chemistry of life - organic molecules

8/3/2019 Chemistry of Life - Organic Molecules

1/52

Chemistry of Life

Organic molecules


2/52


3/52

Organic molecules contain carbon

MethaneNonpolar Hydrophobic

Gas at room tempstable

EthaneEthylene

Plant hormoneCauses ripening of fruits/vegs


4/52

Why study carbon?

All living things are made of cells it isthe most abundant atom in living things Cells

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

Carbohydrates

LipidsProteinsNucleic acids


5/52

Can form a variety of shapes rings inaqueous solution


6/52

Carbohydrates - CH 2O, sugars andstarches


7/52

Monosaccharides usually three to sixcarbons often abbreviated as rings

Most sugar names end in ose6C = hexose (glucose)5C = pentose (fructose, ribose)

3C = triose (glyceraldehyde)


8/52


9/52

Photosynthesis andrespiration

C 6H12O6 + O 2 H 2O + CO 2


10/52

Glucose- energy cycling- open systems importance of carbs


11/52

Dehydration synthesis and hydrolysis

Movie 5-02 ALL BIOLOGICAL REACTIONS requireenzymes and energy

Dehydration synthesis = condensationreactions both are anabolic reactionsBuilding large molecules from small ones

Hydrolysis = digestion both are catabolicreactions

Breaking down larger molecules by addingwater


12/52

Terminology

Polymer Monomer MacromoleculeGlycosidic linkage (carbs)Phosphodiester bonds (nucleic acids)Peptide bonds (proteins)


13/52

Disaccharides* 5-05


14/52

Digestion starch v. cellulose (fiber indiet)

Starch = all theglycosidic linkageare on same side =molecule lies flat

Cellulose = crosslinking between OH(H bonds) = rigidstructure hard todigest

Herbivore (cowwith bacteria v.gorilla supplement withfruits)


15/52

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


16/52

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


17/52

Cellulose-digesting bacteria are foundin grazing animals such as this cow


18/52

Figure 5.10 Chitin, a structural polysaccharide

(a) The structure of thechitin monomer.

O

CH 2OH

OHH

H OH

H

NH

C

CH 3

O

H

H

(b) Chitin forms the exoskeletonof arthropods. This cicadais molting, shedding its oldexoskeleton and emergingin adult form.

(c) Chitin is used to make astrong and flexible surgicalthread that decomposes after the wound or incision heals.

OH


19/52

Lipids * 5-10

Carbon, hydrogen and oxygenRation C:O greater than 2:1 (many morecarbons

Diverse group of moleculesClassified together because they are allhydrophobic (C-H chains make hydrophobic)

Not polymers


20/52

Lipids fats, oils, waxes, steroids and phospholipids


21/52

Triglycerides fats, oils, waxes

Glycerol (C 3H8O3)

3 fatty acidshydrocarbon chain(nonpolar andhydrophobic)carboxyl group

Fats energy rich,cushions and insulates(whale blubber)Waxes different sterolas backbone


22/52

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 lessflexible

Not much fat in plants, no need to move so no need to storeenergy more compactly except in seeds


23/52

Phospholipids amphipathic 2 fatty acidschains and one phosphate group backbonestill glycerol


24/52


25/52

Hydrophilichead

WATER

WATER

Hydrophobictail

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


26/52

Cholesterol maintains cell membrane precursor to other steroid hormones


27/52

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


28/52


29/52

Proteins made of amino acids

Structure:central carbonamino group (NH2)

carboxyl group (acid)R group (side chain)

variable groupconfers unique chemical properties of theamino acid


30/52

Amino acid

H

H

N C

R

H

C

O

OH

Aminogroup

Carboxylgroup

carbon


31/52

Nonpolar amino acids


32/52

Polar amino acids - 20 in all


33/52

Proteins Structure allows function

Made of carbon, hydrogen, oxygen and nitrogen (some sulfur or other atoms in side chains)

Amino acids are building blocksFunctions

structural support (collagen, elastin, keratin-hair and horns,

spider silk) *5t01astorage (egg white or milk casein) btransport of other substances (hemoglobin) chormonal (signaling from one part of the organism to theother) (insulin, glucagon)movement and contraction (actin and myosin) edefense against foreign substances (immune function)(antibodies) f enzymes greceptors (cell membrane) d


