chemistry for changing times 12 th edition hill and kolb chapter 16 biochemistry: a molecular view...
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Chemistry for Changing Times12th Edition
Hill and Kolb
Chapter 16Biochemistry:
A Molecular View of LifeJohn Singer
Jackson Community College, Jackson, MI© 2010 Pearson Prentice Hall, Inc.
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The Living Cell
Biochemistry is the chemistry of living things and life processes.
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The Living Cell
The basic structural unit of all living organisms is the cell.
All cells are enclosed in a cell membrane, which regulates the passage of nutrients and wastes.
In addition to a cell membrane, plant cells are surrounded by a cell wall composed of cellulose.
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The Living CellNucleus: The largest structure within the cell. The nucleus contains the genetic material that controls heredity.
Ribosomes: The structure where protein synthesis occurs.
Mitochrondria: The cell structure where energy production occurs.
Chloroplasts: Found only in plant cells. In the chloroplasts, photosynthesis occurs.
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The Living Cell
Plant Cell
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The Living Cell
Animal Cell
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Energy in Biological SystemsGreen plants contain chloroplasts, which are capable of taking the radiant energy of the sun and storing it as chemical energy in glucose molecules.
6 CO2 + 6 H2O → C6H12O6 + 6 O2
Plant cells can also convert carbohydrate molecules to fat molecules, and some are even capable of converting them to proteins.
Animals cannot produce their own energy. They must obtain such energy by eating plants or other animals that eat plants.
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Energy in Biological Systems
Metabolism is defined as the series of chemical reactions that keep a cell alive. Metabolic reactions are divided into two categories:
1. Catabolism: The process of breaking down molecules to produce energy.
2. Anabolism: The process of synthesizing molecules.
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Carbohydrates
Carbohydrates are polyhydroxy aldehydes or ketones or compounds that can be hydrolyzed to form such compounds.
Monosaccharides: Carbohydrates that cannot be hydrolyzed into simpler compounds.
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Carbohydrates
Monosaccharides: Carbohydrates that cannot be hydrolyzed into simpler compounds.
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Carbohydrates
Most monosaccharides actually exist in cyclic form.
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Carbohydrates
Disaccharides consist of molecules that can be hydrolyzed into two monosaccharide units.
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Carbohydrates
Polysaccharides are composed of large molecules that can be hydrolyzed into many monosaccharide units. Examples include starch, cellulose, and glycogen.
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Carbohydrates
Both starch and cellulose are polymers of glucose. The linkages between glucose molecules in starch are alpha (α) linkages, whereas in cellulose they are beta (β) linkages.
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Carbohydrates
Cellulose makes up the structural units of plants. Cellulose chains are composed of parallel bundles called fibrils.
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CarbohydratesStarch is composed of two polymers, amylose and amylopectin. In amylose, the glucose molecules are connected in long parallel chains. In amylopectin, the chains are branched.
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Carbohydrates
Glycogen is known as animal starch. It is similar to amylopectin in that the glucose polymers are branched.
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Fats and Other Lipids
Lipids are biological molecules that are insoluble in water, but are soluble in nonpolar organic solvents.
Fats are esters of long-chain fatty acids and glycerol. Fats are often called triglycerides or triacylglycerols.
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Fats and Other Lipids
Fatty Acids
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Fats and Other Lipids
Palmitic Acid
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Fats and Other Lipids
Triglycerides are triesters of glycerol and fatty acids.
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Fats and Other Lipids
Saturated fatty acids have no carbon-to-carbon double bonds.
Monounsaturated fatty acids have one carbon-to-carbon double bond.
Polyunsaturated fatty acids have two or more carbon-to-carbon double bonds.
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Fats and Other Lipids
Solid fats have a high proportion of saturated fatty acids.
Liquid oils have only unsaturated fatty acids.
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Fats and Other Lipids
Iodine number is a measure of the degree of unsaturation of a fat or oil. Iodine number is the number of grams of I2 that are consumed by 100 g of a fat or oil.
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Fats and Other Lipids
Iodine Number
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Proteins
Proteins are a vital component of all living things.
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Proteins
Proteins are polymers of amino acids. Amino acids contain both an amine and carboxylate group attached to the same carbon called the alpha carbon.
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ProteinsAmino Acids
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Proteins
Amino acids tend to exist as a dipolar ion or inner ion at physiological pH. Such an ion is called a zwitterion.
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Proteins
Plants can synthesize proteins from carbon dioxide, water, and minerals like nitrates or sulfates.
Animals must consume proteins as part of their diet.
Humans can synthesize some amino acids, but must obtain essential amino acids in a normal diet.
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The Peptide Bond
Amino acids are linked to each other to form proteins by an amide linkage between the amine of one amino acid to the carboxylate of another amino acid. This amide linkage is known as the peptide bond.
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The Peptide Bond
Dipeptide is formed when two amino acids are joined.
Tripeptides contain three amino acid units.
Polypeptides contain ten or more amino acid units.
Proteins may contain 10,000 or more amino acid units.
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The Peptide Bond
The sequence of the amino acids in a protein is critical. The sequence is always denoted from the free amino group (N-terminal) to the free carboxyl group (C-terminal).
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Structure of Proteins
Primary structure: The primary structure of a protein is simply the sequence of amino acids from N-terminal to C-terminal.
Example: The primary structure of angiotensin II is:
Asp-Arg-Val-Tyr-Ile-His-Pro-Phe
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Structure of Proteins
Secondary structure: How the polypeptide chain folds and coils due to hydrogen bonding of the backbone amide groups. Examples include the alpha helix and beta-pleated sheet.
