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AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

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Page 1: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

AP BiologyUnit 1

Chapters 1-7

Introduction, Biochemistry and Cells

Page 2: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Chapter One: Overview: Inquiring About Life

• An organism’s adaptations to its environment are the result of evolution

– For example, the ghost plant is adapted to conserving water; this helps it to survive in the crevices of rock walls

• Evolution is the process of change that has transformed life on Earth

© 2011 Pearson Education, Inc.

Page 3: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 1.1

Page 4: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 1.3

Order

Evolutionary adaptation

Response tothe environment

Reproduction

Growth anddevelopment

Energy processing

Regulation

Page 5: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Theme: New Properties Emerge at Each Level in the Biological Hierarchy

• Life can be studied at different levels, from molecules to the entire living planet

• The study of life can be divided into different levels of biological organization

© 2011 Pearson Education, Inc.

Page 6: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

The biosphere

EcosystemsTissues

Organs andorgan systems

Communities

Populations

Organisms

OrganellesCells

Atoms

Molecules

Figure 1.4

Page 7: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Theme: Organisms Interact with Other Organisms and the Physical Environment

• Every organism interacts with its environment, including nonliving factors and other organisms

• Both organisms and their environments are affected by the interactions between them

© 2011 Pearson Education, Inc.

Page 8: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Animals eatleaves and fruitfrom the tree.

Leaves take incarbon dioxidefrom the airand releaseoxygen.

Sunlight

CO2

O2

Cyclingof

chemicalnutrients

Leaves fall tothe ground andare decomposedby organismsthat returnminerals to thesoil.

Water andminerals inthe soil aretaken up bythe treethroughits roots.

Leaves absorblight energy fromthe sun.

Figure 1.5

Page 9: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Theme: Life Requires Energy Transfer and Transformation

• A fundamental characteristic of living organisms is their use of energy to carry out life’s activities

• Work, including moving, growing, and reproducing, requires a source of energy

• Living organisms transform energy from one form to another– For example, light energy is converted to chemical

energy, then kinetic energy• Energy flows through an ecosystem, usually entering as

light and exiting as heat© 2011 Pearson Education, Inc.

Page 10: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 1.6

Heat

Producers absorb lightenergy and transform it intochemical energy.

Chemicalenergy

Chemical energy infood is transferredfrom plants toconsumers.

(b) Using energy to do work(a) Energy flow from sunlight toproducers to consumers

Sunlight

An animal’s musclecells convertchemical energyfrom food to kineticenergy, the energyof motion.

When energy is usedto do work, someenergy is converted tothermal energy, whichis lost as heat.

A plant’s cells usechemical energy to dowork such as growingnew leaves.

Page 11: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Theme: Structure and Function Are Correlated at All Levels of Biological Organization

• Structure and function of living organisms are closely related

– For example, a leaf is thin and flat, maximizing the capture of light by chloroplasts

– For example, the structure of a bird’s wing is adapted to flight

© 2011 Pearson Education, Inc.

Page 12: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 1.7

(a) Wings(b) Wing bones

Page 13: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Theme: The Cell Is an Organism’s Basic Unit of Structure and Function

• The cell is the lowest level of organization that can perform all activities required for life

• All cells– Are enclosed by a membrane– Use DNA as their genetic information

© 2011 Pearson Education, Inc.

Page 14: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Eukaryotic cellProkaryotic cell

Cytoplasm

DNA(no nucleus)

Membrane

Nucleus(membrane-enclosed)

Membrane

Membrane-enclosed organelles

DNA (throughoutnucleus) 1 m

Figure 1.8

Page 15: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Theme: The Continuity of Life Is Based on Heritable Information in the Form of DNA

• Chromosomes contain most of a cell’s genetic material in the form of DNA (deoxyribonucleic acid)

• DNA is the substance of genes• Genes are the units of inheritance that transmit

information from parents to offspring• The ability of cells to divide is the basis of all

reproduction, growth, and repair of multicellular organisms

© 2011 Pearson Education, Inc.

