Post on 05-Jan-2016
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Chapter 3
Biochemistry
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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
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• The electron configuration of carbon gives it covalent compatibility with many different elements
H O N C
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
HH
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 H
H H
H H
H H H H
H H
H H
HH
HH
H
H
H
C C C C C
C C C C C C C
CCCCCCCC
C
CC
C
C
C
C
CC
C
C
C
H
H
H
HH
H
H
(a) Length
(b) Branching
(c) Double bonds
(d) Rings
Ethane Propane
Butane isobutane
1-Butene 2-Butene
Cyclohexane Benzene
H H H HH
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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
CH3
CH3
OH
Estradiol
Testosterone
Female lion
Male lion
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• 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;
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Some important functional groups of organic compounds
FUNCTIONALGROUP
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 O
C
OH
The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond.
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• 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 (—OPO3
2–) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens).
NH
H
SH
O P
O
OH
OH
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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
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• 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
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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 H1 2 3 HO
HO H1 2 3 4
H
H2O
Short polymer Unlinked monomer
Longer polymer
Dehydration removes a watermolecule, forming a new bond
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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
HO H1 2 3 4
H2O
HHO
Hydrolysis adds a watermolecule, breaking a bond
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Carbohydrates
• Serve as fuel and building material
• Include both sugars and their polymers (starch, cellulose, etc.)
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Sugars
• Monosaccharides– Are the simplest sugars– Can be used for fuel– Can be converted into other
organic molecules– Can be combined into polymers
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• Examples of monosaccharides
Triose sugars(C3H6O3)
Pentose sugars(C5H10O5)
Hexose sugars(C6H12O6)
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
HO C H
H C OH
H C OH
H C OH
H C OH
HO C H
HO C H
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
C OC O
H C OH
H C OH
H C OH
HO C H
H C OH
C O
H
H
H
H H H
H
H H H H
H
H H
C C C COOOO
Ald
oses
Glyceraldehyde
RiboseGlucose Galactose
Dihydroxyacetone
Ribulose
Keto
ses
Fructose
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• Monosaccharides– May be linear– Can form rings
H
H C OH
HO C H
H C OH
H C OH
H C
O
C
H
1
2
3
4
5
6
H
OH
4C
6CH2OH 6CH2OH
5C
HOH
C
H OH
H
2 C
1C
H
O
H
OH
4C
5C
3 C
H
HOH
OH
H
2C
1 C
OH
H
CH2OH
H
H
OHHO
H
OH
OH
H5
3 2
4
(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.
OH3
O H OO
6
1
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• Disaccharides–Consist of two monosaccharides
–Are joined by a glycosidic linkage
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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
HOH H
OH
O H
OH
CH2OH
H
HO
H
HOH
H
OH
O H
OH
CH2OH
H
O
H
HOH H
OH
O H
OH
CH2OH
H
H2O
H2O
H
H
O
H
HOH
OH
O H
CH2OH
CH2OH HO
OHH
CH2OH
HOH
H
H
HO
OHH
CH2OH
HOH H
O
O H
OHH
CH2OH
HOH H
O
HOH
CH2OH
H HO
O
CH2OH
H
H
OH
O
O
1 2
1 41– 4
glycosidiclinkage
1–2glycosidic
linkage
Glucose
Glucose Glucose
Fructose
Maltose
Sucrose
OH
H
H
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Polysaccharides
• Polysaccharides (complex carbohydrates)– Are polymers of sugars– Serve many roles in organisms
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Storage Polysaccharides
• Starch– Is a polymer
consisting entirely of glucose monomers
– Is the major storage form of glucose in plants
Chloroplast Starch
Amylose Amylopectin
1 m
(a) Starch: a plant polysaccharide
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• Glycogen– 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
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Structural Polysaccharides
• Cellulose– Is a polymer of glucose– Its bonding arrangement stabilizes the
chains and make it resist being digested
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– Has different glycosidic linkages than starch
(c) Cellulose: 1– 4 linkage of glucose monomers
H O
O
CH2OH
HOH H
H
OH
OHH
H
HO
4
C
C
C
C
C
C
H
H
H
HO
OH
H
OHOHOH
H
O
CH2OH
HH
H
OH
OHH
H
HO
4 OH
CH2OH
OOH
OH
HO
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O
CH2OH
OOH
OH
O
CH2OH
OOH
OH
CH2OH
O
OH
OH
O O
CH2OH
OOH
OH
HO
4O
1
OH
O
OH
OHO
CH2OH
O
OH
O OH
O
OH
OH
(a) and glucose ring structures
(b) Starch: 1– 4 linkage of glucose monomers
1
glucose glucose
CH2OH
CH2OH
1 4 41 1
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Plant cells
0.5 m
Cell walls
Cellulose microfibrils in a plant cell wall
Microfibril
CH2OH
CH2OH
OH
OH
OO
OHOCH2OH
O
OOH
OCH2OH OH
OH OHO
O
CH2OH
OO
OH
CH2OH
OO
OH
O
O
CH2OHOH
CH2OHOHOOH OH OH OH
O
OH OH
CH2OH
CH2OH
OHO
OH CH2OH
OO
OH CH2OH
OH
Glucose monomer
O
O
O
O
O
O
Parallel cellulose molecules areheld together by hydrogenbonds between hydroxyl
groups attached to carbonatoms 3 and 6.
