Biology Eleventh Edition: Chapter 3 - Protein Chemistry PDF

BIOLOGY ELEVENTH EDITION Chapter 3 The Chemistry of Life: Organic Compounds © 2019 Cengage. All rights reserved.  3.4 Proteins...

BIOLOGY ELEVENTH EDITION Chapter 3 The Chemistry of Life: Organic Compounds © 2019 Cengage. All rights reserved.  3.4 Proteins Proteins: macromolecules composed of amino acids Each cell type contains a characteristic set of thousands of different types of proteins that largely determine what the cell looks like and how it functions – Example: proteins (myosin and actin) in muscle help it contract – Hemoglobin: most abundant protein in blood for oxygen transport Enzymes help accelerate chemical reactions that take place in an organism The sequence of the amino acids in a protein chain determines its shape, which in turn determines its function © 2019 Cengage. All rights reserved. Amino Acids Are the Subunits of Proteins (1 of 4) Amino acids (the constituents of proteins) have an amino group (NH2) and a carboxyl group (COOH) bonded to the same asymmetrical carbon atom, known as the alpha carbon Amino acids in solution at neutral pH are mainly dipolar ions – Each COOH donates a proton and becomes COO- – Each NH2 accepts a proton and becomes NH3+ – Therefore, amino acids in solution resist changes in acidity and alkalinity and are therefore important biological buffers. © 2019 Cengage. All rights reserved. Amino Acids Are the Subunits of Proteins (2 of 4) Ionized form In living cells, amino acids exist mainly in their ionized form, as dipolar ions at pH 7 © 2019 Cengage. All rights reserved. Amino Acids Are the Subunits of Proteins (3 of 4) Twenty amino acids are found in most proteins (see Figure 3-17), each identified by the variable side chain (R group) bonded to the α carbon Amino acids are grouped by properties of their side chains – Nonpolar side chains are hydrophobic – Polar side chains are hydrophilic – A side chain with a carboxyl group is acidic – A side chain where its amino group accepts a hydrogen ion is basic © 2019 Cengage. All rights reserved. Non-polar side chains are hydrophobic © 2019 Cengage. All rights reserved. Non-polar side chains are hydrophobic © 2019 Cengage. All rights reserved. Polar side chains are hydrophilic © 2019 Cengage. All rights reserved. Positively charged side chains are basic (accept hydrogen ion) © 2019 Cengage. All rights reserved. Negatively charged side chains are acidic (carboxyl group) © 2019 Cengage. All rights reserved. Non-polar, aromatic side chains © 2019 Cengage. All rights reserved. Amino Acids Are the Subunits of Proteins (4 of 4) Unusual amino acids in addition to the 20 amino acids: produced by the modification of common amino acids – i.e. incorporation of lysine and proline into collagen, then modified to hydroxylysine and hydroxyproline (they are cross-linked each other to give strength). Essential amino acids are those an animal cannot synthesize in amounts sufficient to meet its needs and must obtain from the diet – Differs in different species – Nine essential amino acids for adult humans: isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and histidine © 2019 Cengage. All rights reserved.  Peptide Bonds Join Amino Acids Amino acids combine chemically by a condensation reaction between the carboxyl carbon of one amino acid and the amino nitrogen of another amino acid – Dipeptide: two amino acids combined – Polypeptide: a longer chain of amino acids A peptide bond is a covalent carbon-to-nitrogen bond linking two amino acids © 2019 Cengage. All rights reserved.  Polypeptides (1 of 2) A protein consists of one or more polypeptide chains, with hundreds of amino acids joined in a specific linear order – N-Cα-C-N-Cα-C-N-Cα-C-N-Cα-C – The two bonds that link the α carbon atoms to the amino and carboxyl groups along with the peptide bonds (shown in red) form the backbone, whereas the R groups of the amino acids extend from the α-carbon atoms – The 20 types of amino acids in proteins are like letters of a protein alphabet; each protein is a very long sentence made up of amino acid letters – An almost infinite variety of protein molecules is possible, differing in number, types, and sequences of amino acids © 2019 Cengage. All rights reserved.  Polypeptides (2 of 2) Polypeptide chains are twisted or folded to form a protein with a specific conformation (3-D shape) A protein’s function is determined by its conformation – Some polypeptide chains form long fibers while others are globular tightly folded into compact – Typical enzymes’ shape is globular, allowing them to catalyze specific chemical reactions – A shape of protein hormones also allows them to combine with receptors on its target cell © 2019 Cengage. All rights reserved. Proteins Have Four Levels of Organization Primary structure: the amino acid sequence, joined by polypeptide bonds Secondary structure: results from hydrogen bonding involving the backbone Tertiary structure: depends on interactions among side chains Quaternary structure: results from interactions among polypeptides © 2019 Cengage. All rights reserved.  