Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings I-2- 1 The Structure and...

• The Structure and Function of Nucleic Acids and Proteins Macromolecules

• Macromolecules

– Are large molecules composed of smaller molecules

– Are complex in their structures

Concept 1: Most macromolecules are polymers, built from monomers

Three of the classes of life’s organic molecules are polymers

– Carbohydrates

– Proteins

– Nucleic acids

The Synthesis and Breakdown of Polymers

• A polymer is a long molecule consisting of many similar building blocks called monomers

• Monomers form larger molecules by condensation reactions called dehydration reactions

(a) Dehydration reaction in the synthesis of a polymer

HO H1 2 3 HO

HO H1 2 3 4

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a watermolecule, forming a new bond

• Polymers can disassemble by

– Hydrolysis

(b) Hydrolysis of a polymer

HO 1 2 3 H

HO H1 2 3 4

Hydrolysis adds a watermolecule, breaking a bond

The Diversity of Polymers

• Each class of polymer

– Is formed from a specific set of monomers

• 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

1 2 3 HOH

Concept 2: Nucleic acids store and transmit hereditary information

• Genes

– Are the units of inheritance

– Program the amino acid sequence of polypeptides

– Are made of nucleic acids

The Roles of Nucleic Acids

• There are two types of nucleic acids

– Deoxyribonucleic acid (DNA)

– Ribonucleic acid (RNA)

• DNA

– Stores information for the synthesis of specific proteins

– Directs RNA synthesis

– Directs protein synthesis through RNA

Synthesis of mRNA in the nucleus

Movement of mRNA into cytoplasm

via nuclear pore

Synthesisof protein

NUCLEUSCYTOPLASM

Ribosome

AminoacidsPolypeptide

The Structure of Nucleic Acids

• Nucleic acids

– Exist as polymers called polynucleotides

(a) Polynucleotide, or nucleic acid

5’ end

3’ endOH

• Each polynucleotide

– Consists of monomers called nucleotides

Nitrogenousbase

Nucleoside

O P CH2

3’CPhosphate

group Pentosesugar

(b) Nucleotide

Nucleotide Monomers

• Nucleotide monomers

– Are made up of nucleosides and phosphate groups

(c) Nucleoside components

Uracil (in RNA)U

Ribose (in RNA)

Nitrogenous bases Pyrimidines

CytosineC

Thymine (in DNA)T

AdenineA

GuanineG

Purines

OHOCH2

Pentose sugars

Deoxyribose (in DNA) Ribose (in RNA)OHOH

Uracil (in RNA)U

3’OH H

3’ 2’

Pyrimidines

Purines

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

• The sequence of bases along a nucleotide polymer

– Is unique for each gene

The DNA Double Helix

• Cellular DNA molecules

– Have two polynucleotides that spiral around an imaginary axis

– Form a double helix

• The DNA double helix

– Consists of two antiparallel nucleotide strands3’ end

Sugar-phosphatebackbone

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to be added to a new strand

3’ end

5’ end

Newstrands

3’ end

5’ end

• The nitrogenous bases in DNA

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

Nitrogenousbase

Nucleoside

O P CH2

3’CPhosphate

group Pentosesugar

(b) Nucleotide

Light absorption and temperature in DNA denaturation

James Watson and Francis Crick with a model of the DNA molecule, the double helix.

X-Ray Diffraction Photograph of a Hydrated DNA Fiber

Dr. Rosalind FranklinPhotograph 51

Rosalind Franklin: The Dark Lady of DNA

(Brenda Maddox, 2002)

Dark Lady of DNA

Electron Micrograph of Part of the E. coli genome

討論：

•DNA有何特徵？– １

– ２

– ３

The chemical structure of RNA

The conformation of an RNA molecule

Transfer RNA (tRNA)

RNA secondary and tertiary structures

Complex Structure of an RNA Molecule

討論：

•RNA有何特徵？– １

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Concept 3: Proteins have many structures, resulting in a wide range of functions

– Proteins

• Have many roles inside the cell

An overview of protein functions

• Enzymes

– Are a type of protein that acts as a catalyst, speeding up chemical reactions

Substrate(sucrose)

Enzyme (sucrase)

Glucose

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.

