Biological Molecules Can Have Complicated Structures

DNA Protein

How complicated are living things?

Even a bacterium is made up of at least 10,000 different kinds of molecules.

But these fall into 4 classes of organic molecules.

4 Kinds of Organic Molecules

Properties of organic molecules:

• Carbon skeletons as backbones

• Side chains bear functional groups that are chemically active

• polymers: chains of subunits

Organic molecules are built around carbon skeletons

Functional Groupschemically active side branches

Organic molecules are polymers

Dehydration (Condensation) Synthesis - Polymer Elongation

Hydrolysis - Polymer Disassembly

Structures are built of large molecules which are built of small molecules

Carbohydrates

• carbohydrates are sugar polymers

• used for:– energy storage– structural features

Sugars are characterized by size, the kinds of functional groups and their position

Another example

Linear carbon chains often become cyclic

Synthesis and breakdown of carbohydrate polymers

Disaccharides

Polysaccharides

Polysaccharides held together by weak bonds are used for energy storage (e.g., starch), whereas those held together by strong bonds are used or

structural purposes (e.g., cellulose)

Cellulose

Lipids

• One end is hydrophilic, the other hydrophobic

• Often polymers (few large instead of many small subunits, fatty acid derivatives)

• Used for:– Energy storage, e.g., fats and oils– Chemical messengers (hormones) , e.g., steroids– Chemical defenses , e.g., terpenes – Membranes , e.g., phospholipids

Fatty Acids

Note: carbon and hydrogen have similar electronegativities and will form non-polar covalent bonds

A simple lipid - triglyceride

Saturated fat

Unsaturated fat

other lipids:

Terpene (citronellol)

Prostaglandin(PGE)

Steroid(cholesterol)

Phospholipid

Phospholipids function in membranes

Membranes - more than lipids

Glycoproteins

(proteins with carbohydrate antennae)

proteins

Membrane(lipid bilayer)

lipid monolayer

membrane systems can be extensive

golgi apparatus

nuclear envelope

rough endoplasmic reticulum

smooth endoplasmic reticulum

ribosomes

Proteins

• Every protein = an unbranched chain of amino acids

• Each kind of protein has a unique amino acid sequence

• Each amino acid sequence confers a specific 3D shape

• Each kind of protein is coded for by a single gene

• Proteins have many functions

Amino acids - 20 kinds

NH2

C COOH

R

R = functional group

each of the 20 amino acids has a

different kind

amino group carboxyl group

H

Acidic and basic amino acids

Non-polar amino acids

Polar amino acids

Peptide bond formation

-

+ The peptide bond is surrounded by two important charges

A short protein - 4 amino acids

four levels of protein structure

primary secondary tertiary quartenary

Secondary Structure and Hydrogen Bonds

Quartenary Structure in Hemoglobin

Quartenary structure:4 proteins (chains)

Hemoglobin and Sickle Cell Anemia:a single amino acid substitution can make a big difference

MUTATION:valine replaces glutamate

hemoglobin polymerizes, forming long rods that

distort the cell

under oxygen stress

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Four levels of protein structure

Proteins differ in their 3D shapes

3D shapes have specific cavities on their surface

these cavities allow “lock and key” fits with other molecules with which

the protein interact

Enzymes Control Chemical Activity

Molecules are modified in pathways, in numerous small controlled steps

Biochemical Pathways

Catalysts Control Chemical Activity

What is the significance of complicated shapes?

Numerous weak bonds among complementary complex surfaces allow molecular recognition and catalysis.

Nucleic Acids: RNA & DNA

• Nucleic acid molecules consist of polynucleotide strands

• DNA has two complementary strands, RNA has one strand

• Both DNA & RNA can replicate and store information

• Nucleotide sequences code for amino acid sequences …DNA genes code for RNA and protein structure

• Like proteins, RNA is single stranded and can fold up into complex 3D shapes ….RNA catalysts are ribozymes

Nucleotides have three subunits

SP

B

Four kinds of DNA nucleotides

RNA is composed of a single polynucleotide strand

DNA is double stranded

DNA can replicate

• DNA unzips

• Single strands act as templates

• Complementary nucleotides added

to form new complementary

second strands

Replication

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DNA Synthesis - Replication

RNA Synthesis - Transcription

DNA structure is too monotonous to serve catalytic functions,but single stranded RNA can assume complicated

shapes

DNA is double strandedcannot be catalytic

RNA is single strandedcan be catalytic (ribozymes)

Protein, RNA and DNA Roles

Protein

RNA

DNA

Heredity

-

√

√

Catalysis

√

√

-

Single strandedness can confer complicated 3D shapes that permit catalytic roles

How does DNA store information for RNA and protein structure?

each kind of molecule is an unbranched sequence of subunits

nucelotide sequences are colinear with the amino acid sequences that they code for

Central Dogma of Biology