module 1d – biochemistry fatty acid has a long hydrocarbon chain with a carboxyl group at one end....

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Module 1D – Biochemistry

Biochemistry is the chemistry of living organisms.

In this module we will focus on the structure, function, and properties of the various organic molecules that make up living organisms.

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Objective # 18

Distinguish between organic and inorganic molecules.

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Objective 18

Inorganic molecules:Relatively small, simple molecules that usually lack C (a few have one C atom).Examples: H2O, CO2, NH3, O2, H2

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Η

ΗCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 4

Objective 18

Organic molecules:Larger, more complex molecules whose structure is based on a backbone of C atoms (always contain C as a major part of their structure).Examples: C6H12O6, C2H5COOH

Living organisms are composed of both inorganic and organic molecules.

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Objective # 19

Identify the characteristics of carbon that allow it to play such an important role in the chemistry of life.

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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.

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Objective 19

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.

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Objective # 20

Explain what isomers are.

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Objective 20

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.

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Structuralisomer

Stereo-isomer

Fructose Glucose Galactose

H OH

O

C

C

C

C

C

C

H

H

HO H

H OH

H OH

H OH

H

OC

C

C

C

C

H

H

HO H

OH

H OH

H OH

OC

C

C

C

C

C

H

H

H

HO H

OH

H OH

H OH

CH OH HO H

Isomers of C6H12O6

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

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Objective # 21

Explain what a functional group is, and be able to identify the structure and characteristics of each of the following functional groups:

a) hydroxylb) carboxylc) amined) methyle) phosphate

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Objective 21

A functional group is a small group of atoms that is part of a larger molecule and gives it specific properties.

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FunctionalGroup

StructuralFormula Example

FoundIn

Hydroxyl

Carbonyl

Carboxyl

O

OH

C

C

O

Ethanol

C

H

H

CH

H

H

OH

Acetic acid

CH

H

H

C

O

OH

Acetaldehyde

CH

H

H

HC

O

carbo-hydrates,proteins,nucleicacids,lipids

carbo-hydrates,nucleicacids

proteins,lipids

OH

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 14

Amino

Sulfhydryl

Phosphate

Methyl

HS

O–P

O–

O

O

HC

H

H

H

HN

Alanine

C

H

CH3

CHO

O

NH

H

Cysteine

Glycerol phosphate

CH

OH

H

C

OH

H H

OC

H

O–

O–

P

O

proteins,nucleicacids

proteins

nucleicacids

proteins

CH

NH2

S HCH2

C

H

C

CHO NH2

HH

Alanine

COOH

HO


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Objective # 22

Define the following terms and be able to give or recognize examples of each:

a) Monomer, dimer, polymerb) Condensation reaction (or

dehydration synthesis)c) Hydrolysis reaction

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Objective 22a

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.

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Objective 22a

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.

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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:

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Condensation or Dehydration Synthesis


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Objective 22c

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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Hydrolysis


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Objective # 23

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) Lipidsc) Proteinsd) Nucleotide-based compounds

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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.

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Objective 23a

Monosaccharides are classified according to the number of C atoms they contain:3 C = triose e.g. glyceraldehyde4 C = tetrose5 C = pentose e.g. ribose, deoxyribose6 C = hexose e.g. glucose, fructose, galactoseMonosaccharides in living organisms generally have 3C, 5C, or 6C:

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Triose(3-carbon sugar)

Pentoses(5-carbon sugars)

Glyceraldehyde

3-carbon Sugar 5-carbon Sugars

C

C

C

H

H OH

OH

H OH

Ribose

CH2OH

HH H H

OH OH

OHO

Deoxyribose

CH2OH

HH H H

OH H

OHO1

3

2 4

5

1

3 2

4

5

1

3 2


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GalactoseFructoseGlucose

Hexoses (6-carbon Sugars)

H

CH2OH

OH

OH

OH

OHH

HH

H

O

HO

CH2OH

H

OH

H

OHOH

HH

H

O

CH2OH

HOH CH2OH

OH H

HO

OH 4

5

6

1

3 2

4

5

6

1

3 2 4

5

6

13

2


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Objective 23a

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:

