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Chapters 4 & 5. Carbon and Macromolecules. CARBON. Atomic #: 6 1st level: 2 2nd Level: 4 # of bonds able to form – 4 - allows the formation of numerous different compounds - compounds that contain carbon are called ORGANIC except for a few very common ones such as CO and CO 2. - PowerPoint PPT Presentation
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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Chapters 4 & 5
Carbon
and
Macromolecules
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
CARBON
Atomic #: 6
1st level: 22nd Level: 4# of bonds able to form – 4- allows the formation of numerous different compounds- compounds that contain carbon are called ORGANIC except for a few very common ones such as CO and CO2
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The bonding versatility of carbon
– Allows it to form many diverse molecules, including carbon skeletons
(a) Methane
(b) Ethane
(c) Ethene (ethylene)
Molecular Formula
Structural Formula
Ball-and-Stick Model
Space-Filling Model
H
H
H
H
H
HH
H
HH
H H
HH
C
C C
C C
CH4
C2H6
C2H4
Name and Comments
Figure 4.3 A-C
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• 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)
Figure 4.4
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
BOND TYPES
Covalent
• single - hydrogen, carbon, nitrogen and hydroxyl
• double - oxygen, carbon, nitrogen
• triple - carbon, nitrogen
• C-H - hydrocarbon - non-polar
• C-O - polar
• C-N- slightly polar
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Molecular Diversity Arising from Carbon Skeleton Variation
• Carbon chains
– Form the skeletons of most organic molecules
– Vary in length and shape
HHH
HH
H H H
HH
H
H H H
H H HH H
H
H
H
H
H
H
HH
HH H H H
H HH H
H H H H
H H
H H
HHHH H
HH
C C C C C
C C C C C C C
CCCCCCCC
C
CC
CC
C
C
CCC
CC
H
H
H
HHH
H
(a) Length
(b) Branching
(c) Double bonds
(d) Rings
Ethane Propane
Butane 2-methylpropane(commonly called isobutane)
1-Butene 2-Butene
Cyclohexane Benzene
H H H HH
Figure 4.5 A-D
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Carbon: Base of All Biological MoleculesDifference between biological molecules
• 1) Structure:
• Isomers: same chemical formula but different structure
• Structual: C4H10
• Butane
• Isobutane (2-methylpropane)
• Geometric: Ethene - cis and trans
• - cis and trans:
• L vs. D.
• - left verses Right
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Three types of isomers are
– Structural
– Geometric
– Enantiomers
H H H H HH
H H H H HH
HHH
HH
H
H
H
H
HHH
H
H
H
H
CO2H
CH3
NH2C
CO2H
HCH3
NH2
X X
X
X
C C C C C
CC
C C C
C C C C
C
(a) Structural isomers
(b) Geometric isomers
(c) Enantiomers
H
Figure 4.7 A-C
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Enantiomers
– Are important in the pharmaceutical industry
L-Dopa
(effective against Parkinson’s disease)
D-Dopa
(biologically inactive)Figure 4.8
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
2) Functional Groups• - different chemical attachments on hydrocarbons that
change the reactivity• TYPES PAGE 54
• a. Hydroxyl - OH - not hydroxide
• alcohols
• ethane vs. ethanol
• b. Carbonyl - C=O
• aldehydes - on end
• keytones - in middle of chain
•
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• c. Carboxyl - -COOH
• carboxylic acid
• - weak acids
• d. Amino - -NH2
• nitrogen containing
• amino acids
• e. Sufhydryl Group - SHthiols
• stabilize proteins – disulfide bridges• f. Phosphate - PO4
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
– Give organic molecules distinctive chemical properties
CH3
OH
HO
O
CH3
CH3
OH
Estradiol
Testosterone
Female lion
Male lionFigure 4.9
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• 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
COH
Figure 4.10
The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Some important functional groups of organic compounds
Acetic acid, which gives vinegar its sour tatste
NAME OF COMPOUNDS
Alcohols (their specific names usually end in -ol)
Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton
Carboxylic acids, or organic acids
EXAMPLE
Propanal, an aldehyde
Acetone, the simplest ketone
Ethanol, the alcohol present in alcoholic beverages
H
H
H
H H
C C OH
H
H
H
HH
H
HC C H
C
C C
C C C
O
H OH
O
H
H
H H
H O
H
Figure 4.10
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Some important functional groups of organic compounds
FUNCTIONALPROPERTIES
Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).
