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Biochemistry. The Structure and Function of Macromolecules. Carbon—Backbone of Biological Molecules. Although cells are 70–95% water, the rest consists mostly of carbon-based compounds Carbon is unique in its ability to form large, complex, and diverse molecules

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biochemistry

Biochemistry

The Structure and Function of Macromolecules

carbon backbone of biological molecules
Carbon—Backbone of Biological Molecules
  • Although cells are 70–95% water, the rest consists mostly of carbon-based compounds
  • Carbon is unique in its ability to form large, complex, and diverse molecules
  • Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds
organic chemistry the study of carbon compounds
Organic chemistry-the study of carbon compounds
  • Organic compounds range from simple molecules to colossal ones
  • Most organic compounds contain hydrogen atoms in addition to carbon atoms
  • With four valence electrons, carbon can form four covalent bonds with a variety of atoms
  • Needs 4 electrons - single, double or triple bonds
  • This tetravalence makes large, complex molecules possible - can form long chains or rings
carbon molecules

Space-Filling

Model

Molecular

Formula

Structural

Formula

Ball-and-Stick

Model

Methane

Ethane

Ethene (ethylene)

Carbon Molecules
  • In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape
  • However, when two carbon atoms are joined by a double bond, the molecule has a flat shape
carbon molecules5

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)

Carbon Molecules
  • The electron configuration of carbon gives it covalent compatibility with many different elements
  • The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules
carbon skeleton diversity

Propane

Ethane

Length

2-methylpropane

(commonly called isobutane)

Butane

Branching

1-Butene

2-Butene

Double bonds

Cyclohexane

Benzene

Rings

Carbon Skeleton Diversity
  • Carbon is a versatile atom
  • Carbon can use its bonds to form an endless diversity of carbon skeletons
  • Carbon chains form the skeletons of most organic molecules
hydrocarbons
Hydrocarbons
  • Hydrocarbons are organic molecules consisting of only carbon and hydrogen
  • Many organic molecules, such as fats, have hydrocarbon components
  • Hydrocarbons can undergo reactions that release a large amount of energy
isomers

Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane.

cis isomer: The two Xs

are on the same side.

trans isomer: The two Xs

are on opposite sides.

Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon.

L isomer

D isomer

Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other.

Isomers
  • Isomers are compounds with the same molecular formula but different structures and properties:
    • Structural isomers have different covalent arrangements of their atoms
    • Geometric isomers have the same covalent arrangements but differ in spatial arrangements
    • Enantiomers are isomers that are mirror images of each other
enantiomers

L-Dopa

(effective against

Parkinson’s disease)

D-Dopa

(biologically

Inactive)

Enantiomers
  • Enantiomers are important in the pharmaceutical industry
  • Two enantiomers of a drug may have different effects
  • Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules
functional groups
Functional Groups
  • Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it
  • Certain groups of atoms called functional groups are often attached to skeletons of organic molecules
  • Functional groups are the parts of molecules involved in chemical reactions
  • The number and arrangement of functional groups give each molecule its unique properties
functional groups11
Functional Groups
  • The six functional groups that are most important in the chemistry of life:
    • Hydroxyl group
    • Carbonyl group
    • Carboxyl group
    • Amino group
    • Sulfhydryl group
    • Phosphate group
slide12

STRUCTURE

(may be written HO—)

Ethanol, the alcohol present in

alcoholic beverages

NAME OF COMPOUNDS

FUNCTIONAL PROPERTIES

Is polar as a result of the

electronegative oxygen atom

drawing electrons toward itself.

Alcohols (their specific names

usually end in -ol)

Attracts water molecules, helping

dissolve organic compounds such

as sugars (see Figure 5.3).

slide13

Acetone, the simplest ketone

EXAMPLE

STRUCTURE

Acetone, the simplest ketone

Propanal, an aldehyde

NAME OF COMPOUNDS

Ketones if the carbonyl group is

within a carbon skeleton

FUNCTIONAL PROPERTIES

Aldehydes if the carbonyl group is

at the end of the carbon skeleton

A ketone and an aldehyde may

be structural isomers with

different properties, as is the case

for acetone and propanal.

slide14

EXAMPLE

STRUCTURE

Acetic acid, which gives vinegar

its sour taste

NAME OF COMPOUNDS

FUNCTIONAL PROPERTIES

Carboxylic acids, or organic acids

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,

Acetic acid

Acetate ion

In cells, found in the ionic form,

which is called a carboxylate group.

slide15

EXAMPLE

STRUCTURE

Glycine

Because it also has a carboxyl

group, glycine is both an amine and

a carboxylic acid; compounds with

both groups are called amino acids.

