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Focus
• Phospholipids are the molecules that make up biological membranes. Below is a picture of a phospholipid. Identify the functional group that we discussed during the last class, give its name and its functional ability.
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PowerPoint Lectures for Biology, Seventh Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero
Macromolecules Part 1Macromolecules Part 1
The Structure and Function of Macromolecules
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Questions we will be able answer
• What is a polymer? What is a monomer?
• What is a monomer
• How does the polymerization of a limited number of monomers allow for the biodiversity in biomolecules that exist in living systems?
• Explain and draw dehydration synthesis (what bond)
• Explain and draw the opposite of dehydration synthesis
• Give examples of carbohydrate monomers and polymers and understand how their physical forms fits their function
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• Overview: The Molecules of Life
– Another level in the hierarchy of biological organization is reached when small organic molecules are joined together
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• Macromolecules
– Are large molecules composed of smaller molecules
– Are complex in their structures
Figure 5.1
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Concept : Most macromolecules are polymers, built from monomers
• Three of the classes of life’s organic molecules are polymers
– Carbohydrates
– Proteins
– Nucleic acids
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• A polymer
– Is a long molecule consisting of many similar building blocks called monomers
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The Synthesis and Breakdown of Polymers
• Monomers form larger molecules by condensation reactions called dehydration reactions
(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
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• Polymers can disassemble by
– Hydrolysis
(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
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The Diversity of Polymers
• Each class of polymer
– Is formed from a specific set of monomers
• 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
1 2 3 HOH
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• Concept : Carbohydrates serve as fuel and building material
• Carbohydrates
– Include both sugars and their polymers
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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
os
es
Glyceraldehyde
RiboseGlucose Galactose
Dihydroxyacetone
Ribulose
Ke
tos
es
FructoseFigure 5.3
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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
Figure 5.4
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• Disaccharides
– Consist of two monosaccharides
– Are joined by a glycosidic linkage
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• Examples of disaccharides 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
OH
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
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Polysaccharides
• Polysaccharides
– 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 polysaccharideFigure 5.6
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Storage Polysaccharides
• Glycogen
– Consists of glucose monomers
– Is the major storage form of glucose in animalsMitochondria Giycogen
granules
0.5 m
(b) Glycogen: an animal polysaccharide
Glycogen
Figure 5.6
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Structural Polysaccharides
• Cellulose
– Is a polymer of glucose
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Cellulose
– 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
OH
OH
OH
H
O
CH2OH
HH
H
OH
OHH
H
HO
4 OH
CH2OH
O
OH
OH
HO41
O
CH2OH
O
OH
OH
O
CH2OH
O
OH
OH
CH2OH
O
OH
OH
O O
CH2OH
O
OH
OH
HO4
O1
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
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Cellulose Structure fits Function
Plant cells
0.5 m
Cell walls
Cellulose microfibrils in a plant cell wall
Microfibril
CH2OH
CH2OH
OH
OH
OO
OHO
CH2OHO
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
– 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
Figure 5.9
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• Chitin, another important structural polysaccharide
– Is found in the exoskeleton of arthropods
– Can be used as surgical thread
(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
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Questions we will be able answer
• What is a polymer? What is a monomer?
• What is a monomer
• How does the polymerization of a limited number of monomers allow for the biodiversity in biomolecules that exist in living systems?
• Explain and draw dehydration synthesis (what bond)
• Explain and draw the opposite of dehydration synthesis
• Give examples of carbohydrate monomers and polymers and understand how their physical forms fits their function
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Focus 9/2
I
•If you see oxygen in the structure of a funtional group what kind of quality is it likely giving to that functional group and why?
•What is the monomer of a carbohydrate?
•Are all macromolecules polymers made of monomers?
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Lipid questions
1. What is a lipid?
2. Are lipids all formed through dehydration synthesis?
3. What is a fat and what alternate names for a fat exist?
4. Is sesame oil a saturated fat? Explain how you know this and how its physical structure dictates its chemical behavior.
