The Structure and Function of Macromolecules Chapter 5 1 -- carbohydrates.
Chapter 5 The Structure and Function of Macromolecules 1.
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Transcript of Chapter 5 The Structure and Function of Macromolecules 1.
Chapter 5
The Structure and Function of Macromolecules
1
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– Big Idea 2: Biological systems utilize Free
Energy and molecular Building Blocks to grow, reproduce, and maintain dynamic homeostasis.
– Big Idea 3: Biological systems store, retrieve, transmit, and respond to information essential to life processes.
2
Macromolecules
•Most macromolecules are polymers, built from monomers• Four classes of life’s organic molecules are polymers– Carbohydrates– Proteins– Nucleic acids– Lipids
3
• 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
4
The Synthesis and Breakdown of Polymers
• Monomers form larger molecules by condensation reactions called dehydration synthesis
5
(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
The Synthesis and Breakdown of Polymers
• Polymers can disassemble by– Hydrolysis (addition of water molecules)
6
(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
• 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
7
Sugars• Monosaccharides– Are the simplest sugars– Can be used for fuel– Can be converted into other organic molecules– Can be combined into polymers
8
Carbohydrates• Serve as fuel and building material• Include both sugars and their polymers
(starch, cellulose, etc.)
• Examples of monosaccharides
9
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
FructoseFigure 5.3
• Monosaccharides– May be linear– Can form rings
10
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
Figure 5.4
11
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
Figure 5.5
• Disaccharides– Consist of two monosaccharides– Are joined by a glycosidic linkage
Polysaccharides
• Polysaccharides– Are polymers of sugars– Serve many roles in organisms
12
Storage Polysaccharides
• Starch– Is a polymer
consisting entirely of glucose monomers
– Is the major storage form of glucose in plants
13
Chloroplast Starch
Amylose Amylopectin
1 m
(a) Starch: a plant polysaccharideFigure 5.6
• Glycogen– Consists of glucose monomers– Is the major storage form of glucose in animals
14
Mitochondria Giycogen granules
0.5 m
(b) Glycogen: an animal polysaccharide
Glycogen
Figure 5.6
Structural Polysaccharides
• Cellulose– Is a polymer of
glucose
15
– 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
41
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
Figure 5.7 A–C
– Is a major component of the tough walls that enclose plant cells
16
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
Figure 5.8
• Cellulose is difficult to digest– Cows have microbes in their stomachs to facilitate
this process
17
Figure 5.9
• Chitin, another important structural polysaccharide– Is found in the exoskeleton of arthropods– Can be used as surgical thread
18
(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
Figure 5.10 A–C
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
19
Triglycerides (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
20
(a) Saturated fat and fatty acid
Stearic acid
Figure 5.12
(b) Unsaturated fat and fatty acidcis double bondcauses bending
Oleic acid
Figure 5.12
21
• Saturated fatty acids– Have the maximum number of hydrogen
atoms possible– Have no double bonds
• Unsaturated fatty acids– Have one or more double bonds
• Phospholipids– Have only two fatty acids– Have a phosphate group instead of a third
fatty acid
22
• Phospholipid structure–Consists of a hydrophilic “head” and
hydrophobic “tails”
23
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+
Figure 5.13
N(CH3)3
• The structure of phospholipids– Results in a bilayer arrangement found in cell
membranes
24
Hydrophilichead
WATER
WATER
Hydrophobictail
Figure 5.14
Steroids• Steroids– Are lipids characterized by a carbon skeleton
consisting of four fused rings
25
• E.g. Cholesterol– Is found in cell membranes– Is a precursor for some hormones
HO
CH3
CH3
H3C CH3
CH3
Figure 5.15
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
26
• An overview of protein functions
27
Table 5.1
• Enzymes– Are a type of protein that acts as a catalyst,
speeding up chemical reactions
28
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.
