Download Identify the characteristics of carbon that allow it to play such an

Module 1D – Biochemistry
„ Biochemistry
Objective # 18
is the chemistry of living
organisms.
Distinguish between organic
and inorganic molecules.
„ In
this module we will focus on the
structure, function, and properties of
the various organic molecules that
make up living organisms.
1
2
Objective 18
Objective 18
„ Organic
molecules:
¾ Larger, more complex molecules
whose structure is based on a
backbone of C atoms (always contain
C as a major part of their structure).
¾ Examples: C6H12O6, C2H5COOH
„ Inorganic
molecules:
¾ Relatively small, simple molecules that
usually lack C (a few have one C
atom).
¾ Examples: H2O, CO2, NH3, O2, H2
Η
„ Living
organisms are composed of
both inorganic and organic molecules.
Ο
Η
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3
4
Objective # 19
Objective 19
„ Carbon
has an atomic # of 6. How
many valence electrons does it have?
„ Carbon can form 4 strong covalent
bonds with up to 4 other atoms.
„ Carbon atoms can form strong
covalent bonds with each other to
produce unbranched chains, branched
chains, and rings.
Identify the characteristics
of carbon that allow it to
play such an important role
in the chemistry of life.
5
6
1
Objective 19
Objective # 20
„ Carbon
rings can join with each other
to form interlocking rings or chains of
rings.
„ Carbon can form single, double, or
triple covalent bonds with other
atoms.
Explain what isomers are.
7
8
Objective 20
Isomers of C6H12O6
„ Isomers
are molecules that have
the same molecular formula
(same number and type of
atoms) but which have different
properties because the atoms
are arranged differently.
H
C
OH
C
O
HO
C
H
H
C
H
H
c)
d)
e)
Stereoisomer
C
O
C
OH
H
C
OH
C
H
HO
C
H
OH
H
C
OH
HO
C
H
C
OH
H
C
OH
H
C
OH
C
OH
H
C
OH
H
C
OH
H
Glucose
H
Galactose
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Objective # 21
b)
O
H
9
a)
C
Structural
isomer
HO
H
Fructose
Explain what a
functional group is,
and be able to
identify the
structure and
characteristics of
each of the
following
functional groups:
H
H
H
10
Objective 21
hydroxyl
carboxyl
amine
methyl
phosphate
„A
functional group is a small group
of atoms that is part of a larger
molecule and gives it specific
properties.
11
12
2
Functional
Group
Structural
Formula
H
Hydroxyl
OH
Found
In
Example
H
H
C
C
H
H
OH
O H
H
Amino
N
H
carbohydrates,
proteins,
nucleic
acids,
lipids
H
HO C C N
CH3
H
proteins,
nucleic
acids
Alanine
Sulfhydryl
COOH
S H
H C CH2 S H
Ethanol
proteins
NH2
Cysteine
H
O
Carbonyl
H
C
O
C
H
C
H
carbohydrates,
nucleic
acids
Phosphate
O–
H
Carboxyl
C
H
OH
C
H
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reproduction or display.
Glycerol phosphate
O
Methyl
HO C C NH2
13
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required for reproduction or display.
Objective # 22
proteins
H C H
H
OH
Acetic acid
O H
H
C H
proteins,
lipids
C
O
O P O– H C C C O P O– nucleic
acids
H H H
O–
O
Acetaldehyde
O
OHOH H
H
Alanine
14
Objective 22a
Define the following terms and be
able to give or recognize examples
of each:
a) Monomer, dimer, polymer
b) Condensation reaction (or
dehydration synthesis)
c) Hydrolysis reaction
„ Large
organic molecules are called
macromolecules.
„ Macromolecules are formed by joining
smaller organic molecules called
subunits, or building bocks, or
monomers.
„ When 2 similar or identical monomers
are joined we get a dimer.
