1. Chapter 3
Biochemistry

2. Why study carbon? All living things are made of cells Cells are…
~72% water
~3% salts
~25% carbon compounds
Carbohydrates
Proteins
Lipids
Nucleic acids

3. Carbon Chemistry Organic chemistry -study of carbon compounds
Carbon atoms can form diverse molecules by bonding to four other atoms
Carbon has four valence electrons and may form single, double, triple, or quadruple bonds

4. The electron configuration of carbon gives it covalent compatibility with many different elements
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4)

5. Hydrocarbons
Hydrocarbons are molecules consisting of only carbon and hydrogen
Hydrocarbons are found in many of a cell’s organic molecules

6. H C
(a) Length
(b) Branching
(c) Double bonds
(d) Rings
Ethane
Propane
Butane
isobutane
1-Butene
2-Butene
Cyclohexane
Benzene

7. Functional Groups
Functional groups are the parts of molecules involved in chemical reactions
They Are the chemically reactive groups of atoms within an organic molecule
Give organic molecules distinctive chemical properties
CH3 OH HO O
Estradiol
Testosterone
Female lion
Male lion

8. Six functional groups are important in the chemistry of life
Hydroxyl – in alcohols, sugar
Carbonyl – in sugars, amino acids, nucleotide bases
Carboxyl – in amino acids, fatty acids; acts as an acid and releases H+
Amino – in amino acids; acts as a weak base
Sulfhydryl – in amino acid cysteine; helps stabilize protein structure
Phosphate – in ATP, nucleotides, proteins, phospholipids; acidic;

9. Some important functional groups of organic compounds
STRUCTURE
(may be written HO )
HYDROXYL CARBONYL CARBOXYL OH
In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.)
When an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (—COOH). C O
The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. 

10. Some important functional groups of organic compounds
The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton.
AMINO SULFHYDRYL PHOSPHATE
(may be written HS )
The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape.
In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P . The phosphate group (—OPO32–) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens). N H SH O P OH

11. Macromolecules Are large molecules composed of smaller molecules
Are complex in their structures

12. Macromolecules Most macromolecules are polymers, built from monomers
Four classes of life’s organic molecules are polymers
Carbohydrates
Proteins
Nucleic acids
Lipids

13. A polymer
Is a long molecule consisting of many similar building blocks called monomers
Specific monomers make up each macromolecule
E.g. amino acids are the monomers for proteins

14. How are organic compounds built?
Enzymes (proteins) are needed to make metabolic reactions proceed much faster than they would on their own.

15. The Synthesis and Breakdown of Polymers
Monomers form larger molecules by condensation reactions called dehydration synthesis
(a) Dehydration reaction in the synthesis of a polymer HO H 1 2 3 4
H2O
Short polymer
Unlinked monomer
Longer polymer
Dehydration removes a water molecule, forming a new bond

16. The Synthesis and Breakdown of Polymers
Polymers can disassemble by a cleavage reaction -Hydrolysis (addition of water molecules)
(b) Hydrolysis of a polymer HO 1 2 3 H 4
H2O
Hydrolysis adds a water molecule, breaking a bond

17. Carbohydrates Serve as fuel and building material
Include both sugars and their polymers (starch, cellulose, etc.)

18. Sugars Monosaccharides Are the simplest sugars Can be used for fuel
Can be converted into other organic molecules
Can be combined into polymers

19. Examples of monosaccharides
Triose sugars (C3H6O3)
Pentose sugars (C5H10O5)
Hexose sugars (C6H12O6)
H C OH
H C OH
HO C H
H C OH
C O
HO C H H C O
Aldoses
Glyceraldehyde
Ribose
Glucose
Galactose
Dihydroxyacetone
Ribulose
Ketoses
Fructose

20. Monosaccharides May be linear Can form rings 4C 3 2 OH
H C OH
HO C H
H C O C 1 2 3 4 5 6 OH 4C
6CH2OH 5C
H OH
2 C 1C
3 C 2C
1 C
CH2OH HO
(a) Linear and ring forms. Chemical equilibrium between the linear and ring
structures greatly favors the formation of rings. To form the glucose ring,
carbon 1 bonds to the oxygen attached to carbon 5.

