CHAPTER 3 LECTURE SLIDES

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CHAPTER 3

LECTURE

SLIDES

Prepared by

Brenda LeadyUniversity of Toledo

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2

Organic Chemistry

Organic molecules contain carbon

Abundant in living organisms

Macromolecules are large, complex

organic molecules

3

Carbon

Carbon has 4 electrons in its outer shell

Needs 4 more electrons to fill the shell

It can make up to 4 bonds

Usually single or double bonds

Carbon can form nonpolar and polar bonds

Molecules with nonpolar bonds (like

hydrocarbons) are poorly water soluble

Molecules with polar bonds are more water

soluble

4

–

–

–

–– –

Nucleus

(a) Orbitals

(b) Simplified depiction of energy shells

–

–

––

–– ++

+

+

+

+

Other energy orbitals

of second shell

contain 1 or 0

electrons

Spherical s

orbital of second

shell is filled with

2 electrons

First shell is filled

with 2 electrons


6

Functional Groups

Groups of atoms with special chemical

features that are functionally important

Each type of functional group exhibits the

same properties in all molecules in which it

occurs

9

Isomers

Two structures with an identical molecular formula but different structures and characteristics

Structural isomers- contain the same atoms but in different bonding relationships

Stereoisomers- identical bonding relationships, but the spatial positioning of the atoms differs in the two isomerscis-trans isomers- positioning around double bond

Enantiomers- mirror image of another molecule

10


Isopropyl alcohol Propyl alcohol

trans-butene

(b) Two types of stereoisomers

(a) Structural isomers

Molecule Mirror image

H C

H

H

C C

H

H

H

H

OH

H C

H

H

C C

HH

H C

H

H

C C

H

H

OH

H

H

C

H

H

H H C

H

H

C C

H

C

H

HH

H

Enantiomers

cis-butene

Cis–trans isomers

Macromolecules

Condensation or dehydration reaction

Links monomers to form polymers

Hydrolysis

Polymers broken down into monomers

11

Figure 3.5

12

HO H H+

Monomers

HO


Figure 3.5

13

HO H H H+

MonomersH2O

HO HO


Figure 3.5

14

HO H H H H

H

+

MonomersH2O H2O

HO

HO

HOHO


Figure 3.5

15

HO H H H HH

H H

+

MonomersH2O H2O

HO

HO HO

HOHO HO

H2O


Figure 3.5

16

HHO


Figure 3.5

17

H H

HHO

H2O

HOHO


Figure 3.5

18

HH H

H HHO HO

H2O H2O

HOHOHO


Figure 3.5

19

HH H HO H H

H H

+

HO HO

H2O H2O H2O

HOHOHOHO


Figure 3.5

20

HO H H H

H

HH

H H

H H HO H H

H H

+

+

Monomers

(a) Polymer formation by dehydration reactions

(b) Breakdown of a polymer by hydrolysis reactions

H2O H2O

HO

HO HO

H2O H2O H2O

HO

HO HO

HOHO HO

HOHOHO

H2O


21

Four major types of organic

molecules and macromolecules

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic acids

22

Carbohydrates

Composed of carbon, hydrogen, and

oxygen atoms

Cn(H2O)n

Most of the carbon atoms in a

carbohydrate are linked to a hydrogen

atom and a hydroxyl group

23

Monosaccharides

Simplest sugars

Most common are 5 or 6 carbons

Pentoses- ribose (C5H10O5), deoxyribose

(C5H10O4)

Hexose- glucose (C6H12O6)

Different ways to depict structures

Ring or linear

25

Glucose isomers

Structural isomers- different arrangement of same elements

Glucose and galactose

Stereoisomers

α- and β-glucose Hydroxyl group of carbon 1 above or below ring

D- and L-glucose Enantiomers- mirror image

26

HO

OHH

H

H

OH

H

4

5

6

1

6

5

23

O

HO

OHH

HOH

H

H

H

OH

4

5

6

1

23

O

HO

OH H

H OHH

H

H

HO

4

5

6

1

2 3

OH OHC

H OHC

H

Enantiomers

-D-galactose

H

OHH

H4

5

6

1

23

O

H

OHHO

OH

H

OH

H

4H OHC

3HO HC

2H OHC

1H C

O

•Linear and ring structures

of -D-glucose

(b) Isomers of glucose

-D-glucose -L-glucose

CH2OH

CH2OH CH2OH CH2OH


D-glucose

(linear)β-D-glucose

(ring)