15
16
Objective 22a
Objective 22b
„ Subunits
are joined during a
type of reaction called
condensation or dehydration
synthesis. An –OH is removed
from one subnunit, an –H is
removed form the other, and
H2O is formed:
„ When
many similar or identical
monomers are joined we get a
polymer.
„ Joining
many similar or identical
subunits together to form a polymer is
called polymerization.
17
18
3
Objective 22c
Condensation or Dehydration
Synthesis
„ The
reverse reaction is called
hydrolysis. It involves breaking
a macromolecule into smaller
subunits. A molecule of water
is added for each subunit that is
removed:
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19
20
Objective # 23
Hydrolysis
„
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Describe the structure and functions
of each of the following groups of
organic compounds. Also be able to
identify examples from each group:
a) Carbohydrates
b) Lipids
c) Proteins
d) Nucleotide-based compounds
21
Objective 23a
22
Objective 23a
„ Carbohydrates
are made of monomers
called simple sugars or monosaccharides.
„ Monosaccharides
are used for short term
energy storage, and serve as structural
components of larger organic molecules.
„ They contain C, H, and O in an
approximate ratio of 1:2:1.
23
„ Monosaccharides
are classified according
to the number of C atoms they contain:
¾ 3 C = triose e.g. glyceraldehyde
¾ 4 C = tetrose
¾ 5 C = pentose e.g. ribose, deoxyribose
¾ 6 C = hexose e.g. glucose, fructose, galactose
ƒMonosaccharides in living organisms
generally have 3C, 5C, or 6C:
24
4
Pentoses
Triose
(3-carbon sugar)
O
5-carbon Sugars
5 CH2OH
C
1
C
2
OH
H
C
3
OH
H
Glyceraldehyde
4
H
H
3
OH
6 CH2OH
5
5 CH2OH
O
H
Hexoses (6-carbon Sugars)
(5-carbon sugars)
3-carbon Sugar
H
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H
OH
1
H
2
OH
Ribose
O
4
H
H
3
OH
H
OH
1
H H
2
H
4
HO
6 CH2OH
H
1
5
OH
HO
4
OH
Glucose
Deoxyribose
O OH
H
H
2
OH
3
H
5
OH
H
2
4
OH
OH
CH2OH
H
1
3
3
H
H
O
O H
H
OH
6 CH2OH
Fructose
H
1
H
2
OH
Galactose
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25
26
Objective 23a
Chain and Ring Forms of Glucose
„ When
monosaccharides with 5 or
more C atoms are dissolved in
water (as they always are in living
systems) most of the molecules
assume a ring shape.
„ Glucose can form 2 types of rings,
α-glucose and β-glucose:
CH2OH
5
C
O
H
H
H
C
C OH
H
4
1
OH
OH 3 C
C2
α-glucose
O
C
1
H
OH
H
H
2C
HO C
3
OH
C
4
H C
5
H C
6
H
OH
H
C H
6
H
5C
O
O
C H
C
OH
H
4
1
OH
C2 H
3C
H
H
H
H
OH
OH
or
CH2OH
5
C
O
OH
C
C H
OH
H
4
1
OH
H
C2
3C
OH
H
OH
H
β-glucose
OH
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27
28
Objective 23a
Fructose and α-glucose can be
joined by a condensation reaction to
produce the disaccharide sucrose:
„ Two
monosaccharides can be
joined by condensation to form a
disaccharide plus H2O.
CH2OH
CH2OH
H
„ Many
organisms transport sugar
within their bodies in the form of
disaccharides.
HO
H
OH
+
H
OH HO
H
OH
α-glucose
CH2OH
O
O H
H
H
OH
H
CH2OH
OH H
Fructose
HO
H2O
H
OH
H
CH2OH
O
O H
H
OH
O
H
OH
Sucrose
H
OH
CH2OH
H
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a.