21. Disaccharides
Consist of two monosaccharides
Are joined by a glycosidic linkage

22. Dehydration reaction in the synthesis of maltose
Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide.
Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring.
(a)
(b) H HO
H OH OH O
CH2OH
H2O 1 2 4
1– 4 glycosidic linkage
1–2 glycosidic linkage
Glucose
Fructose
Maltose
Sucrose

23. Polysaccharides Polysaccharides (complex carbohydrates)
Are polymers of sugars
Serve many roles in organisms

24. Storage Polysaccharides
Chloroplast
Starch
Amylose
Amylopectin
1 m
(a) Starch: a plant polysaccharide
Starch
Is a polymer consisting entirely of glucose monomers
Is the major storage form of glucose in plants

25. (b) Glycogen: an animal polysaccharide
Consists of glucose monomers
Is the major storage form of glucose in animals
Mitochondria
Giycogen granules
0.5 m
(b) Glycogen: an animal polysaccharide
Glycogen

26. Structural Polysaccharides
Cellulose
Is a polymer of glucose
Its bonding arrangement stabilizes the chains and make it resist being digested

27. Has different glycosidic linkages than starch
(c) Cellulose: 1– 4 linkage of  glucose monomers H O
CH2OH OH HO 4 C 1
(a)  and  glucose ring structures
(b) Starch: 1– 4 linkage of  glucose monomers
 glucose
 glucose

28. Is a major component of the tough walls that enclose plant cells
Cell walls
Cellulose microfibrils
in a plant cell wall 
Microfibril
CH2OH OH O
Glucose monomer
Parallel cellulose molecules are
held together by hydrogen
bonds between hydroxyl
groups attached to carbon
atoms 3 and 6.
About 80 cellulose
molecules associate
to form a microfibril, the
main architectural unit
of the plant cell wall.
A cellulose molecule
is an unbranched 
glucose polymer.
Cellulose
molecules

29. Cellulose is difficult to digest
Cows have microbes in their stomachs to facilitate this process

30. Chitin, another important structural polysaccharide
Is found in the exoskeleton of arthropods
Can be used as surgical thread
Has a nitrogen group
(a) The structure of the
chitin monomer. O
CH2OH OH H NH C
CH3
(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.

31. Lipids Lipids are a diverse group of hydrophobic molecules Lipids
Are the one class of large biological molecules that do not consist of polymers
Share the common trait of being hydrophobic

32. Fats
Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids
Vary in the length and number and locations of double bonds they contain

33. (a) Saturated fat and fatty acid
Saturated fatty acids
Have the maximum number of hydrogen atoms possible
Have no double bonds
(a) Saturated fat and fatty acid
Stearic acid

34. (b) Unsaturated fat and fatty acid
Unsaturated fatty acids
Have one or more double bonds
(b) Unsaturated fat and fatty acid
cis double bond
causes bending
Oleic acid

35. Phospholipids Have only two fatty acids
Have a phosphate group instead of a third fatty acid

36. (a) Structural formula (b) Space-filling model
Phospholipid structure
Consists of a hydrophilic “head” and hydrophobic “tails”
CH2 O P CH C
Phosphate
Glycerol
(a) Structural formula
(b) Space-filling model
Fatty acids
(c) Phospholipid
symbol
Hydrophobic tails
Hydrophilic
head
Hydrophobic
tails –
Hydrophilic head
Choline +
N(CH3)3

37. The structure of phospholipids
Results in a bilayer arrangement found in cell membranes
Hydrophilic
head
WATER
Hydrophobic
tail

38. Sterols Sterols (steroids)
Are lipids characterized by a carbon skeleton consisting of four fused rings

39. One steroid, cholesterol
Is found in cell membranes
Is a precursor for some hormones HO
CH3
H3C

40. Proteins
Proteins have many structures, resulting in a wide range of functions
Proteins do most of the work in cells and act as enzymes
Proteins are made of monomers called amino acids

41. An overview of protein functions

42. Enzymes
Are a type of protein that acts as a catalyst, speeding up chemical reactions
Substrate
(sucrose)
Enzyme
(sucrase)
Glucose OH
H O
H2O
Fructose
3 Substrate is converted
to products.
1 Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate binds to
enzyme. 2
4 Products are released.

43. Enzymes vs catalyst

44. Polypeptides Polypeptides A protein
Are polymers (chains) of amino acids
A protein
Consists of one or more polypeptides

45. Amino acids
Are organic molecules possessing both carboxyl and amino groups
Differ in their properties due to differing side chains, called R groups

46. Twenty Amino Acids 20 different amino acids make up proteins O O– H
H3N+ C
CH3 CH
CH2 NH
H2C
H2N
Nonpolar
Glycine (Gly)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Methionine (Met)
Phenylalanine (Phe)
Tryptophan (Trp)
Proline (Pro)
H3C S
20 different amino acids make up proteins