Primary Structure of a Polypeptide Glucagon: small polypeptide made up of 29 amino acids, represented in a linear, “beads-on-a-string” form – One end has a free positive ion (NH3+) ; the other has a free negative ion (COO-) © 2019 Cengage. All rights reserved.  Secondary Structure of a Polypeptide Two common types; both may occur in the same polypeptide chain (see Figure 3-20) 1. α–helix (helical coil) H-bonds form between O and H Basic structural unit of fibrous, elastic proteins (by physical and chemical properties) 2. β-pleated sheet H-bonds form between regions of polypeptides chains Proteins are strong and flexible, but not elastic due to fixed distance between the pleats 3. Combination of both types: spider’s web © 2019 Cengage. All rights reserved.  Tertiary Structure of a Polypeptide Overall 3-D shape of an individual polypeptide chain is determined by four main factors involving interactions among R groups of the same polypeptide chain – 3 weak interactions among R groups: hydrogen bonds, ionic bonds, and hydrophobic interactions by non-polar R groups – 1 strong covalent bond: disulfide bridges (- S – S -, linking the sulfur atoms of two cysteine subunits); a disulfide bridge forms when the sulfhydryl groups (SH-) of two cysteines react © 2019 Cengage. All rights reserved.  α-helical (purple), β-pleated sheet (green), connecting regions (narrow Hydrogen bonds, ioninc bonds, hydrophobic tan, and the interaction among R interactions, and disuflide bridges between R groups (yellow) groups hold the parts of the molecule in the Bovine ribonuclease A. designated shape. © 2019 Cengage. All rights reserved.  Quaternary Structure of a Polypeptide Many functional proteins are composed of two or more polypeptide chains interacting in specific ways to form a biologically active molecule Quaternary structure is the resulting 3-D structure. – Example: hemoglobin, a globular protein consisting of 4 polypeptide chains – Example: collagen, a fibrous protein with 3 polypeptide chains See Figure 3-23 © 2019 Cengage. All rights reserved. Hemoglobin Collagen © 2019 Cengage. All rights reserved.  Antibody molecules: two light-chain and two heavy- chain polypeptides linked together by disulfide bonds. Each of the four chains: internal disulfide linkages © 2019 Cengage. All rights reserved.  The Amino Acid Sequence of a Protein Determines Its Conformation (1 of 3) In vitro, a polypeptide spontaneously folds into its normal, functional conformation: leading to conclusion that amino acid sequence is the ultimate determinant of protein conformation In vivo, molecular chaperones mediate the folding of other protein molecules – Molecular chaperones are thought to:  Make the folding process more orderly and efficient  Prevent partially folded proteins from becoming inappropriately aggregated © 2019 Cengage. All rights reserved.  The Amino Acid Sequence of a Protein Determines Its Conformation (2 of 3) Protein conformation determines function – A single protein may have more than one distinct structural region, called a domain – Each domain is a part of the amino acid sequence that can be independently folded and function free from the other parts of the protein – Each domain may have a different function: Because a domain is a stable structure that has a specific function, one type of domain might be found in a number of different proteins Biological activity can be disrupted by a change in amino acid sequence resulting in protein conformation changes – Example: sickle cell anemia © 2019 Cengage. All rights reserved.  The Amino Acid Sequence of a Protein Determines Its Conformation (3 of 3) Denaturation of a protein – Changes in shape and the accompanying loss of biological activity – Occurs when a protein is heated, subjected to significant pH change, or treated with certain chemicals – Structure becomes disordered and peptide chains unfold – This unfolding, which is mainly due to the disruption of hydrogen bonds and ionic bonds, is typically accompanied by a loss of normal function Misfolded proteins may play an important role in human diseases, such as mad cow disease (prion) Alzheimer’s (tau and amyloid) and Huntington’s disease (huntingtin) © 2019 Cengage. All rights reserved. Cow stomach cheese? Not on my pizza! This case investigates protein types and functions focusing on enzyme activity. © 2019 Cengage. All rights reserved. Cow stomach cheese? Not on my pizza! Types of proteins Proteins have a variety of functions that is dictated by their structure. Types include hormones, structural, enzymes, transport, membrane, etc. In cheese making, chymosin (an enzyme) is used to “cut” casein (a structural protein) which causes milk to curdle. © 2019 Cengage. All rights reserved. Cow stomach cheese? Not on my pizza! Enzyme activity Enzymes are a type of protein that catalyze (speed up) chemical reactions. Enzymes achieve this by lowering the activation energy of a reaction. In cheese making, chymosin (an enzyme) catalyzes the reaction that causes casein to curdle. © 2019 Cengage. All rights reserved. Cow stomach cheese? Not on my pizza! Factors that affect enzyme activity Environmental factors can affect an enzyme’s structure and therefore its function. Enzymes are especially sensitive to changes in pH, temperature, and salt concentration. In cheese making, chymosin (an enzyme) is dependent on pH and temperature. Changing the pH or temperature affects chymosin’s function and therefore the type of cheese that is made. © 2019 Cengage. All rights reserved.  Classroom Response Question #1 Hemoglobin is a protein that binds to oxygen and moves it throughout an organism. What type of protein is hemoglobin? A. Structural B. Enzyme C. Transport D. Signaling © 2019 Cengage. All rights reserved.  Classroom Response Question #2 The enzyme ribonuclease is added to a chemical reaction, what will occur? A. The activation energy will increase. B. The speed of the reaction will slow down. C. The quantity of reactants will increase. D. The quantity of products will increase. © 2019 Cengage. All rights reserved.  Classroom Response Question #3 At what temperature is this enzyme most active? A. ~15 °C B. ~30 °C C. ~40 °C D. ~50 °C © 2019 Cengage. All rights reserved.  Open-ended Question #1 Suppose that you are studying the function of an enzyme but you accidentally dropped it in boiling water for a few minutes. What do you predict would happen to the enzyme? © 2019 Cengage. All rights reserved.  Open-ended Question #2 If you were making cheese, what environmental factors would you need to consider? Why? © 2019 Cengage. All rights reserved.  3.5 Nucleic Acids Nucleic acids: transmit hereditary information and determine what proteins a cell manufactures Two classes of nucleic acids in cells - Deoxyribonucleic acid (DNA): makes up hereditary material of the cell (genes) and contains instructions for making proteins and RNA - Ribonucleic acid (RNA): used in processes that link amino acids to form polypeptides © 2019 Cengage. All rights reserved.  Nucleotides Nucleic acids are polymers of nucleotides, molecular units, made up of three parts: 1. A five-carbon sugar, either deoxyribose (in DNA) or ribose (in RNA) 2. One or more phosphate groups (make the molecule acidic) 3. A nitrogenous base (nitrogen-containing ring compound) © 2019 Cengage. All rights reserved.  Nitrogenous Bases (1 of 2) May be either a double-ring purine or a single-ring pyrimidine – DNA contains four nitrogenous bases:  Two purines: adenine (A) and guanine (G)  Two pyrimidines: cytosine (C) and thymine (T) – RNA contains four nitrogenous bases:  Two purines: adenine (A) and guanine (G)  Two pyrimidines: cytosine (C) and uracil (U) DNA has two chains; RNA a single chain © 2019 Cengage. All rights reserved. Nitrogenous Bases (2 of 2) © 2019 Cengage. All rights reserved.  The molecules of nucleic acids are made of linear chains of nucleotides Joined by phosphodiester linkages Each linkage consists of a phosphate group and the covalent bonds that attach it to the sugars of adjacent nucleotides Example: RNA, -U-A-C-G-, one nucleotide chain © 2019 Cengage. All rights reserved. Some Nucleotides Are Important in Energy Transfers (1 of 2) Adenosine triphosphate (ATP) – The primary energy molecule of all cells – Composed of adenine, ribose, and three phosphates – Transfer a phosphate group to another molecule, making that molecule more reactive Guanosine triphosphate (GTP) – Supports transfer of energy by transferring a phosphate group – Also has a role in cell signaling © 2019 Cengage. All rights reserved. Some Nucleotides Are Important in Energy Transfers (1 of 2) A nucleotide may be converted to an alternative form with specific cell functions. – ATP, for example, is converted to cyclic adenosine monophosphate (cyclic AMP, or cAMP) by the enzyme adenylyl cyclase © 2019 Cengage. All rights reserved. Some Nucleotides Are Important in Energy Transfers (2 of 2) Nicotinamide adenine dinucleotide (NAD+ or NADH) – Primary in oxidation and reduction reactions in cells – An oxidized form (NAD+) is converted to a reduced form (NADH) when it accepts electrons. – These electrons, along with their energy, are transferred to other molecules. © 2019 Cengage. All rights reserved.  3.6 Identifying Biological Molecules Carbohydrates (CHO): – Monosaccharides, disaccharides, and polysaccharides Lipids (CHO): – Fats, phospholipids, steroids, and carotenoids Proteins (CHON) Nucleic Acids (CHONP) Review Table 3-3 © 2019 Cengage. All rights reserved.