Organic Molecules

Organic molecules are found in living things.

Contain Carbon, Hydrogen, and usually oxygen

Organic Molecules are Macromolecules

Macromolecules (polymers) are formed from smaller building blocks called monomers.

Polymer Monomer

carbohydrate monosaccharides

protein amino acid

nucleic acid nucleotide

Monomers combine to make polymers

Organic Molecules are Macromolecules

Organic Molecules are Carbon Compounds

All of life is built on carbon Cells

~72% H2O ~25% carbon compounds

carbohydrates lipids proteins nucleic acids

~3% salts Na, Cl, K…

Organic Molecules are Carbon Compounds Organic chemistry is the study of

carbon compounds C atoms are versatile building blocks

bonding properties 4 stable covalent bonds

HHC

H

H

Hydrocarbons – a component of organic molecules

methane(CH4)

Made of carbons and hydrogens. Come in many shapes (Carbon’s versatility)

Macromolecules

Building Blocksof Life

Macromolecules Smaller organic molecules join together

to form larger molecules macromolecules

4 major classes of macromolecules: carbohydrates lipids proteins nucleic acids

H2O

HO

HO H

H HHO

Polymers Long molecules built by linking repeating

building blocks in a chain monomers

building blocks repeated small units

covalent bonds

Dehydration synthesisDehydration synthesis

H2O

HO

HO H

H HHO

How to build a polymer Synthesis

joins monomers by “taking” H2O out one monomer donates OH–

other monomer donates H+ together these form H2O

requires energy & enzymes

enzymeDehydration synthesisDehydration synthesis

Condensation reactionCondensation reaction

H2O

HO H

HO H HO H

How to break down a polymer

Digestion use H2O to breakdown polymers

reverse of dehydration synthesis cleave off one monomer at a time

H2O is split into H+ and OH–

H+ & OH– attach to ends

requires enzymes releases energy

HydrolysisHydrolysis

DigestionDigestion

enzyme

OH

OH

H

H

HO

CH2OH

HH

H

OH

O

Carbohydratesenergy

molecules

Carbohydrates Carbohydrates are composed of C, H, O

carbo - hydr - ate

CH2O

(CH2O)x C6H12O6

Function: energy energy storage raw materials structural materials

Monomer: sugars

ex: sugars, starches, cellulosesugar sugar sugar sugar sugarsugar

C6H12O6(CH2O)x

Sugars Most names for sugars end in -ose Classified by number of carbons

6C = hexose (glucose) 5C = pentose (ribose)

OH

OH

H

H

HO

CH2OH

HH

H

OH

O

Glucose

H

OH

HO

O H

HHO

H

Ribose

CH2OH

6 5

Simple & complex sugars Monosaccharides

simple 1 monomer sugars glucose

Disaccharides 2 monomers sucrose

Polysaccharides large polymers starch

OH

OH

H

H

HO

CH2OH

H

H

H

OH

O

Glucose

Building sugars Dehydration synthesis

|glucose

|glucose

monosaccharides disaccharide

|maltose

H2O

Building sugars Dehydration synthesis

|fructose

|glucose

monosaccharides

|sucrose

(table sugar)

disaccharide

H2O

Polysaccharides Polymers of sugars

costs little energy to build easily reversible = release energy

Function: energy storage

starch (plants) glycogen (animals)

in liver & muscles

structure cellulose (plants) chitin (arthropods & fungi)

Linear vs. branched polysaccharides

starch(plant)

glycogen(animal)

energystorage

slow release

fast release

Polysaccharide diversity Molecular structure determines function

isomers of glucose structure determines function…

in starch in cellulose

Digesting starch vs. cellulose

starcheasy todigest

starcheasy todigest enzyme

cellulosehard todigest

cellulosehard todigest

Cellulose Most abundant organic

compound on Earth herbivores have evolved a mechanism to

digest cellulose most carnivores have not

that’s why they eat meat to get their energy & nutrients

cellulose = undigestible roughage

Any Questions?

