chapter 16 biochemistry john singer, jackson community college chemistry for changing times,...

Chapter 16Biochemistry

John Singer,

Jackson Community College

Chemistry for Changing Times,

Thirteenth Edition

Lecture Outlines

© 2013 Pearson Education, Inc.

2Chapter 16© 2013 Pearson Education, Inc.

The Living Cell

Biochemistry is the chemistry of living things and life processes.


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.


Nucleus: 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.

The Living Cell


The Living Cell

Plant Cell


The Living Cell

Animal Cell


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.


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.


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.


Carbohydrates

Monosaccharides: Carbohydrates that cannot be hydrolyzed into simpler compounds.


Carbohydrates

Most monosaccharides actually exist in cyclic form.


Carbohydrates

Disaccharides consist of molecules that can be hydrolyzed into two monosaccharide units.


Carbohydrates

Polysaccharides are composed of large molecules that can be hydrolyzed into many monosaccharide units. Examples include starch, cellulose, and glycogen.


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.


Carbohydrates

Cellulose makes up the structural units of plants. Cellulose chains are composed of parallel bundles called fibrils.


Starch 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.

Carbohydrates


Glycogen is known as animal starch. It is similar to amylopectin in that the glucose polymers are branched.

Carbohydrates


Carbohydrates

Amylose, Amylopectin, Glycogen


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.



Fatty Acids



Palmitic Acid



Triglycerides are triesters of glycerol and fatty acids.



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.


Solid fats have a high proportion of saturated fatty acids.

Liquid oils have only unsaturated fatty acids.




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.



Iodine Number


Proteins

Proteins are a vital component of all living things.


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.


Amino Acids

Proteins


Proteins

Amino acids tend to exist as a dipolar ion or inner ion at physiological pH. Such an ion is called a zwitterion.


Proteins

Plants can synthesize proteins from carbon dioxide, water, and minerals contained in compounds 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.


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.


The Peptide Bond

A 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.


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).


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



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.



Alpha Helix



Beta-Pleated Sheet



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.



Quaternary structure: Involves the interaction of more than one peptide chain.


Four Ways to Link Protein Chains1. Hydrogen bond: The secondary structures occur

when hydrogen bonds are formed between amide hydrogen (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.



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.


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


Induced-Fit Model

Enzymes


Inhibition

The action of enzymes can be inhibited. In one mechanism for enzyme inhibition, a molecule bonds to the enzyme protein at a site other than the active site. This changes the shape of the protein and prevents the substrate from bonding at the active site.

Enzymes


Enzymes

Inhibition


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 without cofactors or coenzymes.


Diabetic 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.

Enzymes


Enzymes in Industry

Enzymes have many industrial applications, including the production of baby foods, beer, sweeteners for soft drinks, animal feeds, and blue jeans.


Enzymes and Green Chemistry

Enzymes are continually being investigated for their use in producing specialty chemicals and new drugs.

In addition, enzymes can be used to break down complex pollutants.


Enzymes in Everyday Life

Enzymes are used in stain removers and meat tenderizers. People who 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?


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.


Nucleic Acids


Nucleic Acids

Nucleotides are composed of a sugar, phosphate, and an amine base.


Nucleic Acids

DNA consists of a double helix.


Nucleic Acids

The 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.


Nucleic Acids

Structure of RNA

RNA consists of single strands of nucleic acid.


Chromosomes: Threadlike strands 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.

Enzymes


DNA: Self-Replication


RNA: Protein Synthesis and the Genetic Code

The genetic code is carried in a three-base sequence known as a codon.


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.



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.

vRNA: Protein Synthesis and the Genetic Code


Transcription



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.


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.


The Human GenomeRecombinant DNA


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.


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.