FUNCTIONAL PROPERTIES

NAME OF COMPOUNDS

Acts as a base; can pick up a

proton from the surrounding

solution:

Amine

(nonionized)

(ionized)

Ionized, with a charge of 1+,

under cellular conditions

slide16

EXAMPLE

STRUCTURE

(may be written HS—)

Ethanethiol

NAME OF COMPOUNDS

FUNCTIONAL PROPERTIES

Two sulfhydryl groups can

interact to help stabilize protein

structure (see Figure 5.20).

Thiols

slide17

EXAMPLE

STRUCTURE

Glycerol phosphate

NAME OF COMPOUNDS

FUNCTIONAL PROPERTIES

Makes the molecule of which it

is a part an anion (negatively

charged ion).

Organic phosphates

Can transfer energy between

organic molecules.

biochemistry the molecules of life
Biochemistry: The Molecules of Life
  • Within cells, small organic molecules are joined together to form larger molecules
  • Macromolecules are large molecules composed of thousands of covalently connected atoms
biochemistry19
Biochemistry
  • Living organisms are composed of both inorganic and organic molecules
  • Inorganic molecules
    • Relatively small, simple molecules that usually lack C (a few have one C atom).
    • Examples: CO2, NH3, H2O, O2, H2
  • Organic molecules
    • Larger, more complex, based on a backbone of C atoms (always contain C as a major part of their structure).
    • Examples: C6H12O6, C2H5COOH
macromolecules polymers
Macromolecules - Polymers
  • A polymer is a long molecule consisting of many similar building blocks called monomers
  • Most macromolecules are polymers, built from monomers
  • An immense variety of polymers can be built from a small set of monomers
  • Three of the four classes of life’s organic molecules are polymers:
    • Carbohydrates
    • Proteins
    • Nucleic acids
polymers
Polymers
  • Monomers form larger molecules by condensation reactions called dehydration reactions
  • Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction

Short polymer

Unlinked monomer

Dehydration removes a water

molecule, forming a new bond

Longer polymer

Dehydration reaction in the synthesis of a polymer

Hydrolysis adds a water

molecule, breaking a bond

Hydrolysis of a polymer

carbohydrates
Carbohydrates
  • Carbohydrates serve as fuel and building material
  • They include sugars and the polymers of sugars
  • The simplest carbohydrates are monosaccharides, or single (simple) sugars
  • Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks
sugars
Sugars
  • Monosaccharides have molecular formulas that contain C, H, and O in an approximate ratio of 1:2:1
  • Monosaccharides are used for short term energy storage, and serve as structural components of larger organic molecules
  • Glucose is the most common monosaccharide
monosaccharides
Monosaccharides
  • Monosaccharides are classified by location of the carbonyl group and by number of carbons in the carbon skeleton
  • 3 C = triose e.g. glyceraldehyde
  • 4 C = tetrose
  • 5 C = pentose e.g. ribose, deoxyribose
  • 6 C = hexose e.g. glucose, fructose, galactose
  • Monosaccharides in living organisms generally have 3C, 5C, or 6C:
slide25

Triose sugars

(C3H6O3)

Pentosesugars

(C5H10O5)

Hexose sugars

(C5H12O6)

Aldoses

Glyceraldehyde

Ribose

Galactose

Glucose

Ketoses

Dihydroxyacetone

Ribulose

Fructose

monosaccharides26

Glucose

Fructose

Monosaccharides
  • Monosaccharides serve as a major fuel for cells and as raw material for building molecules
  • The monosaccharides glucose and fructose are isomers
    • They have the same chemical formula
    • Their atoms are arranged differently
  • Though often drawn as a linear skeleton, in aqueous solutions they form rings
monosaccharides27
Monosaccharides
  • In aqueous solutions, monosaccharides form rings