A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.
Has acidic properties because it is a source of hydrogen ions.The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example,
In cells, found in the ionic form, which is called a carboxylate group.
H
H
C
H
H
C
O
OH
H
H
C
O
C
O
+ H+
Figure 4.10
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• 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
SHO P
O
OH
OH
Figure 4.10
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Monomers Vs. Polymersmost biological molecules are polymers
Monomer - one part
Polymer - many repeating part
Macromolecules - combination of polymers
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
BUILDING of POLYMERS• Polymerization reaction: 2 units form one larger unit
• KEY EX: Protein synthesis
Condensation Reaction or Dehydration Synthesis
• bond is formed by the removal of a water
• two hydroxyl groups - one molecule loses OH and one loses an H
• results in a bond based on the remaining O and the H and the OH combine to form water
• Requires energy and a catalyst
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
BREAKING UP IS HARD TO DO• Hydrolysis Reaction - addition of water to break a
polymer chain
• Also requires energy and enzymes - but generally gives off more energy than it uses
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• 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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Dehydration Synthesis and HydrolysisBuild - anabolic - requires energy
• Break - catabolic - releases energy
• NOTE: COMBINATION OF MONOMERS IN DIFFERENT QUANTITIES AND PATTERNS RESULTS IN A WIDE VARIETY OF MOLECULES
• eg. Alphabet
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Four Major Biological Molecules1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic Acids
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
CARBOHYDRATESElements: CHO and sometimes N
• FUNCTION:
• Energy
• Structure
• Protection
• Storage
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Types of Carbohydrates1. Sugars: simplest
Monomers: monosaccharides
Most common glucose : C6H12O6
• Classification:
• Monosaccharides: one sugar unit
• Ex. Glucose - storage of solar energy via photosynthesis• Characteristics:
• Two types of carbonyls:
• aldehyde - carbonyl on end
• ex. Glucose
• ketone - carbonyl in middle
• ex. fructose• carbonyl affects ring formation
• placement of hydroxyl groups give different properties
• Glucose and fructose
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Examples of monosaccharidesTriose 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
Ket
oses
FructoseFigure 5.3
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Monosaccharides
– May be linear
– Can form ringsH
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
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.
OH 3
O H OO
6
1
Figure 5.4
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Glucose + Fructose = Sucrose
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Dissacharides
formation of a 2 sugar unit by dehydration synthesis
• glu + glu = maltose
• glu + galac = lactose
• glu + fruc = sucrose
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• 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
O HCH2OH
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Polysaccharides: many sugar units
• Chains of glucose
• Type of polysaccharide dependent on the type of glucose
• alpha glucose
• beta glucose
– differ in orientation of the hydroxyl group on the number 1 carbon
alpha - down position
beta - up position
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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• STORAGE POLYSACCHARIDES• 1. Starch - storage in plants - as granuals in organelles
called plastids
glucose monomers
linked together a alpha 1-4 glucosidic linkages
two forms of starch
• amalose - unbranched chains
• amylopectin - branched - branches from the sixth carbon• - branches about every 30 units• 2. Glycogen - storage in animals - storage in liver and
muscle cells
• alpha 1-4 linkage• extensivly branched• about every 10 units
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Starch– 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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• 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
provide protection and support
1. Cellulose - long unbranched, straight chains beta 1-4 linkages
makes for alternating bonds
makes for a very rigid structure
makes up cell walls
enzymes that break alpha bonds can't break beta bonds
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Cellulose vs. Starch– 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