About 80 cellulosemolecules associate
to form a microfibril, themain architectural unitof the plant cell wall.
A cellulose moleculeis an unbranched glucose polymer.
OH
OH
O
OOH
Cellulosemolecules
– Is a major component of the tough walls that enclose plant cells
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• Cellulose is difficult to digest– Cows have microbes in their stomachs
to facilitate this process
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• 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
OHHH OH
H
NH
CCH3
O
H
H
(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emergingin adult form.
(c) Chitin is used to make a strong and flexible surgical
thread that decomposes after the wound or incision heals.
OH
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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
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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
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• Saturated fatty acids– Have the maximum number of
hydrogen atoms possible– Have no double bonds
(a) Saturated fat and fatty acid
Stearic acid
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• Unsaturated fatty acids– Have one or more double bonds
(b) Unsaturated fat and fatty acidcis double bondcauses bending
Oleic acid
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• Phospholipids– Have only two fatty acids– Have a phosphate group instead of
a third fatty acid
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• Phospholipid structure– Consists of a hydrophilic “head”
and hydrophobic “tails”CH2
O
PO O
O
CH2CHCH2
OO
C O C O
Phosphate
Glycerol
(a) Structural formula (b) Space-filling model
Fatty acids
(c) Phospholipid symbol
Hyd
rop
hob
i c t
ails
Hydrophilichead
Hydrophobictails
–
Hyd
rop
hi li c
head
CH2 Choline+N(CH3)3
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• The structure of phospholipids– Results in a bilayer arrangement found
in cell membranes
Hydrophilichead
WATER
WATER
Hydrophobictail
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Sterols
• Sterols (steroids)– Are lipids characterized by a carbon
skeleton consisting of four fused rings
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• One steroid, cholesterol– Is found in cell membranes– Is a precursor for some hormones
HO
CH3
CH3
H3C CH3
CH3
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
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• 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 convertedto products.
1 Active site is available for a molecule of substrate, the
reactant on which the enzyme acts.
Substrate binds toenzyme.
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4 Products are released.