Linear and

ring forms

Abbreviated ring

structure

slide29

Triose

(3-carbon sugar)

Pentoses

(5-carbon sugars)

H

O

C

CH2OH

5

CH2OH

5

1

O

O

OH

OH

C

OH

H

2

1

4

4

1

H

H

H

H

OH

H

C

H

H

H

H

3

3

2

2

3

H

H

OH

OH

OH

Glyceraldehyde

Ribose

Deoxyribose

29

disaccharides

Dehydration

reaction in the

synthesis of maltose

1–4

glycosidic

linkage

Glucose

Glucose

Maltose

Dehydration

reaction in the

synthesis of sucrose

1–2

glycosidic

linkage

Sucrose

Fructose

Glucose

Disaccharides
  • A disaccharide is formed when a dehydration reaction joins two monosaccharides
  • Disaccharides are joined by the process of dehydration synthesis
  • This covalent bond is called a glycosidic linkage
disaccharides31
Disaccharides
  • Lactose = Glucose + Galactose
  • Maltose = Glucose + Glucose
  • Sucrose = Glucose + Fructose
  • The most common disaccharide is sucrose, common table sugar
  • Sucrose is extracted from sugar cane and the roots of sugar beets
polysaccharides
Polysaccharides
  • Complex carbohydrates are called polysaccharides
  • They are polymers of monosaccharides - long chains of simple sugar units
  • Polysaccharides have storage and structural roles
  • The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages

(a) Starch

(b) Glycogen

(c) Cellulose

storage polysaccharides starch

Chloroplast

Starch

1 µm

Amylose

Amylopectin

Starch: a plant polysaccharide

Storage Polysaccharides - Starch
  • Starch, a storage polysaccharide of plants, consists entirely of glucose monomers
  • Plants store surplus starch as granules within chloroplasts and other plastids
storage polysaccharides glycogen

Glycogen granules

Mitochondria

0.5 µm

Glycogen

Glycogen: an animal polysaccharide

Storage Polysaccharides - Glycogen
  • Glycogen is a storage polysaccharide in animals
  • Humans and other vertebrates store glycogen mainly in liver and muscle cells
structural polysaccharides

a Glucose

b Glucose

a and b glucose ring structures

Starch: 1–4 linkage of a glucose monomers.

Cellulose: 1–4 linkage of b glucose monomers.

Structural Polysaccharides
  • Cellulose is a major component of the tough wall of plant cells
  • Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ
  • The difference is based on two ring forms for glucose: alpha () and beta ()
    • Polymers with alpha glucose are helical
    • Polymers with beta glucose are straight
cellulose

Cellulose microfibrils

in a plant cell wall

Cell walls

Microfibril

0.5 µm

Plant cells

Cellulose

molecules

b Glucose

monomer

Cellulose
  • Enzymes that digest starch by hydrolyzing alpha linkages can’t hydrolyze beta linkages in cellulose
  • Cellulose in human food passes through the digestive tract as insoluble fiber
  • Some microbes use enzymes to digest cellulose
  • Many herbivores, from cows to termites, have symbiotic relationships with these microbes
chitin
Chitin
  • Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods
  • Chitin also provides structural support for the cell walls of many fungi
  • Chitin can be used as surgical thread
lipids
Lipids
  • Lipids are the one class of large biological molecules that do not form polymers
  • Utilized for energy storage, membranes, insulation, protection
  • Greasy or oily substances
  • The unifying feature of lipids is having little or no affinity for water - insoluble in water
  • Lipids are hydrophobic becausethey consist mostly of hydrocarbons, which form nonpolar covalent bonds
slide39

Fatty acid

(palmitic acid)

Glycerol

Dehydration reaction in the synthesis of a fat

Fats
  • The most biologically important lipids are fats, phospholipids, and steroids
  • Fats are constructed from two types of smaller molecules: glycerol and fatty acids
  • Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon
  • A fatty acid consists of a carboxyl group attached to a long carbon skeleton
fatty acids

Stearate

Oleate

Fatty Acids
  • A fatty acid has a long hydrocarbon chain with a carboxyl group at one end.
  • Fatty acids vary in length (number of carbons) and in the number and locations of double bonds
  • Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds
  • Unsaturated fatty acids have one or more double bonds,
    • Monounsaturated (one double bond)
    • Polyunsaturated (more than one double bond)
  • H can be added to unsaturated fatty acids using a process called hydrogenation
  • The major function of fats is energy storage
slide41

Ester linkage

Fat molecule (triacylglycerol)

Fats
  • Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats
  • In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride
glycerides
Glycerides
  • Glycerol + 1 fatty acid = monoglyceride
  • Glycerol + 2 fatty acids = diglyceride
  • Glycerol + 3 fatty acids = triacylglycerol (also called a triglyceride or fat.)
saturated fats

Stearic acid

Saturated fat and fatty acid.

