chapter 2 small molecules: structure and behavior

CHAPTER 2Small Molecules: Structure and Behavior

Atoms: The Constituents of Matter Matter is composed of atoms with positively

charged nuclei of protons and neutrons surrounded by negatively charged electrons.

Main Elements Found in Living Organisms

Figure 2.1

Isotopes of an element differ in numbers of neutrons

Figure 2.2 Some isotopes are unstable and are termed radioactive. Some isotopes are unstable and are termed radioactive. These radioisotopes are useful for many purposes.These radioisotopes are useful for many purposes.

Electrons are distributed in shells of orbitals

Each orbital contains a max of 2 electrons

Orbital Shell Representations for Several Atoms Figure 2.5

Interaction of atoms via sharing of electrons generates molecules via bonding

Table 2.1

Figure 2.6

Covalent Bonds

Covalent bonds form when two atomic nuclei share one or more pairs of electrons. They have spatial orientations that give molecules three-dimensional shapes

Covalent Bonds

Figure 2.7

Combining electrons in all the orbitals in a particular level often occurs.

sp3 bonds of carbon are the combination of the 2s orbital and the 3 2p orbitals to form 4 sp3 orbitals which each have a single electron that is shared with the single electron in H’s 1s orbital

Table 2.2

Table 2.2

table 02-02.jpg

Chemical Bonds: Linking Atoms Together Nonpolar covalent bonds form when the

electronegativities of two atoms are approximately equal

Polar covalent bond in which one end is + and the other is – forms when atoms with strong electronegativity (such as oxygen) bond to atoms with weaker electronegativity (such as hydrogen)

Hydrogen bonded to a strongly electronegative atom can be donated to a H-bond

Polarity in bonding

Figure 2.8

figure 02-08.jpg

Table 2.3

Table 2.3

table 02-03.jpg

Ionic bonds

Figure 2.10

Complete gain/loss of electron to form a charged species

Oppositely charged ions then interact electrostatically

Hydrogen bonds Hydrogen bonds form between a + hydrogen

atom in one molecule and a – nitrogen, oxygen or sulfur atom in another molecule or in another part of a large molecule.

figure 02-09.jpg

Polar solvents dissolve ionic & polar substances

Figure 2.11

Polar & Non-polar Molecules Nonpolar molecules do not interact directly

with polar substances. They are attracted to each other by very weak bonds called van der Waals forces.

Van der Waals forces are the weak sharing of electons between orbitals of molecules

Water: Structure and Properties Water’s molecular structure and capacity to

form hydrogen bonds give it unusual properties significant for life.

Water: Structure and Properties Cohesion of water molecules results in a high

surface tension. Water’s high heat of vaporization assures cooling when it evaporates.

Solutions are substances dissolved in water. Concentration is the amount of a given substance in a given amount of solution. Most biological substances are dissolved at very low concentrations.

Chemical Reactions: Atoms Change Partners

In chemical reactions, substances change their atomic compositions and properties. Energy is either released or added. Matter and energy are not created or destroyed, but change form.

Acids, Bases, and the pH Scale Acids are substances that donate hydrogen ions.

Bases are those that accept hydrogen ions. The pH of a solution is the negative logarithm of

the hydrogen ion concentration. pH=-log[H+] Values lower than pH 7 indicate an acidic

solution. Values above pH 7 indicate a basic solution

pH Scale

Figure 2.18

Acids, Bases, and the pH Scale Buffers are systems of weak acids and bases that

limit the change in pH when hydrogen ions are added or removed.

The Properties of Molecules Molecules vary in size, shape, reactivity,

solubility, and other chemical properties. Functional groups make up part of a larger

molecule and have particular chemical properties.

The consistent chemical behavior of functional groups helps us understand the properties of the molecules that contain them.

Functional Groups

Figure 2.20 – Part 1

Functional Groups

Figure 2.20 – Part 2

Isomers

Optical Isomers Figure 2.21

•Optical isomers•rotate plain polarized light in opposite directions

•Structural isomers•Differ in position of functional groups

CHAPTER 3Macromolecules: Their Chemistry and

Biology

Macromolecules: Giant Polymers Macromolecules are formed by covalent

bonds between monomers and include polysaccharides, proteins, and nucleic acids.

Lipids are crucial biomolecules, but are not considered ‘macromolecules’

Table 3.1

table 03-01.jpg

Fatty Acid TriglyceridePhospholipid

Macromolecules: Giant Polymers Macromolecules have specific three-

dimensional shapes. Different functional groups give local sites on

macromolecules specific properties.

Condensation Reactions

Monomers are joined by condensation reactions. Hydrolysis reactions break polymers into monomers.

Joining of monomers is typically called polymerization

Proteins: Polymers of Amino Acids Functions of proteins include support,

protection, catalysis, transport, defense, regulation, and movement. They sometimes require an attached prosthetic group.

Proteins: Polymers of Amino Acids Twenty amino acids are found in proteins. Each consists of an amino group, a carboxyl

group, a hydrogen, and a side chain bonded to the carbon atom.