Page 16: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 1.9

25 m

Page 17: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Nucleus

DNA

Cell

Nucleotide

(b) Single strand of DNA

A

C

T

T

A

A

T

C

C

G

T

A

G

T

(a) DNA double helix

A

Figure 1.11

Page 18: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Theme: Feedback Mechanisms Regulate Biological Systems

• Feedback mechanisms allow biological processes to self-regulate

• Negative feedback means that as more of a product accumulates, the process that creates it slows and less of the product is produced

• Positive feedback means that as more of a product accumulates, the process that creates it speeds up and more of the product is produced

© 2011 Pearson Education, Inc.

Animation: Negative Feedback

Animation: Positive Feedback

Page 19: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Negativefeedback

A

B

D

C

Enzyme 2

Enzyme 3

D

DDExcess Dblocks a step.

(a) Negative feedback

Enzyme 1

Figure 1.13a

Page 20: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

W

Enzyme 4

XPositive feedback

Excess Zstimulates a step.

Y

Z

ZZ

Z

(b) Positive feedback

Enzyme 5

Enzyme 6

Figure 1.13b

Page 21: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Evolution, the Overarching Theme of Biology

• Evolution makes sense of everything we know about biology

• Organisms are modified descendants of common ancestors

© 2011 Pearson Education, Inc.

Page 22: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• Evolution explains patterns of unity and diversity in living organisms

• Similar traits among organisms are explained by descent from common ancestors

• Differences among organisms are explained by the accumulation of heritable changes

© 2011 Pearson Education, Inc.

Page 23: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 1.15

(a) Domain Bacteria (b) Domain Archaea

(c) Domain Eukarya

2 m

2 m

100 m

Kingdom Plantae

Kingdom Fungi

Protists

Kingdom Animalia

Page 24: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Unity in the Diversity of Life

• A striking unity underlies the diversity of life; for example

– DNA is the universal genetic language common to all organisms

– Unity is evident in many features of cell structure

© 2011 Pearson Education, Inc.

Page 25: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 1.16

Cilia ofParamecium

15 m

Cross section of a cilium, as viewedwith an electron microscope

0.1 m

Cilia ofwindpipecells

5 m

Page 26: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Concept 1.3: In studying nature, scientists make observations and then form and test hypotheses

• The word science is derived from Latin and means “to know”

• Inquiry is the search for information and explanation• The scientific process includes making observations,

forming logical hypotheses, and testing them

© 2011 Pearson Education, Inc.

Page 27: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 1.23

Page 28: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

The Role of Hypotheses in Inquiry

• A hypothesis is a tentative answer to a well-framed question

• A scientific hypothesis leads to predictions that can be tested by observation or experimentation

© 2011 Pearson Education, Inc.

Page 29: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• For example,– Observation: Your flashlight doesn’t work– Question: Why doesn’t your flashlight work?– Hypothesis 1: The batteries are dead– Hypothesis 2: The bulb is burnt out

• Both these hypotheses are testable

© 2011 Pearson Education, Inc.

Page 30: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• Hypothesis-based science often makes use of two or more alternative hypotheses

• Failure to falsify a hypothesis does not prove that hypothesis– For example, you replace your flashlight bulb, and

it now works; this supports the hypothesis that your bulb was burnt out, but does not prove it (perhaps the first bulb was inserted incorrectly)

© 2011 Pearson Education, Inc.

Page 31: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Questions That Can and Cannot Be Addressed by Science

• A hypothesis must be testable and falsifiable– For example, a hypothesis that ghosts fooled with the

flashlight cannot be tested• Supernatural and religious explanations are outside

the bounds of science

© 2011 Pearson Education, Inc.

Page 32: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

The Flexibility of the Scientific Method

• The scientific method is an idealized process of inquiry• Hypothesis-based science is based on the “textbook”

scientific method but rarely follows all the ordered steps

© 2011 Pearson Education, Inc.

Page 33: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 1.26

(a) Artificial kingsnake

(b) Brown artificial snake that has been attacked

Page 34: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Experimental Controls and Repeatability

• A controlled experiment compares an experimental group (the artificial kingsnakes) with a control group (the artificial brown snakes)

• Ideally, only the variable of interest (the effect of coloration on the behavior of predators) differs between the control and experimental groups

• A controlled experiment means that control groups are used to cancel the effects of unwanted variables

• A controlled experiment does not mean that all unwanted variables are kept constant

© 2011 Pearson Education, Inc.

