92
1 Chapter 3 Biological Molecules http://youtu.be/PYH63o10iTE

1 Chapter 3 Biological Molecules

Embed Size (px)

Citation preview

Page 1: 1 Chapter 3 Biological Molecules

1

Chapter 3Biological Molecules

http://youtu.be/PYH63o10iTE

Page 2: 1 Chapter 3 Biological Molecules

2

Carbon Chemistry• Carbon is the Backbone of Biological

Molecules (macromolecules)• All living organisms Are made up of

chemicals based mostly on the element carbon

Figure 4.1

Video

Page 3: 1 Chapter 3 Biological Molecules

3

There are 4 types of Biological Macromolecules

Carbohydrates like sugar, starch, chiton, cellulose, potatoes and candy!

Lipids like fat, butter, cream and olive oil (all other oils as well including motor oil)

Proteins like steak, collagen (jello), hair and the machinery that runs your cellular metabolism

Nucleic Acids – these are DNA and RNA which are responsible for storing information about how to build proteins

Page 4: 1 Chapter 3 Biological Molecules

4

Carbon Chemistry

• Organic chemistry is the study of carbon compounds

• Carbon atoms can form diverse molecules by bonding to four other atoms or molecules

• Carbon compounds range from simple molecules to complex ones

• Carbon has four valence electrons and may form single, double, triple, or quadruple bonds

Page 5: 1 Chapter 3 Biological Molecules

5

How Many?• A single carbon atom can form a maximum

of ___covalent bond(s)?

Page 6: 1 Chapter 3 Biological Molecules

6

• The electron configuration of carbon gives it covalent compatibility with many different elements

H O N C

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)

Figure 4.4

Page 7: 1 Chapter 3 Biological Molecules

7

• The bonding versatility of carbon allows it to form many diverse molecules, including carbon skeletons

(a) Methane

(b) Ethane

(c) Ethene (ethylene)

Molecular Formula

Structural Formula

Ball-and-Stick Model

Space-Filling Model

H

H

H

H

H

H

H

H

H

H

H H

HH

C

C C

C C

CH4

C2H

6

C2H4

Name and Comments

Figure 4.3 A-C

Page 8: 1 Chapter 3 Biological Molecules

8

• Carbon may bond to itself forming carbon chains• Carbon chains form the skeletons of most

organic molecules• Carbon chains vary in length and shape• The following diagrams show the atoms and

their bonds

HHH

HH

H H H

HH

H

H H H

H H HH H

H

H

H

H

H

H

HH

HH H H H

H HH H

H H H H

H H

H H

HHHH H

H

H

C C C C C

C C C C C C C

CCCCCCCC

C

CC

CC

C

C

CCC

CC

H

H

H

HHH

H

(a) Length

(b) Branching

(c) Double bonds

(d) Rings

Ethane Propane

Butane isobutane

1-Butene 2-Butene

Cyclohexane Benzene

H H H HH

Figure 4.5 A-D

Page 9: 1 Chapter 3 Biological Molecules

9

So….• Carbohydrates look something like this…

• CH3-CH2-CH2-CH2

Page 10: 1 Chapter 3 Biological Molecules

10

                                         Notice that the way the methane is drawn bears no resemblance to the actual shape of the molecule. Methane isn't flat with 90° bond angles. This mismatch between what you draw and what the molecule actually looks like can lead to problems if you aren't careful.

Page 11: 1 Chapter 3 Biological Molecules

11

Hydrocarbons

• Hydrocarbons are molecules consisting of only carbon and hydrogen

• Hydrocarbons Are found within many of a cell’s organic molecules

(a) A fat molecule (b) Mammalian adipose cells100 µm

Fat droplets (stained red)

