Chemistry and Biological Molecules

Bio 9Feb 18, 2010

In covalent bonding, pairs of valence electrons are shared, and molecules are formed

Carbon (always) forms 4 bonds

Carbon can form double bonds

1-Butene 2-Butene

Skeletons may have double bonds, which can vary in location.

Carbon also forms ring structures upon itself

Skeletons may be arranged in rings.

Cyclohexane Benzene

The variety of carbon compounds is limitless

All terrestrial life is based on carbon

FUNCTIONAL GROUPS

A carbon skeleton can be modified by the addition of functional groups- familiar groups of atoms which affect the properties of the molecule

hydroxide group – OHamino group – NH2carboxyl group – COOHphosphate group – PO4methyl group – CH3

Functional groups can radically change the function of a molecule

Estradiol

TestosteroneMale lion

Female lion

Figure 3.5

Which of the following represents an amino group?

1 2 3 4 5

20% 20% 20%20%20%1. -OH2. -PO4

3. -CH3

4. - NH2

5. -COOH

Most molecules in living things fall into four categories

• Carbohydrates• Lipids• Proteins• Nucleic acids

These all exhibit modular construction

Modular housing

Made of interchangeable parts

Freight trains have modular assembly

Modular assembly allows a wide variety of products from a few pieces

Most biopolymers are formed by dehydration synthesis

Hydrolysis is the reverse

reaction (Catabolic)

Metabolism

• all chemical reactions in body• Anabolism- building up• Catabolism- breaking down

Major Macromolecules of Life

• Carbohydrates• Lipids• Proteins• Nucleic Acids

Carbohydrates

Carbohydrates• “Carbon” + “Hydro”• Formula (CH2O)n

• Different from hydrocarbons

• Soluble in water• Includes: table sugar,

honey, starch, glycogen, cellulose, high fructose corn syrup

• Glucose is the primary monomer

A Glucose monomer can cyclize to form a ring structure

Atoms in bonds are free to rotate around the bonds

Glucose + Glucose = Maltose (monosaccharide + monosaccharide = disaccharide)

Glucose + fructose = sucrose

A polysaccharide chain can be extended to thousands- it is theoretically limitless

Glycogen and cellulose

Lipids

Nonpolar molecules of living things: Fats, oils, waxes, steroids, etc.

Lipids

• Non-polar• High-energy molecules• For energy storage• Forms cell membranes• Hormones• Members of family

include oils, fats, waxes, and cholesterol (steroids)

Lipids are non-polar

• Therefore, they are hydrophobic

• C and H are similarly electronegative

• Do not mix easily with water

• C-H bond is high in energy

• Lipids make good energy storage molecules

Triglycerides are a primary lipid structure

Dehydration synthesis links fatty acids to glycerol

Fatty acids can be saturated and unsaturated (“cis” and “trans”)

Monounsaturated vs. Polyunsaturated

Cis- and Trans- fatty acids are isomers

• Melting point is very different because of shape

• Health effects are very different

• Isomers- Same formula, different shape

Triglycerides can be modified to form phospholipids

• Phospholipids are amphipathic- having a polar and nonpolar region

• Hyrophilic head, hydrophobic tails

• Primary constituent of cell membranes

Phospholipids are the primary constituent of cell membranes

Proteins

Amino acid polymers which make us what we are

Proteins have incredible versatility of structure and function

Proteins are incredibly diverse at the molecular level

Insulin

ATP synthase

Rubisco

NitrogenaseFibrin

A few examples

Protein function depends greatly on shape

Figure 2.12

Amino Acids

• Proteins consist of subunits called amino acids

Proteins are made of amino acids

• All amino acids have a backbone and a side group (“R” group)

• Backbone: amino group, carboxyl group, central carbon

• Side group: there are 20 different kinds, each with different chemical properties