Lipids: Fats & Oils

long term energy storageconcentrated energy

Lipids Lipids are composed of C, H, O

long hydrocarbon chains (H-C)

“Family groups” fats phospholipids steroids

Do not form polymers big molecules made of only 3 subunits not a continuing chain

Fats Structure:

glycerol (3C alcohol) + fatty acid fatty acid =

long HC “tail” with carboxyl (COOH) group “head”

dehydration synthesis

H2O

enzyme

Building Fats Triglycerides

3 fatty acids linked to glycerol

Dehydration synthesis

dehydration synthesis

H2O

H2O

H2O

H2O

enzyme

enzyme

enzyme

Fats store energy Long HC chain

polar or non-polar? hydrophilic or hydrophobic?

Function: energy storage

concentrated 2x carbohydrates

cushion organs insulates body

think whale blubber!

Saturated fats All C bonded to H No C=C double bonds

long, straight chain most animal fats solid at room temp.

contributes to cardiovascular disease (atherosclerosis) = plaque deposits

Unsaturated fats C=C double bonds in

the fatty acids plant & fish fats vegetable oils liquid at room temperature

the kinks made by doublebonded C prevent the molecules from packing tightly together

mono-unsaturated?poly-unsaturated?

“Trans” fats are a type of isomer Fatty acid tails are hydrocarbons.

Unsaturated fats have double bonds between carbons.

Form follows function!

Trans fats are straight and solidify at room temperature.

Cis (olive oil)

Trans (partially hydrogenated vegetable oil)

Saturated vs. unsaturatedsaturated unsaturated

Phospholipids Structure:

glycerol + 2 fatty acids + PO4

PO4 = negatively charged

Polar Head

Hydrophilic

Non-polar tail

Hydrophobic

Attracted to Water

Repelled by Water

Why is this important? Phospholipids create a barrier in water

define outside vs. inside they make cell membranes!

Cholesterol Important cell component

animal cell membranes precursor of all other steroids

including vertebrate sex hormones high levels in blood may contribute to

cardiovascular disease

Cholesterol

helps keep cell membranes

fluid & flexible

Important component of cell membrane

Any Questions?

Proteins

Multipurposemolecules

Proteins Most structurally & functionally diverse group Function: involved in almost everything

enzymes (pepsin, DNA polymerase) structure (keratin, collagen) carriers & transport (hemoglobin, aquaporin) cell communication

signals (insulin & other hormones) receptors

defense (antibodies) movement (actin & myosin)

Proteins Structure

monomer = amino acids 20 different amino acids

polymer = polypeptide protein can be one or more polypeptide

chains folded & bonded together large & complex molecules complex 3-D shape

Rubisco

hemoglobin

growthhormones

H2O

Amino acids Structure

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

variable group different for each amino acid confers unique chemical

properties to each amino acid like 20 different letters of an

alphabet can make many words (proteins)

—N—H

HC—OH

||O

R

|—C—

|

H

Oh, I get it!amino = NH2 acid = COOH

Building proteins Peptide bonds

covalent bond between NH2 (amine) of one amino acid & COOH (carboxyl) of another

C–N bond

peptidebond

dehydration synthesisH2O

Effect of different R groups:Nonpolar amino acids

Why are these nonpolar & hydrophobic?Why are these nonpolar & hydrophobic?

nonpolar & hydrophobic

Effect of different R groups:Polar amino acids

polar or charged & hydrophilic

Why are these polar & hydrophillic?Why are these polar & hydrophillic?

Protein structure & function

hemoglobin

Function depends on structure 3-D structure

twisted, folded, coiled into unique shape

collagen

pepsin

Primary (1°) structure Order of amino acids in chain

amino acid sequence determined by gene (DNA)

slight change in amino acid sequence can affect protein’s structure & its function just one amino acid change can

make all the difference!

