Chemical The Building Blocks of Life
Chapter 3
1
Outline
Biological Molecules
Macromolecules
Proteins
Structure and Denaturation
Nucleic Acids
DNA and RNA
Lipids
Fats and Phospholipids
Carbohydrates
Transport and Storage
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Biological Molecules
The framework of biological molecules consists of carbon bonded to other carbon molecules, or other types of atoms.
Hydrocarbons consist of carbon and hydrogen.
Covalent bonds store considerable energy. H H H H C C C H H H H
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Functional Group
Hydroxyl
Structural Formula
OH
Example
H H
Carbonyl
C O
O Carboxyl C OH H Amino N H
Sulfhydryl
S H O
H C C OH H H Ethanol H O H C C H H Acetaldehyde H O H C C OH H Acetic acid O H H HO C C N CH3 H Alanine H H HO C C S H H H -mercaptoethanol OH OH H O
Amino Acids Protein Structure Nucleic Acid Structure
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Phosphate
Methyl
O P O H C C C O P O H H H O O Glycerol phosphate H O O H O C C C H C H H H Pyruvate
Biological Molecules
Functional groups
specific groups of atoms attached to carbon backbones
retain definite chemical properties
Macromolecules
proteins nucleic acids lipids carbohydrates
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Macromolecules
Macromolecules are often polymers.
long molecule built by linking together small, similar subunits
Dehydration synthesis removes OH and H during synthesis of a new molecule. Hydrolysis breaks a covalent bond by adding OH and H.
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Table 3.1
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Proteins
Protein functions:
Enzyme catalysis Defense: Immunoglobulin/Antibodies Transport: Proteins in the membrane for passage of nutrients and ions Support: Collagen/Keratin Motion: Contraction of muscles Regulation: Hormones Storage: Stores ions for long term storage in the cell
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Fig. 3.4
Keratin peacock feather
Fibrin: blood clots
Collagen from gut tissue
Silk: spider's web
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Amino Acids
contain an amino group (-NH2) a carboxyl group (-COOH) and a hydrogen atom, all bonded to a central carbon atom The characteristic of each individual a.a will be determined by the side group R
R H2N C COOH H
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20 amino acids grouped into 5 classes
based on side groups (R) nonpolar amino acids R groups are usually CH2 or CH3 polar uncharged amino acids O or H charged amino acids Acids or bases aromatic amino acids Carbon ring special-function amino acids Methionine is always the 1st a.a. in a protein
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Amino Acids
Peptide bond links two amino acids.
A protein are long chains of amino acids linked by peptide bonds (polypeptides).
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NONAROMATIC Nonpolar
Fig. 3.6a(TE Art)
CH3 CH3 CH3 CH3 CH3 H3 N+ C C O H3 N+ CH C C H O O H3 N+ CH CH2 C C O H O H3 CH3 CH2 H C N+ C H CH3 C O O H3 CH2 N+
AROMATIC
NH C CH2 O H3 N+ C C O H O C C H O
Alanine (Ala) Polar uncharged
H O
Valine (Val)
Leucine Isoleucine Phenylalanine Tryptophan (Leu) (Ile) (Phe) (Trp)
O O NH2 C CH2 C CH2 CH2 C O O H3 N+ C H C O O H3 N+ CH2 C C O H O NH2 OH
OH H H3 N+ C C O H3N+ CH2 C H C O O H H3 N+
CH3 C OH O H3 N+ C C H O
C H
H O
Glycine (Gly) Charged
O C CH2 CH2 H3 N+ C H C O O H3 O
Serine (Ser)
Threonine AsparagineGlutamine (Thr) (Asn) (Gln)
NH2 C CH2 NH3+ NH CH2 CH2 CH2 O H3 N+ C H C O O
+ HC NH CH C N H CH2
Tyrosine (Tyr)
NH2+
O C
O CH2
CH2 CH2 CH2 H3 N+ C C H O
N+
C
C
O
H3
N+
C
C
O
H O
H O
Glutamic Aspartic Histidine acid (Glu) acid (Asp (His)
Lysine (Lys)
Arginine (Arg)
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SPECIAL FUNCTION
Fig. 3.6b(TE Art)
CH3 S CH2 SH CH2
CH2 CH2 CH2 CH NH+ 2 C O Proline (Pro) O
H3N+ C C O H3N+ C C O H O H O Methionine Cysteine (Met) (Cys)
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CH2
Protein Structure
Protein function is determined by its shape. Protein structure primary - specific amino acid sequence secondary - folding of amino acid chains
sheet helix
motifs - folds or creases (supersecondary structure)
motif turn motif
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Interactions that contributes to protein shape
1 Hydrogen bond H R C C C N R O H R C N C C O O C N H H C CS SC C H C O N H 2 Disulfide bridge 3 Ionic bond O C C N (CH2)4 (NH3+) O O C CH2 N C C O O C
N C CH3 CH3 C N C O 4 Van der Waals attraction
CH3
H CH3 C CH3 CH3 CH3 CH2 CH3 C CH3
5 Hydrophobic exclusion
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1 Primary structure
R H H O C C N C C N C C N C C N C C N C H O H H O H H O R R R
Fig. H3.8a(TE Art) R O R H H H
2 Secondary structure
pleated sheet helix
3 Motifs
motif
