Molecular Interactions 2

About this Chapter Atoms, ions, and molecules (self review) Types of chemical bonds (self review) Biomolecules Solutions, concentrations, and pH Water Properties Protein interactions

Types of Biomolecules All four types are composed of either monomers or covalently linked polymers. The first three provide energy to the body. Monomers are connected by dehydration reactions to create polymers Polymers are broken down into monomers by hydrolysis reactions The four groups of biomolecules (organic macromolecules) are: Carbohydrates Lipids Proteins Nucleotides and nucleic acids

Most macromolecules are polymers Polymers are made by stringing together many smaller molecules called monomers Cells link monomers by a process called dehydration synthesis In this process water is removed to unite the two units and form a polymer. Short polymer Monomer Longer polymer Figure 3.7A (a) Dehydration synthesis of a polymer

Polymers broken to monomers Organisms also have to break down macromolecules Cells do this by a process called hydrolysis In hydrolysis a water molecule is used to split a bond between two monomers to reduce the size of the polymer. Figure 3.7B (b) Hydrolysis of a polymer

Carbohydrates Most abundant Simple Complex Carbon Hydrogen Oxygen Monosaccharides (glucose, ribose) Complex Polysaccharides (glycogen, starch) Monomer linked to form polymers by a glycosilic bond

Carbohydrates Figure 2-7 (1 of 3)

Carbohydrates Figure 2-7 (3 of 3)

Fun Facts Americans consume an average of 140 pounds of sugar per person per year Cellulose, found in plant cell walls, is the most abundant organic compound on Earth

Lipids Carbon and hydrogen (little oxygen) Structurally diverse Eicosanoids Steroids Phospholipids Triglycerides Glycerol Fatty acid chains Saturated Unsaturated

High Energy Fuel Source Larger hydrocarbons Are the main molecules in the gasoline we burn in our cars The hydrocarbons of fat molecules provide energy for our bodies Figure 3.4

Lipids and Lipid-Related Molecules Figure 2-8 (1 of 5)

Proteins Amino acids Protein structure Most versatile Essential Amino group Acid group Protein structure Polypeptides Primary through quaternary Most versatile

The four types of proteins (b) Storage proteins (d) Transport proteins (a) Structural proteins (c) Contractile proteins Figure 3.18

Levels of Organization in Protein Molecules Figure 2-9 (1 of 6)

Protein Shape Proteins have four levels of structure Hydrogen bond Pleated sheet Polypeptide (single subunit) Amino acid (a) Primary structure Complete protein, with four polypeptide subunits Hydrogen bond Alpha helix (b) Secondary structure (c) Tertiary structure (d) Quaternary structure Figure 3.23

Proteins Various types of bonds interact to create different types of proteins. The types of bonds that shape the protein affect the structure. Fibrous Globular Figure 2-10

Nucleic Acids Composition Base, sugar, and phosphate(s) Transmit and store Information (genetic code) Energy transfer molecules ATP, cAMP, NAD, and FAD

Nucleotides, DNA, and RNA

Aqueous Solutions Aqueous Solution Solubility Water-based Solute dissolves in solvent Solubility Ease of dissolving Hydrophobic Hydrophilic

Aqueous Solubility Sodium chloride dissolves in water Figure 2-14

Water properties Molecular structure Hydrogen bond-the high amount of hydrogen bond in water give it properties no found in other substances. It makes it less dense as a solid and give a high specific heat. Surface tension- results from cohesion and adhesion Cohesion- water molecules stick together Adhesion-water molecules stick to surfaces Biological Process Water can absorb and store large amounts of heat while only changing a few degrees in temperature thus allowing it to regulate heat in the body.

Water properties These illustrate the properties of water that result from hydrogen bonding.

Hydrogen Ion Concentration (pH)-self review Acid Contributes H+ to solution Base Decreases H+ in solution pH - log [H+] Buffer minimizes changes of pH

Hydrogen Ion Concentration (pH) pH scale Mechanisms in the body closely regulate blood ph to protect from the harmful effects of going beyond the range. Figure 2-15

Protein Interactions Human Proteomics Initiative- determine all the types of proteins in the body. Protein Solubility- the degree to how water soluble a protein is determines influences is role in the body Insoluble – create supportive structures like collagen and keratin Soluble- carry out chemical reactions and interact with molecules Seven categories- these include enzymes, membrane transporters, signal molecules, receptors, binding and regulatory proteins, and antibodies.

Protein Interactions Binding- when proteins binds a conformation change called induce fit occurs. The bind success depends on: Selectivity- protiens bind specific molecules Ligand- generic name for molecules that bind and interact Substrate- ligands that bind enzymes and membrane transporter Binding site- area where ligand attaches and forms reversible or irreversible bonds Specificity- the ability of a protein to bind a certainligand Affinity- degree to which a protein is attracted to a ligand. A high disassociation constant indicates low affinity.

Selective Binding: Induced-Fit Model The induced-fit model of protein-ligand binding Figure 2-16

Factors that affect protein binding Isoforms- proteins with similar function but different affinities for the same ligand. Ex- fetal vs adult hemoglobin Activation – some inactive proteins undergo a physical alteration to become active- like protein hormones and enzymes Cofactors – must bind to protein to enhance affinity to ligand, usually it’s a functional group or ion. Lysis – cleaving a protein section to activate it. Modulators – influences binding or activity of a protein Chemical modulators – bind covalently or non-covalently to alter binding or activity by decreasing or increasing it. Antagonists – decreases activity by blocking binding site Competitive inhibitors – reversible antagonists that competitively bind and can be displaced Allosteric modulators -reversible antagonists that competitively bind but can not be displaced Covalent modulators - bind and alter properties to activate or inactivate- ex. penicillin

Modulators Alter Binding or Activity

Factors that Affect Affinity Figure 2-18

Competitive Inhibition Figure 2-19

Allosteric Modulation Figure 2-20a

Allosteric Modulation Figure 2-20b

Physical Regulators Temperature- each protein has a adequate temperature for it’s function. Outside of the range it may be denatured of inactivated. pH- each protein has a adequate temperature for it’s function. Outside of the range it may be denatured of inactivated. Concentration of protein –amounts in body vary over time to control physiological processes Up-regulation – programmed production of protein Down regulation – programmed removal of protein Concentration of ligand – determines the magnitude of the reponse if the protein concentration is the same. Reaction rates – speed up as ligand concentration increases up until saturation is reached.

Summary Atoms in review Four types of chemical bonds Four kinds of biomolecules Aqueous solutions and pH Proteins in focus