05 macromolecules
Transcript of 05 macromolecules
2
The Molecules of Life• Overview:
– Another level in the hierarchy of biological organization is reached when small organic molecules are joined together
– Atom ---> molecule --- compound
3
Macromolecules– Are large molecules composed of smaller
molecules– Are complex in their structures
Figure 5.1
4
Macromolecules
•Most macromolecules are polymers, built from monomers• Four classes of life’s organic molecules are polymers
– Carbohydrates– Proteins– Nucleic acids– Lipids
5
• 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
6
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
Figure 5.2A
7
The Synthesis and Breakdown of Polymers
• Polymers can disassemble by– 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
Figure 5.2B
8
• Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers
• An immense variety of polymers can be built from a small set of monomers
9
Carbohydrates• Serve as fuel and building
material• Include both sugars and
their polymers (starch, cellulose, etc.)
10
Sugars
• Monosaccharides– Are the simplest sugars– Can be used for fuel– Can be converted into other
organic molecules– Can be combined into polymers
11
• Examples of Monosaccharides
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
FructoseFigure 5.3
Triose sugars(C3H6O3)
Pentose sugars(C5H10O5)
Hexose sugars(C6H12O6)
12
• Monosaccharides– May be linear– Can form rings
H
H C OH
HO C H
H C OH
H C OH
H C
OC
H
1
2
3
4
5
6
H
OH
4C
6CH2OH 6CH2OH
5C
HOH
C
H OH
H2 C
1CH
O
H
OH
4C
5C
3 C
H
HOH
OH
H2C
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.
OH 3
O H OO6
1
Figure 5.4
13
• Disaccharides– Consist of two
monosaccharides– Are joined by a glycosidic
linkage (a bond between an O atom and two different H atoms from different base molecules – see diagram on nest slide)
Dehydration Synthesis (Condensation) Reactions & Hydrolysis Reactions
• These are the two most common types of reactions that occur in living organisms.
• Dehydrations (Condensation) reactions join monomers (or small molecules) together to form larger molecules by removing a water molecule
• Hydrolysis reactions break apart larger, macromolecules in to smaller molecules (monomers) by adding a water molecule and breaking a glycosidic linkage. 14
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.
H2O
CH2OH
Glucose Fructose Sucrose
H
HO
H
HOH
H
OH
O H
OH
CH2OH
H
H
O
H
HOH
OH
O HCH2OH
CH2OH HO
OHH
CH2OH
HOH H
O
HOH
CH2OH
H HO
OH
O
1 21–2
glycosidiclinkage
H
H
HO
H
HOH H
OH
O H
OH
CH2OH
H
O
H
HOH H
OH
O H
OH
CH2OH
H
H2O
H
HO
OHH
CH2OH
HOH H
O H
OHH
CH2OH
HOH H
O H
OHO
1 41– 4
glycosidiclinkage
Glucose Glucose Maltose
OH
H
17
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 µm
(a) Starch: a plant polysaccharideFigure 5.6
18
• Glycogen– Consists of glucose monomers– Is the major storage form of glucose in
animals Mitochondria Giycogen granules
0.5 µm
(b) Glycogen: an animal polysaccharide
Glycogen
Figure 5.6
20
– Has different glycosidic linkages than starch
(c) Cellulose: 1– 4 linkage of β glucose monomers
H O
O
CH2OH
HOH H
H
OHO
HH
H
HO
4
C
C
C
C
C
C
H
H
H
HO
OH
HOHOHOH
H
O
CH2OH
HH
H
OH
OHH
H
HO
4 OH
CH2OH O
OH
OH
HO
41O
CH2OH
OOH
OH
O
CH2OH
OOH
OH
CH2OH
OOH
OH
O O
CH2OH O
OH
OH
HO
4O
1
OH
O
OH
OHO
CH2OH O
OH
O OH
O
OH
OH
(a) α and β glucose ring structures
(b) Starch: 1– 4 linkage of α glucose monomers
1
α glucose β glucose
CH2OH
CH2OH
1 4 41 1
Figure 5.7 A–C
Plant cells
0.5 µm
Cell walls
Cellulose microfibrils in a plant cell wall
∩
Microfibril
CH2OH
CH2OH
OHOH
OO
OHOCH2OH
OO
OHO
CH2OH OH
OH OHO
O
CH2OHO
O OH
CH2OH
OO
OH
O
O
CH2OHOH
CH2OHOHOOH OH OH OH
O
OH OH
CH2OH
CH2OHOHO
OH CH2OH
OO
OH CH2OH
OH
β 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 associateto form a microfibril, the main architectural unit of the plant cell wall.
A cellulose moleculeis an unbranched βglucose polymer.