22
4 Products are released.Figure 5.16
Polypeptides• Polypeptides– Are polymers (chains) of amino acids
• A protein– Consists of one or more polypeptides
• Amino acids– Are organic molecules possessing both carboxyl
and amino groups– Differ in their properties due to differing side
chains, called R groups
29
Twenty Amino Acids
• 20 different amino acids make up proteins
30
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
Figure 5.17
S
O
O–
31
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)
Amino Acid Polymers
• Amino acids– Are linked by peptide bonds
32
Protein Conformation and Function
• A protein’s specific conformation (shape) determines how it functions
33
Four Levels of Protein Structure
• Primary structure– Is the unique sequence
of amino acids in a polypeptide
34
Figure 5.20–
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
• Secondary structure– Is the folding or coiling of the polypeptide into a
repeating configuration– Includes the helix and the pleated sheet
35
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
H H
Figure 5.20
• Tertiary structure– Is the overall three-dimensional shape of a
polypeptide– Results from interactions between amino acids
and R groups
36
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
• Quaternary structure– Is the overall protein structure that results from
the aggregation of two or more polypeptide subunits
37
Polypeptidechain
Collagen
Chains
ChainsHemoglobin
IronHeme
Review of Protein Structure
38
+H3NAmino end
Amino acidsubunits
helix
39
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 . . .. . .
Figure 5.21
Exposed hydrophobic
region
Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu
Sickle-Cell Disease: A Simple Change in Primary Structure
What Determines Protein Conformation?
• Protein conformation Depends on the physical and chemical conditions of the protein’s environment
• Temperature, pH, etc. affect protein structure
40
•Denaturation is when a protein unravels and loses its native conformation(shape)
41
Denaturation
Renaturation
Denatured protein
Normal protein
Figure 5.22
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
42
• Chaperonins– Are protein molecules that assist in the proper
folding of other proteins
43
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.
Correctlyfoldedprotein
Polypeptide
2
1
3
Figure 5.23
• X-ray crystallography– Is used to determine a protein’s three-
dimensional structure
44
X-raydiffraction pattern
Photographic filmDiffracted X-
raysX-ray
source
X-ray
beam
CrystalNucleic acid Protein
(a) X-ray diffraction pattern(b) 3D computer modelFigure 5.24
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
45
The Roles of Nucleic Acids• There are two types of nucleic acids– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)
46
Deoxyribonucleic Acid• DNA– Stores information for
the synthesis of specific proteins
– Found in the nucleus of cells
– Directs RNA synthesis (transcription)
– Directs protein synthesis through RNA (translation)
47
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
The Structure of Nucleic Acids– Consists of monomers called
nucleotides– Sugar + phosphate + nitrogen
base
48
(a) Polynucleotide, or nucleic acid
3’C
5’ end
5’C
3’C
5’C
3’ endOH
Figure 5.26
O
O
O
O
Nitrogenousbase
Nucleoside
O
O
O
O P CH2
5’C
3’CPhosphate
group Pentosesugar
(b) NucleotideFigure 5.26
O
The Nitrogen bases: A, T, U, G, and C
• Purine Rings:• Adenine, Guanine
• Pyrimidine Rings:• Cytosine, Uracil, thymine
49
Nucleotide Polymers• Nucleotide polymers are linked by
phosphodiester bonds. – OH group on the 3´ carbon to phosphate of 5’
carbon on next molecule.
50
The DNA Double Helix• Cellular DNA molecules– Have two anti-parallel strands that spiral around
an imaginary axis forming a double helix– Are held together by hydrogen bonding between
nitrogen bases on anti-paralle strands
51
complementary base pair rules: A with T only in DNA/ A with U only in RNAC with G only
DNA and Proteins as Tape Measures of Evolution
• Molecular comparisons – Help biologists sort out the evolutionary
connections among species – We will come back to this in Investigation 3:
Using BLAST to compare DNA sequences to determine evolutionary sequences
52
Big Ideas 2 and 3
• Big Idea 2: Biological systems utilize Free Energy and molecular Building Blocks to grow, reproduce, and maintain dynamic homeostasis.
• Big Idea 3: Biological systems store, retrieve, transmit, and respond to information essential to life processes.
53