Figure 4.6 A, B

Page 12: 1 Chapter 3 Biological Molecules

12

Functional Groups• Functional groups

are the parts of molecules involved in chemical reactions

• They Are the chemically reactive groups of atoms within an organic molecule

• Give organic molecules distinctive chemical properties

CH3

OH

HO

O

CH3

CH3

OH

Estradiol

Testosterone

Female lion

Male lionFigure 4.9

Page 13: 1 Chapter 3 Biological Molecules

13

Macromolecules– Are large molecules composed of smaller

molecules– Are complex in their structures

Figure 5.1

Page 14: 1 Chapter 3 Biological Molecules

14

Macromolecules•Most macromolecules are polymers, built from monomers•A monomer is a single unit of a polymer like legos!• Four classes of life’s organic molecules are polymers

– Carbohydrates (include sugars, starches etc)– Proteins– Nucleic acids– Lipids (fats)

Page 15: 1 Chapter 3 Biological Molecules

15

• A polymer– Is a long molecule consisting of many

similar building blocks called monomers– Specific monomers make up each

macromolecule– E.g. amino acids are the monomers for

proteins

Page 16: 1 Chapter 3 Biological Molecules

16

The Synthesis and Breakdown of Polymers

• Monomers form larger molecules by condensation reactions called dehydration synthesis

• DRAW THIS AND CHECK WITH YOUR GROUP THAT IT IS RIGHT!

(a) Dehydration reaction in the synthesis of a polymer

HO H1 2 3 HO

HO H1 2 3 4

H

H2O

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a watermolecule, forming a new bond

Figure 5.2A

Page 17: 1 Chapter 3 Biological Molecules

17

Building up and breaking down

• When you are building a biochemical, you put monomers together and it’s called “DEHYDRATION SYNTHESIS”

• When you break it down to release energy, it is called “hydrolysis”

• Hydro=water lysis=to break• If water is a product, then it’s hydrolysis

• Ex: galactose+glucose = lactose + water

Page 18: 1 Chapter 3 Biological Molecules

18

The Synthesis and Breakdown of Polymers

• Polymers can disassemble by– Hydrolysis (addition of water molecules)– DRAW THIS AND COMPARE IT WITH YOUR GROUP TO

MAKE SURE IT’S RIGHT!

(b) Hydrolysis of a polymer

HO 1 2 3 H

HO H1 2 3 4

H2O

HHO

Hydrolysis adds a watermolecule, breaking a bond

Figure 5.2B

Page 19: 1 Chapter 3 Biological Molecules

19

• Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers

• An immense variety of polymers can be built from a small set of monomers

Page 20: 1 Chapter 3 Biological Molecules

20

Carbohydrates• Serve as fuel and building material• Include both sugars and their polymers

(starch, cellulose, etc.)• Carbohydrates are either:• Monosaccharides – a single monomer

Disaccharides - two monomers• Polysaccharides – three or more

monos

Page 21: 1 Chapter 3 Biological Molecules

21

Sugars

•Monosaccharides–Are the simplest sugars–Can be used for fuel–Can be converted into other organic molecules

–Can be combined into polymers

Page 22: 1 Chapter 3 Biological Molecules

22

Monosaccharides• Glucose• Maltose• Sucrose• Fructose

• Note the “ose”

Page 23: 1 Chapter 3 Biological Molecules

23

• Examples of monosaccharides

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

Keto

ses

FructoseFigure 5.3

Page 24: 1 Chapter 3 Biological Molecules

24

• Monosaccharides– May be linear– Can form rings

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

(a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5.

OH3

O H OO

6

1

Figure 5.4

Page 25: 1 Chapter 3 Biological Molecules

25

• Disaccharides– Consist of two monosaccharides– Are joined by a glycosidic linkage– a glycosidic bond is a type of covalent

bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.

– To clarify: Disaccharides are formed when two monosaccharides join together by the dehydration synthesis reaction resulting in a glycosidic bond

Page 26: 1 Chapter 3 Biological Molecules

26

Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide.

Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring.