lysozyme: enzyme in tears & mucus that kills bacteria

Secondary (2°) structure “Local folding”

folding along short sections of polypeptide interactions between

adjacent amino acids H bonds

weak bonds between R groups

forms sections of 3-D structure -helix -pleated sheet

Tertiary (3°) structure “Whole molecule folding”

interactions between distant amino acids hydrophobic interactions

cytoplasm is water-based

nonpolar amino acids cluster away from water

H bonds & ionic bonds disulfide bridges

covalent bonds between sulfurs in sulfhydryls (S–H)

anchors 3-D shape

Quaternary (4°) structure More than one polypeptide chain bonded

together only then does polypeptide become

functional protein hydrophobic interactions

collagen = skin & tendons hemoglobin

Protein structure (review)

amino acid sequence

peptide bonds

1°

determinedby DNA R groups

H bonds

R groupshydrophobic interactions

(H & ionic bonds)

3°multiple

polypeptideshydrophobic interactions

4°

2°

Sickle cell anemia

I’mhydrophilic!

But I’mhydrophobic!

Just 1out of 146

amino acids!

Protein denaturation Unfolding a protein

conditions that disrupt H bonds, ionic bonds temperature pH salinity

alter 2° & 3° structure alter 3-D shape

destroys functionality

Nucleic AcidsInformation

storage

proteinsproteins

DNADNA

Nucleic Acids Function:

genetic material stores information

genesblueprint for building proteins

DNA RNA proteins

transfers informationblueprint for new cellsblueprint for next generation

AA

A

A

TC

G

CG

TG

C

T

Nucleic Acids Examples:

RNA (ribonucleic acid) single helix

DNA (deoxyribonucleic acid) double helix

Structure: monomers = nucleotides

RNADNA

Nucleotides 3 parts

nitrogen base (C-N ring) pentose sugar (5C)

ribose in RNA deoxyribose in DNA

phosphate (PO4) group

Nitrogen baseI’m the

A,T,C,G or Upart!

Types of nucleotides 2 types of nucleotides

different nitrogen bases purines

double ring N base adenine (A) guanine (G)

pyrimidines single ring N base cytosine (C) thymine (T) uracil (U)

Purine = AGPure silver!

Nucleic polymer Backbone

Sugar-phosphate N bases hang off the

sugar-phosphate backbone

Dangling bases?Why is this important?

Pairing of nucleotides Nucleotides bond between

DNA strands H bonds purine :: pyrimidine A :: T

2 H bonds G :: C

3 H bonds

Matching bases?Why is this important?

DNA molecule Double helix

H bonds between bases join the 2 strands A :: T C :: G

H bonds?Why is this important?

Copying DNA Replication

2 strands of DNA helix are complementary have one, can build other

Matching halves?Why is this

a good system?

When does a cell copy DNA? When in the life of a cell does DNA have

to be copied? cell reproduction

mitosis gamete production

meiosis

DNA replication“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”

James WatsonFrancis Crick

1953

Watson and Crick … and others…

Maurice Wilkins… and…

Rosalind Franklin (1920-1958)

MacromoleculesReview Carbohydrates

Empirical formula CH2O Functions: Quick energy (sugar), energy

storage in plants (starch), structure (cellulose in plants, chitin in fungi + arthropods)

Monomer = monosaccharide Polymer = polysaccharide

OH

OH

H

H

HO

CH2OH

HH

H

OH

O

MacromoleculesReview Lipids

Made of C, H, and a few O Functions: Energy storage in

animals (triglycerides), Cell membrane structure (phospholipids), hormones (steroids)

Fats made of 1 Glycerol, 3 Fatty acids

Fatty acids can be saturated (no C-C double bonds) or unsaturated (C-C double bonds)

MacromoleculesReview Proteins

Made of C, H, O, N, S, P Many diverse functions

Enzymes Membrane channels Hormones Structure

Monomer = amino acids Polymer = polypeptide 3-D shape determined by amino acid

sequence. Crucial to protein function 1°, 2°, 3°, 4° levels of organization

Macromolecules Review Nucleic Acids

Information storage Examples: DNA and RNA Complementary base pairing

genetic code can be copied A – T C – G Purine – Pyrimidine Hydrogen bonds hold nitrogenous

bases together Monomer = nucleotides

Sugar, phosphate, nitrogenous base