27

Disaccharides

Carbohydrates composed of two

monosaccharides

Joined by dehydration or condensation

reaction

Glycosidic bond

Broken apart by hydrolysis

Examples − sucrose, maltose, lactose

28

HO

OHH

HOHH

H

O H

HO

H

HOH

HOH

O

+

OH

Glucose Fructose

CH2OH

CH2OH

CH2OH


29

H

+

H

HOH

H

O

O

HO

HO

OHH

HOH

H

H

O H

HO

HO

OHH

HOH

H

H O

Glucose + Fructose

Sucrose + Water

H

HOH

HOH

O

+

OH

Glucose Fructose

Sucrose

CH2OH

CH2OH

CH2OH

CH2OH

CH2OH

CH2OH

H2O

Glycosidic

bond


30

Polysaccharides

Many monosaccharides linked together to

form long polymers

Examples

Energy storage – starch, glycogen

Structural role – cellulose, chitin,

glycosaminoglycans

32

Lipids

Composed predominantly of hydrogen and

carbon atoms

Defining feature of lipids is that they are

nonpolar and therefore very insoluble in

water

33

Fats

Also known as triglycerides or

triacylglycerols

Formed by bonding glycerol to three fatty

acids


reaction


35

Fatty acids

Saturated- all carbons are linked by single covalent bonds Tend to be solid at room temperature

Unsaturated- contain one or more double bonds Tend to be liquid at room temperature (oils)

cis forms naturally

trans formed by synthetic process – disease link

36

Saturated fatty acid

(Stearic acid)

Unsaturated fatty acid

(Linoleic acid)

CH2

O

HOC

CH

CH

CH

CH

O

HOC

CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3

CH2 CH2 CH3CH2 CH2

CH2

CH2CH2CH2CH2CH2CH2CH2


37

Fats are important for energy storage

1 gram of fat stores more energy than 1 gram

of glycogen or starch

Fats can also be structural in providing

cushioning and insulation

38

Phospholipids

Glycerol, 2 fatty acids and a phosphate

group

Amphipathic molecule

Phosphate region- polar, hydrophillic, head

Fatty acid chains- nonpolar, hydrophobic, tail

39

Phosphate

CH2

CH2

CH2

CH2

O

CH3 CH3

CH3

CH

H2C

N+

O

O

O

C O

O

O–P

C O

CH2

CH2

CH2

CH2

CH2

CH2

CH2

H2C

(a) Structure and model of a phospholipid

Charged

nitrogen-

containing

region

Glycerol

backbone

Ends of

fatty acids

Polar head

(hydrophilic)

Membrane

bilayer

Schematic

drawing of a

phospholipid

Nonpolar tail

(hydrophobic)