29
30
5
Galactose and α-glucose can be
joined by a condensation reaction to
produce the disaccharide lactose:
Two α-glucose molecules can be
joined by a condensation reaction to
produce the disaccharide maltose:
CH2OH
H
HO
CH2OH
O
H
H
OH
H
H
OH
H
O
O
H
OH
H
H
OH
H
OH
OH
H
Maltose
H
H
OH
Glucose
H
OH
Galactose
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31
CH2OH
O
H
OH H
CH2OH
O
H H
H
OH
H
O
OH
Lactose
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reproduction or display.
Objective 23a
32
Objective 23a
„ Storage
„ Polysaccharides
consist of many
monosaccharides joined by
condensation to form long
branched or unbranched chains.
„ Some polysaccharides are used to
store excess sugars, while others
are used as structural materials.
Polysaccharides:
subunits can be joined by α-1,4
linkages to form long unbranched chains
¾ α-glucose
CH2OH
H
4 H
OH
HO
O H
1
H
OH
H
H
OH
α-glucose
CH2OH
O
OH
H
H
OH
H
O
CH2OH
O
OH
H
H
O
H
OH
α-1,4 linkages
CH2OH
O
OH
H
H
OH
H
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33
Objective 23a
Objective 23a
use α-glucose to make starches,
including amylose (coiled and unbranched)
and amylopectin (coiled and branched):
¾ Plants
¾ Branches
can be added to the chain
using α-1,6 linkages:
H
34
CH2OH
O H
H
OH H
O
α-1,6 linkage
H
OH
CH2
CH2OH
O H
O H
H
H
H
H
OH H
OH
H
O
H
OH
OH
H
α-1,4 linkage
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35
Amylose
+
Amylopectin
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36
6
Objective 23a
¾ Animals use α-glucose to make glycogen
which is more extensively branched than
amylopectin:
Objective 23a
„ Structural
Polysaccharides:
¾ Cellulose
is a long unbranched chain of
β-glucose subunits. It is a major
component of plant cell walls.
CH2OH
H
4 H
OH
HO
H
CH2OH
O OH
1
H
H
OH
β-glucose
H
O
H
O
O
H
OH
H
H
OH
H H
OH
H
OH
H
CH2OH
H
H
O
O
CH2OH
β-1,4 linkages
O
H
OH
H
H
OH
O
H
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Glycogen
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37
38
Objective 23a
Objective 23b
„ Lipids
are structurally diverse molecules
that are greasy and insoluble in H2O.
„ We will examine 4 types of lipids:
¾ Fats and oils
¾ Phospholipids
¾ Terpenes
¾ Steroids
¾ Chitin
is similar to cellulose, but a
nitrogen group is added to each glucose.
It is found in the exoskeleton of
arthropods and cell walls of fungi.
39
40
Objective 23b
Objective 23b
„ Fats
and oils are composed of 2 types
of subunits: glycerol and fatty acids.
„ Glycerol is an alcohol with 3 carbons,
each bearing a hydroxyl group:
„A
41
fatty acid has a long hydrocarbon
chain with a carboxyl group at one end.
ƒIt may be saturated (no double bonds
between the C atoms of the hydrocarbon
chain), monounsaturated (one double
bond), or polyunsaturated (more than
one double bond).
ƒH can be added to unsaturated fatty acids
using a process called hydrogenation.
42
7
Objective 23b
Fatty Acids:
„ Glycerol
+ 1 fatty acid = monoglyceride
„ Glycerol + 2 fatty acids = diglyceride
+ 3 fatty acids = triacylglycerol
(also called a triglyceride or fat.)
„ Glycerol
43
Saturated fat
44
Unsaturated fat
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45
46
Objective 23b
Objective 23b
„ Most
animal fats contain saturated fatty
acids and tend to be solid at room
temperature.
„ Because
fats and oils are such
concentrated sources of energy,
they are often used for long term
energy storage.
„ In animals, fats also act as
insulators and cushions.
„ Most
plant fats contain unsaturated fatty
acids. They tend to be liquid at room
temperature, and are called oils.