5. What is a steroid? What is cholesterol? How much cholesterol does vegetable oil have in it?
6. What structure to phospholipids and cholesterols both play an important role in?
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• Concept : Lipids are a diverse group of hydrophobic molecules
• Lipids
– Are the one class of large biological molecules that do not consist of polymers ( however some lipids are formed through dehydration synthesis)
– Share the common trait of being hydrophobic
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Fats
• Fats
– Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids
(b) Fat molecule (triacylglycerol)
H HH H
HHH
HH
HH
HH
HH
HOH O HC
C
C
H
H OH
OH
H
HH
HH
HH
HH
HH
HH
HH
H
HCCC
CC
CC
CC
CC
CC
CC C
Glycerol
Fatty acid(palmitic acid)
H
H
H
H
HH
HH
HH
HH
HH
HH
HH
HH
HHHH
HHHHHHHHHHHH
H
HH
H HH
H HH
HH
HH
HH
HH
HHHHHHHHHHH
HH
H
H H H H H H H H HH
HH H H H
H
HH
HHHHHH
HHHHH
HH
HO
O
O
O
OC
C
C C C C C C C C C C C C C C C C C
C
CCCCCCC
CCCCCCCCC
C C C C C C C C C C C CC
CC
O
O
(a) Dehydration reaction in the synthesis of a fatEster linkage
Figure 5.11
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Fatty acids
• Vary in the length and number and locations of double bonds they contain
• 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
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• Unsaturated fatty acids
– Have one or more double bonds
(b) Unsaturated fat and fatty acidcis double bondcauses bending
Oleic acid
Figure 5.12
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Phospholipids
• Phospholipids
– Have only two fatty acids
– Have a phosphate group instead of a third fatty acid
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Fat with a twist
• 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
Hy
dro
ph
ob
ic t
ail
s
Hydrophilichead
Hydrophobictails
–
Hy
dro
ph
ilic
he
ad CH2 Choline
+
Figure 5.13
N(CH3)3
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• The structure of phospholipids
– Results in a bilayer arrangement found in cell membranes
Hydrophilichead
WATER
WATER
Hydrophobictail
Figure 5.14
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Steroids
• 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
Figure 5.15
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Lipid questions
1. What is a lipid?
2. Are lipids all formed through dehydration synthesis?
3. What is a fat and what alternate names for a fat exist?
4. Is sesame oil a saturated fat? Explain how you know this and how its physical structure dictates its chemical behavior.
5. What is a steroid? What is cholesterol? How much cholesterol does vegetable oil have in it?
6. What structure to phospholipids and cholesterols both play an important role in?
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Protein questions
1. What 2 functional groups do all amino acids have
2. List the roles of Proteins. Give examples.
3. What are the general steps of an enzymatic reaction?
4. Name and describe the qualities of the primary bonds in a protein.
5. What are the levels of proteins structure and which associations hold them together.
6. What is denaturation and how does it happen?
7. What is a cahperonin? What role do they play in protein structure
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Proteins
• Concept 5.4: Proteins have many structures, resulting in a wide range of functions
– Proteins
• Have many roles inside the cell
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• An overview of protein functions
Table 5.1
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• 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.
22
4 Products are released.
Figure 5.16
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Polypeptides
• Polypeptides
– Are polymers of amino acids
• A protein
– Consists of one or more polypeptides
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Amino Acid Monomers
• 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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• 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+
CH3
CH3
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–
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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 C
O
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)
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Amino Acid Polymers
• Amino acids
– Are linked by peptide bondsOH
DESMOSOMES
DESMOSOMESDESMOSOMES
OH
CH2
C
N
H
C
H O
H OH OH
Peptidebond
OH
OH
OH
H H
HH
H
H
H
H
H
H H
H
N
N N
N N
SHSide
chains
SH
OO
O O O
H2O
CH2 CH2
CH2 CH2CH2
C C C C C C
C CC C
Peptidebond
Amino end(N-terminus)
Backbone
(a)
Figure 5.18 (b) Carboxyl end(C-terminus)
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Determining the Amino Acid Sequence of a Polypeptide
• The amino acid sequences of polypeptides
– Were first determined using chemical means
– Can now be determined by automated machines
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Protein Conformation and Function
• A protein’s specific conformation
– Determines how it functions
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• Two models of protein conformation
(a) A ribbon model
(b) A space-filling model
Groove
Groove
Figure 5.19
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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
ValLeu
AspAlaVal ArgGly
SerPro
Ala
Gly
lle
SerProPheHisGluHis
Ala
GluVal
ValPheThrAlaAsn
AspSer
GlyProArg
ArgTyrThr
lleAla
Ala
Leu
LeuSer
ProTyrSerTyrSerThr
Thr
Ala
ValVal
ThrAsnProLysGlu
ThrLys
SerTyrTrpLysAlaLeu
GluLle Asp
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O C helix
pleated sheet
Amino acidsubunits NC
H
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
O
N
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 H
O 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
Figure 5.20
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• 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
Polypeptidebackbone
Hyrdogenbond
Ionic bond
CH2
Disulfide bridge
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• Quaternary structure
– Is the overall protein structure that results from the aggregation of two or more polypeptide subunits
Polypeptidechain
Collagen Chains
ChainsHemoglobin
IronHeme
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• The four levels of protein structure
+H3NAmino end
Amino acidsubunits
helix
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Sickle-Cell Disease: A Simple Change in Primary Structure
• Sickle-cell disease
– Results from a single amino acid substitution in the protein hemoglobin
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• Hemoglobin structure and sickle-cell disease
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 S
Molecules 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
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What Determines Protein Conformation?
