Chapter 2
Molecular
Interactions
About this Chapter
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Chemistry Review
Molecular Bonds and Shapes
Biomolecules
Solutions, Acids, Bases, and Buffers
Protein interactions
Atoms
• Structure of an atom
• Nucleus
• Electron orbitals or shells
• Atom has three components
• Protons
• Electrons
• Neutrons
Elements
• Simplest type of matter
• Essential
• Trace
• Atomic number
• Atomic mass
Isotopes
• Isotopes have different numbers of neutrons
• Different atomic mass
• Radioisotopes
• Unstable and emit energy
• Alpha, beta, gamma emissions
• Medical uses as tracers
Ions
• Ions are charged atoms
• Cations
• Positively charged (+)
• Anions
• Negatively charged (–)
Ionic Bonds and Ions
Table 2-1
Atoms, Elements, Ions, and Isotopes
ATOMS
• A map showing the
relationship among
atoms, elements,
ions, and isotopes
Helium, He
consist of
Electrons
Protons
An atom that
gains or loses
electrons
becomes an
Ion of the
same element
Neutrons
An atom that
gains or loses
protons
becomes a
An atom that
gains or loses
neutrons
becomes an
Different
element
Isotope of the
same element
Helium loses a proton
(and two neutrons) to
become hydrogen
loses
an
electron
H + is a
hydrogen ion.
gains
a
neutron
Hydrogen-1, H
Hydrogen-2, or
deuterium, 2H, is an
isotope of hydrogen.
Figure 2-1
Four Primary Roles of Electrons
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Covalent bonds
Ions
High-energy electrons
Free radicals
• Unpaired electron
• highly reactive
• Antioxidants
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
• Hydrogen bonds - between molecules
Molecules and Compounds
• Shared electrons in the outer shells of atoms
form covalent bonds
Figure 2-2b
Types of Chemical Bonds
• Water is a polar molecule
Figure 2-3
Types of Chemical Bonds
• Covalent bonds
• Polar versus nonpolar
• Ionic bonds
• Hydrogen bonds
Covalent and Ionic Bonds
• Covalent bonds
• Share a pair of electrons
• Ionic bonds
• Atoms gain or lose electrons
• Opposite charges attract
• Exchange of electrons
Covalent and Ionic Bonds
• Ions and ionic bonds
Figure 2-4, step 1
Covalent and Ionic
Figure 2-4, step 2
Covalent and Ionic
Figure 2-4, step 3
Hydrogen and Van der Waals
• Hydrogen bonds
• Weak and partial
• Water surface tension
• Van der Waals forces
• Weak and nonspecific
Hydrogen bonds and Van der Waals
• Hydrogen bonds between water molecules
Figure 2-5a
Hydrogen bonds and surface tension
Figure 2-5b
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
give unique functions
Molecular Shape and Function
• Different ways of drawing chemical structures
and formulas of glucose
Figure 2-6b
Functional Groups
• Combinations of atoms that occur frequently in
biological molecules
• Move among molecules as a single group
Functional Groups
Table 2-2
Types of Biomolecules
Know 4 major
biomolecule groups,
functions,
composition and
examples.
Monomer / Polymer
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Carbohydrates
Lipids
Proteins
Nucleotides and
nucleic acids
Carbohydrates
• (CH2O)n
• Most abundant
• Made of carbon, hydrogen, oxygen
• Simple
• Monosaccharides (glucose, ribose)
• Complex
• Polysaccharides (glycogen, starch)
Carbohydrates
MONOSACCHARIDES
Fructose
Glucose (dextrose)
Galactose*
* Notice that the only difference between glucose and galactose is the spatial arrangement of the
hydroxyl groups.
Figure 2-7 (1 of 3)
Carbohydrates
DISACCHARIDES
Sucrose (table sugar)
Glucose + Fructose
Maltose
Glucose + Glucose
Lactose
Galactose + Glucose
Polymers: X 100s or 1000s
Figure 2-7 (2 of 3)
Carbohydrates
POLYSACCHARIDES
Animals
Yeasts
and
bacteria
Plants
Glycogen
Chitin
(invertebrates
only)
Cellulose
Dextran
Starch
Glycogen
Glucose
molecules
Starch
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
• Thromboxanes, leukotrienes and prostaglandins
Lipids and Lipid-Related Molecules
Figure 2-8 (1 of 5)
Lipids and Lipid-Related Molecules
Figure 2-8 (2 of 5)
Lipids and Lipid-Related Molecules
Figure 2-8 (3 of 5)
Lipids and Lipid-Related Molecules
Figure 2-8 (4 of 5)
Lipids and Lipid-Related Molecules
Figure 2-8 (5 of 5)
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
• Most versatile
Amino Acids
• Taurine?
