1 Organic Chemistry The Structure and Function of Macromolecules.
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Transcript of 1 Organic Chemistry The Structure and Function of Macromolecules.
1
Organic Chemistry
The Structure and Function of
Macromolecules
•Organic compounds contain carbon and are associated with living things.
•Carbon is so vital to life, an entire branch of chemistry is devoted to its study: organic chemistry
Carbon!
Characteristics of Carbon!
4
The Molecules of Life
• Overview:– Another level in the hierarchy of
biological organization is reached when small organic molecules are joined together
– Atom molecule macromolecule
Macromolecules
Large molecules are called macromolecules
The macromolecules are composed of submits called MONOMERS.
A POLYMER is composed of many monomers.
Building PolymersWhy it is called Dehydration
7
Macromolecules
•Most macromolecules are polymers, built from monomers• Four classes of life’s organic molecules are polymers
– Carbohydrates– Proteins– Nucleic acids– Lipids
CARBOHYDRATES
LIPIDS
PROTEINS
NUCLEIC ACIDS
4 Classes of Biological Macromolecules
CARBOHYDRATESCARBOHYDRATESMonomer is monosaccharide Monosaccharides are the simple
sugars• They contain C, H and O in a 1:2:1 ratio
and may be represented by the general formula CH2O
glucose fructose
Complex CarbohydratesComplex CarbohydratesTwo monosaccharides = a disaccharide More than two = polysaccharide
+ H2O
glucose fructose
sucrose
11
Complex CarbohydratesComplex Carbohydrates
• Serve as fuel (energy) and building material (cellular structure)
• Include both sugars and their polymers (starch, cellulose, glycogen, chitin)
Complex CarbohydratesComplex Carbohydrates
Glycogen (animals) Starch (plants) are energy
storing Cellulose is in plant cells Chitin is the major component
in the exoskeleton of arthropods
Complex CarbohydratesComplex Carbohydrates
Monosaccharides– May be linear– Can form rings
13
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
OH3
O H OO
6
1
Figure 5.4
Complex CarbohydratesComplex Carbohydrates
Examples of monosaccharides
14
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
Ket
oses
FructoseFigure 5.3
Complex CarbohydratesComplex CarbohydratesDisaccharides
– Consist of two monosaccharides– Are joined by a glycosidic linkage
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
Storage Polysaccharides• Starch
– Is a polymer consisting entirely of glucose monomers
– Is the major storage form of glucose in plants
• Glycogen– Consists of glucose
monomers– Is the major storage
form of glucose in animals
Chloroplast Starch
Amylose Amylopectin
1 m
Starch: a plant polysaccharide
Mitochondria Giycogen granules
0.5 m
Glycogen: an animal polysaccharide
Glycogen
17
Structural Polysaccharides
• Cellulose– Is a polymer of glucose– 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
CH2OHO
OH
OH
HO41
O
CH2OH
O
OH
OH
O
CH2OH
O
OH
OH
CH2OH
O
OH
OH
O O
CH2OHO
OH
OH
HO4
O1
OH
O
OH OHO
CH2OHO
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
18
Plant cells
0.5 m
Cell walls
Cellulose microfibrils in a plant cell wall
Microfibril
CH2OH
CH2OH
OH
OHO
OOHO
CH2OHO
OOH
OCH2OH OH
OH OHO
O
CH2OH
OO
OH
CH2OH
OO
OHO
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 unit
of the plant cell wall.
A cellulose moleculeis an unbranched
glucose polymer.
OH
OH
O
OOH
Cellulosemolecules
Figure 5.8
– Cellulose is a major component of the tough walls that enclose plant cells
19
• Cellulose is difficult to digest– Cows have microbes in their stomachs to
facilitate this process
Figure 5.9
20
• 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.
OCH2OH
OHHH OH
H
NH
CCH3
O
H
H
(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging
in 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
21
Lipids• Lipids are a diverse group of hydrophobic molecules
– Are the one class of large biological molecules that do not consist of polymers
– Share the common trait of being hydrophobic– fats and oils– waxes – sterols
Monomer is the fatty acidStructure is mostly C and H
Fig. 3.8a, p. 40stearic acid oleic acid linolenic acid
22
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
23
• 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
24
• Unsaturated fatty acids– Have one or more double bonds
(b) Unsaturated fat and fatty acidcis double bondcauses bending
Oleic acid
Figure 5.12
25
• Phospholipids– Have only two fatty acids– Have a phosphate group instead of a
third fatty acid
26
• Phospholipid structure– Consists of a hydrophilic “head” and
hydrophobic “tails”
27
• The structure of phospholipids– Results in a bilayer arrangement found in cell
membranes
Hydrophilichead
WATER
WATER
Hydrophobictail
Figure 5.14
28
LipidsLipids• Function– Energy Storage– Fats store twice as many
calories as carbohydrates– Protection of vital organs
and insulation– Fat is stored in adipose
cells.