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H

CH2OH

H

OH

OH HH

H

C

CC

C

C O

C

C

H

C H

HO

OHH

OHH C

OHH C

OHH C

H

OH

C HH

OH

H

OH

H

OH

H

OH

H

OH HH

H

CCC

C

C O

CH2OH

OH

OH HH

H

C

CC

COC

OH

OH

OH

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5

14

6

5

4

3

2

1

23

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14

23

5

14

α-glucose

or

β-glucose

O

Chain and Ring Forms of Glucose


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Objective 23a

Two monosaccharides can be joined by condensation to form a disaccharide plus H2O.

Many organisms transport sugar within their bodies in the form of disaccharides.

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Fructose and α-glucose can be joined by a condensation reaction to produce the disaccharide sucrose:

OH

H2OSucroseFructoseα-glucose

HO

CH2OH

H

OH

H

OHH

H

H

O

CH2OH

H CH2OH

OH H

HO

HO

CH2OH

H

OH

H

OH OHH

H

OCH2OH

H OHCH2OH

OH H

HO

+

a.

OHHO


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Two α-glucose molecules can be joined by a condensation reaction to produce the disaccharide maltose:

Maltose

HO

CH2OH

H

OH

HOH OHH

H

OCH2OH

H

OH

HOH

OHH

H

H

O


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Galactose and α-glucose can be joined by a condensation reaction to produce the disaccharide lactose:

Lactose

OH

OHH

H

HH H

OH

OH

OH

O

H

H

OH

HH

OH

O

GalactoseGlucose

CH2OHCH2OH


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Objective 23a

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.

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Objective 23a

Storage Polysaccharides:α-glucose subunits can be joined by α-1,4 linkages to form long unbranched chains

α-1,4 linkagesα-glucose

HO

CH2OH

H

OH

H

OH HH

H

OCH2OH

OH

H

OH H

H

OCH2OH

OH

H

OH H

H

OCH2OH

OH

H

OH H

H

O

OH4 1

O O

H


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Objective 23a

Branches can be added to the chain using α-1,6 linkages:

α-1,4 linkage

α-1,6 linkage

CH2OH

O

H

OH

HOH HH

H

O

CH2

H

OH

H

OH HH

H

O

O

CH2OHH

OH

H

OH HH

H

O


Objective 23aPlants use α-glucose to make starches,including amylose (coiled and unbranched) and amylopectin (coiled and branched):

Amylose + AmylopectinCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

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Objective 23aAnimals use α-glucose to make glycogenwhich is more extensively branched than amylopectin:

GlycogenCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 38

Objective 23a

Structural Polysaccharides:Cellulose is a long unbranched chain of β-glucose subunits. It is a major component of plant cell walls.

HO

CH2OH

H

OH

HOH HH

H

OCH2OH

H H

OH

HOH HH

H

O

O

CH2OH

H

OH

HOH HH

H

OOHH

HOH HH

CH2OHO

β-glucose β-1,4 linkages

OH O O

O4 1


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Objective 23a

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.

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Objective 23b

Lipids are structurally diverse molecules that are greasy and insoluble in H2O.We will examine 4 types of lipids:Fats and oilsPhospholipidsTerpenesSteroids

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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:

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Objective 23b

A fatty acid has a long hydrocarbon chain with a carboxyl group at one end.It 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).H can be added to unsaturated fatty acids using a process called hydrogenation.

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Fatty Acids:

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Objective 23b

Glycerol + 1 fatty acid = monoglycerideGlycerol + 2 fatty acids = diglycerideGlycerol + 3 fatty acids = triacylglycerol

(also called a triglyceride or fat.)

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Saturated fat


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Unsaturated fat


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Objective 23b

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.

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Objective 23b

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.

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Objective 23b

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).

