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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) 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 Proteins have many functions in the cell. Table 5.1 1 Enzymes – Structure is Important to Function • Enzymes – Are a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate (sucrose) 2 Substrate binds to enzyme. Glucose OH Enzyme (sucrase) H2O Fructose H O 4 Products are released. Figure 5.16 3 Substrate is converted to products. Polypeptides • Polypeptides – Are polymers of amino acids • A protein – Consists of one or more polypeptides 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) 2 • 20 different amino acids make up proteins H H3N+ CH3 O H3N+ C C O– H Glycine (Gly) H3N+ C H Alanine (Ala) CH CH3 CH3 O C O– C CH2 CH2 O H3N+ C O– H Valine (Val) CH3 CH3 CH3 CH3 H3C O C CH H3N+ C H Leucine (Leu) C O C O– O– H Isoleucine (Ile) Nonpolar CH3 CH2 S NH CH2 CH2 H3N+ CH2 O C H3N+ C H3N+ C C O– H CH2 O C O C O– H C O– H Phenylalanine (Phe) Methionine (Met) C CH2 O O– H H2C H2N Proline (Pro) Tryptophan (Trp) Figure 5.17 OH OH Polar CH2 H3N+ C CH O H3N+ C O– H Serine (Ser) C CH2 O H3N+ C O– H NH2 O C CH2 O C O– H H3N+ C CH2 O H3N+ C C O– H CH2 H3N+ C O NH2 CH2 C CH2 CH2 CH2 O CH2 C O– H3N+ H C CH2 O O C O– H Glutamine (Gln) O– H3N+ C H3N+ CH2 O C O– H CH2 H3N+ C H Lysine (Lys) Glutamic acid (Glu) NH+ NH2+ CH2 CH2 C H Aspartic acid (Asp) O– C Basic NH3+ C O– O C Electrically charged CH2 H3N+ C Asparagine (Asn) Acidic –O CH2 O H Tyrosine (Tyr) Cysteine (Cys) Threonine (Thr) C NH2 O C SH CH3 OH NH CH2 O C C O– H O C O– Arginine (Arg) Histidine (His) Amino Acid Polymers • Amino acids – Are linked by peptide bonds Peptide bond OH OH SH CH2 CH2 H N H CH2 H C C H N C C OH H N C H O H O H (a) C OH O DESMOSOMES H2O OH DESMOSOMES DESMOSOMES SH Peptide CH2 bond CH2 OH CH2 H H N C C H O Figure 5.18 (b) Amino end (N-terminus) H H N C C H O N C C OH Side chains Backbone H O Carboxyl end (C-terminus) 3 Protein Conformation and Function • A protein’s specific conformation – Determines how it functions • Conformation is determined at four different levels. Four Levels of Protein Structure • Primary structure – Is the unique sequence of amino acids in a polypeptide +H N 3 Amino end GlyProThr Gly Thr Gly Amino acid subunits Glu CysLysSeu LeuPro Met Val Lys Val Leu Asp AlaVal Arg Gly Ser Pro Ala – Is what is coded for by the DNA of genes. GluLle LeuAla Gly Asp Thr Lys Ser Lys Trp Tyr lle Ser ProPheHisGlu Ala Thr PheVal Asn His Ala Glu Val Thr Asp Tyr Arg Ser Arg GlyPro Thr Ser Tyr lle Ala Ala Leu Leu Ser Pro SerTyr Thr Ala Val Val ThrAsnProLysGlu Figure 5.20 c o o– Carboxyl end 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 α helix and β pleated sheet β pleated sheet Amino acid subunits O H H C C N C N H R R O H H C C N C C N O H H O O H H O H H R R C C N C C N N C C N R C C R C C OH H OH H O R R O O C H C H H H C N HC C N HC N C N H H C O C O R R O C R R R H H C C O C O C N H N H N H N H C O C H C R H C R H C R H C R N H O C N H O C O C O C N H N H C H C H R R R O C H H NH C N C H O C R R H C N HC N H O C α helix Figure 5.20 4 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’. Hyrdogen bond CH CH22 CH O H O H3C H3C CH3 CH3 CH Hydrophobic interactions and van der Waals interactions Polypeptide backbone HO C CH2 CH2 S S CH2 Disulfide bridge O CH2 NH3+ -O C CH2 Ionic bond Quaternary structure – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen β Chains Iron Heme α Chains Hemoglobin 