1. BSC 2010 - Exam I Lectures and Text Pages I. Intro to Biology (2-29) II. Chemistry of Life – Chemistry review (30-46) – Water (47-57) – Carbon (58-67) – Macromolecules (68-91) continued…proteins and nucleic acids III. Cells and Membranes – Cell structure (92-123) – Membranes (124-140) IV. Introductory Biochemistry – Energy and Metabolism (141-159) – Cellular Respiration (160-180) – Photosynthesis (181-200)

2. Proteins Proteins have many structures, resulting in a wide range of functions – Proteins Have many roles inside the cell Make up 50% of the dry weight (after removal of water) of cells. Have amino acids as their monomer

3. Proteins have many functions in the cell. Table 5.1

4. Enzymes – Structure is Important to Function Enzymes – Are a type of protein that acts as a catalyst, speeding up chemical reactions Substrate (sucrose) Enzyme (sucrase) Glucose OH H O H2OH2O Fructose 3 Substrate is converted to products. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate binds to enzyme. 22 4 Products are released. Figure 5.16

5. Polypeptides – Are polymers of amino acids A protein – Consists of one or more polypeptides

6. Amino Acid Monomers Amino acids – Are organic molecules possessing both carboxyl and amino groups – Differ in their properties due to differing side chains, called R groups (can be polar, nonpolar, or charged)

7. 20 different amino acids make up proteins O O–O– H H3N+H3N+ C C O O–O– H CH 3 H3N+H3N+ C H C O O–O– C C O O–O– H H3N+H3N+ CH CH 3 CH 2 C H H3N+H3N+ CH 3 CH 2 CH C H H3N+H3N+ C CH 3 CH 2 C H3N+H3N+ H C O O–O– C H3N+H3N+ H C O O–O– NH H C O O–O– H3N+H3N+ C CH 2 H2CH2C H2NH2N C H C Nonpolar Glycine (Gly) Alanine (Ala) Valine (Val)Leucine (Leu)Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) C O O–O– Tryptophan (Trp) Proline (Pro) H3CH3C Figure 5.17 S O O–O–

9. Amino Acid Polymers Amino acids – Are linked by peptide bonds OH DESMOSOMES OH CH 2 C N H C H O HOH Peptide bond OH H H HH H H H H H H H H N N N N N SH Side chains SH OO OO O H2OH2O CH 2 C C C CCC C C C C Peptide bond Amino end (N-terminus) Backbone (a) Figure 5.18 (b) Carboxyl end (C-terminus)

10. Protein Conformation and Function A protein’s specific conformation – Determines how it functions Conformation is determined at four different levels.

11. Four Levels of Protein Structure Primary structure – Is the unique sequence of amino acids in a polypeptide – Is what is coded for by the DNA of genes. Figure 5.20 – Amino acid subunits + H 3 N Amino end o Carboxyl end o c Gly ProThr Gly Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Val Arg Gly Ser Pro Ala Gly lle Ser Pro Phe His Glu His Ala Glu Val Phe Thr Ala Asn Asp Ser Gly Pro Arg Tyr Thr lle Ala Leu Ser Pro Tyr Ser Tyr Ser Thr Ala Val Thr Asn Pro Lys Glu Thr Lys Ser Tyr Trp Lys Ala Leu Glu Lle Asp

12. OC  helix  pleated sheet Amino acid subunits N C H C O C N H C O H R C N H C O H C R N H H R C O R C H N H C O H N C O R C H N H H C R C O C O C N H H R C C O N H H C R C O N H R C H C O N H H C R C O N H R C H C O N H H C R C O N H H C R N H O O C N C R C H O C H R N H O C R C H N H O C H C R N H C C N R H O C H C R N H O C R C H H C R N H C O C N H R C H C O N H C Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration caused by H-bonds between peptide linkages. – Includes the predictable shapes of the  helix and  pleated sheet H H Figure 5.20

13. Tertiary structure – Is the overall three-dimensional shape of a polypeptide – Results from interactions between the R groups of amino acids. Shapes are less predictable than 2’. CH 2 CH OHOH O C HO CH 2 NH 3 + C -O-O CH 2 O SS CH CH 3 H3CH3C H3CH3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hyrdogen bond Ionic bond CH 2 Disulfide bridge

14. Quaternary structure – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen  Chains  Chains Hemoglobin Iron Heme

15. The four levels of protein structure Amino acid sequence determines the way the protein molecule forms the higher levels of structure. Heat, pH, salinity can all affect the structure of the molecule, and if it is changed too much, the protein is said to be denatured. A change in amino acid sequence, as could be caused by a mutation in the DNA, might result in a non-functional molecule. + H 3 N Amino end Amino acid subunits  helix