Levels of Organization in Protein Molecules
Figure 2-9 (1 of 5)
Levels of Organization in Protein Molecules
Figure 2-9 (2 of 5)
Levels of Organization in Protein Molecules
Figure 2-9 (3 of 5)
Levels of Organization in Protein Molecules
Figure 2-9 (4 of 5)
Levels of Organization in Protein Molecules
Figure 2-9 (5 of 5)
Proteins
• Globular protein structure
Figure 2-10
Combination Biomolecules
• Lipoproteins
• Blood transport molecules
• Glycoproteins
• Cell membranes
• Glycolipids
• Cell membranes
Nucleotides, DNA, and RNA
• Composition
• Base, sugar, and phosphate
• Transmit and store information
• DNA, RNA
• Transmit and store energy
• ATP, cAMP, NAD, and FAD
Nucleotides, DNA, and RNA
NUCLEOTIDE
consists of
Sugar
Nitrogenous base
Purine
Adenine (A) Guanine (G)
Pyrimidine
Ribose
Phosphates
Deoxyribose
Thymine (T)
Cytosine (C)
Uracil (U)
Figure 2-11 (1 of 2)
Nucleotides, DNA, and RNA
• Nucleotides are made of bases, sugars, and
phosphate groups
NUCLEOTIDES
ATP
ADP
cAMP
NAD
FAD
Bases
=
=
=
=
=
Adenine
Adenine
Adenine
Adenine
Adenine
Sugar
Phosphate groups
+
+
+
+
+
Ribose
Ribose
Ribose
2 Ribose
Ribose
+
+
+
+
+
3
2
1
2
2
+
+
Deoxyribose
Ribose
+
+
1 per nucleotide
1 per nucleotide
Other component
+
+
Nicotinamide
Riboflavin
NUCLEIC ACIDS:
DNA
RNA
= A,G,C,T
= A,G,C,U
Figure 2-11 (2 of 2)
Nucleotides, DNA, and RNA
Cytosine
Guanine
Guanine-Cytosine base pair
Adenine
Thymine
Adenine-Thymine base pair
(b) Complementary Base Pairs
KEY
Adenine
Thymine
Guanine
Cytosine
Uracil
Hydrogen bonds
(a) Ribbon model of DNA
Figure 2-12a–b
Nucleotides, DNA, and RNA
Sugar-phosphate
backbone
Hydrogen
bonds
KEY
Adenine
Thymine
Guanine
Cytosine
Uracil
Hydrogen bonds
(c) Stylized ribbon model of DNA
Figure 2-12c
Nucleotides, DNA, and RNA
Bases
Sugar-phosphate
backbone
KEY
Adenine
Thymine
Guanine
Cytosine
Uracil
Hydrogen bonds
(d) Stylized ribbon model of RNA
Figure 2-12d
Aqueous Solutions
• Aqueous
• Water-based
• Solution
• Solute dissolves in solvent
• Solubility
• Ease of dissolving
• Hydrophobic
• Hydrophilic
Aqueous Solubility
• Sodium chloride dissolves in water
Figure 2-14
Concentrations
• Amount of solute in a unit volume of solution
• Mass of solute before it dissolves
• Number of molecules or ions
Concentrations
• Mole
• 6.02  1023 units of substance
• Gram molecular mass
• Expressed in Daltons
• Molarity
• One mole in one liter
• Equivalents
• Molarity multiplied by charge
Concentrations
• Weight /volume
• Grams solute/ml solvent
• Volume/volume
• Percent solution
Hydrogen Ion Concentration (pH)
• Acid
• Contributes H+ to solution
• Base
• Decreases H+ in solution
• pH
• - log [H+]
• Buffer minimizes changes of pH
Hydrogen Ion Concentration (pH)
1 M NaOH
• pH scale
Chemical hair removers
Household ammonia
Soap solutions
Baking soda
Pancreatic secretions
Compatible with human life
Saliva
Urine (4.5–7)
Tomatoes, grapes
Vinegar, cola
Lemon juice
Stomach acid
Figure 2-15
Protein Interactions
• Soluble and insoluble
• Soluble include
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Enzymes
Membrane transporters
Signal molecules
Receptors
Binding proteins
Regulatory proteins
Immunoglobulins
Protein Interactions
• Binding
• Noncovalent bonds with other molecules
• Proteins are selective about bonding
• Molecular complementarity
• Specificity
• Affinity
Selective Binding: Induced-Fit Model
• The induced-fit model of protein-ligand (L)
binding
Figure 2-16
Factors that Affect Protein Binding
• Isoforms
• Activation
• Cofactors
• Lysis
• Modulation
Factors that Affect Protein Binding
• Attachment of cofactors activates the protein
Figure 2-18
Modulators Alter Binding or Activity
Table 2-3
Competitive Inhibition
Figure 2-19
Allosteric Modulation
ALLOSTERIC ACTIVATION
Protein without
modulator is inactive.
Modulator binds to protein
away from binding site.
Ligand
Ligand
Binding
site
INACTIVE
PROTEIN
ACTIVE
PROTEIN
Allosteric activator
Figure 2-20 (1 of 2)
Allosteric Modulation
ALLOSTERIC INHIBITION
Protein without
modulator is active.
Modulator binds to protein away
from binding site and inactivates
the binding site.
Ligand
Ligand
Binding
site
ACTIVE
PROTEIN
INACTIVE
PROTEIN
Allosteric
inhibitor
Figure 2-20 (2 of 2)
Physical Factors
• Temperature
• pH
• Concentration of protein
• Up-regulation
• Down-regulation
• Concentration of ligand
• Maximum reaction rate
• Saturation
Physical Factors
Figure 2-21
Summary
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Atoms in review
Four types of chemical bonds
Four kinds of biomolecules
Aqueous solutions and pH
Proteins in focus