47
48
8
„ In
Nonpolar Hydrophobic Tails
phospholipids, two of the –OH
groups on glycerol are joined to fatty
acids. The third –OH joins to a
phosphate group which joins, in turn,
to another polar group of atoms.
„ The phosphate and polar groups are
hydrophilic (polar head) while the
hydrocarbon chains of the 2 fatty acids
are hydrophobic (nonpolar tails).
Polar Hydrophilic Heads
Objective 23b
N+(CH3)3
CH2
CH2
Phospholipid
O
O
Choline
O
H2C
C
O
O
Glycerol
F
a
t
t
y
a
c
I
d
a
c
I
d
O–
H
Phosphate
F
a
t
t
y
P
CH2
C OC O
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH2 CH2
CH3 CH3
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49
Objective 23b
50
Micelle
Lipid head
(hydrophilic)
„ In
water, phospholipids will
spontaneously orient so that the
nonpolar tails are shielded from
contact with the polar H2O
molecules.
„ Phospholipids are major
components of cell membranes.
Lipid tail
(hydrophobic)
Water
Phospholipid bilayer
Water
Water
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51
Objective 23b
52
Objective 23b
„ Terpenes
are long-chain lipids
that are components of many
important biological pigments
such as chlorophyll.
CH3
CH2
C
CH2
CH2
CH2
CH3
OH
CH
CH2
CH2
Terpene (citronellol)
53
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54
9
Objective 23b
Objective 23b
„ Steroids
are lipids whose principle
component is the steroid nucleus, a
structure made of 4 interlocking rings
of carbon atoms.
H3C
CH2
CH
CH3
CH3
CH2
CH2
CH
CH3
CH3
„ Examples:
¾ Cholesterol
is a component of animal
cell membranes.
Steroid (cholesterol)
HO
55
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56
Objective 23b
¾ Testosterone
and estrogen are steroids
that function as sex hormones.
Hormones are chemical messengers.
After being secreted by endocrine
glands, they are carried by the blood to
specific target cells where they trigger a
response, such as the production or
activation of a protein:
57
Objective 23c
Proteins perform many essential functions
in living organisms:
Function
Class of Protein
Catalysis
enzymes
Defense
immunoglobulins,
toxins
Cell recognition
antigens
Transport through
globins
the body
Objective 23c
„
Membrane transport transporters
58
59
Function
Structure/support
Class of Protein
fibers
Motion
muscle
Osmotic regulation
albumin
Gene regulation
repressors, activators
Messengers
hormones
Storage
Ion binding
60
10
Objective 23c
„ One
of the most important groups of
proteins are enzymes.
„ Enzymes are proteins that function as
catalysts – substances that facilitate or
speed up specific chemical reactions
without being altered themselves:
61
Objective 23c
62
Three amino acids with the central
carbon in red, the amino group in blue,
and the R group shaded in white:
„ Proteins
are composed of monomers
called amino acids.
„ An amino acid consists of a central
carbon atom joined to 4 other groups:
¾ H atom
¾ Amino group (NH2)
¾ Carboxyl group (COOH)
¾ R group (varies)
OH
NH
CH2
H3N+ C
CH2
CH2
H O
Phenylalanine
(Phe)
63
C
C O–
H3N+ C
H3N+ C
C O–
C O–
H O
H O
Tryptophan
(Trp)
Tyrosine
(Tyr)
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64
Objective 23c
„ About
20 different amino acids occur
naturally in proteins. They are
identical except for the R group.
„ Two amino acids can join by
condensation to form a dipeptide plus
H2O.
„ The bond between 2 amino acids is
called a peptide bond.
H
H
R
N
C
C
H
O
H
OH
H
R
N
C
C
H
O
Amino acid
OH
Amino acid
H 2O
H
H
R
N
C
C
H
O
H
R
N
C
C
H
O
OH
Dipeptide
65
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66
11
Objective 23c
Objective 23c
„A
polypeptide consists of many amino
acids joined by peptide bonds to form
a long unbranched chain:
R
H H O
R
H H O
R
„A
protein consists of one or more
polypeptides which are coiled and
folded into a specific 3-D shape.