Page 35: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• In science, observations and experimental results must be repeatable

© 2011 Pearson Education, Inc.

Page 36: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Chapter TWO:The Chemical Context of Life

Chapter 2

Page 37: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• Atoms in a molecule attract electrons to varying degrees

• Electronegativity is an atom’s attraction for the electrons in a covalent bond

• The more electronegative an atom, the more strongly it pulls shared electrons toward itself

© 2011 Pearson Education, Inc.

Page 38: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 2.13

H H

H2O+ +

O

Page 39: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Hydrogen Bonds

• A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

• In living cells, the electronegative partners are usually oxygen or nitrogen atoms

© 2011 Pearson Education, Inc.

Page 40: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 2.16

Water (H2O)

Ammonia (NH3)

Hydrogen bond

+

+

+

+

+

Page 41: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Chapter THREE:Water and Life

Chapter 3

Page 42: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Concept 3.1: Polar covalent bonds in water molecules result in hydrogen bonding

• The water molecule is a polar molecule: the opposite ends have opposite charges

• Polarity allows water molecules to form hydrogen bonds with each other

© 2011 Pearson Education, Inc.

Animation: Water Structure

Page 43: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 3.2

Hydrogenbond

Polar covalentbonds

+

+

+

+

Page 44: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 3.UN02

2 H2O Hydroxideion (OH)

Hydroniumion (H3O+)

+

Page 45: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Acidification: A Threat to Water Quality

• Human activities such as burning fossil fuels threaten water quality

• CO2 is the main product of fossil fuel combustion

• About 25% of human-generated CO2 is absorbed by the oceans

• CO2 dissolved in sea water forms carbonic acid; this process is called ocean acidification

© 2011 Pearson Education, Inc.

Page 46: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 3.11

CO2

CO2 + H2O H2CO3

H+ + HCO3

H+ + CO32 HCO3

CaCO3 CO32 + Ca2+

H2CO3

Page 47: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Chapter FOUR: Carbon and the Molecular Diversity of Life

Chapter 4

Page 48: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 4.4

Hydrogen(valence 1)

Oxygen(valence 2)

Nitrogen(valence 3)

Carbon(valence 4)

Page 49: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 4.UN02

Estradiol

Testosterone

Page 50: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• The seven functional groups that are most important in the chemistry of life:

– Hydroxyl group– Carbonyl group– Carboxyl group– Amino group– Sulfhydryl group– Phosphate group– Methyl group

© 2011 Pearson Education, Inc.

Page 51: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 4.9f

Phosphate

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Organic phosphates

Glycerol phosphate

• Contributes negativecharge to the moleculeof which it is a part(2– when at the end ofa molecule, as at left;1– when locatedinternally in a chain ofphosphates).

• Molecules containingphosphate groups havethe potential to reactwith water, releasingenergy.

Page 52: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

ATP: An Important Source of Energy for Cellular Processes

• One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell

• ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups

© 2011 Pearson Education, Inc.

Page 53: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 4. UN04

Adenosine

Page 54: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 4. UN05

AdenosineAdenosine

Reactswith H2O

Inorganicphosphate

ATP ADP

Energy

Page 55: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Chapter FIVE: The Structure and Function of Large Biological Molecules

Chapter 5

Page 56: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.2a

(a) Dehydration reaction: synthesizing a polymer

Short polymer Unlinked monomer

Dehydration removesa water molecule,forming a new bond.

Longer polymer

1 2 3 4

1 2 3

Page 57: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.2b

(b) Hydrolysis: breaking down a polymer

Hydrolysis addsa water molecule,breaking a bond.

1 2 3 4

1 2 3

Page 58: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.7b

(b) Starch: 1–4 linkage of glucose monomers

(c) Cellulose: 1–4 linkage of glucose monomers

41

41

Page 59: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.9

Chitin forms the exoskeletonof arthropods.

The structureof the chitinmonomer

Chitin is used to make a strong and flexiblesurgical thread that decomposes after thewound or incision heals.