Polar

heads

Nonpolar

fatty acid

tails

Polar

headsSpace-filling

model

Chemical

structure

Nonpolar

tails

Polar

heads

H2C

H2C

H2C

H2C

H2C

H2C

H2C

H3C

CH2

CH2

CH2

CH2

CH2

CH2

H2C

H2C

H2C

H2C

H2C

H2C

H3C

(b) Arrangement of phospholipids in a bilayer


40

Steroids

Four interconnected rings of carbon atoms

Usually not very water soluble

Cholesterol

Tiny differences in chemical structure can

lead to profoundly different biological

properties

Estrogen vs. testosterone

41

CH3

CHH3C CH3

CH3

H

H H

HO

CH3

CH2

CH2CH

CH2

3

Cholesterol


42


Female cardinal Male cardinal

O

TestosteroneEstrogen

OH

H

H

H

OHH3C

CH3

CH3

H

H H

HO

CHH3C CH3

CH3

H

H H

HO

CH3

CH2

CH2CH

CH2

3

Cholesterol

H3C

b: © Adam Jones/Photo Researchers; c: © Adam Jones/Photo Researchers

43

Proteins

Composed of carbon, hydrogen, oxygen,

nitrogen, and small amounts of other

elements, notably sulfur

Amino acids are the monomers

Common structure with variable R-group

20 amino acids

Side-chain determines structure and function

44

C

H

-carbon

O–H

OH

CN+H

R


46


reaction

Peptide bond

Forms polypeptides

Proteins are made up of 1 or more

polypeptides


47

O

O–

N+ C

H

H

H

H

H C

Carboxyl

group

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

48

O

O–

N+ C

H

H

H

H

H

H

H

C

O

O–

N+ C

CH3

C

H

H

Amino

groupCarboxyl

group

AlanineGlycine

+


49

O

O–

N+ C

H

H

H

H

H

H

H

H

H

H

C

O

O–

N+ C

CH3

C

O

N+ C

H

H H

C

O

O–

N C

CH3

C

H H

H

Peptide

bondAmino

groupCarboxyl

group

AlanineGlycine

+


50

H3N+

N-terminus C-terminus

COO–

O

O–

N+ C

H

H

H

H

H

H

H

H

H

H

C

O

O–

N+ C

CH3

C

O

N+ C

H

H H

C

O

O–

N C

CH3

C

O

N+ C

H

H

H

N N NH C

O

C

O

C

O

C

O

C

O

C

O

C

O–

OH

O

CN C C

CH3

H H

CH2

C

CH2

H H HHH

C

CH2

H

SH

C

CH2

H

N

H HH

N

H

N

H

OH

H H H

C

CH

H3C CH3

C

CH2

H

O

O–

C

(a) Formation of a peptide bond between 2 amino acids

(b) Polypeptide—a linear chain of amino acids

(c) Numbering system of amino acids in a polypeptide

Gly

1 2 3 4 5 6 7 8

Ala Ser Asp Phe Val Tyr Cys

Peptide

bondAmino

groupCarboxyl

group

AlanineGlycine

Free carboxyl

groupFree amino

group

H2O+ +


51

Protein Structure

Primary

Secondary

Tertiary

Quaternary

53

Primary structure

Amino acid sequence

Determined by genes

55

Secondary Structure

Chemical and physical interactions cause folding

Repeating patterns

α helices and β pleated sheets

Key determinants of a protein’s characteristics

“Random coiled regions”

Not α helix or β pleated sheet

Shape is specific and important to function

56

S SCH2 CH2

CH2

CH2

C

O–

COO–

O

CH2

CH2

CH2

CH2

NH3

CH2

NH2

O

CH2 OH

CH3

HC CH3

CH2

C CH2

+

NH3+


57

Tertiary structure

Folding gives complex three-dimensional

shape

Final level of structure for single

polypeptide chain

58

Quaternary structure

Made up of 2 or more polypeptides

Protein subunits – individual polypeptides

Multimeric proteins – proteins with multiple

parts

60

5 factors promoting protein folding

and stability

1. Hydrogen bonds

2. Ionic bonds and other polar interactions

3. Hydrophobic effects

4. Van der Waals forces

5. Disulfide bridges

61

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62

Protein-protein interactions

Many cellular processes involve steps in

which two or more different proteins

interact with each other

Specific binding at surface

Use first 4 factors1. Hydrogen bonds

2. Ionic bonds and other polar interactions

3. Hydrophobic effects

4. Van der Waals forces

Anfinsen Showed That the Primary Structure

of Ribonuclease Determines Its Three-

Dimensional Structure

Prior to the 1960s, the mechanisms by which proteins assume their three-dimensional structures were not understood.