„ The final overall shape of a protein
determines its function.
H H
C C N C C N C C N C C N C C N C
H O
H H O
H H O
R
R
R
Peptide bond
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67
68
Objective 23c
Objective 23c
Scientists generally recognize 4 levels
of protein structure:
1) Primary structure is the sequence of
amino acids in the polypeptide
chains that make up a protein
„
Primary Structure of a protein
R
R
H
H
O
C C N
C
C N C C N C
H O
R
e.g. Ala-Gly-Val-Ser-Glu-Val-His-
H H O
H H
R
The primary structure can fold
into a pleated sheet, or turn into a helix
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69
70
Objective 23c
Objective 23c
2) Secondary structure is the regular,
repeated pattern of coiling or folding
that occurs in certain areas of the
polypeptide chain.
¾ the two most common patterns are the
β-pleated sheet and the α-helix
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Secondary Structure
β-pleated sheet
71
Secondary Structure
α-helix
72
12
Objective 23c
Objective 23c
3) Tertiary structure – the final overall
shape of a protein. Proteins can be
classified into 2 basic shapes:
¾ Globular – compact, round shape;
these proteins are soluble in H2O
¾ Fibrous – thin, threadlike shape;
these proteins are insoluble in H2O
Tertiary Structure
73
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Objective 23c
Objective 23c
4) Quaternary structure – the way the
different polypeptide chains of a
protein fit together. Only present in
proteins composed of more than
one polypeptide chain.
Quaternary Structure
75
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R
C
H
O
H
H
O
N
C
C
R
R
N
C
C
H
H
O
H
H
N
C
R
Four Levels of
Protein Structure
„ The
way a polypeptide coils and folds
is determined by a variety of chemical
interactions. The stability of these
interactions is affected by
environmental conditions such
temperature and pH.
„ In addition, cells have chaperone
proteins, which help the polypeptides
fold correctly.
The primary structure can fold
into a pleated sheet, or turn into a helix
Secondary Structure
Secondary Structure
β-pleated sheet
Tertiary Structure
α-helix
Quaternary Structure
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76
Objective 23c
Primary Structure
C
74
77
78
13
Objective 23c
Interactions that Contribute to a Protein’s Shape
Objective 23c
Interactions that Contribute to a Protein’s Shape
79
Objective 23c
Interactions that Contribute to a Protein’s Shape
80
Objective 23c
Interactions that Contribute to a Protein’s Shape
81
82
Objective 23c
Interactions that Contribute to a Protein’s Shape
Objective 23c
„ If
a protein’s environment is altered,
the protein may change its shape or
even unfold completely. This process
is called denaturation.
„ When proteins are denatured, they are
usually rendered biologically inactive.
83
84
14
Objective 23d
„ Nucleotide-
based compounds are
composed of subunits called nucleotides.
„A
nucleotide consists of 3 parts:
¾ Pentose (5 C) sugar – ribose/deoxyribose
¾ Nitrogenous base attached to 1′ C
¾ Phosphate group (-PO4) attached to 5′ C
85
Phosphate group
O
–O
P
O–
Objective 23d
Nitrogenous base
NH2
6
7N 5
N1
8
2
9 N 4 N3
Structure of a
Nucleotide
„ There
have a double ring structure and
include adenine (A) and guanine (G).
O
¾ Pyrimidines
have a single ring structure
and include cytosine (C), thymine (T),
and uracil (U).