Page 60: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.10

(a) One of three dehydration reactions in the synthesis of a fat

(b) Fat molecule (triacylglycerol)

Fatty acid(in this case, palmitic acid)

Glycerol

Ester linkage

Page 61: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.11

(a) Saturated fat(b) Unsaturated fat

Structuralformula of asaturated fatmolecule

Space-fillingmodel of stearicacid, a saturatedfatty acid

Structuralformula of anunsaturated fatmolecule

Space-filling modelof oleic acid, anunsaturated fattyacid

Cis double bondcauses bending.

Page 62: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.12

Choline

Phosphate

Glycerol

Fatty acids

Hydrophilichead

Hydrophobictails

(c) Phospholipid symbol(b) Space-filling model(a) Structural formula

Hyd

roph

ilic

head

Hyd

roph

obic

tails

Page 63: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.13

Hydrophilichead

Hydrophobictail

WATER

WATER

Page 64: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.15a

Enzymatic proteins

Enzyme

Example: Digestive enzymes catalyze the hydrolysisof bonds in food molecules.

Function: Selective acceleration of chemical reactions

Page 65: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.15b

Storage proteins

Ovalbumin Amino acidsfor embryo

Function: Storage of amino acidsExamples: Casein, the protein of milk, is the majorsource of amino acids for baby mammals. Plants havestorage proteins in their seeds. Ovalbumin is theprotein of egg white, used as an amino acid sourcefor the developing embryo.

Page 66: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.15c

Hormonal proteins

Function: Coordination of an organism’s activitiesExample: Insulin, a hormone secreted by thepancreas, causes other tissues to take up glucose,thus regulating blood sugar concentration

Highblood sugar

Normalblood sugar

Insulinsecreted

Page 67: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.15d

Muscle tissue

Actin Myosin

100 m

Contractile and motor proteins

Function: Movement

Examples: Motor proteins are responsible for theundulations of cilia and flagella. Actin and myosinproteins are responsible for the contraction ofmuscles.

Page 68: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.15e

Defensive proteins

Virus

Antibodies

Bacterium

Function: Protection against diseaseExample: Antibodies inactivate and help destroyviruses and bacteria.

Page 69: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.15f

Transport proteins

Transportprotein

Cell membrane

Function: Transport of substancesExamples: Hemoglobin, the iron-containing protein ofvertebrate blood, transports oxygen from the lungs toother parts of the body. Other proteins transportmolecules across cell membranes.

Page 70: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.15g

Signalingmolecules

Receptorprotein

Receptor proteins

Function: Response of cell to chemical stimuliExample: Receptors built into the membrane of anerve cell detect signaling molecules released byother nerve cells.

Page 71: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.15h

60 m

Collagen

Connectivetissue

Structural proteins

Function: SupportExamples: Keratin is the protein of hair, horns,feathers, and other skin appendages. Insects andspiders use silk fibers to make their cocoons and webs,respectively. Collagen and elastin proteins provide afibrous framework in animal connective tissues.

Page 72: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

© 2011 Pearson Education, Inc.

Animation: Structural Proteins

Animation: Storage Proteins

Animation: Transport Proteins

Animation: Receptor Proteins

Animation: Contractile Proteins

Animation: Defensive Proteins

Animation: Hormonal Proteins

Animation: Sensory Proteins

Animation: Gene Regulatory Proteins

Page 73: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Polypeptides

• Polypeptides are unbranched polymers built from the same set of 20 amino acids

• A protein is a biologically functional molecule that consists of one or more polypeptides

© 2011 Pearson Education, Inc.

Page 74: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Four Levels of Protein Structure

• The primary structure of a protein is its unique sequence of amino acids

• Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain

• Tertiary structure is determined by interactions among various side chains (R groups)

• Quaternary structure results when a protein consists of multiple polypeptide chains

© 2011 Pearson Education, Inc.

Animation: Protein Structure Introduction

Page 75: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.20aPrimary structure

Aminoacids

Amino end

Carboxyl end

Primary structure of transthyretin

Page 76: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word

• Primary structure is determined by inherited genetic information

© 2011 Pearson Education, Inc.