4 Products are released.

Polypeptides

• Polypeptides

– Are polymers of amino acids

• A protein

– Consists of one or more polypeptides

Amino Acid Monomers

• Amino acids

– Are organic molecules possessing both carboxyl and amino groups

– Differ in their properties due to differing side chains, called R groups

• 20 different amino acids make up proteins

H3N+ C C

H3N+ C

CH3 CH3

H3N+ C

Nonpolar

Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

Tryptophan (Trp) Proline (Pro)

OH CH3

H3N+ C

H3N+ C C

C CH3N+

Electricallycharged

–O O

C CH3N+

O– O

C CH3N+

C NH2+

C CH3N+

Serine (Ser) Threonine (Thr)Cysteine

(Cys)Tyrosine

(Tyr)Asparagine

(Asn)Glutamine

Acidic Basic

Aspartic acid (Asp)

Glutamic acid (Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)

Amino Acid Polymers

• Amino acids

– Are linked by peptide bondsOH

DESMOSOMES

DESMOSOMESDESMOSOMES

H OH OH

Peptidebond

SHSide

chains

CH2 CH2

CH2 CH2CH2

C C C C C C

C CC C

Peptidebond

Amino end(N-terminus)

Backbone

(b) Carboxyl end(C-terminus)

Determining the Amino Acid Sequence of a Polypeptide

• The amino acid sequences of polypeptides

– Were first determined using chemical means

– Can now be determined by automated machines

Protein Conformation and Function

• A protein’s specific conformation

– Determines how it functions

• Two models of protein

• conformation:

(a) A ribbon model

(b) A space-filling model

Groove

Four Levels of Protein Structure

• Primary structure

– Is the unique sequence of amino acids in a polypeptide

Amino acid subunits

+H3NAmino

oCarboxyl end

GlyProThrGlyThr

GluSeuLysCysProLeu

MetVal

ValLeu

AspAlaVal ArgGly

SerPro

SerProPheHisGluHis

GluVal

ValPheThrAlaAsn

AspSer

GlyProArg

ArgTyrThr

lleAla

LeuSer

ProTyrSerTyrSerThr

ValVal

ThrAsnProLysGlu

ThrLys

SerTyrTrpLysAlaLeu

GluLle Asp

O C helix

pleated sheet

Amino acidsubunits NC

O CH C R

• Secondary structure

– Is the folding or coiling of the polypeptide into a repeating configuration

– Includes the helix and the pleated sheet

• Tertiary structure

– Is the overall three-dimensional shape of a polypeptide

– Results from interactions between amino acids and R groups

CH2 NH3+ C-O CH2

CH2SSCH2

Hydrophobic interactions and van der Waalsinteractions

Polypeptidebackbone

Hyrdogenbond

Ionic bond

Disulfide bridge

• Quaternary structure

– Is the overall protein structure that results from the aggregation of two or more polypeptide subunits

Polypeptidechain

Collagen Chains

ChainsHemoglobin

IronHeme

• The four levels of protein structure

+H3NAmino end

Amino acidsubunits

Sickle-Cell Disease: A Simple Change in Primary Structure

• Sickle-cell disease

– Results from a single amino acid substitution in the protein hemoglobin

• Hemoglobin structure and sickle-cell disease

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 S

Molecules 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. . .. . . Exposed

hydrophobic region

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

What Determines Protein Conformation?

• Protein conformation

– Depends on the physical and chemical conditions of the protein’s environment

Denaturation

• Is when a protein unravels and loses its native conformation

Denaturation

Renaturation

Denatured proteinNormal protein

Flexibility and Function: the protein lactoferrin

The Protein-Folding Problem

• Most proteins

– Probably go through several intermediate states on their way to a stable conformation

Chaperonins

– Are protein molecules that assist in the proper folding of other proteins

Hollowcylinder

Chaperonin(fully assembled)

Steps of ChaperoninAction: An unfolded polypeptide 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

X-ray crystallography

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

diffraction pattern

Photographic film

Diffracted X-rays

X-raysource

X-ray beam

Crystal Nucleic acid Protein

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

An overview of protein functions

討論：

•蛋白質有何特徵？– １

– ２

– ３

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings I-2- 1 The Structure and...

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