) Glycine(Gly or G) Leucine(Leu or L) Methionine(Met or M) Phenylalanine(Phe or F) Tryptophan(Trp or W) Proline(Pro or P)

31. Figure 5.16b Polar side chains; hydrophilic Threonine(Thr or T) Serine(Ser or S) Cysteine(Cys or C) Tyrosine(Tyr or Y) Asparagine(Asn or N) Glutamine(Gln or Q)

32. Figure 5.16c Electrically charged side chains; hydrophilic Basic (positively charged) Acidic (negatively charged) Glutamic acid(Glu or E) Histidine(His or H) Aspartic acid(Asp or D) Lysine(Lys or K) Arginine(Arg or R)

33. Proteins = AA polymers • Condensation reaction results in peptide bond Peptide bond New peptidebond forming Side chains Back-bone Peptidebond Carboxyl end(C-terminus) Amino end(N-terminus)

34. Proteins – Form and Function • A functional protein – A polypeptide that is properly twisted, folded, and coiled into its unique shape • AA sequence determines the three-dimensional structure • Structure determines the function

35. Protein – Form and Function Groove Groove (a) A ribbon model (b) A space-filling model

36. Protein – Form and Function Antibody protein Protein from flu virus

37. Proteins - Form • Three levels of protein structure • Primary Structure – The unique sequence of amino acids. • Secondary structure- Coils and folds in the polypeptide chain. • Tertiary structure - Determined by interactions among various side chains (R groups). • Some have a fourth level • Quaternary structure - Results when a protein consists of multiple polypeptide chains.

38. Proteins – Form – Primary Structure • The sequence of amino acids in a protein. • Kinda like the order of letters in a long word • Read left to right • Starts with amino group – N-terminus • Ends with carboxy group – C-terminus

39. Figure 5.20a Primary structure Aminoacids Amino end Primary structure of transthyretin Carboxyl end

40. Proteins – Form – Secondary Structure • Secondary structure – Regular, repeated folds and twists • Stabilized by hydrogen bonds • Determined by aa sequence (primary structure) • Two main Secondary Structures: • helix – Coils • pleated sheet- folds

41. Proteins – Secondary Structurea Helix

42. Proteins – Secondary Structurea Helix • Function follows form • A helices • DNA binding (transcription factors, hox proteins, chromatin proteins…) • Membrane spanning proteins

43. Proteins – Secondary Structureb Pleated Sheets

44. Proteins – Secondary Structureb Pleated Sheets • Usually part of Protein/Protein interactions • Silk is an example of b pleated sheets • Made up of multiple polypeptides packed together • Amyloid Proteins • Implicated in Alzheimer's, Parkinson’s & Huntington’s disease • Mad Cow’s disease (Transmissible spongiform encephalopathy) • Rheumatoid arthritis • Chronic traumatic encephalopathy • Accumulation of Tau Protein & Beta Amyloid plaques

45. Proteins – Tertiary Structure • The 3 dimensional shape of the whole protein