Animation: Primary Protein Structure

Page 77: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.20b

Secondarystructure

Tertiarystructure

Quaternarystructure

Hydrogen bond

helix

pleated sheet strand

Hydrogenbond

Transthyretinpolypeptide

Transthyretinprotein

Page 78: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone

• Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet

© 2011 Pearson Education, Inc.

Animation: Secondary Protein Structure

Page 79: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents

• These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions

• Strong covalent bonds called disulfide bridges may reinforce the protein’s structure

© 2011 Pearson Education, Inc.

Animation: Tertiary Protein Structure

Page 80: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• Quaternary structure results when two or more polypeptide chains form one macromolecule

• Collagen is a fibrous protein consisting of three polypeptides coiled like a rope

• Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains

© 2011 Pearson Education, Inc.

Animation: Quaternary Protein Structure

Page 81: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.25-3

Synthesis ofmRNA

mRNA

DNA

NUCLEUSCYTOPLASM

mRNA

Ribosome

AminoacidsPolypeptide

Movement ofmRNA intocytoplasm

Synthesisof protein

1

2

3

Page 82: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 5.26ab

Sugar-phosphate backbone5 end

5C

3C

5C

3C

3 end(a) Polynucleotide, or nucleic acid

(b) Nucleotide

Phosphategroup Sugar

(pentose)

Nucleoside

Nitrogenousbase

5C

3C

1C

Page 83: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Chapter SIX: A Tour of the Cell

Chapter 6

Page 84: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 6.2 10 m

1 m

0.1 m

1 cm

1 mm

100 m

10 m

1 m

100 nm

10 nm

1 nm

0.1 nm Atoms

Small molecules

Lipids

Proteins

Ribosomes

VirusesSmallest bacteria

MitochondrionMost bacteriaNucleus

Most plant andanimal cells

Human egg

Frog egg

Chicken egg

Length of somenerve andmuscle cells

Human height

Una

ided

eye

Ligh

t mic

rosc

opy

Elec

tron

mic

rosc

opy

Super-resolution

microscopy

Page 85: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Brightfield(unstained specimen)

Brightfield(stained specimen)

50 m

Confocal

Differential-interference-contrast (Nomarski)

Fluorescence

10 m

Deconvolution

Super-resolution

Scanning electronmicroscopy (SEM)

Transmission electronmicroscopy (TEM)

Cross sectionof cilium

Longitudinal sectionof cilium

Cilia

Electron Microscopy (EM)

1 m

10 m

50 m

2 m

2 m

Light Microscopy (LM)

Phase-contrast

Figure 6.3

Page 86: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Concept 6.2: Eukaryotic cells have internal membranes that compartmentalize their functions

• The basic structural and functional unit of every organism is one of two types of cells: prokaryotic or eukaryotic

• Only organisms of the domains Bacteria and Archaea consist of prokaryotic cells

• Protists, fungi, animals, and plants all consist of eukaryotic cells

© 2011 Pearson Education, Inc.

Page 87: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• Metabolic requirements set upper limits on the size of cells

• The surface area to volume ratio of a cell is critical• As the surface area increases by a factor of n2, the

volume increases by a factor of n3

• Small cells have a greater surface area relative to volume

© 2011 Pearson Education, Inc.

Page 88: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Surface area increases whiletotal volume remains constant

Total surface area[sum of the surface areas(height width) of all boxsides number of boxes]

Total volume[height width length number of boxes]

Surface-to-volume(S-to-V) ratio[surface area volume]

1

5

6 150 750

1

1251251

1.26 6

Figure 6.7

Page 89: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

A Panoramic View of the Eukaryotic Cell

• A eukaryotic cell has internal membranes that partition the cell into organelles

• Plant and animal cells have most of the same organelles

© 2011 Pearson Education, Inc.