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Pola

r Hyd

roph

ilic

Hea

dsN

onpo

larH

ydro

phob

icTa

ils

CH2

CH2

CH2H2C

O

O

O P

CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3

C

O O

OO

C

H

C

Choline

Phosphate

Glycerol

O–

N+(CH3)3

CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3

Fatty

acId

Fatty

acId

Phospholipid


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Objective 23b

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.

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Water

Lipid head(hydrophilic)

Lipid tail(hydrophobic)

Water

Water

Micelle

Phospholipid bilayer


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Objective 23b

Terpenes are long-chain lipids that are components of many important biological pigments such as chlorophyll.

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Objective 23b

Terpene (citronellol)

COH

CH2

CHCH2 CH2 CH2

CH2CH2

CH3 CH3


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Objective 23b

Steroids are lipids whose principle component is the steroid nucleus, a structure made of 4 interlocking rings of carbon atoms.

Examples:Cholesterol is a component of animal cell membranes.

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Objective 23b

Steroid (cholesterol)HO

CH3

CHH3C CH2

CHCH3 CH3

CH2 CH3

CH2


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Objective 23b

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:

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Objective 23cProteins perform many essential functions in living organisms:

globinsTransport through the body

transportersMembrane transport

antigensCell recognition

immunoglobulins, toxins

DefenseenzymesCatalysisClass of ProteinFunction

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Objective 23c

Class of ProteinFunction

Ion bindingStorage

hormonesMessengers

repressors, activatorsGene regulation

albuminOsmotic regulation

muscleMotion

fibersStructure/support

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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:

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Objective 23c

Proteins are composed of monomers called amino acids.An amino acid consists of a central carbon atom joined to 4 other groups:H atomAmino group (NH2)Carboxyl group (COOH)R group (varies)

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Three amino acids with the central carbon in red, the amino group in blue, and the R group shaded in white:

Tryptophan(Trp)

CH2

NHC

H OPhenylalanine

(Phe)

CH2

H O

Tyrosine(Tyr)

OH

CH2

H O

H3N+ CC O–H3N+ CC O–

H3N+ CC O–


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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.

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Amino acidAmino acid

Dipeptide

H C N

RH

H

R

H O

R

OH

H C OH

RH

OH

H2O

H

O

H N

H

N C

N C C C OH

C C OH


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Objective 23c

A polypeptide consists of many amino acids joined by peptide bonds to form a long unbranched chain:

N N NH

H

H

H

H H

HC C C C C C N C C N CCC

O

OO

O H H

OH H

R

R

R R

R R

Peptide bondCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

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Objective 23c

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.

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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

e.g. Ala-Gly-Val-Ser-Glu-Val-His-

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Objective 23c

The primary structure can foldinto a pleated sheet, or turn into a helix

Primary Structure of a protein

N

H

H H

C C C N C C N CC

O

O H H

OH H

R R

R R


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Objective 23c

2) Secondary structure is the regular, repeated pattern of coiling or folding that occurs in certain areas of the polypeptide chain.the two most common patterns are theβ-pleated sheet and the α-helix

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Objective 23c

β-pleated sheet α-helix

Secondary Structure Secondary StructureCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

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Objective 23c

3) Tertiary structure – the final overall shape of a protein. Proteins can be classified into 2 basic shapes:Globular – compact, round shape; these proteins are soluble in H2OFibrous – thin, threadlike shape; these proteins are insoluble in H2O

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Objective 23c

Tertiary Structure


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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.

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Objective 23c

Quaternary Structure


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Four Levels of Protein Structure

Tertiary Structure

β-pleated sheet α-helix

The primary structure can foldinto a pleated sheet, or turn into a helix

Primary Structure

Secondary Structure Secondary Structure

Quaternary Structure

N

H

H H

C C C N C C N CC

O

O H H

OH H

R R

R R


Objective 23c

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.

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Objective 23cInteractions that Contribute to a Protein’s Shape

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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.

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85 86

Objective 23d

Nucleotide- based compounds are composed of subunits called nucleotides.