OH
OH
O
OOH
Cellulosemolecules
– Is a major component of the tough walls that enclose plant cells
22
• Cellulose is difficult to digest– Cows have microbes in their stomachs to
facilitate this process
Figure 5.9
• Chitin, another important structural polysaccharide– Is found in the exoskeleton of arthropods– Can be used as surgical thread
(c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.
(a) The structure of the chitin monomer.
O
CH2OH
OHHH OH
HNHCCH3
O
H
H
(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emergingin adult form.
OH
Figure 5.10 A–C
24
Lipids
• Lipids are a diverse group of hydrophobic molecules
• Lipids– Are the one class of large biological
molecules that do not always consist of polymers
– Share the common trait of being hydrophobic
25
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
26
Fats– Are constructed from two types of smaller
molecules, a single glycerol and usually three fatty acids
– Fatty Acids have a “carboxyl” group at the end of the chain
29
• Saturated fatty acids– Have the maximum number of
hydrogen atoms possible– Have no double bonds
(a) Saturated fat and fatty acid
Stearic acid
Figure 5.12
30
• Unsaturated fatty acids– Have one or more double bonds
(b) Unsaturated fat and fatty acidcis double bondcauses bending
Oleic acid
Figure 5.12
32
• Phospholipid structure– Consists of a hydrophilic “head” and a
hydrophobic “tail”CH2
OPO OOCH2CHCH2
OO
C O C O
Phosphate
Glycerol
(a) Structural formula (b) Space-filling model
Fatty acids
(c) Phospholipid symbol
Hyd
roph
obic t
ails
Hydrophilichead
Hydrophobictails
–
Hyd
roph
ilic
head CH2 Choline+
Figure 5.13
N(CH3)3
33
• The structure of phospholipids results in a bilayer arrangement found in cell membranes
Hydrophilichead
WATER
WATER
Hydrophobictail
Figure 5.14
34
Steroids• Steroids are lipids characterized by a
carbon skeleton consisting of four fused rings
HO
CH3
CH3
H3C CH3
CH3
Figure 5.15
Steroids• Steroids include estrogen, progesterone and
testosterone.
• Estrogen and progesterone are made primarily in the ovary and in the placenta during pregnancy
• Testosterone is made in the testes.Testosterone is also converted into estrogen to regulate the supply of each, in the bodies of both females and males.
35
36
• One steroid, cholesterol– Is found in cell membranes and prevents
them “freezing”– Is a precursor for some hormones
HO
CH3
CH3
H3C CH3
CH3
Figure 5.15
37
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
39
• Enzymes– Are a type of protein that acts as a
catalyst, speeding up chemical reactions
Substrate(sucrose)
Enzyme (sucrase)
Glucose
OH
H O
H2OFructose
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.
22
4 Products are released.Figure 5.16
40
Polypeptides• Polypeptides
– Are polymers (chains) of amino acids
• A protein– Consists of one or more polypeptides
41
• Amino acids– Are organic molecules possessing both carboxyl and amino groups
– Differ in their properties due to differing side chains, called R groups
42
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
CO
O–
CH2
NH
H
CO
O–
H3N+ C
CH2
H2C
H2
NC
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
Figure 5.17
S
O
O–
43
O–
OH
CH2
C C
H
H3N+O
O–
H3N+
OH CH3
CH
C C
H O–
O
SH
CH2
C
H
H3N+ CO
O–H3N+ C C
CH2
OH
H H H
H3N+
NH2
CH2
OC
C CO
O–
NH2 OC
CH2
CH2
C CH3N+O
O–
OPolar
Electricallycharged
–O OC
CH2
C CH3N+
H
O
O–
O– OC
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)
45
Protein Conformation and Function
• A protein’s specific conformation (shape) determines how it functions
46
Four Levels of Protein Structure
• Primary structure– Is the unique
sequence of amino acids in a polypeptide
Figure 5.20–
Amino acid
subunits
+H3NAmino end
oCarboxyl end
oc
GlyProThrGlyThr
Gly
GluSeuLysCysProLeu
MetVal
Lys
ValLeuAsp
AlaValArgGlySer
ProAla
GlylleSerProPheHisGluHis
AlaGlu
ValValPheThrAlaAsn
AspSer
GlyProArgArgTyrThrlle
AlaAlaLeu
LeuSerProTyrSerTyrSerThr
ThrAlaVal
ValThrAsnProLysGlu
ThrLysSer
TyrTrpLysAlaLeu
GluLle Asp
47
O C α helix
β pleated sheet
Amino acidsubunits NC
H
CO
C NH
CO H
RC N
H
CO H
CR
NHH
R CO
RCH
NH
CO H
NCO
RCH
NH
H
CR
CO
CO
C
NH
H
RC
CO
NH
H
CR
CO
NH
RCH C
ONH H
CR
CO
NH
RCH C
ONH H
CR
CO
N H
H C RN H O
O C N
C
RC
H O
CHR
N HO C
RC H
N H
O CH C R
N H
CC
N
RH
O C
H C R
N HO C
RC
H
H
CR
NH
CO
C
NH
RCH C
ONH
C
• Secondary structure– Is the coiling or folding of the polypeptide
into a repeating configuration– Includes the α helix (coiled) and the β
pleated (folded) sheet
H H
Figure 5.20
48
• Tertiary structure– Is the overall three-dimensional shape of
a polypeptide– Results from interactions between amino
acids and R groupsCH2
CH
OHOCHOCH2
CH2 NH3+ C-O CH2
O
CH2SSCH2
CH
CH3
CH3
H3CH3C
Hydrophobic interactions and
van der Waalsinteractions
Polypeptidebackbone
Hyrdogenbond
Ionic bond
CH2
Disulfide bridge
49
• Quaternary structure– Is the overall protein
structure that results from the aggregation of two or more polypeptide subunits
Polypeptidechain
Collagenβ Chains
α ChainsHemoglobin
IronHeme
50
Review of Protein Structure
+H3NAmino end
Amino acidsubunits
α helix
Primary Secondary Tertiary Quaternary
51
Sickle-Cell Disease: A Simple Change in Primary Structure
• Sickle-cell disease– Results from a single amino acid
substitution in the protein hemoglobin
52
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
α
β
β
α
10 µm 10 µm
α
β
β α
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.
