Biology II -Part 1 PDF

Biology II -Paart1 FUNCTIONAL GROUPS AND PROTEINS 1  Biology II -Paart1 Polar Functional Groups CHEMICAL Hydroxyl Carbonyl...

Biology II -Paart1 FUNCTIONAL GROUPS AND PROTEINS 1  Biology II -Paart1 Polar Functional Groups CHEMICAL Hydroxyl Carbonyl Carboxyl GROUP STRUCTURE (may be written HO—) Alcohols Ketone/Aldehyde Carboxylic acids, COMPOUND (Specific name usually or organic acids NAME end in -ol.) EXAMPLE Ethanol Acetone Acetic acid Propanal Figure 4.9 2  Biology II -Paart1 CARBOXYL O R‐C‐OH (R‐COOH) O‐H bond is so polar that the hydrogen can reversibly dissociate as H+ Since it donates a proton, this functional group has ________ acidic properties _____________ Compounds with carboxyl groups are called _____________ carboxylic acids Nonionized Ionized 3  Biology II -Paart1 AMINO H R‐N H (R‐NH2) Unshared pair of electrons on nitrogen can accept a proton and therefore this functional group acts as a weak base ______________ Compounds with an amino group are called ________ amines Nonionized Ionized 4  Biology II -Paart1 Polar Functional Groups (cont) CHEMICAL Amino Sulfhydryl Phosphate GROUP STRUCTURE (may be written HS—) COMPOUND NAME Amines Thiols Organic phosphates EXAMPLE Glycine Cysteine Glycerol phosphate Can form disulfide bonds Important in the storage and transfer of cellular energy when 2 sulfhydryl (ex. ATP) come togeether make that bond dans nucleque acid , play an important part in storing Figure 4.9 5  Biology II -Paart1 Nonpolar Functional Group CHEMICAL Methyl GROUP STRUCTURE COMPOUND Methylated NAME compound EXAMPLE 5-Methylcytosine Figure 4.9 6  Biology II -Paart1 Macromolecules ‐ Large polymers formed from monomers Classes of Macromolecules: 1)Proteins 2)Nucleic acides (DNA,RNA) 3)Carbohydrates 4)Lipids (not true polymers) Formation of Macromolecules: dehydration (condensation reaction) occurs through Breakdown of Macromolecules: occurs through Hydrolysis (reverse of hydration) 7  Biology II -Paart1 Dehydration reactions link 1 2 3 monomers together to build Short polymer Unlinked monomer macromolecules Dehydration removes a water molecule, (water is removed) forming a new bond. 1 2 3 4 (dehydration = condensation) Longer polymer 1 2 3 4 Hydrolysis reactions break Hydrolysis adds down macromolecules a water molecule, breaking a bond. (water is added) Formation dehydration -> removing water to form covalent bond 1 2 3 8  Biology II -Paart1 REVIEW: PROTEINS: molecular tools of the cell have a wide range of functions Enzymatic proteins Defensive proteins Function: Selective acceleration of chemical reactions Function: Protection against disease Example: Digestive enzymes catalyze the hydrolysis Example: Antibodies inactivate and help destroy of bonds in food molecules. viruses and bacteria. Antibodies Enzyme Virus Bacterium Storage proteins Transport proteins Function: Storage of amino acids Function: Transport of substances Examples: Casein, the protein of milk, is the major Examples: Hemoglobin, the iron-containing protein of source of amino acids for baby mammals. Plants have vertebrate blood, transports oxygen from the lungs to storage proteins in their seeds. Ovalbumin is the other parts of the body. Other proteins transport protein of egg white, used as an amino acid source molecules across cell membranes. for the developing embryo. Transport protein Ovalbumin Amino acids for embryo Cell membrane Figure 5.14 9  Biology II -Paart1 Protein Functions (cont) : Hormonal proteins Receptor proteins Function: Coordination of an organism’s activities Function: Response of cell to chemical stimuli Example: Insulin, a hormone secreted by the Example: Receptors built into the membrane of a pancreas, causes other tissues to take up glucose, nerve cell detect signaling molecules released by thus regulating blood sugar concentration other nerve cells. Receptor Signaling protein Insulin High secreted Normal molecules blood sugar blood sugar Contractile and motor proteins Structural proteins Function: Movement Function: Support Examples: Motor proteins are responsible for the Examples: Keratin is the protein of hair, horns, undulations of cilia and flagella. Actin and myosin feathers, and other skin appendages. Insects and proteins are responsible for the contraction of spiders use silk fibers to make their cocoons and webs, muscles. respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Actin Myosin Collagen Muscle tissue Connective 100 m tissue 60 m Figure 5.14 10  Biology II -Paart1 Monomer: Amino Acids (20 total) Side chain (R group) ‐ 4 components attached to central carbon: i. hydrogen ii. carboxyl group iii. amino group Amino Carboxyl iv. R group (side chain): group group Speci c for each Amino Acid Determines characteristics of each Amino Acids 11  Biology II -Paart1 Amino acids can exist in 3 ionic states i) Physiological pH (pH 7): H Zwitterion: a neutral molecule that H 3 N+ C COO‐ has both positive and negative Want to get rid of its proton charges (charges cancel out) R H ii) Acidic pH (< pH 2) H 3 N+ C COOH Carboxyl group gains proton (H+) Everything Will be protanted R iii) Basic pH (> pH 10) H Amino group loses proton (H+) H2N C COO‐ Negative charges R 12  Biology II -Paart1 Amino acids can exist in 3 ionic states: Summary pH < 2 pH = 7 pH > 10 H H H H3N+ C COOH H3N+ C COO‐ H2N C COO‐ R R R Carboxyl groups in Amino groups in backbone and in R group backbone and R group gain protons (H+) lose