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Structure of Proteins
Alpha Helix
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Structure of Proteins
Beta-Pleated Sheet
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Structure of Proteins
Tertiary structure: The three-dimensional shape of a protein due to the spatial relationships of groups that are far apart on the protein chain. One example is the protein chain in globular proteins.
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Structure of Proteins
Quaternary structure: Involves the interaction of more than one peptide chain.
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Structure of ProteinsFour Ways to Link Protein Chains1. Hydrogen bond: The secondary structures occur when
hydrogen bonds are formed between amide nitrogen (N-H) and carboxyl oxygen (C=O). Tertiary structures also involve hydrogen bonding between side chains of the amino acids.
2. Ionic bonds: Sometimes called salt bridges. These occur between oppositely charged side chains.
3. Disulfide linkages: When two cysteine side chains are oxidized, a (-S-S-) disulfide linkage can form.
4. Dispersion forces: These are attractive forces between two nonpolar side chains.
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Structure of Proteins
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Enzymes
Enzymes are biological catalysts. Most are proteins. Many are highly specific, only catalyzing a single reaction or related group of reactions. The substrate is the reactant molecule whose reaction the enzyme catalyzes.
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Enzymes
The activity of many enzymes can be explained by the induced fit model. According to the induced fit model, the substrate molecule bonds to the enzyme at the active site, forming an enzyme-substrate complex. This complex can then catalyze the reaction of the substrate and form products.
Enzyme + Substrate → Enzyme-substrate complex ↔ Enzyme + Products
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EnzymesInduced Fit Model
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Enzymes
Inhibition
The action of enzymes can be inhibited. One mechanism of enzyme inhibition has a molecule bonding to the enzyme protein at another site other than the active site. This changes the shape of the protein and prevents the substrate from bonding at the active site. This mechanism is used to control the action of certain enzymes.
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Enzymes
Inhibition
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Enzymes
Cofactors: Some enzymes require another molecule to be present for proper functioning of the enzyme. Cofactors can be inorganic ions (Zn2+, Mg2+, …) or organic molecules.
Coenzyme: A cofactor that is a nonprotein organic molecule.
Apoenzyme: The pure protein part of an enzyme.
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Enzymes in MedicineDiabetic test strips use two enzymes to measure blood sugar. One enzyme catalyzes the oxidation of glucose, producing hydrogen peroxide as a by-product. The other enzyme catalyzes the breakdown of hydrogen peroxide and oxidizes a dye to produce a color change.
Enzymes can be monitored to diagnose liver damage or heart damage.
Enzymes can also be used to break up clots after a heart attack or to increase clotting to treat hemophelia.
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Enzymes in Industry
Enzymes have many industrial applications, including the production of baby foods, beer, sweeteners for soft drinks, animal feeds, and blue jeans.
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Enzymes and Green Chemistry
Enzymes are being investigated for producing specialty chemicals and new drugs.
In addition, enzymes can be used to break down complex pollutants.
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Enzymes in Everyday Life
Enzymes are used in stain removers and meat tenderizers. Those that are lactose-intolerant can also take enzymes to reduce the discomfort caused by ingesting dairy foods. Worldwide production of enzymes is worth more than $1 billion per year.
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Nucleic Acids
Nucleic acids serve as the information and control centers of the cell. They are in two major forms: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Both consist of long chains called nucleotides. Each nucleotide is composed of a sugar unit, phosphate unit, and a heterocyclic amine base.
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Nucleic Acids
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Nucleic Acids
Nucleotides are composed of a sugar, phosphate, and an amine base.
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Nucleic AcidsDNA consists of a double helix.
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Nucleic AcidsThe double helix of DNA is held together by base-pairing. Complimentary bases are thymine and adenine, and cytosine and guanine. These complimentary bases are held together by hydrogen bonding.
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Nucleic AcidsStructure of RNA
RNA consists of single strands of nucleic acid.
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DNA: Self-Replication
Chromosomes: Threadlike bodies of DNA that are tightly coiled into x-shaped bodies. Human body cells contain 46 chromosomes. Twenty-three come from the egg of the mother, 23 come from the sperm of the father.
Gene: Section of a DNA molecule that controls the synthesis of protein.
Replication: Copying of DNA during cell division.
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DNA: Self-Replication
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RNA: Protein Synthesis and the Genetic Code
The genetic code is carried in a three-base sequence known as a codon.
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RNA: Protein Synthesis and the Genetic Code
During protein synthesis, the genetic information of DNA is transferred to RNA by a process known as transcription. During transcription, messenger RNA (mRNA) is synthesized.
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RNA: Protein Synthesis and the Genetic Code
The genetic code is carried on a sequence of three bases known as a codon. The codon codes for a specific protein by base-pairing the anticodon with a specific transfer RNA (tRNA) through a process known as transcription.
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RNA: Protein Synthesis and the Genetic Code
Transcription
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The Human Genome
Genetic Testing
One DNA sequencing technique is known as polymerase chain reaction (PCR). In the PCR technique, the DNA is cleaved by enzymes; bacterial enzymes called DNA polymerases are used to multiply the amount of DNA fragments. The fragments are separated from longest to shortest and a “print” is obtained.
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The Human Genome
Recombinant DNA is DNA that is produced artificially and contains DNA from two different sources. In one technique, restriction enzymes are used to cleave the DNA. The DNA fragments can then be inserted into bacterial plasmids and the plasmid inserted into a host organism. There it replicates, producing exact copies of itself.
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The Human GenomeRecombinant DNA
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The Human Genome
Gene therapy involves introducing a functioning gene into a person’s cells to correct the action of a defective gene. Viruses are used to carry the DNA into cells. Gene therapy is still experimental.
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The Human Genome
Controversy and Promise in Genetic Engineering
Cloning of animals and plants holds much promise for food production and treatment of disease. There is also much controversy and concern.