BioFlix: Tour of an Animal Cell

BioFlix: Tour of a Plant Cell

Page 90: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 6.8a

ENDOPLASMIC RETICULUM (ER)

RoughER

SmoothER

NuclearenvelopeNucleolusChromatin

Plasmamembrane

Ribosomes

Golgi apparatus

LysosomeMitochondrion

Peroxisome

Microvilli

MicrotubulesIntermediate filaments

Microfilaments

Centrosome

CYTOSKELETON:

Flagellum NUCLEUS

Page 91: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

NUCLEUS

Nuclearenvelope

Nucleolus

Chromatin

Golgiapparatus

Mitochondrion

Peroxisome

Plasma membrane

Cell wall

Wall of adjacent cell

Plasmodesmata

Chloroplast

Microtubules

Intermediatefilaments

Microfilaments

CYTOSKELETON

Central vacuole

Ribosomes

Smoothendoplasmicreticulum

Roughendoplasmic

reticulum

Figure 6.8c

Page 92: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Concept 6.4: The endomembrane system regulates protein traffic and performs metabolic functions in the cell

• Components of the endomembrane system– Nuclear envelope– Endoplasmic reticulum– Golgi apparatus– Lysosomes– Vacuoles– Plasma membrane

• These components are either continuous or connected via transfer by vesicles

© 2011 Pearson Education, Inc.

Page 93: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 6.11 Smooth ER

Rough ER

ER lumen

CisternaeRibosomes

Smooth ERTransport vesicle

Transitional ER

Rough ER 200 nm

Nuclearenvelope

Page 94: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 6.12

cis face(“receiving” side ofGolgi apparatus)

trans face(“shipping” side ofGolgi apparatus)

0.1 m

TEM of Golgi apparatus

Cisternae

Page 95: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 6.15-3

Smooth ER

Nucleus

Rough ER

Plasmamembrane

cis Golgi

trans Golgi

Page 96: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

NucleusEndoplasmicreticulum

Nuclear envelope

Ancestor ofeukaryotic cells(host cell)

Engulfing of oxygen-using nonphotosyntheticprokaryote, whichbecomes a mitochondrion

Mitochondrion

Nonphotosyntheticeukaryote

Mitochondrion

At leastone cell

Photosynthetic eukaryote

Engulfing ofphotosyntheticprokaryote

Chloroplast

Figure 6.16

Page 97: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 6.17a

Intermembrane space

Outer

DNA

Innermembrane

Cristae

Matrix

Freeribosomesin themitochondrialmatrix

(a) Diagram and TEM of mitochondrion0.1 m

membrane

Page 98: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 6.18a

RibosomesStroma

Inner and outermembranes

Granum

1 mIntermembrane spaceThylakoid(a) Diagram and TEM of chloroplast

DNA

Page 99: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Peroxisomes: Oxidation

• Peroxisomes are specialized metabolic compartments bounded by a single membrane

• Peroxisomes produce hydrogen peroxide and convert it to water

• Peroxisomes perform reactions with many different functions

• How peroxisomes are related to other organelles is still unknown

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Page 100: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 6.19

ChloroplastPeroxisome

Mitochondrion

1 m

Page 101: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Centrosomes and Centrioles• In many cells, microtubules grow out from a

centrosome near the nucleus• The centrosome is a “microtubule-organizing center”• In animal cells, the centrosome has a pair of

centrioles, each with nine triplets of microtubules arranged in a ring

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Page 102: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Centrosome

Longitudinalsection ofone centriole

Centrioles

Microtubule

0.25 m

Microtubules Cross sectionof the other centriole

Figure 6.22

Page 103: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 6.30a

EXTRACELLULAR FLUIDCollagen

Fibronectin

Plasmamembrane

Micro-filaments

CYTOPLASM

Integrins

Proteoglycancomplex

Page 104: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• Functions of the ECM– Support– Adhesion– Movement– Regulation

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Page 105: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Chapter SEVEN: Membrane Structure and Function

Chapter 7

Page 106: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.2

Hydrophilichead

Hydrophobictail

WATER

WATER

Page 107: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.3

Phospholipidbilayer

Hydrophobic regionsof protein

Hydrophilicregions of protein

Page 108: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.4

Knife

Plasma membrane Cytoplasmic layer

Proteins

Extracellularlayer

Inside of extracellular layer Inside of cytoplasmic layer

TECHNIQUE

RESULTS

Page 109: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.5

Glyco-protein

Carbohydrate

Glycolipid

Microfilamentsof cytoskeleton

EXTRACELLULARSIDE OFMEMBRANE

CYTOPLASMIC SIDEOF MEMBRANE

Integralprotein

Peripheralproteins

Cholesterol

Fibers of extra-cellular matrix (ECM)