Enzymes vs catalyst
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Polypeptides
• Polypeptides– 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
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Twenty Amino Acids
• 20 different amino acids make up proteins
O
O–
H
H3N+ C C
O
O–
H
CH3
H3N+ C
H
C
O
O–
CH3 CH3
CH3
C C
O
O–
H
H3N+
CH
CH3
CH2
C
H
H3N+
CH3CH3
CH2
CH
C
H
H3N+
C
CH3
CH2
CH2
CH3N+
H
C
O
O–
CH2
CH3N+
H
C
O
O–
CH2
NH
H
C
O
O–
H3N+ C
CH2
H2C
H2N C
CH2
H
C
Nonpolar
Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)
Methionine (Met) Phenylalanine (Phe)
C
O
O–
Tryptophan (Trp) Proline (Pro)
H3C
S
O
O–
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O–
OH
CH2
C C
H
H3N+
O
O–
H3N+
OH CH3
CH
C C
HO–
O
SH
CH2
C
H
H3N+ C
O
O–
H3N+
C C
CH2
OH
H H H
H3N+
NH2
CH2
OC
C CO
O–
NH2 O
C
CH2
CH2
C CH3N
+
O
O–
O
Polar
Electricallycharged
–O O
C
CH2
C CH3N
+
H
O
O–
O– O
C
CH2
C CH3N
+
H
O
O–
CH2
CH2
CH2
CH2
NH3+
CH2
C CH3N
+
H
O
O–
NH2
C NH2+
CH2
CH2
CH2
C CH3N
+
H
O
O–
CH2
NH+
NHCH2
C CH3N
+
H
O
O–
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
+H3NAmino
end
oCarboxyl end
oc
GlyProThrGlyThr
Gly
GluSeuLysCysProLeu
MetVal
Lys
ValLeu
AspAlaValArgGly
SerPro
Ala
Gly
lle
SerProPheHisGluHis
Ala
GluValValPheThrAla
Asn
AspSer
GlyProArg
ArgTyrThr
lleAla
Ala
Leu
LeuSer
ProTyrSerTyrSerThr
Thr
Ala
ValVal
ThrAsnProLysGlu
ThrLys
SerTyrTrpLysAlaLeu
GluLleAsp
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O C helix
pleated sheetAmino acid
subunitsNCH
C
O
C N
H
CO H
R
C NH
C
O H
C
R
N
HH
R C
O
R
C
H
NH
C
O H
NCO
R
C
H
NH
H
C
R
C
O
C
O
C
NH
H
R
C
C
ON
HH
C
R
C
O
NH
R
C
H C
ON
HH
C
R
C
O
NH
R
C
H C
ON
HH
C
R
C
O
N H
H C R
N HO
O C N
C
RC
H O
CHR
N HO C
RC
H
N H
O CH C R
N H
CC
N
R
H
O C
H C R
N H
O C
RC
H
H
C
RN
H
CO
C
NH
R
C
H C
O
N
H
C
• Secondary structure– Is the folding or coiling of the
polypeptide into a repeating configuration
– Includes the helix and the pleated sheet
H H
52
• Tertiary structure– Is the overall three-dimensional shape
of a polypeptide– Results from interactions between
amino acids and R groups
CH2CH
OH
O
CHO
CH2
CH2 NH3+ C-O CH2
O
CH2SSCH2
CH
CH3
CH3
H3C
H3C
Hydrophobic interactions and van der Waalsinteractions Polypeptid
ebackbone
Hyrdogenbond
Ionic bond
CH2
Disulfide bridge
53
• Quaternary structure– Is the overall protein structure that
results from the aggregation of two or more polypeptide subunits
Polypeptidechain
Collagen
Chains
ChainsHemoglobin
IronHeme
54
Review of Protein Structure
+H3NAmino end
Amino acidsubunits
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)
Denaturation
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
• Sickle-cell disease– Results from a single amino
acid substitution in the protein hemoglobin
59
Fibers of abnormalhemoglobin deform cell into sickle shape.
Primary structure
Secondaryand tertiarystructures
Quaternary structure
Function
Red bloodcell shape
Hemoglobin A
Molecules donot associatewith oneanother, eachcarries oxygen.Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen
10 m 10 m
Primary structure
Secondaryand tertiarystructures
Quaternary structure
Function
Red bloodcell shape
Hemoglobin SMolecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.
subunit subunit
1 2 3 4 5 6 7 3 4 5 6 721
Normal hemoglobin
Sickle-cell hemoglobin . . .. . . Exposed
hydrophobic region
Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu
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
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
Synthesisof protein
NUCLEUSCYTOPLASM
DNA
mRNA
Ribosome
AminoacidsPolypeptide
mRNA
65
The Structure of Nucleic Acids
• Nucleic acids– Exist as polymers called
polynucleotides
(a) Polynucleotide, or nucleic acid
3’C
5’ end
5’C
3’C
5’C
3’ endOH
O
O
O
O
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• Each polynucleotide– Consists of monomers called nucleotides– Sugar + phosphate + nitrogen base
Nitrogenousbase
Nucleoside
O
O
O
O P CH2
5’C
3’CPhosphate
group Pentosesugar
(b) Nucleotide
O
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