34/52

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

Amino acids bonded bypeptide bondBond formed bydehydration synthesisBroken by hydrolysisBond between aminogroup on one amino acidand carboxyl group onsecond amino acid


35/52

Sickle cell anemia change in primarystructure of hemoglobin


36/52

Secondary structurehydrogen bonding between atoms of backbone*

E l i L l f P i S


37/52

O C helix

pleated sheet Amino acid

subunits NC

H

C

O

C N

H

C

OH

R

C N

H

C

O H

C

R

N

HH

RC

O

R

C

H

N

H

C

OH

N

C

O

R

C

H

N

H

H

C

R

C

O H

C

R

N

H

C

O

C

C

O

C

N

HH

R

C

C

O

N

H

H

C

R

C

O

N

H

R

C

HC

ON

HH

C

R

C

O

N

H

R

C

H C

O

N

HH

C

R

C

O

N

H

R

C

H C

O

N

H

C

N H

H C R

N HO

O C N

C

RC

H

H O

CHR

N H

O C

R

CH

N H

O C

H C R

N H

C

CN

R H

H

O C

H C R

N H

O C

R

CH

Exploring Levels of Protein Structure:Secondary structure


38/52

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


39/52

Quaternary * 5-24d


40/52

Exploring Levels of Protein Structure:Tertiary structure

CH 2OH

O

COH

CH 2

CH 2 NH3+ C-O CH 2

O

CH 2SSCH 2

CH

CH

CH 3CH 3

H3C

H3C

Hydrophobicinteractions andvan der Waalsinteractions

Polypeptidebackbone

Hydrogenbond

Ionic bond

Disulfide bridge


41/52


42/52

Abdominal glands of thespider secrete silk fibers

that form the web

The radiating strands, madeof dry silk fibers maintained

the shape of the web

The spiral strands (capturestrands) are elastic, stretching

in response to wind, rain,and the touch of insects

Spider silk: a structural proteincontaining pleated sheets


43/52

Protein structure (review)


44/52

Denaturation unravels protein

Disrupt 3 structurepH, 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


45/52

Chaperonin type of protein

Aid in folding proteins into their proper shape ShapeCRITICAL to protein function


46/52

Nucleic Acids

DNA, RNA, ATPFunction in information transfer from onegeneration to the next

Energy transfer (ATP)Nucleotides are the building block(phosphodiester bond)

5-carbon sugar

Phosphate groupNitrogenous base

Adenine, guanine, cytosine, thymine, uracil


47/52


48/52

DNA form fits function antiparallel

The components of nucleic acids


49/52

The components of nucleic acids

3C

CHCH

Uracil (in RNA)U

5 end

5C

3C

5C

O

O

O

O

3 endOH

Nitrogenousbase

Nucleoside

O

O

O

O P CH 2 O

5C

3CPhosphategroup Pentose

sugar

(b) Nucleotide

C

NN

CO

H

NH2

CHCHO

CNH

CHHN

C

O

C

CH 3

NHN

C

C

HO

O

CytosineC

Thymine (in DNA)T

NHC

N C

CN

C

CH

N

NH2 ON

HCNHH

C

C

C

N

NH

C NH2

Adenine A

GuanineG

Purines

OHOCH 2

H

H H

OH

HOHOH

OHOCH 2

H

H H

OH

HOH H

5

4

3 2

1

3 2

14

5 Pentose sugars

Deoxyribose (in DNA) Ribose (in RNA)

Nitrogenous basesPyrimidines

(c) Nucleoside components

(a) Polynucleotide,or nucleic acid

The DNA double helix and its replication


50/52

e doub e e a d ts ep cat o3 end

Sugar-phosphatebackbone

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to be

added to anew strand

A

3 end

3 end

5 end

Newstrands

3 end

5 end

5 endC G

C G

AT

C G

A T

A T

G C

A T

A T

T A

G

A C

C

C

G G T

A

A

T

C

G

A

T

G

C

A

T

A

T

T

A

C

G A

T A

T G

C

T

A

A

T

T

A

C

G

A

T T

A C

G

T

A C

G

G

C

T

C

G

5 end


51/52


52/52

ATP

chemistry of life - organic molecules

Documents