β subunit β subunit
1 2 3 4 5 6 7 3 4 5 6 721
Normal hemoglobin Sickle-cell hemoglobin. . .. . .
Figure 5.21
Exposed hydrophobic
region
Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu
53
What Determines Protein Conformation?
• Protein conformation Depends on the physical and chemical conditions of the protein’s environment
• Temperature, pH, etc. affect protein structure
54
•Denaturation is when a protein unravels and loses its native conformation(shape)
Denaturation
Renaturation
Denatured proteinNormal protein
Figure 5.22
55
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
56
• Chaperonins– Are protein molecules that assist in the
proper folding of other proteins
Hollowcylinder
Cap
Chaperonin(fully assembled)
Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end.
The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide.
The cap comesoff, and the properlyfolded protein is released.
CorrectlyfoldedproteinPolypeptide
2
1
3
Figure 5.23
57
• X-ray crystallography– Is used to determine a protein’s three-
dimensional structure X-raydiffraction pattern
Photographic filmDiffracted X-
raysX-raysource
X-ray beam
Crystal Nucleic acid Protein
(a) X-ray diffraction pattern(b) 3D computer modelFigure 5.24
58
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
59
The Roles of Nucleic Acids• There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)
60
Deoxyribonucleic Acid• DNA
– Stores information for the synthesis of specific proteins
– Found in the nucleus of cells
61
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
Figure 5.25
62
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
Figure 5.26
O
O
O
O
63
• Each polynucleotide– Consists of monomers called nucleotides– Sugar + phosphate + nitrogen base
Nitrogenousbase
Nucleoside
O
O
O−
−O P CH2
5’C
3’CPhosphategroup Pentose
sugar
(b) NucleotideFigure 5.26
O
64
Nucleotide Monomers
• Nucleotide monomers – Are made up of
nucleosides (sugar + base) and phosphate groups
(c) Nucleoside componentsFigure 5.26
CHCH
Uracil (in RNA)U
Ribose (in RNA)
Nitrogenous bases Pyrimidines
CN
NCO
H
NH2
CHCH
OC
NH
CHHN C
O
CCH3
N
HNC
CH
O
O
CytosineC
Thymine (in DNA)T
NHC
N C
C N
C
CHN
NH2 ON
HCNHH
C C
N
NHC NH2
AdenineA
GuanineG
Purines
OHOCH2
HH H
OH
H
OHOCH2
HH H
OH
H
Pentose sugars
Deoxyribose (in DNA) Ribose (in RNA)OHOH
CHCH
Uracil (in RNA)U
4’
5”
3’OH H
2’
1’
5”
4’
3’ 2’
1’
65
Nucleotide Polymers• Nucleotide polymers
– Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next
67
The DNA Double Helix• Cellular DNA molecules
– Have two polynucleotides that spiral around an imaginary axis
– Form a double helix
68
• The DNA double helix– Consists of two antiparallel nucleotide
strands 3’ end
Sugar-phosphatebackbone
Base pair (joined byhydrogen bonding)Old strands
Nucleotideabout to be added to a new strand
A
3’ end
3’ end
5’ end
Newstrands
3’ end
5’ end
5’ end
Figure 5.27
69
A,T,C,G• The nitrogenous bases in DNA
– Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)
70
DNA and Proteins as Tape Measures of Evolution
• Molecular comparisons – Help biologists sort out the
evolutionary connections among species