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. + H3N Amino end Amino acid subunits α helix 5 Chaperonins – Are protein molecules that assist in the proper folding of other proteins Correctly folded protein Polypeptide Cap Hollow cylinder 2 The cap attaches, causing 3 The cap comes Steps of Chaperonin the cylinder to change shape in off, and the properly Action: folded protein is such a way that it creates a 1 An unfolded polyhydrophilic environment for the released. peptide enters the cylinder from one end. folding of the polypeptide. Chaperonin (fully assembled) Figure 5.23 Denaturation – When a protein unravels and loses its native conformation Denaturation Normal protein Denatured protein Renaturation Figure 5.22 Sickle-Cell Disease: A Simple Change in Primary Structure • Sickle-cell disease – a single change in one a.a. Primary structure Normal hemoglobin Val His Leu Thr Pro Glul Glu 1 2 3 4 5 6 7 Secondary and tertiary structures Sickle-cell hemoglobin . . . Primary Val His Leu Thr Secondary β subunit and tertiary structures Quaternary Hemoglobin A structure α β Function Molecules do not associate with one another, each carries oxygen. Red blood cell shape Normal cells are full of individual hemoglobin molecules, each carrying oxygen β α Pro Val Glu ... structure 1 2 3 4 5 6 7 Quaternary structure β subunit α β β α Function 10 μm 10 μm Red blood cell shape Exposed hydrophobic region Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced. Fibers of abnormal hemoglobin deform cell into sickle shape. Figure 5.21 6 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 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 DNA to Protein 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 Figure 5.25 Polypeptide Amino acids 7 The Structure of Nucleic Acids • Nucleic acids – Exist as polymers called polynucleotides 5’ end 5’C O 3’C O O 5’C O 3’C OH 3’ end (a) Polynucleotide, or nucleic acid Figure 5.26 • Each polynucleotide – Consists of monomers called nucleotides Nucleoside Nitrogenous base O − O P 5’C O CH2 O O− Phosphate group Figure 5.26 3’C Pentose sugar (b) Nucleotide Nucleotide Monomers Are made up of nucleosides and phosphate groups Nucleoside Nitrogenous base O − O P Nitrogenous bases Pyrimidines O O C C CH3 CH N C CH HN HN CH C CH C C CH N N O N O O H H H Cytosine Thymine (in DNA) Uracil (in RNA) RNA) Uracil (in U C U T NH2 C Purines 5’C O CH2 O O− Phosphate group 3’C Pentose sugar O NH2 N C C N CC NH N HC HC C CH N C N NH2 N N H H Adenine Guanine A G 5” Pentose sugars (b) Nucleotide Figure 5.26 5” HOCH2 O OH H H 1’ H H 1’ 4’ H H H 3’ 2’ H 3’ 2’ OH OH OH H Deoxyribose (in DNA) Ribose (in RNA) HOCH2 O OH Figure 5.26 4’ (c) Nucleoside components 8 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 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 5’ end 5’C O 3’C O O 5’C O 3’C OH 3’ end Figure 5.26 • The sequence of bases along a nucleotide polymer – Is unique for each gene 9 The DNA Double Helix • Cellular DNA molecules – Consists of two antiparallel nucleotide strands that spiral around to form a “double helix). 5’ end 3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands A 3’ end Nucleotide about to be added to a new strand 5’ end 3’ end Figure 5.27 New strands 5’ end 3’ end 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. 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. 10 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 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) 11