Protein Structure and Function

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. Table 5.1 Proteins have many functions in the cell.

4. Substrate binds to enzyme. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. 2 2 Substrate (sucrose) Glucose Enzyme (sucrase) OH H2O Fructose H O 4 Products are released. 3 Substrate is converted to products. Figure 5.16 Enzymes – Structure is Important to Function • Enzymes • Are a type of protein that acts as a catalyst, speeding up chemical reactions

5. Polypeptides • 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. CH3 CH3 CH3 CH CH2 CH3 CH3 H CH3 H3C CH3 CH2 CH O O O O O H3N+ C H3N+ C H3N+ H3N+ C C C C C C H3N+ C C O– O– O– O– O– H H H H H Valine (Val) Leucine (Leu) Isoleucine (Ile) Glycine (Gly) Alanine (Ala) Nonpolar CH3 CH2 S H2C CH2 O NH CH2 C C H2N CH2 CH2 O– CH2 O O O H H3N+ H3N+ C C C C H3N+ C C O– O– O– H H H Phenylalanine (Phe) Proline (Pro) Methionine (Met) Tryptophan (Trp) Figure 5.17 • 20 different amino acids make up proteins

8. OH NH2 O C NH2 O C OH SH CH2 CH3 OH Polar CH2 CH CH2 CH2 CH2 CH2 O O O O O O H3N+ C H3N+ C H3N+ C C H3N+ C C H3N+ C C C C C H3N+ C O– O– O– O– O– O– H H H H H H Glutamine (Gln) Tyrosine (Tyr) Asparagine (Asn) Cysteine (Cys) Serine (Ser) Threonine (Thr) Basic Acidic NH3+ NH2 NH+ O– O –O O CH2 C NH2+ C C NH Electrically charged CH2 CH2 CH2 CH2 CH2 O O CH2 CH2 C CH2 C H3N+ C H3N+ C O O– O– CH2 C H3N+ CH2 C H O H O– C C H3N+ CH2 H O O– C C H3N+ H O– H Lysine (Lys) Histidine (His) Arginine (Arg) Glutamic acid (Glu) Aspartic acid (Asp)

9. Peptidebond OH SH CH2 CH2 CH2 H H H C C H C C N C OH H C OH N N DESMOSOMES H O H O H O (a) H2O OH DESMOSOMES DESMOSOMES Side chains SH OH Peptidebond CH2 CH2 CH2 H H H N OH C C C C C H C N N Backbone H H O O H O Amino end(N-terminus) Carboxyl end(C-terminus) Figure 5.18 (b) Amino Acid Polymers • Amino acids • Are linked by peptide bonds OH

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

11. +H3NAmino end Pro Thr Gly Gly Amino acid subunits Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Arg Val Gly Ser Pro Ala Glu Lle Asp Thr Lys Ser Tyr Trp Lys Ala Leu Gly lle Ser Pro Phe His Glu His Ala Glu Val Thr Phe Val Ala Asn lle Thr Asp Ala Tyr Arg Ser Ala Arg Pro Gly Leu Leu Ser Pro Tyr Ser Tyr Ser Thr Thr Ala o Val c Val Glu – Lys o Thr Pro Asn Carboxyl end Figure 5.20 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.

12. H H H H H H O O O O O O O H H H H H H R R R R R R R C C C C C C C C C C C C C N N N N N N N N N N N N N C C C C C C C C C C C C C C R R R R R R H H H H H H H O O O O O O O H H H H H H H  pleated sheet H O H H Amino acidsubunits C C N N N C C C R H O H H H H H H N N N N N N  helix C C O C H H H C C C R R R R R H H C C C C C C O O O O H C R O C C O H C O N N H C C H R H R Figure 5.20 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

13. Hydrophobic interactions and van der Waalsinteractions CH CH2 CH2 H3C CH3 OH Polypeptidebackbone H3C CH3 Hyrdogenbond CH O HO C CH2 CH2 S S CH2 Disulfide bridge O -O C CH2 CH2 NH3+ Ionic bond 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’.

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

15. +H3N Amino end Amino acid subunits helix 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.

16. Correctlyfoldedprotein Polypeptide Cap Hollowcylinder The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comesoff, and the properlyfolded protein is released. Chaperonin(fully assembled) Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end. 2 1 3 Figure 5.23 Chaperonins • Are protein molecules that assist in the proper folding of other proteins

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

18. Normal hemoglobin Sickle-cell hemoglobin Primary structure Primary structure . . . . . . Exposed hydrophobic region Val His Leu Thr Pro Glul Glu Val His Leu Pro Glu Thr Val 5 6 7 3 4 5 6 7 1 2 1 2 3 4 Secondaryand tertiarystructures Secondaryand tertiarystructures  subunit  subunit     Quaternary structure Hemoglobin A Quaternary structure Hemoglobin S     Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced. Function Molecules donot associatewith oneanother, eachcarries oxygen. Function 10 m 10 m Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen Red bloodcell shape Red bloodcell shape Figure 5.21 Sickle-Cell Disease:A Simple Change in Primary Structure • Sickle-cell disease – a single change in one a.a. Fibers of abnormalhemoglobin deform cell into sickle shape.

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

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

23. Nucleoside Nitrogenous base O 5’C O O CH2 P O O Phosphate group 3’C Pentose sugar Figure 5.26 (b) Nucleotide • Each polynucleotide • Consists of monomers called nucleotides

24. Nitrogenous bases Pyrimidines NH2 O O Nucleoside C C CH3 C N CH HN C CH HN CH CH C CH C C CH CH N N O N O O Nitrogenous base H H H Cytosine C Uracil (in RNA) U Thymine (in DNA) T Uracil (in RNA) U Purines O 5’C O NH2 C C N N O O CH2 P C C NH N O HC HC C CH C N N NH2 N O N H H Adenine A Guanine G Phosphate group 3’C Pentose sugar Pentose sugars 5” 5” OH OH HOCH2 HOCH2 O O H H H H 1’ 1’ 4’ 4’ Figure 5.26 (b) Nucleotide H H H H 3’ 2’ 3’ 2’ H OH OH OH Deoxyribose (in DNA) Ribose (in RNA) Ribose (in RNA) Nucleotide Monomers Are made up of nucleosides and phosphate groups Figure 5.26 (c) Nucleoside components

25. Nucleotides • 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

26. 5’ end 5’C O 3’C O O 5’C O 3’C 3’ end OH Figure 5.26 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

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

28. 3’ end 5’ end Sugar-phosphatebackbone Base pair (joined byhydrogen bonding) Old strands Nucleotideabout to be added to a new strand 3’ end A 5’ end Newstrands 3’ end 3’ end 5’ end Figure 5.27 The DNA Double Helix • Cellular DNA molecules • Consists of two antiparallel nucleotide strands that spiral around to form a “double helix).

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, ATPb. coenzymes for metabolism - NAD and FADc. 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)