Table 3.2 – Part 1

table 03-02a.jpg

Amino Acids

table 03-02bc.jpgAmino Acids

Proteins: Synthesis

Amino acids are covalently bonded together by peptide linkages or peptide bond

Chemically this is an amide bond

Each amino acid is called a residue

Reaction proceeds leaving the amino terminus of the 1st aa and the carboxyl terminus of the last aa unmodified (free)

Proteins: Structure Polypeptide chains of proteins are folded into

specific three-dimensional shapes There are 4 levels of structure

Primary (1o) – amino acid sequence Secondary (2o) – localized structures of adjacent residues Tertiary (3o) – folding of units of secondary structure Quaternary – association of multiple individual proteins

(subunits) to form a functional complex

H-bonds stabilize 2o structures

Protein Structure

3.5 – Part 2

Figure 3.5 – Part 2Protein Structure

Covalent bonds (disulfide bridges), H-bonds & ionic bonds (salt bridges) stabilize 3o and 4o structures

Figure 3.3

figure 03-03.jpg

The SH groups of cysteine residues The SH groups of cysteine residues can form disulfide bridges that link can form disulfide bridges that link distant regions of proteins togetherdistant regions of proteins together

Protein Structure

3.7

Figure 3.7

figure 03-07.jpg

Proteins: Structure

• Chemical interactions important for binding of proteins to other molecules. • H-bonds• Van der Waals

interactions• Ionic interactions

Proteins: Structure Proteins can be

denatured heat, acid, or

chemicals Loss of tertiary

and secondary structures and biological function.

Proteins: Structure Proper folding of proteins is critical for their function Chaperonins assist protein folding

Carbohydrates: Sugars and Sugar Polymers• Monosaccharides

• 3-carbons – trioses• 5-carbons - pentoses• 6-carbons – hexoses

• Disaccharides• Two monosaccharides

• Maltose• Sucrose• Lactose

• Oligosaccharide• <10 glycoside residues

• Polysaccharide• >10 glycoside residues

Carbohydrates: Structures

Hemiacetal forms

Carbohydrates Structure

Glyceraldehyde

4 carbon sugar is erythrose

Carbohydrates Structure figure 03-12b.jpg

Isomers

Carbohydrate Polymerization

Glycosidic linkages may have either or orientation in spaceNumbering of bond refers to carbon position of hemiacetal ring

Carbohydrate polymerization

Figure 3.14 – Part 1An unbranched polysaccharide

Carbohydrate polymerization

Figure 3.14 – Part 2Branched chain polysaccharides

Carbohydrates modified sugars• Chemically modified

monosaccharides• Phosphates, • Acetyl groups• Sulfates• Amino groups

• Derivative of glucosamine polymerizes to form the polysaccharide chitin• Used as the basis of

arthropod exoskeletons• Proteoglycans &

Glycoproteins• Proteins with attached

carbohydrates• Heparin sulfate• Chondroitin sulfate

Nucleic Acids: Informational Macromolecules

• In cells, DNA is the hereditary material. DNA and RNA play roles in protein formation.

Nucleotide Structures

Nucleotides – The Sugars

Nucleotides – The Bases

Nucleosides – Sugar + Base

Nucleotide – Nucleoside + Phosphates

Nucleic Acids – Polymers of Nucleotides

Nucleic Acid Structure

Nucleic Acids Complementary Base Pairing

A-T or U G-C Watson-Crick Pairing

Specificity Fidelity of DNA replication Fidelity of transcription Fidelity of any nucleic acid-nucleic acid

interaction ie. mRNA – tRNA Hybridization

Our manipulation of nucleic acids

16S rRNA Secondary Structures

tRNA Secondary Structure

DNA Double Helix

Figure 3.18

Major Groove

Minor Groove

Spacing of base-pairs – 3.4ÅHelix diameter ~ 20Å10 base-pairs per helical turn

DNA – The Genetic Material Genes

Coding sequences Regulatory sequences

Genes encode proteins Information flow DNA RNA protein Central Dogma

DNA sequences

Nucleic Acids: Manipulation Molecular Biology

• DNA amplification – PCR• DNA cloning – gene isolation and

identification• DNA sequencing – gene characterization• DNA-RNA & DNA-DNA hybridization – Gene

Chips

Lipids Fatty Acids

Triglycerides Phospholipids

Steroids Steroid hormones Retinoids

Fatty Acids

Triglyceride Formation

Figure 3.19

Phospholipids:

• Phospholipids have a hydrophobic hydrocarbon “tail” and a hydrophilic “head” group.

• Head group• Phosphate connection• Base

• Choline• Ethanolamine

• Sugar• Inositol

• Amino acid• Serine

Lipid Bilayer Formation

Figure 3.22

Steroid Lipids:• Carotenoids trap light energy in green plants. β-Carotene

can be split to form vitamin A (retinol), a lipid vitamin.

All-trans retinol

Steroid Lipids

Figure 3.24