Page 110: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.7

Membrane proteins

Mouse cellHuman cell Hybrid cell

Mixed proteinsafter 1 hour

RESULTS

Page 111: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.8

Fluid

Unsaturated hydrocarbontails

Viscous

Saturated hydrocarbon tails

(a) Unsaturated versus saturated hydrocarbon tails

(b) Cholesterol within the animal cell membrane

Cholesterol

Page 112: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.10

Enzymes

Signaling molecule

Receptor

Signal transduction

Glyco-protein

ATP

(a) Transport (b) Enzymatic activity (c) Signal transduction

(d) Cell-cell recognition (e) Intercellular joining (f) Attachment to the cytoskeleton and extracellular matrix (ECM)

Page 113: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.11

Receptor(CD4)

Co-receptor(CCR5)

HIV

Receptor (CD4)but no CCR5 Plasma

membrane

HIV can infect a cell thathas CCR5 on its surface,as in most people.

HIV cannot infect a cell lackingCCR5 on its surface, as in resistant individuals.

Page 114: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.12

Transmembraneglycoproteins

ER

ER lumen

Glycolipid

Plasma membrane:Cytoplasmic face

Extracellular face

Secretoryprotein

Golgiapparatus

Vesicle

Transmembraneglycoprotein Secreted

protein

Membraneglycolipid

Page 115: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.15

Hypotonicsolution

Osmosis

Isotonicsolution

Hypertonicsolution

(a) Animal cell

(b) Plant cell

H2O H2O H2O H2O

H2O H2O H2O H2OCell wall

Lysed Normal Shriveled

Turgid (normal) Flaccid Plasmolyzed

Page 116: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.17

EXTRACELLULARFLUID

CYTOPLASM

Channel protein Solute

SoluteCarrier protein

(a) A channel protein

(b) A carrier protein

Page 117: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.18-6

EXTRACELLULARFLUID

[Na] high[K] low

[Na] low[K] high

CYTOPLASM

Na

Na

Na

1 2 3

456

Na

Na

Na

Na

Na

Na

K

K

K

K

K

K

P P

PP i

ATP

ADP

Page 118: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.19Passive transport Active transport

Diffusion Facilitated diffusion ATP

Page 119: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

How Ion Pumps Maintain Membrane Potential

• Membrane potential is the voltage difference across a membrane

• Voltage is created by differences in the distribution of positive and negative ions across a membrane

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Page 120: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• Two combined forces, collectively called the electrochemical gradient, drive the diffusion of ions across a membrane

– A chemical force (the ion’s concentration gradient)– An electrical force (the effect of the membrane

potential on the ion’s movement)

© 2011 Pearson Education, Inc.

Page 121: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

• An electrogenic pump is a transport protein that generates voltage across a membrane

• The sodium-potassium pump is the major electrogenic pump of animal cells

• The main electrogenic pump of plants, fungi, and bacteria is a proton pump

• Electrogenic pumps help store energy that can be used for cellular work

© 2011 Pearson Education, Inc.

Page 122: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.20

CYTOPLASM

ATP EXTRACELLULARFLUID

Proton pumpH

H

H

H

H

H

Page 123: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Cotransport: Coupled Transport by a Membrane Protein

• Cotransport occurs when active transport of a solute indirectly drives transport of other solutes

• Plants commonly use the gradient of hydrogen ions generated by proton pumps to drive active transport of nutrients into the cell

© 2011 Pearson Education, Inc.

Page 124: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.21

ATP

H

H

HH

H

H

H

H

Proton pump

Sucrose-H

cotransporter

SucroseSucrose

Diffusion of H

Page 125: AP Biology Unit 1 Chapters 1-7 Introduction, Biochemistry and Cells

Figure 7.22

Solutes

Pseudopodium

“Food” orother particle

Foodvacuole

CYTOPLASM

Plasmamembrane

Vesicle

Receptor

Ligand

Coat proteins

Coatedpit

Coatedvesicle

EXTRACELLULARFLUID

Phagocytosis Pinocytosis Receptor-Mediated Endocytosis