turn motif
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Protein Structure
tertiary - final folded shape of globular protein (3D-shape)
Positions nonpolar groups in the interior
domains - functional units (independent of other parts of the protein) quaternary - forms when two or more polypeptide chains associate to form a functional protein
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Fig. 3.8b(TE Art) 4 Tertiary
structure
5 Domains Domain 1 6
Domain 2 Domain 3
Quaternary structure
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Unfolding Proteins
Denaturation refers to the process of changing a protein's shape. usually rendered biologically inactive pH Temperature ionic concentration of the solution
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Nucleic Acids
Deoxyribonucleic Acid (DNA)
Encodes information used to assemble proteins.
Ribonucleic Acid (RNA)
Reads DNA-encoded information to direct protein synthesis.
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Nucleic Acid Structure
Nucleic acids are polymers of repeating subunits, nucleotides. five-carbon sugar phosphate nitrogenous base Purines : adenine and guanine Pyrimidines: cytosine, thymine, and uracil
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Structure of a nucleotide Fig.
3.14(TE Art)
Phosphate group O
O
P O CH2 59 O 49 39
Nitrogenous base NH2 6 7N 5 N1 8 2 N 4 N 3 9
O 19 29 OH in RNA H in DNA
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OH
R
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Sugar
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59
Fig. 3.15a(TE Art)
P O P Phosphodiester bonds
Phosphate group
O P
O P OH 39
5-carbon sugar Nitrogenous base O
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N P U R I N E S H C N H N H C N H
NH2 Adenine CC N P H Y H CN C H R I O Guanine M I CN H C D H3C I H C N C NH2 N E S
Fig. 3.15b(TE CArt)
C
NH2
N CN C O H Thymine O C N H (DNA only) C
Cytosine (both DNA and RNA)
CN C O H Uracil O (RNA only) H CC N H H CN C O H
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Fig. 3.16(TE Art)
Sugar-phosphate "backbone"
O
P
O
C
G
O
P
O
P
O
G T
O
C
P
Hydrogen bonds between nitrogenous bases
O
P
A
P
O
P
O
C
G T A
P
O OH
Phosphodiester bond
P
O
39 end
P
59 end
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Nucleic Acid Structure
DNA: Deoxiribonucleic Acid
exists as double-stranded (ds) molecules. double helix complementary base pairing
hydrogen bonding
RNA (Ribonucleic Acid)
exists as a single stand (ss) . contains ribose instead of deoxyribose contains uracil in place of thymine
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Structure of DNA
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Lipids
Lipids are loosely defined as groups of molecules that are insoluble in water. fats and oils Phospholipids form the core of all biological membranes. composed of three subunits glycerol fatty acid phosphate group
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CH2 N+(CH3)3 CH2 Polar hydrophilic heads Choline Phosphate Glycerol F a t t y a c i d F a t t y a c i d H 2C O
CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3
O O P O O H C CH2 O
CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH CH CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3
C O CO
Nonpolar hydrophobic tails
Schematic
Formula
Space-filling model
Icon
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Water
Fig. 3.20(TE Art) head Lipid
(hydrophilic)
Micelle
Lipid tail (hydrophobic) Water
Phospholipid bilayer
Water
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H
O H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Fig. 3.22(TE Art)
H O H H H H H H H H H H H H H H H
H H H H
H H H H H H H H H H H
H C O C C C C C C C C C C C C C C C C C C HH C O C C C C C C C C C C C C C C C C C C H O H H H H H H H H H H H H H H H H H O H H H H H H H H H H H H H H H H H C O C C C C C C C C C C C C C C C C C C HH C O C C C C C C C C C C C C C C C C C C H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H O H H H H H H H H H H H H H H H H H OH H H H H H H H H H H H H H H C O C C C C C C C C C C C C C C C C C C H H C O C C C C C C C C C C C C C C C C C H H H H H H H H H H H H H H H H H H H H H H H H H H H H HH H H H H
Saturated fat Unsaturated fat
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Fats and Other Lipids
Fats : a of glycerol molecule with three attached fatty acids (triglyceride / triglycerol). Saturated fats - all internal carbon atoms are bonded to at least two hydrogen atoms Unsaturated fats - at least one double bond between successive carbon atoms Polyunsaturated - contains more than one double bond usually liquid at room temperature
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Fats as Energy Storage Molecules
Fats, on average, yield about 9 kcal per gram versus 4 kcal per gram for carbohydrates.