• Protein conformation
– Depends on the physical and chemical conditions of the protein’s environment
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• Denaturation
– Is when a protein unravels and loses its native conformation
Denaturation
Renaturation
Denatured proteinNormal protein
Figure 5.22
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The Protein-Folding Problem
• Most proteins
– Probably go through several intermediate states on their way to a stable conformation
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• 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.
Correctlyfoldedprotein
Polypeptide
2
1
3
Figure 5.23
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• X-ray crystallography
– Is used to determine a protein’s three-dimensional structure X-ray
diffraction pattern
Photographic film
Diffracted X-raysX-ray
sourceX-ray beam
Crystal Nucleic acid Protein
(a) X-ray diffraction pattern (b) 3D computer modelFigure 5.24
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Protein questions
1. What 2 functional groups do all amino acids have
2. List the roles of Proteins. Give examples.
3. What are the general steps of an enzymatic reaction?
4. Name and describe the qualities of the primary bonds in a protein.
5. What are the levels of proteins structure and which associations hold them together.
6. What is denaturation and how does it happen?
7. What is a cahperonin? What role do they play in protein structure
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• Concept 5.5: Nucleic acids store and transmit hereditary information
• Genes
– Are the units of inheritance
– Program the amino acid sequence of polypeptides
– Are made of nucleic acids
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The Roles of Nucleic Acids
• There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
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• DNA
– Stores information for the synthesis of specific proteins
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– Directs RNA synthesis
– Directs protein synthesis through RNA
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
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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
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• Each polynucleotide
– Consists of monomers called nucleotides
Nitrogenousbase
Nucleoside
O
O
O
O P CH2
5’C
3’CPhosphate
group Pentosesugar
(b) NucleotideFigure 5.26
O
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Nucleotide Monomers
• Nucleotide monomers
– Are made up of nucleosides and phosphate groups
(c) Nucleoside componentsFigure 5.26
CHCH
Uracil (in RNA)U
Ribose (in RNA)
Nitrogenous bases Pyrimidines
CN
NC
OH
NH2
CHCH
OC
NH
CH
HNC
O
CCH3
N
HNC
C
HO
O
CytosineC
Thymine (in DNA)T
NHC
N C
CN
C
CH
N
NH2 O
NHC
NHH
CC
N
NH
C NH2
AdenineA
GuanineG
Purines
OHOCH2
H
H H
OH
H
OHOCH2
HH H
OH
H
Pentose sugars
Deoxyribose (in DNA) Ribose (in RNA)OHOH
CH
CH
Uracil (in RNA)U
4’
5”
3’OH H
2’
1’
5”
4’
3’ 2’
1’
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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
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• The sequence of bases along a nucleotide polymer
– Is unique for each gene
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The DNA Double Helix
• Cellular DNA molecules
– Have two polynucleotides that spiral around an imaginary axis
– Form a double helix
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• The DNA double helix
– Consists of two antiparallel nucleotide strands3’ 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
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• The nitrogenous bases in DNA
– Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)
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DNA and Proteins as Tape Measures of Evolution
• Molecular comparisons
– Help biologists sort out the evolutionary connections among species
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The Theme of Emergent Properties in the Chemistry of Life: A Review
• Higher levels of organization
– Result in the emergence of new properties
• Organization
– Is the key to the chemistry of life
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