Macromolecules of LifeProteins and Nucleic Acids

Chapter 5

You already know a lot about proteins!

• Biuret – [protein]• Gel Electrophoresis• Enzymes

You’ve been working with them in lab for the past 2-3 weeks!

Protein Definition• Consists of one or more polypeptides folded, coiled,

and twisted into a specific 3D shape• Proteios – “first place”

• There are many different shapes of proteins depending on its FUNCTION– Enzymes– Cell signaling– Defense– Structural support– Transport– Receptors

Two similar terms

• Protein – already defined

• Polypeptide – polymer made of repeating subunits of amino

acids (monomer)– usually refers to a long linear strand of amino

acids that will then get folded into a 3D shape (protein)

Fig. 5-2a

Dehydration removes a watermolecule, forming a new bond

Short polymer Unlinked monomer

Longer polymer

Dehydration reaction in the synthesis of a polymer

HO

HO

HO

H2O

H

HH

4321

1 2 3

(a)

Fig. 5-2b

Hydrolysis adds a watermolecule, breaking a bond

Hydrolysis of a polymer

HO

HO HO

H2O

H

H

H321

1 2 3 4

(b)

Fig. 5-UN1

Aminogroup

Carboxylgroup

carbon

Fig. 5-17Nonpolar

Glycine(Gly or G)

Alanine(Ala or A)

Valine(Val or V)

Leucine(Leu or L)

Isoleucine(Ile or I)

Methionine(Met or M)

Phenylalanine(Phe or F)

Trypotphan(Trp or W)

Proline(Pro or P)

Polar

Serine(Ser or S)

Threonine(Thr or T)

Cysteine(Cys or C)

Tyrosine(Tyr or Y)

Asparagine(Asn or N)

Glutamine(Gln or Q)

Electricallycharged

Acidic Basic

Aspartic acid(Asp or D)

Glutamic acid(Glu or E)

Lysine(Lys or K)

Arginine(Arg or R)

Histidine(His or H)

Fig. 5-17a

Nonpolar

Glycine (Gly or G)

Alanine (Ala or A)

Valine (Val or V)

Leucine (Leu or L)

Isoleucine (Ile or I)

Methionine (Met or M)

Phenylalanine (Phe or F)

Tryptophan (Trp or W)

Proline (Pro or P)

Fig. 5-17b

Polar

Asparagine (Asn or N)

Glutamine (Gln or Q)

Serine (Ser or S)

Threonine (Thr or T)

Cysteine (Cys or C)

Tyrosine (Tyr or Y)

Fig. 5-17c

Acidic

Arginine (Arg or R)

Histidine (His or H)

Aspartic acid (Asp or D)

Glutamic acid (Glu or E)

Lysine (Lys or K)

Basic

Electricallycharged

Peptidebond

Fig. 5-18

Amino end(N-terminus)

Peptidebond

Side chains

Backbone

Carboxyl end(C-terminus)

(a)

(b)

Fig. 5-UN5

Fig. 5-21

PrimaryStructure

SecondaryStructure

TertiaryStructure

pleated sheet

Examples ofamino acidsubunits

+H3N Amino end

helix

QuaternaryStructure

Fig. 5-21a

Amino acidsubunits

+H3N Amino end

25

20

15

10

5

1

Primary Structure

Fig. 5-21b

Amino acidsubunits

+H3N Amino end

Carboxyl end125

120

115

110

105

100

95

9085

80

75

20

25

15

10

5

1

Fig. 5-21c

Secondary Structure

pleated sheet

Examples ofamino acidsubunits

helix

Fig. 5-21f

Polypeptidebackbone

Hydrophobicinteractions andvan der Waalsinteractions

Disulfide bridge

Ionic bond

Hydrogenbond

Fig. 5-21e

Tertiary Structure Quaternary Structure

Fig. 5-21g

Polypeptidechain

Chains

HemeIron

Chains

CollagenHemoglobin

Fig. 5-22a

Primarystructure

Secondaryand tertiarystructures

Function

Quaternarystructure

Molecules donot associatewith oneanother; eachcarries oxygen.

Normalhemoglobin(top view)

subunit

Normal hemoglobin

7654321

GluVal His Leu Thr Pro Glu

Fig. 5-22b

Primarystructure

Secondaryand tertiarystructures

Function

Quaternarystructure

Molecules interact with one another andcrystallize into a fiber; capacity to carry oxygenis greatly reduced.

Sickle-cellhemoglobin

subunit

Sickle-cell hemoglobin

7654321

ValVal His Leu Thr Pro Glu

Exposedhydrophobicregion

Fig. 5-22c

Normal red bloodcells are full ofindividualhemoglobinmolecules, each carrying oxygen.

Fibers of abnormalhemoglobin deformred blood cell intosickle shape.

10 µm 10 µm

What Determines Protein Structure?

• In addition to primary structure, physical and chemical conditions can affect structure

• Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel

• This loss of a protein’s native structure is called denaturation

• A denatured protein is biologically inactive

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 5-23

Normal protein Denatured protein

Denaturation

Renaturation

The Roles of Nucleic Acids

• There are two types of nucleic acids:

– Deoxyribonucleic acid (DNA)

– Ribonucleic acid (RNA)

• DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis

• Protein synthesis occurs in ribosomes

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 5-26-3

mRNA

Synthesis ofmRNA in thenucleus

DNA

NUCLEUS

mRNA

CYTOPLASM

Movement ofmRNA into cytoplasmvia nuclear pore

Ribosome

AminoacidsPolypeptide

Synthesisof protein

1

2

3

Fig. 5-27ab5' end

5'C

3'C

5'C

3'C

3' end

(a) Polynucleotide, or nucleic acid

(b) Nucleotide

Nucleoside

Nitrogenousbase

3'C

5'C

Phosphategroup Sugar

(pentose)

Fig. 5-27c-1

(c) Nucleoside components: nitrogenous bases

Purines

Guanine (G)Adenine (A)

Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)

Nitrogenous bases

Pyrimidines

Fig. 5-27c-2

Ribose (in RNA)Deoxyribose (in DNA)

Sugars

(c) Nucleoside components: sugars

Nucleotide Polymers

• Adjacent nucleotides are joined by covalent bonds (phosphodiester linkage)

• The nitrogenous bases in DNA pair up and form hydrogen bonds:

– adenine (A) always with thymine (T)

– guanine (G) always with cytosine (C)

• Forms a double helix

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 5-28

Sugar-phosphatebackbones

3' end

3' end

3' end

3' end

5' end

5' end

5' end

5' end

Base pair (joined byhydrogen bonding)

Old strands

Newstrands

Nucleotideabout to beadded to anew strand