HO4 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
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
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Cellulose
Plant cells
0.5 m
Cell walls
Cellulose microfibrils in a plant cell wall
Microfibril
CH2OH
CH2OH
OHOH
OO
OHOCH2OH
OO
OHO
CH2OH OH
OH OHO
O
CH2OHO
OOH
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 – mutualism
Figure 5.9
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Structural Polysaccharides
2. Chitin - structure of arthropod exoskeletons and cell walls of fungus
differs: glucose with a nitrogen compound attached
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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
HNHCCH3
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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LIPIDS
• CHOP - mostly HYDROPHOBIC
• - MOSTLY hydrocarbons
• NET affect - NON-POLAR
• Types: fats, phospholipids, steroids, waxes
• Function: energy storage, structure, chemical commumication, repel water
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
FATS AND OILSStructure - two parts
1. glycerol - three carbon chain with three hydroxyls
2. fatty acid - long chain of hydrocabons with a carboxyl head
• carboxyl head combines with hydroxyl of glycerol by dehydration synthesis so 3 fatty acids combine with the glycerols = triglycerol or triglyceride
• The massive amounts of hydrocarbons in the tail make fats NONPOLAR
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Fats and Oils
Constructed from a glycerol and three fatty acids
Result = TRIGLYCERIDE
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
FATS vs. OILS
• FATS - animal derived - solid at room temp
• OILS - mostly plant derived - liquid at room temp
• crucial difference?
• bonding in the fatty acids
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Saturation vs. Unsaturation
Saturated - all carbon bonds are single bonded - all possible hydrogens
• straight chains
• atheriosclerosis
Unsaturated - carbons may have double bonds
• - causes a bend in the chain
• - chains can't stack as neatly
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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
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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PARTIALLY HYDROGENATED OILS
BAD BAD BAD BAD BAD
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ENERGY Content of Fats and Oils
9 Cal/g
• - carbs: 4 Cal/g
• - protein: 4 Cal/g
• - alcohol: 7 Cal/g
• Protection and Insulation
Ex: Blubber
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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
PHOSPHOLIPIDS
• Function: STRUCTURE - cell membranes
• Composition:
• Hydrophyillic head:
• phosphate joined to glycerol
• POLAR
• - joins with other polar molecules - choline
• Hydrophobic tail:
• two chains not three
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• Phospholipid structure - amphipathic
– Consists of a hydrophilic “head” and hydrophobic “tails”
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
tails
Hydrophilichead
Hydrophobictails
–
Hyd
roph
ilic
hea d CH2 Choline
+
Figure 5.13
N(CH3)3
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• Reaction with water
• heads out tails in
• 2 structures
• 1. micelle
• 2. lyposome
• - cell membrane – PHOSPHOLIPID BILAYER
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Phospholipids in Water
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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
four fused rings
• examples:
• testosterone
• estrogen
• cholesterol - stabilize cell membranes
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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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PROTEINS: molecular tools of cells
Function: PAGE 68
• support
• storage
• Transport
• Communication
• Movement
• Protection
• *****CATALYST*******
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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
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
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Structure of a ProteinPOLYPEPTIDE - chain of amino acids
• amino acid - monomer
Four parts of amino acid
1. alpha carbon
2. carboxyl group
3. amino group
- carboxyl and amino change with pH of environment
- very acidic: amino and carboxyl have H+
- as increase in pH # of H + decreases so H+ dissociate
- until reaches no H+ on amino or carboxyl
- point in between where amino group is positively charged and carboxyl is negatively charged is called the ZWITTERION
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Zwitterion
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Amino Acid Structure (cont.)
