CHAPTER 3

Carbon & the Molecular Diversity of Life

Carbon: The Organic Element

• Compounds that are synthesized by cells and contain carbon are organic

• So what is inorganic?

•Why are carbon compounds so prevalent?

• 4 valence electron configuration

• completes shell by sharing 4

• the 4 electron orbitals are shaped like teardrops

• this forms a 3-D tetrahedron

Hydrocarbons

• organic molecules consisting of only hydrogen and carbon

• The molecules’ chain of carbon atoms is called the carbon skeleton –C-C-C-C-

• Ex: methane, ethane, propane

Isomer – compounds with the same molecular formula but different structure

3 types of isomers

1. structural – covalent arrangements

2. geometric – spatial arrangements

3. enantiomers – mirror images

Functional Groups Fig. 3.5 p.43

- Attachments replace one or more of the H on the C skeleton & usually participate in chemical reactions

- All are polar & therefore hydrophilic

Hydroxyl Group

• H bonded to O (-OH or HO-)

•Known as alcohols

Carbonyl Group

• C double bonded to O (-CO) C=O

• Usually sugars w/hydroxyl groups

•Compounds are called aldehydes when –CO is at the end of the chain

•Compounds are called ketones when –CO is in the middle

•Chain must have at least 3 carbons if ketone

Carboxyl Group

• O double bonded to C which is also bonded to a hydroxyl group (-COOH)

• Forms carboxylic acids such as acetic acid in vinegar

Amino Group

• N bonded with 2 H (-NH2)

• Forms compounds called amines

• The amino group acts like a base

• Amino acid combines an amino group with a carboxyl group

Sulfhydryl Group

• S bonded to H

• Compounds called thiols

• Helps stabilize proteins

“I had sulfur for breakfast!”

Phosphate Group

•P bonded w/4 oxygen atoms (-OPO3)

•Used in energy transfer

•Forms organic phosphates

Methyl Group

• C bonded to 3 H

• Methlyated compounds

• Works as a tag more so than a functional group

The Structure and Function of Large Biological

Molecules

Macromolecules

Polymer – a large molecule consisting of similar or identical subunits strung together

Monomers - subunits

Making a Polymer

• Dehydration synthesis – monomers linked together by the removal of water

• One monomer loses a hydroxyl (-OH), the other loses a hydrogen (H)

• One H2O molecule must be removed for every link in the chain of monomers

p. 45

Breaking a Polymer

• Hydrolysis – the reverse of dehydration synthesis (adding water)

• It breaks the molecule by using H2O

Carbohydrates

• Monosaccharides

• Disaccharides

• Polysaccharides

Monosaccharides

• Simple sugars with a molecular formula in multiples of CH2O ex:C6H12O6

• Carbons in the chain each have an –OH group bonded to them; except one which is bonded to form a carbonyl group

• sugar is either an aldehyde or a ketone depending on the location of the carbonyl group (p. 46)

•this changes taste

• monosaccharides are major nutrients for cells

Disaccharides

• double sugars (2 monomers)

• 2 monosaccharides joined by glycosidic linkage – 1 monomer gives up a H from a hydroxyl group and the other gives up an entire hydroxyl group

• bond formed by dehydration synthesis ex: p. 47 (fig. 3.9)

Polysaccharides

• contain a few hundred to a few thousand monosaccharides linked together

Storage polysaccharides – are hydrolyzed as needed to provide sugar for the cell

2 Storage Types

Starch – in plants – consists of many glucose molecules in a helical shape

Glycogen – in animals – stored in the livers and muscles in a branched format

2 Structural Types

- serve as building materials for structures protecting cells

Cellulose – the major component of the tough cell walls in plants (fiber for humans)

- rod formation

- enzymes that digest starch are unable to hydrolyze the linkages here (exception: cows & termites)

Chitin – structural polysaccharides are used by arthropods to build their exoskeletons

Lipids (hydrophobic – water fearing)

• Fats

• Phospholipid

• Waxes

• steroids

Fats

- large molecules composed of glycerol and fatty acids

Glycerol – an alcohol w/3 carbons, each w/a hydroxyl group

Fatty acids – have long carbon chains (p. 49)

Fatty Acids

-One end has a –COOH head

-Other end is a long hydrocarbon tail

-Insoluble in water

-can be linked to glycerol by dehydration synthesis

-ester linkage bond

-triglyceride can be made this way – 3 fatty acids and a gylcerol

-vary in length and # & location of double bonds

Vs.

