Molecular Interactions

Chapter 2

About this Chapter

• Chemistry Review

• Molecular Bonds and Shapes

• Biomolecules

• Solutions, Acids, Bases, and Buffers

Atoms

• Structure of an atom

• Nucleus

• Electron orbitals or shells

• Atom has three components

• Protons

• Electrons

Elements

• Simplest type of matter

• Essential

• Trace

• Atomic number

Isotopes

• Isotopes have different numbers of neutrons

• Different atomic mass

• Radioisotopes

• Unstable and emit energy

• Alpha, beta, gamma emissions

Ions

• Ions are charged atoms

• Cations

• Positively charged (+)

• Anions

Ionic Bonds and Ions

Atoms, Elements, Ions, and Isotopes

• A map showing the relationship among atoms, elements, ions, and isotopes

Figure 2-1

Helium loses a proton (and two neutrons) to become hydrogen

Different element

Isotope of the same element Ion of the

same element

An atom that gains or loses

protons becomes a

An atom that gains or loses

neutrons becomes an An atom that

gains or loses electrons becomes an loses an electron gains a neutron

Hydrogen-1, H Hydrogen-2, or deuterium,2H, is an isotope of hydrogen. H+is a

Four Primary Roles of Electrons

• Covalent bonds

• Ions

• High-energy electrons

• Free radicals

• Unpaired electron

• highly reactive

Molecules and Compounds

• Bonds capture energy

• Bonds link atoms

• Molecules versus compounds

• 2 or more linked atoms

• A compounds contain different kinds of atoms.

H₂O vs O₂

• The forces holding atoms in a molecule are chemical bonds.

Types of bonds:

• Ionic - exchange of electronics making ions

• Covalent - shared electrons

• Polar unequal sharing

Molecules and Compounds

• Shared electrons in the outer shells of atoms form covalent bonds

Types of Chemical Bonds

• Water is a polar molecule

Types of Chemical Bonds

• Covalent bonds

• Polar versus nonpolar

• Ionic bonds

Covalent and Ionic Bonds

• Covalent bonds

• Share a pair of electrons • Ionic bonds

• Atoms gain or lose electrons

• Opposite charges attract

Covalent and Ionic Bonds

• Ions and ionic bonds

Covalent and Ionic

Covalent and Ionic

Hydrogen and Van der Waals

• Hydrogen bonds

• Weak and partial

• Water surface tension

• Van der Waals forces

Hydrogen bonds and Van der Waals

• Hydrogen bonds between water molecules

Hydrogen bonds and surface tension

Molecular Shape and Function

• Molecular bonds determine shape

• Shape influences function

• Chemical formula

• Atoms in a molecule (no relation is given)

• Functional groups

• Molecular groups that often move together and

Molecular Shape and Function

• Different ways of drawing chemical structures and formulas of glucose

Functional Groups

• Combinations of atoms that occur frequently in biological molecules

Functional Groups

Types of Biomolecules

Know 4 major

biomolecule groups, functions,

composition and examples.

Monomer / Polymer

• Carbohydrates

• Lipids

• Proteins

Carbohydrates

• (CH₂O)_n

• Most abundant

• Made of carbon, hydrogen, oxygen

• Simple

• Monosaccharides (glucose, ribose)

• Complex

Carbohydrates

Figure 2-7 (1 of 3)

Fructose Glucose

(dextrose)

Galactose* MONOSACCHARIDES

Carbohydrates

Figure 2-7 (2 of 3)

Glucose + Fructose Glucose + Glucose Galactose + Glucose

Sucrose (table sugar) _Maltos

e

Lactos e

DISACCHARIDES

Carbohydrates

Figure 2-7 (3 of 3)

Lipids

• Carbon and hydrogen (little oxygen)

• Structurally diverse

• Triglycerides / Neutral Fats – energy storage

• Glycerol

• Fatty acid chains

• Saturated and unsaturated

• Phospholipids - membranes

• Steroids – membranes/hormones

• Eicosanoids

Lipids and Lipid-Related Molecules

Lipids and Lipid-Related Molecules

Lipids and Lipid-Related Molecules

Lipids and Lipid-Related Molecules

Lipids and Lipid-Related Molecules

Proteins

• 20 Amino acids

• Amino group

• Acid group

• Essential amino acids must be obtained

• Four levels of protein structure

• Primary through quaternary

• Peptides, polypeptides, oligopeptides

Amino Acids

Levels of Organization in Protein Molecules

Levels of Organization in Protein Molecules

Levels of Organization in Protein Molecules

Levels of Organization in Protein Molecules

Levels of Organization in Protein Molecules

Proteins

• Globular protein structure

Combination Biomolecules

• Lipoproteins

• Blood transport molecules

• Glycoproteins

• Cell membranes

• Glycolipids

Nucleotides, DNA, and RNA

• Composition

• Base, sugar, and phosphate

• Transmit and store information

• DNA, RNA

• Transmit and store energy

Nucleotides, DNA, and RNA

Figure 2-11 (1 of 2)