(a)

(b)

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

Figure 5.5

Page 27: 1 Chapter 3 Biological Molecules

27

Polysaccharides• Polysaccharides (poly = many)

– Are polymers of sugars– Serve many roles in organisms

Page 28: 1 Chapter 3 Biological Molecules

28

Storage Polysaccharides• Starch

– Is a polymer consisting entirely of glucose monomers

– Is the major storage form of glucose in plants

Chloroplast Starch

Amylose Amylopectin

1 m

(a) Starch: a plant polysaccharideFigure 5.6

Page 29: 1 Chapter 3 Biological Molecules

29

• Glycogen– Consists of glucose monomers– Is the major storage form of glucose in animals

Mitochondria Giycogen granules

0.5 m

(b) Glycogen: an animal polysaccharide

Glycogen

Figure 5.6

Page 30: 1 Chapter 3 Biological Molecules

30

Structural Polysaccharides

• Cellulose– Is a polymer of glucose and is considered a

fiber! It is indigestible by humans– Cows can digest it because they have four

stomachs

Page 31: 1 Chapter 3 Biological Molecules

31

– 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

OHOHOH

H

O

CH2OH

HH

H

OH

OHH

H

HO

4 OH

CH2OH

OOH

OH

HO

41

O

CH2OH

OOH

OH

O

CH2OH

OOH

OH

CH2OH

O

OH

OH

O O

CH2OH

OOH

OH

HO

4O

1

OH

O

OH

OHO

CH2OH

O

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

Page 32: 1 Chapter 3 Biological Molecules

32

The formulae for both glucose and fructose are identical. How do they differ?

Page 33: 1 Chapter 3 Biological Molecules

33

Plant cells

0.5 m

Cell walls

Cellulose microfibrils in a plant cell wall

Microfibril

CH2OH

CH2OH

OH

OH

OO

OHOCH2OH

O

OOH

OCH2OH OH

OH OHO

O

CH2OH

OO

OH

CH2OH

OO

OH

O

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 unitof the plant cell wall.

A cellulose moleculeis an unbranched glucose polymer.

OH

OH

O

OOH

Cellulosemolecules

Figure 5.8

– Is a major component of the tough walls that enclose plant cells

Page 34: 1 Chapter 3 Biological Molecules

34

• Cellulose is difficult to digest– Cows have microbes in their stomachs to facilitate this

process

Figure 5.9

Page 35: 1 Chapter 3 Biological Molecules

35

• 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.

O

CH2OH

OHHH OH

H

NH

CCH3

O

H

H

(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emergingin 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

Page 36: 1 Chapter 3 Biological Molecules

36

Lipids• Lipids are a diverse group of

hydrophobic (water fearing) molecules• Lipids

– Are the one class of large biological molecules that do not consist of polymers

– Share the common trait of being hydrophobic

Page 37: 1 Chapter 3 Biological Molecules

37

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

Page 38: 1 Chapter 3 Biological Molecules

38

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

Page 39: 1 Chapter 3 Biological Molecules

39

Fats• Are constructed from two types of smaller molecules, a single

glycerol and usually three fatty acids

Page 40: 1 Chapter 3 Biological Molecules

40

Page 41: 1 Chapter 3 Biological Molecules

41

Fats• Vary in the length and number and locations of double

bonds they contain

Page 42: 1 Chapter 3 Biological Molecules

42

• Saturated fatty acids (saturated with hydrogen)

– Have the maximum number of hydrogen atoms possible

– Have no double bonds

(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12

Page 43: 1 Chapter 3 Biological Molecules

43

• Unsaturated fatty acids– Have one or more double bonds

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12

Page 44: 1 Chapter 3 Biological Molecules

44

• Phospholipids– Have only two fatty acids– Have a phosphate group instead of a third fatty

acid

Page 45: 1 Chapter 3 Biological Molecules

45

• A hydrogenated fat is more solid - butter

• An unsaturated fat is liquid - oils

Page 46: 1 Chapter 3 Biological Molecules

46

• Phospholipid structure– Consists of a hydrophilic “head” and

hydrophobic “tails”