Some amino acids are polar, others nonpolar

Others have sulfur, others are acidic, still others are

basic

Many are sold as nutritional supplements

Amino acids are added one by one to form a polypeptide chain of a protein

• Dehydration synthesis forms a peptide bond• DNA contains the instructions for the proper

sequence for a specific protein

DNA carries the information to make a specific protein

Proteins have four levels of structure

• Primary- amino acid sequence of polypeptide

• Secondary- coiling of amino acid backbone

• Tertiary- Polypeptide folding from amino acid side groups

• Quaternary- more than one polypeptide

• Protein structure depends on all these levels of interaction

A protein’s Primary (1o) structure is its amino acid sequence

• Determined by the sequence of amino acids

• Amino acids linked by peptide bonds

• Chain is called polypeptide• Sequence proceeds from “N-

terminus” to “C-terminus”• Amino acid sequence

determined by DNA code

Figure 2.15a

Levels of Protein Structure

• The primary structure is a polypeptide chain

Secondary (2o) structure

• Hydrogen bonding between amino acid backbones• Amino group H’s H-bond with O’s from carboxyl end • 2 basic 2o 2o structures: α- helix and β-pleated sheet

Alpha-helix and Beta-sheet are two important 2o structural motifs

Tertiary structure• The folding interactions

from amino acid side chains of a polypeptide

• The folding of 2o domains upon each other

• Interactions can be ionic, H-bonds, hydrophobic, or covalent

• Proper 3o structure depends on pH, temperature

A lightbulb filament has multiple levels of structure

Quaternary structure• The interactions of multiple polypeptides to form a

functional protein• Polypeptides can be the same (collagen is a homotrimer)

or different (hemoglobin is a heterotetramer)

Changes in the 1o structure of a protein can have far-reaching effects

The tertiary structure of proteins is sensitive to denaturation

• Heat or chemicals (incl. acids and bases) can temporarily or permanently change a protein’s 3o structure

Enzymes-Catalytic proteins

Enzymes are a special kind of protein

Enzymes are protein catalysts

• Catalysts- things which speed up chemical reactions

• Catalysts are not consumed in a reaction

• -ase: The enzyme suffix

Catalase

How enzymes work Structure aids

function An active site

naturally fits substrate

Enzyme specificity depends on shape

Shape changes to fit substrate- induced fit

Enzymes increase the rates of reactions by 108 or more

Enzymes are not consumed by the reactions they catalyze

Enzyme availablewith empty activesite

Active site

Glucose

Fructose

Products arereleased

Enzyme(sucrase)

Substrate(sucrose)

H2O

Substrate isconverted toproducts

Substrate bindsto enzyme withinduced fit

-galactosidase

11

lactose

galactose

glucose

H2O

- galactosidase(aka lactase in humans)

Enzymes are catalysts made of protein. Which of these factors can slow their proper functioning?

1. Temperature2. pH3. Salts4. All of the above5. None of these

Effects of Temperature and pH

• Each enzyme has an optimal temperature in which it can function

• Each enzyme has an optimal pH in which it can function

• Tertiary structure can be radically altered by changes in pH

In salad dressings, oil quickly separates from vinegar because oils are

1. heavier than water. 2. polar. 3. nonpolar. 4. hydrophilic. 5. amphiphilic.

A protein containing more than one polypeptide chain exhibits the __________ level of protein

structure.

1. A) primary 2. B) secondary 3. C) tertiary 4. D) quaternary 5. E) infinite

Nucleic acids

DNA, RNA, and ATP

Nucleic acids• (Primarily)

Informational molecules in cells

• Include DNA, RNA, and ATP/ADP

• DNA is the code to make a protein

• Living things are made up of protein

Nulceotides are the monomers of nucleic acid polymers

• Consist of a sugar, a phosphate, and a nitrogen-containing base

• Sugar can be deoxygenated

• Bases contain the genetic information

Hydrogen bonds hold the two sides of the DNA ladder together

• DNA bases have –OH and –NH2 groups

• Sides of ladder are covalently bonded

• Rungs held together with H-bonds

There are 4 kinds of DNA bases

• Adenine and Thymine, Cytosine and Guanine

• A, T, C, and G• RNA has Uracil instead

of Thymine

RNA’s major task is to carry out the instructions of DNA

• DNA is double-stranded, RNA single

• DNA has thymine, RNA has uracil

ATP

A nucleotide-based

ATP, a single RNA nucleotide, is the basic energy currency of all cells

LE 8-12

Pi

ADP

Energy for cellular work(endergonic, energy-consuming processes)

Energy from catabolism(exergonic, energy-yielding processes)

ATP

+

The Regeneration of ATP

What powers this cycle?