Christian Anfinsen, however, postulated that proteins contain all the information necessary to fold into their proper conformation without the need for organelles or cellular factors

He hypothesized that proteins spontaneously assume their most stable conformation based on the laws of chemistry and physics

Ribonuclease experiment

Nobel Prize 1972

In vitro- no other cellular components present

Chemicals that disrupt bonds cause the enzyme to lose function

Removal of those chemicals restored function Even in the complete absence of any cellular factors

or organelles, an unfolded protein can refold into its functional structure

We have learned that some proteins do require assistance in folding

1

Experimental level Conceptual level

1

2

3

-mercaptoethanol

+Urea

Urea-mercaptoethanol

S

S

S S

S

S

S

S

SH

SH

SH

SH SH

SH

SH

0

50

100Activity restored

6

54 THE D ATA

HYPOTHESIS Within their amino acid sequence, proteins contain all the information needed to fold into their correct, 3-dimensional shapes.

KEY MATERIALS Purified ribonuclease, RNA, denaturing chemicals, size-exclusion columns.

Incubate purified

ribonuclease in test tube

with RNA, and measure its

ability to degrade RNA.

Layer mixture from step 2

atop a chromatography

column. Beads in the column

allow ribonuclease to escape,

while -mercaptoethanol and

urea are retained. Collect

ribonuclease in a test tube

and measure its ability to

degrade RNA.

Mixture from

step 2 containing

denatured

ribonuclease,

-mercaptoethanol,

and urea

Column containing

beads suspended

in a watery solution

Collection port

with filter to prevent

beads from escaping

Solution of

ribonuclease

Numerous H bonds

(not shown) and 4

S—S bonds. Protein

is properly folded.

No more H bonds,

ionic bonds, or S—S

bonds. Protein is

unfolded.

Denatured

ribonuclease

Beads have

microscopic pores

that trap -mercapto-

ethanol and urea, but

not ribonuclease.

Denatured

ribonuclease

Renatured

ribonuclease

CONCLUSION Certain proteins, like ribonuclease, can

spontaneously fold into their final,

functional

shapes without assistance from other cellular

structures or factors. (Howeve r , as described in your text, this is not

true of many other proteins.)

SOURCE Habe r , E., and Anfinsen, C.B. 1961. Regeneration of

enzyme activity by air oxidation of reduced subtilisin-modified

ribonuclease. Journal of Biological Chemistry 236:422–424.

Purified

ribonuclease

Denature ribonuclease

by adding -mercaptoethanol

(breaks S—S bonds) and

urea (breaks H bonds and

ionic bonds). Measure its

ability to degrade RNA.

Ribonuclease

function (%)

Purified

ribonuclease

(step 1)

Denatured

ribonuclease

(step 2)

Ribonuclease

after column

chromatography

(step 3)


Proteins Contain Functional

Domains Within Their Structures

Module or domains in proteins have

distinct structures and function

Signal transducer and activator of

transcription (STAT) protein example

Each domain of this protein is involved in a

distinct biological function

Proteins that share one of these domains

also share that function

HN3+

COO–

STAT

protein


69

Nucleic Acids

Responsible for the storage, expression, and transmission of genetic information

Two classes Deoxyribonucleic acid (DNA)

Store genetic information coded in the sequence of their monomer building blocks

Ribonucleic acid (RNA) Involved in decoding this information into instructions for

linking together a specific sequence of amino acids to form a polypeptide chain

70

Monomer is a nucleotide

Made up of phosphate group, a five-carbon

sugar (either ribose or deoxyribose), and a

single or double ring of carbon and nitrogen

atoms known as a base

Monomers linked into polymer with a

sugar-phosphate backbone

72

Adenine

Guanine

Bases

Backbone

Thymine

Cytosine

OHH

H

4

5

3 2•

1

HH

N

OOO P

CH3

CH2

O–

HH

H

HH

OO

O

CH2

O–

NH2

N

N

H

H

N

N

HH

H

HH

OOO

O

P CH2

O–

NH2

HN

N

N

N

HH

HOH

HH

OOO

O

P CH2

O–

Phosphate

Sugar

5

5

4 1

2

3

3

3

5

4

4

1

1

2

2

N

PO

NH2

N

N

O–


73

DNA vs. RNA

DNA RNA

Deoxyribonucleic acid Ribonucleic acid

Deoxyribose Ribose

Thymine (T) Uracil (U)

Adenine (A), guanine (G), cytosine (C)

used in both

2 strands- double helix Single strand

1 form Several forms

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