4. functional group - DISTINGUISHES ONE AA FROM ANOTHER - a.k.a. R group - gives specific chemical properties
- some hydrophilic - can be acidic or basic
- some hydrophobic
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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+
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–
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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–
O
Polar
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)
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BUILDING A PROTEIN
process called protein synthesis
• AA bond by dehydration synthesis between amino and carboxyl
• FORM A PEPTIDE BOND
• as build get different conformations based on the AA sequence and the interactions of the R groups - resulting structure will determine function
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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 CH2 CH2
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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STRUCTURE OF A PROTEIN
• 1. Primary structure: sequence of amino acids - determined by genetic information of DNA - change in one AA can alter function
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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
lleSerProPheHisGluHis
Ala
GluValValPheThrAla
Asn
AspSer
GlyProArg
ArgTyrThr
lleAla
Ala
Leu
LeuSer
ProTyrSerTyrSerThrThr
AlaVal
ValThrAsnProLysGlu
ThrLys
SerTyrTrpLysAlaLeu
GluLle Asp
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• 2. Secondary structure: alpha helix or pleated sheets
- from interactions of Hydrogen bonds amino and carboxyl groups of AA
• alpha helix - H bonds every 4th AA
• pleated sheets - two regions of the chain lie next to one another
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O C helix
pleated sheet
Amino acidsubunits NC
H
C
OC N
H
CO H
R
C NH
C
O H
CR
NHH
R CO
R
CH
NH
C
O H
NCO
R
CH
NH
H
CR
C
O
C
O
C
NH
H
R
CCO
NH
H
CR
C
O
NH
R
CH C
ONH H
CR
C
ONH
R
CH C
ONH H
CR
C
O
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
R
H
O C
H C R
N H
O C
RC
H
H
CR
NH
CO
C
NH
R
CH C
ONH
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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• 3. Tertiary Structure: interactions that hold the different areas of a protein together
• hydrogen bonds
• hydrophobic region attracted to one another
• Van der Walls
• Disulfide bridges - bonds between two sulfurs in R groups – Between 2 cysteine AA
• STRONG
• Ionic Bonds between R groups
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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
OHO
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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• 4. Quaternary Structure: putting other proteins together in a cluster
EX: hemoglobin, collagen
• Shaping of the protein aided by CHAPERONE PROTEINS (chaperonins) -direct conformation
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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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Environmental Effects on Protein Structure
Denaturation - changing the protein so its no longer effective
• pH, salt, temperature - cause protein to unravel by breaking interlinking bonds
Denaturation
Renaturation
Denatured proteinNormal protein
Figure 5.22
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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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NUCLEIC ACIDS• - direct cell function - informational polymers
• DNA – deoxyribonucleic acid
• RNA – ribonucleic acid
• Differences
• DNA -deoxyribose, two chains, adenine, thymine, guanine, cytosine
• RNA - ribose sugar, one chain, uracil instead of thymine
• DNA makes RNA which directs formation of proteins which direct the chemical reactions of the cell
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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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• Nucleic Acid Monomers: NUCLEOTIDES1. sugar: deoxribose or ribose - difference C #2
• 2. phosphate
• 3. nitrogenous base:
• purines (bigger) : adenine and guanine
- 6 C ring + 5 C ring
• pyrimidines (smaller): thymine/uracil, cytosine
- 6 C ring
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• Each polynucleotide
– Consists of monomers called nucleotides
Nitrogenousbase
Nucleoside
O
O
O
O P CH2
5’C
3’CPhosphategroup Pentose
sugar
(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
NCO
H
NH2
CHCH
OC
NH
CHHN
CO
CCH3
N
HNC
C
HO
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’
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• In DNA Nitrogenous bases link together by hydrogen bonds
• A bonds to T
• G bonds to C
• - must pair purine with pyrimidine – Page 298
• pur with pur to big
• pyr with pyr to small
• - # of correlating H bonds
• Sequence of A, C, T, and G determines genetic info
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N H O CH3
N
N
O
N
N
N
N H
Sugar
Sugar
Adenine (A) Thymine (T)
N
N
N
N
Sugar
O H N
H
NH
N OH
H
N
Sugar
Guanine (G) Cytosine (C)Figure 16.8
H
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