A nucleotide consists of 3 parts:Pentose (5 C) sugar – ribose/deoxyriboseNitrogenous base attached to 1′ CPhosphate group (-PO4) attached to 5′ C

87Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Phosphate group

Sugar

Nitrogenous base

N

N

O

4’

5’

1’

3’ 2’

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7 6

39 4

5

P CH2

O–O

O–

OH ROH in RNA

H in DNA

O

N

NH2

N1

Structure of a Nucleotide

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Objective 23d

There are 2 types of 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).

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Nitrogenous Bases

Adenine Guanine

NH2CCNN

N

C

HN

CCH

O

H

H

Cytosine(both DNA and RNA)

Thymine(DNA only)

Uracil(RNA only)

OCNC

HN

CNH2

HCH

Purin

esPy

rimid

ines

O

O

CNC

HN

CH3CCH

HO

O

CNC

HN

CHCH

NH2

CCNN

N

C

HN

CCH

H


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Objective 23d

We will examine 3 groups of nucleotide-based compounds:Adenosine phosphatesNucleotide coenzymesNucleic acids

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91

Objective 23d

Adenosine phosphates:Ribose + Adenine = AdenosineAdenosine + 1 phosphate = AMP (adenosine monophosphate)Adenosine + 2 phosphates = ADP (adenosine diphosphate)Adenosine + 3 phosphates = ATP (adenosine triphosphate)

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4’

5’

56

1

239 4

8

7

1’

3’ 2’

Triphosphate group

Ribose

Nitrogenous base(adenine)

OP CH2

O

O

O–

P

O

O

O–

P

O–O

O–

OH OH

NH2

N

N

N

N

ATP

O


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Objective 23d

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

Nucleotide coenzymes:consist of 2 nucleotides joined by condensation e.g. NAD+, FAD, NADP+

function as electron carriers. They transport e- and H+ within the cell for use in chemical reactions.

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NAD+: Oxidized form of nicotinamide NADH: Reduced form of nicotinamide

H H

O Reduction

OxidationC

CH2O

O

O CH2

HH

NH2

Adenine

H

OH OH

O

H

OH OH

O

N

N

N

CH2O

O

O CH2

H

H

NH2

Adenine

H

OH OH

O

H

OH OH

O

NN

N

H H O

N

N;

H H

H

N N

O P O–

O P O–O P O–

NH2 + 2H C NH2 + 2H

O P O–

Nicotinamide Adenine Dinucleotide


Objective 23d

Nucleic acids (RNA and DNA) are polynucleotides.

The nucleotides in RNA contain the sugar ribose and the bases A, G, C, U.

The nucleotides in DNA contain the sugar deoxyribose and the bases A, G, C, T.

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97

Objective 23d

RNA:consists of a single, unbranchedchain of RNA nucleotides.plays several important roles during the process of protein synthesis.

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5’ end

3’ end

P

P

P

P

OH

5-carbon sugar (ribose)

Nitrogenous base(A,C,G or U)

Phosphate group

Phosphodiesterbonds

O

O

O

O

RNA

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Objective 23d

DNA:consists of 2 unbranched chains of DNA nucleotides twisted into a double helix.the 2 chains are held together by H bonds between the nitogenous bases.A always pairs with T, and G with C.functions as the heredity information in all living organisms.


Sugar-phosphate "backbone"Hydrogen bonds betweennitrogenous bases

Phosphodiesterbond

P

P

P

P

P

P

P

P

C

C

G

G

A

A

T

T

P

C G

3’ endOH

P

5’ end

DNA

101 102

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DNA Deoxyribose-phosphatebackbone

Bases

Hydrogen bondingoccurs between base-pairs

RNARibose-phosphate

backbone

Bases

G

CG

G

G

C

C

T

AA

AA

A

A

T

TT

GC

U

U

PP

P

P

PP

P

P

PPP

P

P

P

P

P

P

P

P

P

P

P

DNA vs. RNA

module 1d – biochemistry fatty acid has a long hydrocarbon chain with a carboxyl group at one end....

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