SterolsSterols
Characterized by a carbon skeleton consisting of four fused rings
Steroids- differ from other lipids in structure but are classified as a lipid because they are insoluble in water
– Examples• Cholesterol• Progesterone• Vitamin D
ProteinsProteins• Many structures, resulting in a wide range of
functions
• Amino acids are the building blocks of proteins.
• Needed for
• Structural support and movement(bone, cartilage, muscle)
• Storage/transport molecules (hemoglobin)
• Hormones (insulin-sugar breakdown)
• Enzymes (control of cellular reactions)
• Amino acids joined together by special covalent bonds called peptide bonds
Amino AcidAmino Acid -COOH, which is a
carboxyl group (acidic).
-NH2, which is an amino group (basic).
-H hydrogen. -R which varies
depending on the amino acid
Amino AcidAmino Acid All 20 different amino acids 10 essential - you must get them from food10 non-essential – your body can make themThe amino acids are the alphabet in which the proteins are written.
33
• 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
34
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+
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–
35
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)
36
Protein Conformation and Function
• Instrumental in nearly everything organisms do; 50% dry weight of cells
• The most structurally sophisticated molecules known
• A protein’s specific conformation (shape) determines how it functions
37
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
Gly ProThr GlyThr
Gly
GluSeuLysCysProLeu
MetVal
Lys
ValLeu
AspAlaVal ArgGly
SerPro
Ala
Gly
lle
SerProPheHis Glu His
Ala
GluValValPheThrAla
Asn
AspSer
Gly ProArg
ArgTyrThr
lleAla
Ala
Leu
LeuSer
ProTyrSerTyrSerThr
Thr
Ala
ValVal
ThrAsnProLysGlu
ThrLys
SerTyrTrpLysAlaLeu
Glu Lle Asp
38
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
ON
HH
C
R
C
O
NH
R
C
H C
ON
H H
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
Figure 5.20
39
• 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
40
• Quaternary structure– Is the overall protein structure that results from
the aggregation of two or more polypeptide subunits
41
Review Structure of ProteinsReview Structure of Proteins
• Primary Structure - the sequence of amino acids, which form a chain
• Secondary structure
•Alpha helix
•Beta-sheets
•Random coil
• Tertiary structure – folding of the coil
• Quaternary structure – two or more chains joined together
Types of ProteinsTypes of Proteins
Normal Sickle cell
Sickle cell disease, abnormal hemoglobins, is due to a single amino acid substitution.
43
What Determines Protein Conformation?
• Protein conformation depends on the physical and chemical conditions of the protein’s environment
• Temperature, pH, etc. affect protein structure
44
•Denaturation is when a protein unravels and loses its native conformation(shape)
Denaturation
Renaturation
Denatured proteinNormal protein
Figure 5.22
45
Types of ProteinsTypes of Proteins
46
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
47
Nucleic AcidsNucleic Acids Provide blueprint of life Nucleotides are the monomers that make
– DNA – RNA – ATP
Nitrogen Base Pentose (5 carbon sugar) Phosphate
48
Nucleotide BasesNucleotide Bases
PyrimidinesC = CytosineT = ThymineU = Uracil
PurinesA = AdenineG = Guanine
CHCH
Uracil (in RNA)U
Ribose (in RNA)
Nitrogenous bases Pyrimidines
CN
NC
OH
NH2
CH
CHO
CN
H
CH
HNC
O
CCH3
N
HNC
C
HO
O
CytosineC
Thymine (in DNA)T
NHC
N C
CN
C
CH
N
NH2 O
N
HCNHH
CC
N
NH
CNH2
AdenineA
GuanineG
Purines
OHOCH2
H
H H
OH
H
OHOCH2
H
H H
OH
H
Pentose sugars
Deoxyribose (in DNA) Ribose (in RNA)OHOH
CH
CH
Uracil (in RNA)U
4’
5”
3’
OH H2’
1’
5”
4’
3’ 2’
1’
49
Deoxyribonucleic acid (DNA)
– Double stranded– Form double helix– Stores hereditary
information– Provides instruction
for every protein in the body
Nucleic AcidsNucleic Acids
50
Ribonucleic acid (RNA)– Single stranded– Builds proteins– Acts as enzymes– Three types
• mRNA• tRNA• rRNA
Nucleic AcidsNucleic Acids
51
Adenosine triphosphate (ATP)
– Called Life’s Energy Currency
– Single nucleotide – Energy storing phosphate
groups– Energy transfer and
storage used by all cells– Energy is released by
breaking high energy phosphate bond
Nucleic AcidsNucleic Acids
52
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