biological molecules. the hydrocarbon skeleton provides a basic framework: biological molecules...

Biological Molecules

The hydrocarbon skeleton provides a basic framework:

Biological Molecules Small and Large

Figure 3-3Figure 3-3

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 4.5 Variations in carbon skeletons

HH H HH C

H H H HH

H

HH

H

H

H H H

H

H

H

H H H

H H H

H H

H

H

H

H

H

H

HH

H

H H H H

H H

H H

H H H H

H H

H H

HH

HH

H

H

H

C C C C C

C C C C C C C

CCCCCCCC

C

CC

C

C

C

C

CC

C

C

C

H

H

H

HH

H

H

(a) Length

(b) Branching

(c) Double bonds

(d) Rings

Ethane Propane

Butane 2-methylpropane(commonly called isobutane)

1-Butene 2-Butene

Cyclohexane Benzene

Functional Groups• Hydroxyl group R-OH

• Carbonyl group R-C-H (or R)

• Carboxyl group R-C

• Amino group R-N

• Sulfhydryl group R-SH

• Phosphate group R-O-P-O–

O

O

OH

H

H

O

O–

Four Classes of Building Blocks

• Lipids

• Sugars – polysaccharides

• Nucleotides – nucleic acids

• Amino acids – proteins

Condensation : monomer oligomer polymer

Four Classes of Building Blocks

• Lipids

• Sugars – polysaccharides

• Nucleotides – nucleic acids

• Amino acids – proteins

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Figure 5.12 Examples of saturated and unsaturated fats and fatty acids

(a) Saturated fat and fatty acid

Stearic acid

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Hydrogenated oil

trans double bond

三酸甘油酯

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Hydrophilichead

WATER

WATER

Hydrophobictail

Figure 5.14 Bilayer structure formed by self-assembly of phospholipids in an aqueous environment

膽固醇

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Figure 4.9 A comparison of functional groups of female (estradiol) and male (testosterone) sex hormones

CH3

OH

HO

O

CH3

CH3

OH

Estradiol

Testosterone

Female lion

Male lion

Four Classes of Building Blocks

• Lipids

• Sugars – polysaccharides

Carbohydrate (C:H2O = 1:1)

• Nucleotides – nucleic acids

• Amino acids – proteins

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 5.4 Linear and ring forms of glucose

(b) Abbreviated ring structure. Each corner represents a carbon. The ring’s thicker edge indicates that you are looking at the ring edge-on; the components attached to the ring lie above or below the plane of the ring.

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

4 C

6 CH2OH 6 CH2OH

5 C

HOH

C

H OH

H

2 C

1C

H

O

H

OH

4 C

5 C

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

Here are twomonosaccharides …

and a disaccharide(sucrose) formed by a condensation reactionbetween the two mono-saccharides.

Biological Molecules Small and Large

Figure 3-11Figure 3-11

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Figure 5.6 Storage polysaccharides of plants and animals

Mitochondria Giycogen granulesChloroplast Starch

Amylose Amylopectin

1 m

0.5 m

(a) Starch: a plant polysaccharide (b) Glycogen: an animal polysaccharide

Glycogen

Four Classes of Building Blocks

• Lipids

• Sugars – polysaccharides

• Nucleotides – nucleic acids

• Amino acids – proteins

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 5.25 DNA RNA protein: a diagrammatic overview of information flow in a cell

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

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Figure 5.27 The DNA double helix and its replication3 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

C G

C G

AT

C G

A T

A T

G C

A T

A T

T A

G

AC

C

C

G G

T

A

A

T

C

G

A

T

G

C

A

T

A

T

T

A

C

GA

T

A

T

G

C

T

AA

TT

A

C

G

A

T

T

A

C

G

T

A

C

GG

C

T

CG

5 end

Four Classes of Building Blocks

• Lipids

• Sugars – polysaccharides

• Nucleotides – nucleic acids

• Amino acids – proteins

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

S

Figure 5.17 The 20 amino acids of proteins

O

O–

O

O–

H

H3N+ C C

O

O–

H

CH3

H3N+ C

H

C

O

O–

CH3 CH3

CH3

C C

O

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3

CH3

CH2

CH

C

H

H3N+ C

CH3

CH2

CH2

CH3N+

H

C

O

O–

CH2

CH3N+

H

C

O

O–

CH2

NH

H

C

O

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

Nonpolar

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

Methionine (Met) Phenylalanine (Phe)

C

O

O–

Tryptophan (Trp) Proline (Pro)

H3C

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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 C

O

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)

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Figure 5.18 Making a polypeptide chain

Carboxyl end

(C-terminus)

DESMOSOMES

OH

DESMOSOMESDESMOSOMES

OH

CH2

C

N

H

C

H O

H OH OH

Peptidebond

OH

OH

OH

H H

HH

H

H

H

H

H

H H

H

N

N N

N N

SH Side chains

SH

OO

O O O

H2O

CH2 CH2

CH2 CH2CH2

C C C C C C

C CC C

Peptidebond

Amino end(N-terminus)

Backbone

(a)

(b)

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Figure 5.20 Exploring Levels of Protein Structure: Tertiary structure

Figure 5.20 Exploring Levels of Protein Structure: Tertiary structure

CH2

OH

O

COH

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH

CH3

CH3

H3C

H3C

Hydrophobic interactions and van der Waalsinteractions

Polypeptidebackbone

Hydrogenbond

Ionic bond

Disulfide bridge

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Polypeptidechain

Collagen

Chains

ChainsHemoglobin

IronHeme

Figure 5.20 Exploring Levels of Protein Structure: Quaternary Structure

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Exposed hydrophobic region

Figure 5.21 A single amino acid substitution in a protein causes sickle-cell disease

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

Fibers of abnormalhemoglobin deform cell into sickle shape

subunit subunit

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

Normal hemoglobin Sickle-cell hemoglobin. . .. . .Val His Leu Thr Pro Glu Glu Val His Leu Thr Pro Val Glu

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 5.16 The catalytic cycle of an enzyme

Substrate(sucrose)

Enzyme (sucrase)

Glucose

OH

H O

H2O

Fructose

1 Active site is available for a molecule of substrate, the

reactant on which the enzyme acts.