CH2

O

PO O

O

CH2CHCH2

OO

C O C O

Phosphate

Glycerol

(a) Structural formula (b) Space-filling model

Fatty acids

(c) Phospholipid symbol

Hyd

rop

hob

i c t

ails

Hydrophilichead

Hydrophobictails

Hyd

rop

hi li c

head

CH2 Choline+

Figure 5.13

N(CH3)3

Page 47: 1 Chapter 3 Biological Molecules

47

• The structure of phospholipids– Results in a bilayer arrangement found in cell

membranes

Hydrophilichead

WATER

WATER

Hydrophobictail

Figure 5.14

Page 48: 1 Chapter 3 Biological Molecules

48

Steroids• Steroids

– Are lipids characterized by a carbon skeleton consisting of four fused rings

– Examples are hormones such as estrogen and testosterone

Page 49: 1 Chapter 3 Biological Molecules

49

• One steroid, cholesterol– Is found in cell membranes– Is a precursor for some hormones

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15

Page 50: 1 Chapter 3 Biological Molecules

50

Proteins• Proteins have many structures, resulting in a wide

range of functions• Proteins do most of the work in cells and act as

enzymes. Enzymes are proteins.• Proteins are made of monomers called amino

acids

Page 51: 1 Chapter 3 Biological Molecules

51

• An overview of protein functions

Table 5.1

Page 52: 1 Chapter 3 Biological Molecules

52

• 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

Page 53: 1 Chapter 3 Biological Molecules

53

Polypeptides• Polypeptides

– Are polymers (chains) of amino acids

• A protein– Consists of one or more polypeptides

Page 54: 1 Chapter 3 Biological Molecules

54

• Amino acids– Are organic molecules possessing both carboxyl

and amino groups– Differ in their properties due to differing side chains,

called R groups– YOU MUST REMEMBER THIS!

Page 55: 1 Chapter 3 Biological Molecules

55

Twenty Amino Acids• 20 different amino acids make up proteins

O

O–

H

H3N+ C CO

O–

H

CH3

H3N+ C

H

CO

O–

CH3 CH3

CH3

C CO

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3

CH3CH2

CH

C

H

H3N+

C

CH3

CH2CH2

CH3N+

H

CO

O–

CH2

CH3N+

H

CO

O–

CH2

NH

H

CO

O–

H3N+ C

CH2H2

CH2

NC

CH2

H

C

Nonpolar

Glycine (Gly)Alanine

(Ala)Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

CO

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–

Page 56: 1 Chapter 3 Biological Molecules

56

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 CO

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)

Page 57: 1 Chapter 3 Biological Molecules

57

Amino Acid Polymers

• Amino acids– Are linked by peptide bonds

Page 58: 1 Chapter 3 Biological Molecules

58

• Again, building proteins is dehydration synthesis and breaking proteins is hydrolysis

• Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure and secondary structure which is present in their native state

Page 59: 1 Chapter 3 Biological Molecules

59

Protein Conformation and Function

• A protein’s specific conformation (shape) determines how it functions

Page 60: 1 Chapter 3 Biological Molecules

60

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

GlyProThrGlyThr

Gly

GluSeuLysCysProLeu

MetVal

Lys

ValLeu

AspAlaValArgGly

SerPro

Ala

Gly

lle

SerProPheHisGluHis

Ala

GluValValPheThrAla

Asn

AspSer

GlyProArg

ArgTyrThr

lleAla

Ala

Leu

LeuSer

ProTyrSerTyrSerThr

Thr

Ala

ValVal

ThrAsnProLysGlu

ThrLys

SerTyrTrpLysAlaLeu

GluLleAsp

Page 61: 1 Chapter 3 Biological Molecules

61

O C helix

pleated sheetAmino acid

subunitsNCH

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

HH

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– Be sure that you can identify what this structure looks

like!