47. Polar Electrically chargedOH
CH2 C H
H3N+ O
CH3 CH SH
NH2
Polar
Electrically
charged –O
NH3+
NH2+
NH+ NH
Serine (Ser)
Threonine (Thr)
Cysteine
(Cys)
Tyrosine
(Tyr)
Asparagine
(Asn)
Glutamine
(Gln)
Acidic
Basic
Aspartic acid
(Asp)
Glutamic acid
(Glu)
Lysine (Lys)
Arginine (Arg)
Histidine (His)

48. Amino Acid Polymers
Amino acids
Are linked by peptide bonds

49. Protein Conformation and Function
A protein’s specific conformation (shape) determines how it functions

50. Four Levels of Protein Structure
Primary structure
Is the unique sequence of amino acids in a polypeptide –
Amino acid subunits
+H3N Amino end o
Carboxyl end c
Gly
Pro
Thr
Glu
Seu
Lys
Cys
Leu
Met
Val
Asp
Ala
Arg
Ser
lle
Phe
His
Asn
Tyr
Trp
Lle

51. Secondary structure
Is the folding or coiling of the polypeptide into a repeating configuration
Includes the  helix and the  pleated sheet O C
 helix
 pleated sheet
Amino acid subunits N H R H

52. Is the overall three-dimensional shape of a polypeptide
Tertiary structure
Is the overall three-dimensional shape of a polypeptide
Results from interactions between amino acids and R groups
CH2 CH
O H O C HO
NH3+ -O S
CH3
H3C
Hydrophobic interactions and van der Waals interactions
Polypeptide backbone
Hyrdogen bond
Ionic bond
Disulfide bridge

53. Quaternary structure
Is the overall protein structure that results from the aggregation of two or more polypeptide subunits
Polypeptide chain
Collagen
 Chains
 Chains
Hemoglobin
Iron
Heme

54. Review of Protein Structure
+H3N
Amino end
Amino acid
subunits
helix

55. What Determines Protein Conformation?
Protein conformation Depends on the physical and chemical conditions of the protein’s environment
Temperature, pH, etc. affect protein structure

56. Denaturation is when a protein unravels and loses its native conformation (shape)
Renaturation
Denatured protein
Normal protein

57. The Protein-Folding Problem
Most proteins
Probably go through several intermediate states on their way to a stable conformation
Denaturated proteins no longer work in their unfolded condition
Proteins may be denaturated by extreme changes in pH or temperature

58. Sickle-Cell Disease: A Simple Change in Primary Structure
Results from a single amino acid substitution in the protein hemoglobin

59. Sickle-cell hemoglobin
Primary structure
Secondary and tertiary structures
Quaternary structure
Function
Red blood cell shape
Hemoglobin A
Molecules do not associate with one another, each carries oxygen.
Normal cells are full of individual hemoglobin molecules, each carrying oxygen  
10 m
Hemoglobin S
Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced.
 subunit 1 2 3 4 5 6 7
Normal hemoglobin
Sickle-cell hemoglobin
. . .
Exposed hydrophobic region
Val
Thr
His
Leu
Pro
Glul
Glu
Fibers of abnormal hemoglobin deform cell into sickle shape.

60. Nucleotides
Consist of sugar, phosphate group, and nitrogen-containing bases
ATP – adenosine triphosphate contains 3 phosphate groups; important source of energy
Coenzymes – enzyme helpers that accept hydrogen atoms and electrons

61. Nucleic Acids Nucleic acids store and transmit hereditary information
Genes
Are the units of inheritance
Program the amino acid sequence of polypeptides
Are made of nucleotide sequences on DNA

62. The Roles of Nucleic Acids
There are two types of nucleic acids
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)

63. Deoxyribonucleic Acid
DNA
Stores information for the synthesis of specific proteins
Found in the nucleus of cells

64. Synthesis of mRNA in the nucleus
DNA Functions
Directs RNA synthesis (transcription)
Directs protein synthesis through RNA (translation) 1 2 3
Synthesis of mRNA in the nucleus
Movement of
mRNA into cytoplasm
via nuclear pore
Synthesis
of protein
NUCLEUS
CYTOPLASM
DNA
mRNA
Ribosome
Amino acids
Polypeptide

65. The Structure of Nucleic Acids
5’ end
5’C
3’ end OH O
Nucleic acids
Exist as polymers called polynucleotides
(a) Polynucleotide,
or nucleic acid

66. Each polynucleotide Consists of monomers called nucleotides
Sugar + phosphate + nitrogen base
Nitrogenous
base
Nucleoside O O O P
CH2
5’C
3’C
Phosphate
group
Pentose
sugar
(b) Nucleotide