Saturated – no double bonds in the tail of the molecule (animal fats – solid at room temperature), causes plaque build up in arteries (p.50)

Transfats – unsaturated fat that has been converted to saturated by adding hydrogen

Unsaturated – have one or more double bonds in the tail (plant fats – liquid at room temperature)

•Major function of fats is energy storage (more than twice as much as sugar)

•Stored in adipose cells

•Cells shrink and swell

Phospholipid

•Structurally related to fats in structure, but only have 2 fatty acids

•Third carbon of glycerol is joined to a phosphate group (p. 51)

•The major component of cell membranes (phospholipid bilayer)

Waxes

• Have one fatty acid linked to an alcohol & are more hydrophobic than fats

• Used as water-resistant coatings on surfaces of fruits, leaves, and insects

Steroids

• Are lipids w/ a carbon skeleton consisting of 4 fused rings (p. 51)

• Cholesterol – precursor from which most other steroids are made

• Are all steroids bad?

No! Cancer treatments, poison ivy

Anabolic Steroids – synthetic variants of testosterone, indiscriminate usage can cause liver damage, cancer, infertility, aggressive behavior and reduced sex drive Who uses anabolic steroids?

You would be surprised!!

Athletes of ALL types, body builders, people who want the perfect body, etc.

Proteins

-structural, storage, enzyme (biological catalyst)

-Made up of amino acids

Amino Acids (aa)

• Building blocks of proteins

• Consist of an asymmetric carbon bonded to 4 different covalent partners

• C (alpha carbon) bonds to a H, a carboxyl group and an amino group

•Fourth bond is to a variable group (chemical group) called the R group or side chain

•There are 20 amino acids that make millions of different proteins

p. 53

Polypeptide Chains

• 2 amino acids joined by dehydration synthesis by a peptide bond (p. 54)

• Polypeptide chain – many aa’s joined by peptide bonds

Protein Conformation

• A protein consists of one or more polypeptide chains twisted in a 3-D shape or conformation

•When a cell makes a polypeptide, the chain folds spontaneously into its conformation

Levels of Protein Structure (p. 56-57)

• Primary

• Secondary

• Tertiary

• Quaternary

Primary – protein’s unique sequence of

aa’s (one aa change in hemoglobin causes sickle cell)

Secondary – describes how the primary structure is folded into it’s conformation

*this results from H bonding between peptides

*alpha helix (spring coil) or beta pleated sheet

Tertiary – describes additional, less regular contortions of the molecule (its 3-D shape)

-caused by hydrophobic interactions, H bonds, ionic bonds, etc.

-Disulfide bridges reinforce conformation

Quaternary – results from the relationship (bonding interactions) between subunits – each polypeptide chain is a subunit

Chaperonins – protein molecules that help fold other proteins

Denaturation

What is this?

-when a protein unravels & loses its conformation

- Changes in pH, salt [ ], temperature

What causes denaturation?

Nucleic Acids

• Polynucleotides – another name for nucleic acid, phosphodiester linkages (phosphate and sugar) join monomers

• RNA and DNA are made up of monomers called nucleotides – contains 3 parts: nitrogenous base, a sugar, & a phosphate group (sugar-phosphate backbone)

RNA & DNA

• Ribonucleic acid

• Has the sugar ribose (pentose=5-C)

• Adenine, Guanine, Uracil, Cytosine

• Deoxyribonucleic acid

• Has the sugar deoxyribose (pentose=5-C)

• Adenine, Guanine, Thymine, Cytosine

The Double Helix

-consists of 2 polynucleotide chains that spiral

-Genes are specific stretches of DNA that program the aa sequences (primary structure) of proteins

Who all played a part in discovering the double helix?

How do base pairings ALWAYS occur?

Adenine – Thymine

Guanine - Cytosine