H H

Figure 5.20

Page 62: 1 Chapter 3 Biological Molecules

62

• 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 Polypeptid

ebackbone

Hyrdogenbond

Ionic bond

CH2

Disulfide bridge

Page 63: 1 Chapter 3 Biological Molecules

63

• Quaternary structure– Is the overall protein structure that results from the

aggregation of two or more polypeptide subunits

Polypeptidechain

Collagen

Chains

ChainsHemoglobin

IronHeme

Page 64: 1 Chapter 3 Biological Molecules

64

Review of Protein Structure

+H3NAmino end

Amino acidsubunits

helix

Page 65: 1 Chapter 3 Biological Molecules

65

Sickle-Cell Disease: A Simple Change in Primary Structure

• Sickle-cell disease– Results from a single amino acid

substitution in the protein hemoglobin

Page 66: 1 Chapter 3 Biological Molecules

66

Fibers of abnormalhemoglobin deform cell into sickle shape.

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin A

Molecules donot associatewith oneanother, eachcarries oxygen.Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen

10 m 10 m

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin SMolecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.

subunit subunit

1 2 3 4 5 6 7 3 4 5 6 721

Normal hemoglobin

Sickle-cell hemoglobin . . .. . .

Figure 5.21

Exposed hydrophobic

region

Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu

Page 67: 1 Chapter 3 Biological Molecules

67

What Determines Protein Conformation?

• Protein conformation Depends on the physical and chemical conditions of the protein’s environment

• Temperature, pH, etc. affect protein structure

Page 68: 1 Chapter 3 Biological Molecules

68

•Denaturation is when a protein unravels and loses its native conformation(shape)

Denaturation

Renaturation

Denatured protein

Normal protein

Figure 5.22

Page 69: 1 Chapter 3 Biological Molecules

69

The Protein-Folding Problem

• Most proteins– Probably go through several intermediate states on their way

to a stable conformation – Denaturated proteins no longer work in their unfolded

condition– Proteins may be denaturated by extreme changes in pH or

temperature

Page 70: 1 Chapter 3 Biological Molecules

70

• Chaperonins– Are protein molecules that assist in the proper folding of

other proteins

Hollowcylinder

Cap

Chaperonin(fully assembled)

Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end.

The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide.

The cap comesoff, and the properlyfolded protein is released.

Correctlyfoldedprotein

Polypeptide

2

1

3

Figure 5.23

Page 71: 1 Chapter 3 Biological Molecules

71

• X-ray crystallography– Is used to determine a protein’s three-dimensional

structure

X-raydiffraction pattern

Photographic filmDiffracted X-

raysX-ray

source

X-ray

beam

CrystalNucleic acid Protein

(a) X-ray diffraction pattern(b) 3D computer modelFigure 5.24

Page 72: 1 Chapter 3 Biological Molecules

72

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

Page 73: 1 Chapter 3 Biological Molecules

73

The Roles of Nucleic Acids

• There are two types of nucleic acids– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)

Page 74: 1 Chapter 3 Biological Molecules

74

Deoxyribonucleic Acid

• DNA– Stores information for the synthesis of

specific proteins– Found in the nucleus of cells

Page 75: 1 Chapter 3 Biological Molecules

75

DNA Functions– Directs RNA synthesis (transcription)– Directs protein synthesis through RNA (translation)

1

2

3

Synthesis of mRNA in the nucleus

Movement of mRNA into cytoplasm

via nuclear pore

Synthesisof protein

NUCLEUSCYTOPLASM

DNA

mRNA

Ribosome

AminoacidsPolypeptide

mRNA

Figure 5.25

Page 76: 1 Chapter 3 Biological Molecules

76

The Structure of Nucleic Acids

• Nucleic acids– Exist as polymers called

polynucleotides– Nucleic acids are polymers of

nucleotides

(a) Polynucleotide, or nucleic acid

3’C

5’ end

5’C

3’C

5’C

3’ endOH

Figure 5.26

O

O

O

O

Page 77: 1 Chapter 3 Biological Molecules

77

Page 78: 1 Chapter 3 Biological Molecules

78

• Each polynucleotide– Consists of monomers called nucleotides– Sugar + phosphate + nitrogen base

