Chemistry of Life

Organic molecules

Figure 4.1 Life is based on carbon

Organic molecules contain carbon

Methane Nonpolar Hydrophobic Gas at room temp stable Ethane Ethylene Plant hormone Causes ripening of fruits/vegs

Why study carbon?

All living things are made of cells it is

the most abundant atom in living things Cells

~72% H2O ~3% salts (Na, Cl, K) ~25% carbon compounds

Carbohydrates Lipids Proteins Nucleic acids

Can form a variety of shapes rings in

aqueous solution

Carbohydrates - CH2O, sugars and starches

Monosaccharides usually three to six carbons often abbreviated as rings

Most sugar names end in ose 6C = hexose (glucose) 5C = pentose (fructose, ribose) 3C = triose (glyceraldehyde)

Photosynthesis and respiration

C6H12O6 + O2 H2O + CO2

Glucose- energy cycling- open systems importance of carbs

Dehydration synthesis and hydrolysis

Movie 5-02 ALL BIOLOGICAL REACTIONS require

enzymes and energy Dehydration synthesis = condensation reactions both are anabolic reactions

Building large molecules from small ones

Hydrolysis = digestion both are catabolic

reactions

Breaking down larger molecules by adding water

Terminology
Polymer Monomer Macromolecule Glycosidic linkage (carbs) Phosphodiester bonds (nucleic acids) Peptide bonds (proteins)

Disaccharides* 5-05

Digestion starch v. cellulose (fiber in diet)

Starch = all the

glycosidic linkage are on same side = molecule lies flat Cellulose = cross linking between OH (H bonds) = rigid structure hard to digest Herbivore (cow with bacteria v. gorilla supplement with fruits)

Carbohydrates main function energy storage(glycogen is animal starch)*5-7

Cellulose(fiber) and chitin (crabs and fungi) are structural polysaccharides

Cellulose-digesting bacteria are found in grazing animals such as this cow

Figure 5.10 Chitin, a structural polysaccharide

CH2OH H OH H OH H H O OH H

NH C CH3 O

(a) The structure of the chitin monomer.

(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form.

(c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.

Lipids * 5-10
Carbon, hydrogen and oxygen Ration C:O greater than 2:1 (many more

carbons Diverse group of molecules Classified together because they are all hydrophobic (C-H chains make hydrophobic) Not polymers

Lipids fats, oils, waxes, steroids and phospholipids

Triglycerides fats, oils, waxes

Glycerol (C3H8O3) 3 fatty acids hydrocarbon chain (nonpolar and hydrophobic) carboxyl group Fats energy rich,

cushions and insulates (whale blubber) Waxes different sterol as backbone

Saturated versus unsaturated fats

Saturated (with hydrogens) v. unsaturated (double bonds) Saturated solid at room temp no kinks (animal fat usually)

Hardening arteries plaque buildup makes vessels less flexible Not much fat in plants, no need to move so no need to store energy more compactly except in seeds

Phospholipids amphipathic 2 fatty acids chains and one phosphate group backbone still glycerol

Bilayer structure formed by self-assembly of phospholipids in an aqueous environment

WATER Hydrophilic head

WATER Hydrophobic tail

Cholesterol maintains cell membrane precursor to other steroid hormones

Steroidscholesterol/hormones4 rings
(note only diff in male and female hormone is one functional group)

Proteins made of amino acids

Structure:

central carbon amino group (NH2) carboxyl group (acid) R group (side chain)

variable group confers unique chemical properties of the amino acid

Amino acid
carbon R H N H H Amino group Carboxyl group C C OH O

Nonpolar amino acids

Polar amino acids - 20 in all

Proteins Structure allows function

Made of carbon, hydrogen, oxygen and nitrogen (some sulfur or

other atoms in side chains) Amino acids are building blocks Functions structural support (collagen, elastin, keratin-hair and horns, spider silk) *5t01a storage (egg white or milk casein) b transport of other substances (hemoglobin) c hormonal (signaling from one part of the organism to the other) (insulin, glucagon) movement and contraction (actin and myosin) e defense against foreign substances (immune function) (antibodies) f enzymes g receptors (cell membrane) d

Primary structure of proteins order of amino acids * 5-24a

Amino acids bonded by

peptide bond Bond formed by dehydration synthesis Broken by hydrolysis Bond between amino group on one amino acid and carboxyl group on second amino acid

Sickle cell anemia change in primary structure of hemoglobin

Secondary structurehydrogen bonding between atoms of backbone*

Exploring Levels of Protein Structure: Secondary structure

pleated sheet
Amino acid subunits
C N O C H C R H R O C C N H C H C O H N C N H H N C O R C H N H R C H C O H N C R O H C N H O C H C R H N C O R C H N H R C H C O H N C R O H C N H O C H C R H N C O C H N H R C H C O H N C O R C H C R H N C O C

OH C

R C N H O N O H C C N O C C R H R H H O N C R C H O C H O N

H H O N C N C C R H R H H O N C C H C

R C

C H

H R

helix

Tertiary structure hydrogen and other bonds between R groups *5-24c

Quaternary * 5-24d

Exploring Levels of Protein Structure: Tertiary structure

CH2

Hydrogen bond

O H O CH2

H3C

CH

CH3 H3C CH3 CH

Hydrophobic interactions and van der Waals interactions Polypeptide backbone

OH C CH2 S S CH2 Disulfide bridge

O
CH2 NH3+ -O C CH2 Ionic bond

Abdominal glands of the spider secrete silk fibers that form the web The radiating strands, made of dry silk fibers maintained the shape of the web The spiral strands (capture strands) are elastic, stretching in response to wind, rain, and the touch of insects

Spider silk: a structural protein containing pleated sheets

Protein structure (review)

Denaturation unravels protein

Disrupt 3 structure

pH, salt, temperature, etc. disrupts H bonds, ionic bonds & disulfide bridges Frying an egg Some proteins can return to their functional shape after denaturation others cannot

Chaperonin type of protein

Aid in folding proteins into their proper shape Shape

CRITICAL to protein function

Nucleic Acids
DNA, RNA, ATP Function in information transfer from one

generation to the next Energy transfer (ATP) Nucleotides are the building block (phosphodiester bond)
5-carbon sugar Phosphate group Nitrogenous base

Adenine, guanine, cytosine, thymine, uracil

DNA form fits function antiparallel

The components of nucleic acids

5 end 5C 3C Nucleoside O Nitrogenous base O

Nitrogenous bases Pyrimidines NH2 N O C C CH CH O CH3 C HN C HN CH C CH C CH N O N O H H Thymine (in DNA) Uracil (in RNA) U T Purines NH2 HC N C C N CH HC O N C C NH N C N H Guanine G
5

O C

N H Cytosine C

5C CH2 O

O P O

5C 3C OH

O Phosphate 3C Pentose group sugar (b) Nucleotide

N C N H Adenine A

NH2

3 end (a) Polynucleotide, or nucleic acid

5

Pentose sugars

HOCH2 O OH 4 H H 1 H 3 2 H OH H Deoxyribose (in DNA)

HOCH2 O OH 4 H H 1 H 3 2 H OH OH Ribose (in RNA)

(c) Nucleoside components

The DNA double helix and its replication

5 end
C C G G

3 end

T C

A G A A T
T

Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand

G A A T A T T

G C

C G

C G T C G A A T A C A T G A T A T G C
T

A G

3 end
C G G

T A G A T A
T

5 end
T

G A

3 end

New strands

5 end

5 end

3 end

ATP