Saturated Fats
  • Fats made from saturated fatty acids are called saturated fats
  • Most animal fats are saturated
  • Saturated fats are solid at room temperature
  • A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits
unsaturated fats

Oleic acid

cis double bond

causes bending

Unsaturated fat and fatty acid.

Unsaturated Fats
  • Fats made from unsaturated fatty acids are called unsaturated fats
  • Plant fats and fish fats are usually unsaturated
  • Plant fats and fish fats are liquid at room temperature and are called oils
fat sources
Fat Sources
  • Most animal fats contain saturated fatty acids and tend to be solid at room temperature
  • Most plant fats contain unsaturated fatty acids. They tend to be liquid at room temperature, and are called oils.
phospholipids

Choline

Hydrophilic head

Phosphate

Glycerol

Hydrophobic tails

Fatty acids

Hydrophilic

head

Hydrophobic

tails

Space-filling model

Structural formula

Phospholipid symbol

Phospholipids
  • In 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).
phospholipids49

Water

Lipid head

(hydrophilic)

Lipid tail

(hydrophobic)

Micelle

Water

Water

Phospholipid bilayer

Phospholipids
  • When phospholipids are added to water, they orient so that the nonpolar tails are shielded from contact with the polar H2O may form micelles
  • Phosopholipids also may self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior
phospholipids50

WATER

Hydrophilic

head

Hydrophobic

tails

WATER

Phospholipids
  • The structure of phospholipids results in a bilayer arrangement found in cell membranes
  • Phospholipids are the major component of all cell membranes
steroids
Steroids
  • Steroids are lipids characterized by a carbon skeleton consisting of four fused rings
  • Cholesterol, an important steroid, is a component in animal cell membranes
  • Testosterone and estrogen function as sex hormones
proteins
Proteins
  • Proteins have many structures, resulting in a wide range of functions
  • They account for more than 50% of the dry mass of most cells
  • Protein functions
    • Structural support / storage / movement - fibers
    • Catalysis - Enzymes
    • Defense against foreign substances– Immunoglobulins
    • Transport – globins, membrane transporters
    • Messengers for cellular communications - hormones
proteins55
Proteins
  • A protein is composed of one or more polypeptides that performs a function
  • A polypeptide is a polymer of amino acids joined by peptide bonds to form a long chain
  • Polypeptides range in length from a few monomers to more than a thousand
  • Each polypeptide has a unique linear sequence of amino acids
  • A protein consists of one or more polypeptides which are coiled and folded into a specific 3-D shape.
  • The shape of a protein determines its function.
amino acids

a carbon

Carboxyl

group

Amino

group

Amino Acids
  • Amino acids are monomers of polypetides
  • They composed of a carboxyl group, amino group, and an “R”Group
  • Amino acids differ in their properties due to differing side chains, called R groups
  • Cells use 20 amino acids to make thousands of proteins
amino acids58

CH3

CH3

CH3

CH

CH2

CH3

CH3

H

CH3

H3C

CH3

CH2

CH

O

O

O

O

O

H3N+

C

H3N+

C

H3N+

H3N+

C

C

C

C

C

C

H3N+

C

C

O–

O–

O–

O–

O–

H

H

H

H

H

Valine (Val)

Leucine (Leu)

Isoleucine (Ile)

Glycine (Gly)

Alanine (Ala)

Nonpolar

CH3

CH2

S

H2C

CH2

O

NH

CH2

C

C

H2N

CH2

CH2

O–

CH2

O

O

O

H

H3N+

H3N+

C

C

C

C

H3N+

C

C

O–

O–

O–

H

H

H

Phenylalanine (Phe)

Proline (Pro)