protons (H+) 13  Biology II -Paart1 Grouping of amino acids ‐ Amino acids are classified into different groups based on the R‐group Hydrophobic: Nonpolar side chains ‐ Figure 5.15 14  Biology II -Paart1 Grouping of amino acids (cont) Hydrophilic: Polar side chains (If one i group is polar , i) it will make eveything polar) Figure 5.15 15  Biology II -Paart1 Grouping of amino acids (cont) Hydrophilic: ii) charged side chains Acidic (carboxylic acids); negatively charged at pH 7 Basic (amino groups); positively charged at pH 7 Figure 5.15 16  Biology II -Paart1 Nonpolar side chains; hydrophobic Side chain (R group) Glycine Alanine Valine Leucine Isoleucine (Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I) All amino acids at Methionine Phenylalanine Tryptophan Proline physiological (Met or M) (Phe or F) (Trp or W) (Pro or P) Polar side chains; hydrophilic pH (~7): Serine Threonine Cysteine Tyrosine Asparagine Glutamine (Ser or S) (Thr or T) (Cys or C) (Tyr or Y) (Asn or N) (Gln or Q) Electrically charged side chains; hydrophilic Basic (positively charged) Acidic (negatively charged) Aspartic acid Glutamic acid Lysine Arginine Histidine (Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H) Figure 5.15 17  Biology II -Paart1 Formation of a Polypeptide Figure 5.16 Amino acids are linked together by peptide bonds formed by condensation reactions Peptide bond Peptide bionds link the carboxyle group of one amino acid to the amino group of another New peptide bond forming Side chains C-N we know that there’s a peptide bond because the amino group is connected to a Back- carbonyle group. bone We can see terminus free amine group c-terminus free carnyle Amino end Peptide bond Carboxyl end (N-terminus) (C-terminus) 18  Biology II -Paart1 Features of Polypeptides Polypeptides range from a few amino acids to thousands Each polypeptide has: ‐ a unique linear sequence of amino acids ‐ directionality:  An amino group at one end (N-terminus) and a carbonyl group at the otheer (C-terminus)) ‐ a unique isoelectric point pH at which a molecule has no net charge Isoelectric point = 19  Biology II -Paart1 Protein Structure & Function The function of a protein depends on its shape the shape will ditermine if they will func. properly Four levels of Protein Structure: Primary Secondary Tertiary Quaternary 20  Biology II -Paart1 All proteins have 3 levels of structure Only proteins with 2 or more polypeptides 21  Biology II -Paart1 Primary Structure: Amino end linear sequence of amino acids determined by the DNA sequence held together by___________________ peptide bonds Dna ->mRNA->Protein txn translation Carboxyl end Ex: NH3+‐Lys‐Val‐Phe‐Gly‐Arg‐Cys‐Leu‐Ala‐COO‐ Figure 5.19 22  Biology II -Paart1 Secondary Structure: includes coils (α‐helices) and folds (β‐pleated sheets) stabilized by H‐bonds between the carbonyl (C=O) and amino (N‐H) groups of the polypeptide backbone R groups are not involved in H‐bonding Two types: i) α‐helix: occurs due to H‐ o ii) β‐pleated sheets: two bonding between every fourth regions of the polypeptide amino acid chain lie parallel to each other β‐pleated sheets -helix H- H-bond R-group to prove it bond Figure 5.19 doesnt e ect 23  Biology II -Paart1 Tertiary Structure: folding of the polypeptide into its final 3D shape formed through the interactions between amino acid side chains/R groups α ‐helices and β‐sheets interact to form a variety of shapes! Figure 5.19 24  Biology II -Paart1 Bonds which contribute to tertiary structure Side chains interact through covalent and non‐covalent interactions to form the tertiary structure Non‐covalent interactions (weak): between polar side chains ‐ Hydrogen bonds between charges side chains (forms salt bridges) ‐ Ionic bonds ‐ Hydrophobic interactions between nonpolar side chains Covalent interactions (strong): ‐ Disulfide bridges between two thiol groups (i.e.,invloves -SH) 25  Biology II -Paart1 Bonds which contribute to tertiary structure: Hydrogen bond Hydrophobic interactions and van der Waals interactions Disulfide bridge Ionic bond Polypeptide backbone Figure 5.19 26  Biology II -Paart1 Quaternary Structure: two or more polypeptides interact to form a protein polypeptides held together by same bonds as tertiary Examples: Collagen: Hemoglobin: Na,K‐ATPase: 3 helical A globular protein Integral polypeptides composed of 4 membrane coiled into a polypeptides protein composed of triple helix 3 subunits Figure 5.19 27  Biology II -Paart1 What Determines Protein Structure? Primary structure Physical & chemical conditions Note: any change leads to denaturation Protein unravels, loses its shape and function. 28  Biology II -Paart1 Denaturation: ‐ Disruptiing the protein structure ‐ Protein unable to function primary structure Figure 5.21 29  Biology II -Paart1 Conditions that can denature proteins 1) Temperature: Disrupts non- covalent interactions such as H-bonds Ex with Protein Albumen in egg white 2) pH: Changes the ionic state of changed side chains Creates regions of charge repulsion or disruption of ionic bonds. 3) Salts: Changes the ionic environment 30  Biology II -Paart1 Conditions that can denature proteins (cont) 4) Detergents/organic solvents: Disruot hydrophobic interactions Hydrophobic side chains move from inside to outside Hydrophilic side chains move away from the detergent/solvent, towards interior of protein 5) Reducing Agents: Breaks covalent disul de bridges (S-S->S-H H-S) 31 fi