1’
3’
2’
OH
OH in RNA
R
Sugar
H in DNA
87
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88
Objective 23d
Nitrogenous Bases
„ We
will examine 3 groups of
nucleotide-based compounds:
¾Adenosine phosphates
¾Nucleotide coenzymes
¾Nucleic acids
Pyrimidines
Purines
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H C
NH2
N C C N
N C N C H
H
Adenine
H C
H C
NH2
C
N
N
C O
H
Cytosine
(both DNA and RNA)
H C
O
N C C N H
N C N C NH2
H
Guanine
O
H3C C
H C
C
N
O
N H
H C
C O
H C
H
Thymine
(DNA only)
are 2 types of nitrogenous bases:
¾ Purines
O CH2
5’
4’
86
C
N
N H
C O
H
Uracil
(RNA only)
89
90
15
Objective 23d
Nitrogenous base
(adenine)
ATP
„ Adenosine
phosphates:
¾ Ribose + Adenine = Adenosine
¾ Adenosine + 1 phosphate = AMP
(adenosine monophosphate)
¾ Adenosine + 2 phosphates = ADP
(adenosine diphosphate)
¾ Adenosine + 3 phosphates = ATP
(adenosine triphosphate)
7N 5
Triphosphate group
O
–O
P
O
O
O
O–
P
O
P
O–
NH2
6
N1
8
5’
O CH2
9N
4
N
2
3
O–
O
1’
4’
3’
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2’
OH OH
Ribose
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Objective 23d
Objective 23d
„ Nucleotide
coenzymes:
¾ consist of 2 nucleotides joined by
condensation
e.g. NAD+, FAD, NADP+
¾ function as electron carriers. They
transport e- and H+ within the cell
for use in chemical reactions.
„ cAMP
plays an important role as a
second messenger.
„ ATP is called the “energy currency” of
the cell. The energy stored in the bond
that connects the third phosphate to
the rest of the molecule supplies the
energy needed for most cell activities.
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Objective 23d
Nicotinamide Adenine Dinucleotide
H
„ Nucleic
O
C
O
O
P
NH2 + 2H
O
O
OH
P
O
O–
CH2
N
O
O
H
H
H
OH
„ The
P
O
O–
NH2
OH
NAD+: Oxidized form of nicotinamide
N
H
N
CH2
O
N
Adenine
H
„ The
H
H
OH
OH
nucleotides in RNA contain the
sugar ribose and the bases A, G, C, U.
H
H
N
N
N
Adenine
O
OH
H
CH2
NH2 + 2H
acids (RNA and DNA) are
polynucleotides.
N
O–
O
NH2
OH
N
O
P
H
H
O
O
C
O
O–
H
Oxidation
;
N
CH2
H
Reduction
OH
NADH: Reduced form of nicotinamide
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95
nucleotides in DNA contain the
sugar deoxyribose and the bases A, G,
C, T.
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Objective 23d
5’ end
„ RNA:
RNA
P
of a single, unbranched
chain of RNA nucleotides.
¾ plays several important roles
during the process of protein
synthesis.
Phosphate group
O
¾ consists
Phosphodiester
bonds
P
O
P
5-carbon sugar (ribose)
P
O
OH
3’ end
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Objective 23d
O
Nitrogenous base
(A,C,G or U)
98
DNA
„ DNA:
of 2 unbranched chains of DNA
nucleotides twisted into a double helix.
¾ the 2 chains are held together by H
bonds between the nitogenous bases.
¾ A always pairs with T, and G with C.
¾ functions as the heredity information in
all living organisms.
Sugar-phosphate "backbone"
¾ consists
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101
P
C
Hydrogen bonds between
nitrogenous bases
P
G
C
P
P
G
P
A
P
T
P
G
C
P
T
Phosphodiester
bond
A
P
P
OH
3’ end
5’ end
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100
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17
DNA
P
P
T T
A P
G
C
G
A
P
P
Deoxyribose-phosphate
backbone
P
P
T
Bases P
P
Hydrogen bonding
occurs between base-pairs
RNA
P
AP G
C
T
P
P
P
P
Ribose-phosphate
backbone
P
P
P
P
P
A
C
C
A
G
U
A
Bases
DNA vs. RNA
U P
P
G
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