Methionine (Met)

Tryptophan (Trp)

Figure 5.17

Amino Acids
amino acids59

OH

NH2

O

C

NH2

O

C

OH

SH

CH2

CH3

OH

Polar

CH2

CH

CH2

CH2

CH2

CH2

O

O

O

O

O

O

H3N+

C

H3N+

C

H3N+

C

C

H3N+

C

C

H3N+

C

C

C

C

C

H3N+

C

O–

O–

O–

O–

O–

O–

H

H

H

H

H

H

Glutamine

(Gln)

Tyrosine

(Tyr)

Asparagine

(Asn)

Cysteine

(Cys)

Serine (Ser)

Threonine (Thr)

Basic

Acidic

NH3+

NH2

NH+

O–

O

–O

O

CH2

C

NH2+

C

C

NH

Electrically

charged

CH2

CH2

CH2

CH2

CH2

O

O

CH2

CH2

C

CH2

C

H3N+

C

H3N+

C

O

O–

O–

CH2

C

H3N+

CH2

C

H

O

H

O–

C

C

H3N+

CH2

H

O

O–

C

C

H3N+

H

O–

H

Lysine (Lys)

Histidine (His)

Arginine (Arg)

Glutamic acid

(Glu)

Aspartic acid

(Asp)

Amino Acids
amino acids and peptide bonds
Amino Acids and Peptide Bonds
  • Two amino acids can join by condensation to form a dipeptide plus H2O.
  • The bond between 2 amino acids is called a peptide bond.
protein conformation and function

Groove

A ribbon model

Groove

A space-filling model

Protein Conformation and Function
  • A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape
  • The sequence of amino acids determines a protein’s three-dimensional conformation
  • A protein’s conformation determines its function
  • Ribbon models and space-filling models can depict a protein’s conformation
four levels of protein structure

b pleated sheet

Amino acid

subunits

 helix

Four Levels of Protein Structure
  • The primary structure of a protein is its unique sequence of amino acids
  • Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain
  • Tertiary structure is determined by interactions among various side chains (R groups)
  • Quaternary structure results when a protein consists of multiple polypeptide chains
primary structure

Amino end

Amino acid

subunits

Carboxyl end

Primary Structure
  • Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word
  • Primary structure is determined by inherited genetic information
secondary structure

b pleated sheet

Amino acid

subunits

 helix

Secondary Structure
  • The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone
  • Typical secondary structures are a coil called an alpha helix and a folded structure called a beta pleated sheet
tertiary structure

Hydrophobic

interactions and

van der Waals

interactions

Polypeptide

backbone

Hydrogen

bond

Disulfide bridge

Ionic bond

Tertiary Structure
  • Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents
  • These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions
  • Strong covalent bonds called disulfide bridges may reinforce the protein’s conformation
quaternary structure

b Chains

Polypeptide

chain

Iron

Heme

a Chains

Hemoglobin

Polypeptide chain

Collagen

Quaternary Structure
  • Quaternary structure results when two or more polypeptide chains form one macromolecule
  • Collagen is a fibrous protein consisting of three polypeptides coiled like a rope
  • Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains
sickle cell disease a simple change in primary structure

10 µm

10 µm

Red blood

cell shape

Fibers of abnormal

hemoglobin deform

cell into sickle

shape.

Red blood

cell shape

Normal cells are

full of individual

hemoglobin

molecules, each

carrying oxygen.

Sickle-Cell Disease: A Simple Change in Primary Structure
  • A slight change in primary structure can affect a protein’s conformation and ability to function
  • Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin
sickle cell anemia

Sickle-cell hemoglobin

Normal hemoglobin

Primary

structure

Primary

structure

Val

Val

His

His

Thr

Pro

Glu

Glu

Thr

Pro

Val

Glu

Leu

Leu

1

1

2

4

6

2

4

6

7

7

3

5

3

5

Exposed

hydrophobic

region

Secondary

and tertiary

structures

Secondary

and tertiary

structures

b subunit

b subunit

a

a

Quaternary

structure

Sickle-cell

hemoglobin

Normal

hemoglobin

(top view)

Quaternary

structure

a

a

Function

Molecules do

not associate

with one

another; each

carries oxygen.