16. Chaperonins – Are protein molecules that assist in the proper folding of other proteins Hollow cylinder Cap Chaperonin (fully assembled) Steps of Chaperonin Action: An unfolded poly- peptide enters the cylinder from one end. The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. Correctly folded protein Polypeptide 2 1 3 Figure 5.23

17. Denaturation – When a protein unravels and loses its native conformation Denaturation Renaturation Denatured proteinNormal protein Figure 5.22

18. Sickle-Cell Disease : A Simple Change in Primary Structure Sickle-cell disease – a single change in one a.a. Fibers of abnormal hemoglobin deform cell into sickle shape. Primary structure Secondary and tertiary structures Quaternary structure Function Red blood cell shape Hemoglobin A Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen     10  m     Primary structure Secondary and tertiary structures Quaternary structure Function Red blood cell shape Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced.  subunit 12 3 4 567 34 567 21 Normal hemoglobin Sickle-cell hemoglobin... Figure 5.21 Exposed hydrophobic region ValThrHisLeuProGlulGluValHisLeu Thr Pro Val Glu

19. Nucleic Acids Nucleic acids store and transmit hereditary information Genes – Are the units of inheritance – Program the amino acid sequence of polypeptides – Are made of nucleic acids

20. The Roles of Nucleic Acid Polymers There are two types of polynucleotides – Deoxyribonucleic acid (DNA) (genes) Stores information for the synthesis of specific proteins Directs RNA synthesis – Ribonucleic acid (RNA) Translates the DNA code into polypeptides

21. DNA to Protein 1 2 3 Synthesis of mRNA in the nucleus Movement of mRNA into cytoplasm via nuclear pore Synthesis of protein NUCLEUS CYTOPLASM DNA mRNA Ribosome Amino acids Polypeptide mRNA Figure 5.25

22. The Structure of Nucleic Acids Nucleic acids – Exist as polymers called polynucleotides (a) Polynucleotide, or nucleic acid 3’C 5’ end 5’C 3’C 5’C 3’ end OH Figure 5.26 O O O O

23. Each polynucleotide – Consists of monomers called nucleotides Nitrogenous base Nucleoside O O OO OO P CH 2 5’C 3’C Phosphate group Pentose sugar (b) Nucleotide Figure 5.26 O

24. Nucleotide Monomers Are made up of nucleosides and phosphate groups (c) Nucleoside components Figure 5.26 CH Uracil (in RNA) U Ribose (in RNA) Nitrogenous bases Pyrimidines C N N C O H NH 2 CH O C N H HN C O C CH 3 N HN C C H O O Cytosine C Thymine (in DNA) T N HC N C C N C CH N NH 2 O N HC N H H C C N NH C NH 2 Adenine A Guanine G Purines O HOCH 2 H H H OH H O HOCH 2 H H H OH H Pentose sugars Deoxyribose (in DNA) Ribose (in RNA) OH CH Uracil (in RNA) U 4’ 5”5” 3’ OH H 2’ 1’ 5”5” 4’ 3’ 2’ 1’ Nitrogenous base Nucleoside O O OO OO P CH 2 5’C 3’C Phosphate group Pentose sugar (b) Nucleotide Figure 5.26 O

25. Structure: nucleotides are made up of a nitrogenous base, a pentose sugar, and a phosphate group. The sugar and nitrogenous base are also called a nucleoside. The nitrogenous bases include: – The pyrimidines (single ring structure) cytosine and thymine (and uracil in RNA) – The purines (double ring structure) adenine and guanine Nucleotides

26. Nucleotide Polymers – Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next 3’C 5’ end 5’C 3’C 5’C 3’ end OH Figure 5.26 O O O O

27. The sequence of bases along a nucleotide polymer – Is unique for each gene

28. The DNA Double Helix Cellular DNA molecules – Consists of two antiparallel nucleotide strands that spiral around to form a “double helix). 3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand A 3’ end 5’ end New strands 3’ end 5’ end Figure 5.27

29. Base-Pairing Rules The nitrogenous bases in DNA – Form hydrogen bonds in a complementary fashion (A with T only, and C with G only) In RNA, Uracil is substituted for Thymine.

30. DNA and Proteins as Tape Measures of Evolution Molecular comparisons – Help biologists sort out the evolutionary connections among species The more closely related two species are the more nucleic acid and protein sequences they will have in common. Various classes of nucleic acids mutate at characteristic rates.

31. Other nucleic acids There are other nucleic acids in the cell (besides DNA and RNA) and they have other functions: a. energy transfer - AMP, ADP, ATP b. coenzymes for metabolism - NAD and FAD c. messenger within the cell - cAMP

32. Organic molecules may be formed in combinations Examples include: – Lipoproteins: carry cholesterol in blood. LDL (low density lipoprotein) = bad; HDL (high density lipoprotein) = good – Glycoproteins: (in cell membranes)