Animal fats are saturated while most plant fats are unsaturated.
Consumption of excess carbohydrates leads to conversion into starch, glycogen, or fats for future use.
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Carbohydrates
Carbohydrates are loosely defined as molecules that contain carbon, hydrogen, and oxygen in a 1:2:1 ratio.
monosaccharides - simple sugars disaccharides - two monosaccharides joined by a covalent bond polysaccharides - macromolecules made of monosaccharide subunits
isomers - alternative forms of the same substance
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3-carbon sugar
H O 1C
Fig. 3.23(TE Art)
5 CH2OH OH 1 4 H H H H 3 2 OH OH Ribose O 5 CH2OH OH 4 1 H H H3 H 2 OH H Deoxyribose O
5-carbon sugars
H C OH 2 H C OH 3 H Glyceraldehyde
6-carbon sugars
6 CH2OH O H H5 H 4 OH H 1 OH HO3 2 H OH Glucose 6 CH2OH O H 5 H HO 2 CH2OH HO 3 1 4 OH H Fructose 6 CH2OH 5 OH OH H 1 4 OH H H H 2 3 H OH Galactose
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Structure of Glucose C6H12O6 Fig. 3.24(TE Art)
6 O C H 1 H C OH 2 HO C H 3 H C OH 4 H C OH 5 H C OH 6 H OH H C H 6 5 C OH O H H C C H OH H 1 OH 4 C C 2 3 H OH 4 6 O C H H 5H C OH H C OH 4 OH C 1 C 2 H 3 OH HO CH2OH 5
1 2 3 H 6 CH2OH HO 4 H H 5 O 2 HO 1 OH H 3 H
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Disaccharides
Fig. 3.25(TE Art)
CH2OH CH2OH O H H H O H OH H O H HO HO CH2OH OH H H OH Glucose Fructose
CH2OH CH2OH H H O H H H OH OH H O OH H HO OH H OH H OH Glucose Glucose
Maltose
Sucrose
CH2OH CH2OH H H O H O OH O OH HO OH H OH H H H OH H H OH Glucose Galactose
Lactose
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Carbohydrate Transport and Storage
Transport disaccharides
Humans transport glucose as a simple monosaccharide. Plants transform glucose into a disaccharide transport form.
Storage polysaccharides
plant polysaccharides formed from glucose starches
most is amylopectin
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Fig. 3.27(TE Art)
CH2OH O H H H OH H HO OH H OH Glucose CH2OH O H H H OH H OH HO OH H Glucose CH2OH O HO H H HO CH2OH OH H Fructose H 2O CH2OH CH2OH O O H H H H OH H H HO O HO CH2OH H OH OH Sucrose H
CH2OH O H H H H OH OH HO H OH Glucose H2 O
CH2OH CH2OH O O H H H H H H OH H OH H O HO OH H OH H Maltose OH
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CH2OH O H H H 1 4 OH H OH HO H OH
Fig. 3.28(TE Art)
H OH H OH H OH H
CH2OH CH2OH CH2OH CH2OH H H O H H O O H H O H H H H H 14 H OH H O OH H O OH H O OH H OH
form of glucose
Starch: chain of -glucose subunits
O Plant cell wall CH2OH H H O OH 4 OH H 1 HO H H OH OH H O H H OH O CH2OH O O H OH H CH2OH HH H H H H CH2OH O H O H OH H O OH O OH H 14 H H CH2OH H OH
form of glucose
Cellulose: chain of - glucose subunits
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Structural Carbohydrates
Cellulose - plants
alpha form or beta form of ring
Chitin - arthropods and fungi
modified form of cellulose
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Summary
Biological Molecules
Macromolecules
Proteins
Structure and Denaturation
Nucleic Acids
DNA and RNA
Lipids
Fats and Phospholipids
Carbohydrates
Transport and Storage
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