Molecules

interact with

one another to

crystallize into

a fiber; capacity

to carry oxygen

is greatly reduced.

Function

Sickle Cell Anemia

conformation

Denaturation

Normal protein

Denatured protein

Renaturation

Conformation
  • In addition to primary structure, physical and chemical conditions can affect conformation
  • Alternations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel
  • This loss of a protein’s native conformation is called denaturation
  • A denatured protein is biologically inactive
nucleic acids
Nucleic Acids
  • Nucleic acids store and transmit hereditary information
  • The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene
  • Genes are made of DNA, a nucleic acid
the roles of nucleic acids
The Roles of Nucleic Acids
  • There are two types of nucleic acids:
    • Deoxyribonucleic acid (DNA)
    • Ribonucleic acid (RNA)
  • DNA provides directions for its own replication
  • DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis
  • Protein synthesis occurs in ribosomes
slide75

DNA

Synthesis of

mRNA in the nucleus

mRNA

NUCLEUS

CYTOPLASM

mRNA

Movement of

mRNA into cytoplasm

via nuclear pore

Ribosome

Synthesis

of protein

Amino

acids

Polypeptide

the structure of nucleic acids
The Structure of Nucleic Acids
  • Nucleic acids are polymers called polynucleotides
  • Each polynucleotide is made of monomers called nucleotides
  • Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group
  • The portion of a nucleotide without the phosphate group is called a nucleoside
slide77

5¢ end

Nucleoside

Nitrogenous

base

Phosphate

group

Pentose

sugar

Nucleotide

3¢ end

Polynucleotide, or

nucleic acid

slide78

Nitrogenous base

NH2

6

7

N

5

N

1

8

Phosphate group

2

9

N

4

N

O

3

O

P

O

CH2

5’

O

O

4’

1’

3’

2’

OH in RNA

OH

R

H in DNA

Sugar

nucleotide monomers

Nitrogenous bases

Pyrimidines

Uracil (in RNA)

U

Cytosine

C

Thymine (in DNA)

T

Purines

Guanine

G

Adenine

A

Pentose sugars

Deoxyribose (in DNA)

Ribose (in RNA)

Nucleoside components

Nucleotide Monomers
  • Nucleotide monomers are made up of nucleosides and phosphate groups
  • Nucleoside = nitrogenous base + sugar
  • There are two families of nitrogenous bases:
    • Pyrimidines have a single six-membered ring
    • Purines have a six-membered ring fused to a five-membered ring
  • In DNA, the sugar is deoxyribose
  • In RNA, the sugar is ribose
nitrogenous bases

NH2

NH2

Adenine

Cytosine

(both DNA

and RNA)

N

C

C

C

C

H

N

N

P

Y

R

I

M

I

D

I

N

E

S

H

C

P

U

R

I

N

E

S

C

C

H

O

H

C

C

N

N

N

H

H

O

O

Guanine

Thymine

(DNA only)

N

C

C

C

N

H

N

H

C

H3C

H

C

C

NH2

N

C

H

C

O

C

N

N

H

H

Uracil

(RNA only)

O

C

N

C

H

H

H

C

O

C

N

H

Nitrogenous bases
  • Purines have a double ring structure and include adenine (A) and guanine (G).
  • Pyrimidines have a single ring structure and include cytosine (C), thymine (T), and uracil (U) – found only in RNA
nucleotide polymers
Nucleotide Polymers
  • Nucleotide polymers are linked together, building a polynucleotide
  • Adjacent nucleotides are joined by covalent bonds that form between the –OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next
  • These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages
  • The sequence of bases along a DNA or mRNA polymer is unique for each gene
the dna double helix

5¢ end

3¢ end

Sugar-phosphate

backbone

Base pair (joined by

hydrogen bonding)

Old strands

Nucleotide

about to be

added to a

new strand

5¢ end

New

strands

5¢ end

3¢ end

5¢ end

3¢ end

The DNA Double Helix
  • A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix
  • In the DNA double helix, the two backbones run in opposite 5´ to 3´ directions from each other, an arrangement referred to as antiparallel
  • One DNA molecule includes many genes
  • The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion: A always with T, and G always with C
slide84
ATP
  • Adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell
  • ATP is the “energy currency” of the cell
  • ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups
  • 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