Nitrogenousbase

Nucleoside

O

O

O

O P CH2

5’C

3’CPhosphate

group Pentosesugar

(b) NucleotideFigure 5.26

O

Page 79: 1 Chapter 3 Biological Molecules

79

Nucleotide Monomers• Nucleotide monomers

– Are made up of nucleosides (sugar + base) and phosphate groups

(c) Nucleoside componentsFigure 5.26

CHCH

Uracil (in RNA)U

Ribose (in RNA)

Nitrogenous bases Pyrimidines

CN

NC

OH

NH2

CHCH

OC

NH

CHHN

CO

CCH3

N

HNC

C

HO

O

CytosineC

Thymine (in DNA)T

NHC

N C

CN

C

CH

N

NH2 O

NHC

NHH

C C

N

NH

C NH2

AdenineA

GuanineG

Purines

OHOCH2

HH H

OH

H

OHOCH2

HH H

OH

H

Pentose sugars

Deoxyribose (in DNA)Ribose (in RNA)OHOH

CH

CH

Uracil (in RNA)U

4’

5”

3’OH H

2’

1’

5”

4’

3’ 2’

1’

Page 80: 1 Chapter 3 Biological Molecules

80

Nucleotide Polymers• Nucleotide polymers

– Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

Page 81: 1 Chapter 3 Biological Molecules

81

Page 82: 1 Chapter 3 Biological Molecules

82

DNA nucleotides

Page 83: 1 Chapter 3 Biological Molecules

83

Be sure that you can recognize a single strand of DNA

Page 84: 1 Chapter 3 Biological Molecules

84

Can you do this?

• In DNA, A always pairs with T and G always pairs with C

• Therefore, can you tell me what the compliment of this is?

• AGTACTG

Page 85: 1 Chapter 3 Biological Molecules

85

• TCATGAC

Page 86: 1 Chapter 3 Biological Molecules

86

Gene

• A specific stretch of DNA that programs the amino acid sequence of a polypeptide is a gene

• The sequence of bases along a nucleotide polymer– Is unique for each gene

Page 87: 1 Chapter 3 Biological Molecules

87

The DNA Double Helix• Cellular DNA molecules

– Have two polynucleotides that spiral around an imaginary axis

– Form a double helix

– Check this out

Page 88: 1 Chapter 3 Biological Molecules

88

• The DNA double helix– Consists of two antiparallel nucleotide strands

3’ end

Sugar-phosphatebackbone

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to be added to a new strand

A

3’ end

3’ end

5’ end

Newstrands

3’ end

5’ end

5’ end

Figure 5.27

Page 89: 1 Chapter 3 Biological Molecules

89

A,T,C,G• The nitrogenous bases in DNA

– Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)

– RNA substitutes Uracil for Thymine

Page 90: 1 Chapter 3 Biological Molecules

90

DNA and Proteins as Tape Measures of Evolution

• Molecular comparisons – Help biologists sort out the

evolutionary connections among species

Page 91: 1 Chapter 3 Biological Molecules

91

The Theme of Emergent Properties in the Chemistry of

Life: A Review• Higher levels of organization

– Result in the emergence of new properties

• Organization– Is the key to the chemistry of life

Page 92: 1 Chapter 3 Biological Molecules

92

Large biologicalmolecules

Functions Components Examples

Carbohydrates

Lipids

Proteins

Nucleic acids

Dietary energy;storage; plantstructure

Long-termenergy storagefats;hormonessteroids

Enzymes, structure,storage, contraction,transport, and others

Informationstorage

Monosaccharides:glucose, fructoseDisaccharides:lactose, sucrosePolysaccharides:starch, cellulose

Fats triglycerides;Steroidstestosterone,estrogen

Lactasean enzyme,hemoglobina transport protein

DNA, RNA

Monosaccharide

Components ofa triglyceride

Amino acid

Nucleotide

Fatty acid

Glycerol

Aminogroup

Carboxylgroup

Sidegroup

Phosphate

Base

Sugar

Figure UN3-2