8/3/2019 Chemistry of Life - Organic Molecules
1/52
Chemistry of Life
Organic molecules
8/3/2019 Chemistry of Life - Organic Molecules
2/52
8/3/2019 Chemistry of Life - Organic Molecules
3/52
Organic molecules contain carbon
MethaneNonpolar Hydrophobic
Gas at room tempstable
EthaneEthylene
Plant hormoneCauses ripening of fruits/vegs
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
5/52
Can form a variety of shapes rings inaqueous solution
8/3/2019 Chemistry of Life - Organic Molecules
6/52
Carbohydrates - CH 2O, sugars andstarches
8/3/2019 Chemistry of Life - Organic Molecules
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)
8/3/2019 Chemistry of Life - Organic Molecules
8/52
8/3/2019 Chemistry of Life - Organic Molecules
9/52
Photosynthesis andrespiration
C 6H12O6 + O 2 H 2O + CO 2
8/3/2019 Chemistry of Life - Organic Molecules
10/52
Glucose- energy cycling- open systems importance of carbs
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
12/52
Terminology
Polymer Monomer MacromoleculeGlycosidic linkage (carbs)Phosphodiester bonds (nucleic acids)Peptide bonds (proteins)
8/3/2019 Chemistry of Life - Organic Molecules
13/52
Disaccharides* 5-05
8/3/2019 Chemistry of Life - Organic Molecules
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)
8/3/2019 Chemistry of Life - Organic Molecules
15/52
Carbohydrates main function energystorage(glycogen is animal starch)*5-7
8/3/2019 Chemistry of Life - Organic Molecules
16/52
Cellulose(fiber) and chitin (crabs andfungi) are structural polysaccharides
8/3/2019 Chemistry of Life - Organic Molecules
17/52
Cellulose-digesting bacteria are foundin grazing animals such as this cow
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
20/52
Lipids fats, oils, waxes, steroids and phospholipids
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
23/52
Phospholipids amphipathic 2 fatty acidschains and one phosphate group backbonestill glycerol
8/3/2019 Chemistry of Life - Organic Molecules
24/52
8/3/2019 Chemistry of Life - Organic Molecules
25/52
Hydrophilichead
WATER
WATER
Hydrophobictail
Bilayer structure formed by self-assembly of phospholipids in an aqueous environment
8/3/2019 Chemistry of Life - Organic Molecules
26/52
Cholesterol maintains cell membrane precursor to other steroid hormones
8/3/2019 Chemistry of Life - Organic Molecules
27/52
Steroidscholesterol/hormones4 rings(note only diff in male and female hormone is onefunctional group)
8/3/2019 Chemistry of Life - Organic Molecules
28/52
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
30/52
Amino acid
H
H
N C
R
H
C
O
OH
Aminogroup
Carboxylgroup
carbon
8/3/2019 Chemistry of Life - Organic Molecules
31/52
Nonpolar amino acids
8/3/2019 Chemistry of Life - Organic Molecules
32/52
Polar amino acids - 20 in all
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
35/52
Sickle cell anemia change in primarystructure of hemoglobin
8/3/2019 Chemistry of Life - Organic Molecules
36/52
Secondary structurehydrogen bonding between atoms of backbone*
E l i L l f P i S
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
38/52
Tertiary structure hydrogen andother bonds between R groups *5-24c
8/3/2019 Chemistry of Life - Organic Molecules
39/52
Quaternary * 5-24d
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
41/52
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
43/52
Protein structure (review)
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
45/52
Chaperonin type of protein
Aid in folding proteins into their proper shape ShapeCRITICAL to protein function
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
47/52
8/3/2019 Chemistry of Life - Organic Molecules
48/52
DNA form fits function antiparallel
The components of nucleic acids
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
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
8/3/2019 Chemistry of Life - Organic Molecules
51/52
8/3/2019 Chemistry of Life - Organic Molecules
52/52
ATP