consists of Purin e Pyrimidin e Ribos e Deoxyribos e

Adenine (A) Guanine (G)

Figure 2-11 (2 of 2)

Nucleotides, DNA, and RNA

• Nucleotides are made of bases, sugars, and phosphate groups ATP AD P cAMP NA D DN A RN A + + + + + + + + + + + + + = = = = = = Adenine Adenine Adenine Adenine A,G,C,T A,G,C,U 2 Ribose Ribose Ribose Ribose Ribose Deoxyribose 3 2 1 2

1 per nucleotide 1 per nucleotide

Nicotinamide

FAD = Adenine + Ribose + 2 + Riboflavin

NUCLEIC ACIDS:

NUCLEOTIDES Bases Suga

r

Phosphate groups

Other

Nucleotides, DNA, and RNA Figure 2-12a–b Adenin e Thymin e Guanin e Cytosin e Uraci l_Hydrogen bonds Guanin e Adenin e Cytosin e Thymin e KEY

(a) Ribbon model of DNA

(b) Complementary Base Pairs

Guanine-Cytosine base pair

Nucleotides, DNA, and RNA Figure 2-12c Adenin e Thymin e Guanin e Cytosin e Uraci l Hydrogen bonds KEY

Nucleotides, DNA, and RNA Figure 2-12d Adenin e Thymin e Guanin e_Cytosin e Uraci l Hydrogen bonds KEY

(d) Stylized ribbon model of RNA Base

s

Sugar-phosphat e

Aqueous Solutions

• Aqueous

• Water-based

• Solution

• Solute dissolves in solvent

• Solubility

• Ease of dissolving

• Hydrophobic

Aqueous Solubility

• Sodium chloride dissolves in water

Concentrations

• Amount of solute in a unit volume of solution

• Mass of solute before it dissolves

Concentrations

• Mole

• 6.02 × 1023 units of substance

• Gram molecular mass

• Expressed in Daltons

• Molarity

• One mole in one liter

• Equivalents

Concentrations

• Weight /volume

• Grams solute/ml solvent

• Volume/volume

Hydrogen Ion Concentration (pH)

• Acid

• Contributes H+ to solution • Base

• Decreases H+ in solution

• pH

• - log [H+]

Hydrogen Ion Concentration (pH)

• pH scale

Figure 2-15 Stomach acid Lemon juice Vinegar, cola Tomatoes, grapes Urine (4.5–7) Pancreatic secretions Baking soda Soap solutions

Protein Interactions

• Soluble and insoluble

• Soluble include

• Enzymes

• Membrane transporters

• Signal molecules

• Receptors

• Binding proteins

• Regulatory proteins

Protein Interactions

• Binding

• Noncovalent bonds with other molecules

• Proteins are selective about bonding

• Molecular complementarity

• Specificity

Selective Binding: Induced-Fit Model

• The induced-fit model of protein-ligand (L) binding

Factors that Affect Protein Binding

• Isoforms

• Activation

• Cofactors

• Lysis

Factors that Affect Protein Binding

• Attachment of cofactors activates the protein

Modulators Alter Binding or Activity

Competitive Inhibition

Allosteric Modulation

Figure 2-20 (1 of 2)

Binding site ACTIVE PROTEI N Allosteric activator INACTIV E PROTEIN

Modulator binds to protein away from binding site. Protein without

modulator is inactive.

ALLOSTERIC ACTIVATION

Allosteric Modulation

Figure 2-20 (2 of 2)

Protein without modulator is active.

Modulator binds to protein away from binding site and

inactivates the binding site.

Physical Factors

• Temperature

• pH

• Concentration of protein

• Up-regulation

• Down-regulation

• Concentration of ligand

• Maximum reaction rate

Physical Factors

Summary

• Atoms in review

• Four types of chemical bonds

• Four kinds of biomolecules

• Aqueous solutions and pH