2 Substrate binds toenzyme.

4 Products are released. 3 Substrate is convertedto products.

Four Classes of Building Blocks

• Lipids

• Sugars – polysaccharides

• Nucleotides – nucleic acids

• Amino acids – proteins

Why are All Organisms Made of Cells?

• All Organisms Are Made of Cells

• Cell Theory– All organisms are composed of one or more

cells.– Cells are the basic unit of organization of all

organisms.– All cells come from existing cells.

Every Cell Consists of a Boundary, a Cell Body, and a Set of Genes

– The Plasma Membrane • The boundary of the cell which serves to define the limits of the cell and selectively admit and excrete specific molecules.

– A set of Genetic Instructions• It is contained in one or more molecules of DNA.• Nucleus/nucleoid

– The Cell Body• The cytoplasm, which is the portion of the cell outside the nucleus but inside the membrane.

• Cytosol, organelles, cytoskeleton

Why Are All Organisms Made of Cells?

• Every Cell Consists of a Boundary, a Cell Body, and a Set of Genes

• Two Major Cell Types• Prokaryotic Cells

– pro = before, Karyo = nucleus – Prokaryotic cells lack a nucleus and other membrane bou

nd organelles.

– Bacteria and blue green algae are examples.

– They are generally smaller than eukaryotic cells

0.4 to 5 micrometers (μm) vs. 10-100 μm

Why Are All Organisms Made of Cells?

How Are Cells Alive?How Are Cells Alive?Cells are the fundamental living units of life Cells are the fundamental living units of life and all contain the characteristics of life and all contain the characteristics of life discussed in Chapter 1.discussed in Chapter 1.

organizationorganization chemical transformationschemical transformationsenergy transformationsenergy transformations changechangeresponsivenessresponsiveness continuitycontinuity

reproductionreproduction

Copyright 2001 by Harcourt, Inc.

Why Are All Organisms Made of Cells?Why Are All Organisms Made of Cells?

6

Copyright 2001 by Harcourt, Inc.

Individual Cells May Specialize for Different TasksIndividual Cells May Specialize for Different Tasks

Cellular organization allows organisms to make a division Cellular organization allows organisms to make a division of labor among specialized cells.of labor among specialized cells.

If you were one big cell, organizing your body to perform If you were one big cell, organizing your body to perform all its different jobs would be difficult.all its different jobs would be difficult.

MulticellularityMulticellularity allows individual specialization.allows individual specialization.For example, your red blood cells specialize in carrying oxygen For example, your red blood cells specialize in carrying oxygen and your heart cells function to pump blood throughout your bodyand your heart cells function to pump blood throughout your body..

Why Are All Organisms Made of Cells?Why Are All Organisms Made of Cells?

3-D Animation of Vessel Trafficking© 1995 Robert Ezzell

Traffic Through the Golgi Apparatus© 1997 The Mona Group LLC

The Endomembrane System in Action© 1997 The Mona Group LLC

Lysosome and Mitochondria Transport© Mark Cooper

Golgi Bodies© 1994 Cytographics

Endoplasmic Reticulum Extension© Mark Cooper

Videos and AnimationsChapter 9: Protein Sorting and Transport: The Endoplasmic Reticulum,

Golgi Apparatus, and Lysosomes

Dynamic mitochondria

Microtubule Assembly and Breakdown© 1997 The Mona Group LLC

Organization of a Thin Filament in Skeletal Muscle© 1997 The Mona Group LLC

Assembly of an Actin Filament© 1997 The Mona Group LLC

Gelsolin Catalyzes the Breakdown of Actin Filaments© 1997 The Mona Group LLC

A Flagellum© 1997 The Mona Group LLC

Kinesin is a Motor Protein© 1997 The Mona Group LLC

Videos and AnimationsChapter 11: The Cytoskeleton and Cell Movement

Ca2+ Wave at Fertilization of Xenopus Egg© L. Jaffe and Linda Runft

Neuronal Growth Cone Motility© Paul Forscher Laboratory, Dept. Molecular, Cellular & Developmental Biology, Yale University

Cell Locomotion in a Flagellate,Part 2© Sidney Tamm

Cell Locomotion in a Flagellate,Part 1© Sidney Tamm

Proteus Swarm Cells© 1995 James Shapiro[swarm_cells.mov]

Slime Mold Morphogenesis© 1991 John Bonner[slimemold.mov]

Videos and AnimationsChapter 12: The Cell Surface

WHAT DO MEMBRANES DO?

– Membranes are essential boundaries that separate the inside from the outside;

– Membranes regulate the contents of the spaces they enclose;

– Membranes serve as a “workbench” for a variety of biochemical reactions;

– Membranes participate in energy conversions.

Why Are All Organisms Made of Cells?

membrane