Essential knowledge 1.D.1 There are several hypotheses about the natural origin of life on Earth, each with supporting scientific evidence. a. Scientific.

• Essential knowledge 1.D.1 There are several hypotheses about the natural origin of life on Earth, each with supporting scientific evidence.

• a. Scientific evidence supports the various models• 1. Primitive Earth provided inorganic precursors from which organic molecules could

have been synthesized due to the presence of available free energy and the absence of a significant quantity of oxygen.

• 2. In turn, these molecules served as monomers or building blocks for the formation of more complex molecules, including amino acids and nucleotides. [See also 4.A.1]

3. The joining of these monomers produced polymers with the ability to replicate, store and transfer information.

4. These complex reaction sets could have occurred in solution (organic soup model) or as reactions on solid reactive surfaces. [See also 2.B.1]

5. The RNA World hypothesis proposes that RNA could have been the earliest genetic material.

Enduring understanding 1.D: The origin of living systems is explained by natural

processes.

1.D.1 Learning Objectives• Learning Objectives:• LO 1.27 The student is able to describe a scientific hypothesis

about the origin of life on Earth. [See SP 1.2]• LO 1.28 The student is able to evaluate scientific questions based

on hypotheses about the origin of life on Earth. [See SP 3.3]• LO 1.29 The student is able to describe the reasons for revisions of

scientific hypotheses of the origin of life on Earth. [See SP 6.3]• LO 1.30 The student is able to evaluate scientific hypotheses about

the origin of life on Earth. [See SP 6.5]• LO 1.31 The student is able to evaluate the accuracy and legitimacy

of data to answer scientific questions about the origin of life on Earth. [See SP 4.4]

Organic Molecules and the Origin of Life on Earth

• Stanley Miller’s classic experiment demonstrated the abiotic synthesis of organic compounds

• Experiments support the idea that abiotic synthesis of organic compounds, perhaps near volcanoes, could have been a stage in the origin of life

© 2011 Pearson Education, Inc.

Figure 4.2EXPERIMENT

“Atmosphere”

Electrode

Condenser

CH4

H 2NH

3

Water vapor

Cooled “rain”containingorganicmolecules

Cold water

Sample for chemical analysis

H2O “sea”

L.O. 1.28

• Essential knowledge 2.A.3: Organisms must exchange matter with the environment to grow, reproduce and maintain organization

a. Molecules and atoms from the environment are necessary to build new molecules.

1. Carbon moves from the environment to organisms where it is used to build carbohydrates, proteins, lipids or nucleic acids. Carbon is used in storage compounds and cell formation in all organisms.

2. Nitrogen moves from the environment to organisms where it is used in building proteins and nucleic acids. Phosphorus moves from the environment to organisms where it is used in nucleic acids and certain lipids.

3. Living systems depend on properties of water that result from its polarity and hydrogen bonding. To foster student understanding of this concept, instructors can choose an illustrative example such as:

• Cohesion

• Adhesion

• High specific heat capacity

• Universal solvent supports reactions

• Heat of vaporization

• Heat of fusion

• Water’s thermal conductivity

Enduring understanding 2.A: Growth, reproduction and maintenance of the organization of living

systems require free energy and matter.

• b. Surface area-to-volume ratios affect a biological system’s ability to obtain necessary resources or eliminate waste products.1. As cells increase in volume, the relative surface area decreases and demand for material resources increases; more cellular structures are necessary to adequately exchange materials and energy with the environment. These limitations restrict cell size.

• Root hairs• Cells of the alveoli• Cells of the villi• Microvilli

2. The surface area of the plasma membrane must be large enough to adequately exchange materials; smaller cells have a more favorable surface area-to-volume ratio for exchange of materials with the environment.

• 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


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

2.A.3 Learning Objectives• LO 2.6 The student is able to use calculated surface area-to-volume

ratios to predict which cell(s) might eliminate wastes or procure nutrients faster by diffusion. [See SP 2.2]

• LO 2.7 Students will be able to explain how cell size and shape affect the overall rate of nutrient intake and the rate of waste elimination. [See SP 6.2]

• LO 2.8 The student is able to justify the selection of data regarding the types of molecules that an animal, plant or bacterium will take up as necessary building blocks and excrete as waste products. [See SP 4.1]

• LO 2.9 The student is able to represent graphically or model quantitatively the exchange of molecules between an organism and its environment, and the subsequent use of these molecules to build new molecules that facilitate dynamic homeostasis, growth and reproduction. [See SP 1.1, 1.4]

L.O. 2.6

Essential knowledge 2.B.2: Growth and dynamic homeostasis aremaintained by the constant movement of molecules across

membranes

a. Passive transport does not require the input of metabolic energy; the net movement of molecules is from high concentration to low concentration.Evidence of student learning is a demonstrated understanding of each of the following:1. Passive transport plays a primary role in the import ofresources and the export of wastes.2. Membrane proteins play a role in facilitated diffusion ofcharged and polar molecules through a membrane.To foster student understanding of this concept, instructors canchoose an illustrative example such as:• Glucose transport• Na+/K+ transport

✘✘ There is no particular membrane protein that is required forteaching this concept.3. External environments can be hypotonic, hypertonic or isotonic to internal environments of cells.

Concept 7.3: Passive transport is diffusion of a substance

across a membrane with no energy investment

• Diffusion is the tendency for molecules to spread out evenly into the available space

• Although each molecule moves randomly, diffusion of a population of molecules may be directional

• At dynamic equilibrium, as many molecules cross the membrane in one direction as in the other



Animation: Membrane Selectivity Right-click slide / select “Play”


Animation: Diffusion Right-click slide / select “Play”

Figure 7.13Molecules of dye

Membrane (cross section)

WATER

(a) Diffusion of one solute

(b) Diffusion of two solutes

Net diffusion Net diffusion



Equilibrium

Equilibrium

Equilibrium

• Substances diffuse down their concentration gradient, the region along which the density of a chemical substance increases or decreases

• No work must be done to move substances down the concentration gradient

• The diffusion of a substance across a biological membrane is passive transport because no energy is expended by the cell to make it happen


Effects of Osmosis on Water Balance

• Osmosis is the diffusion of water across a selectively permeable membrane

• Water diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration until the solute concentration is equal on both sides


Figure 7.14Lowerconcentrationof solute (sugar)

Higher concentrationof solute

Sugarmolecule

H2O

Same concentrationof solute

Selectivelypermeablemembrane

Osmosis

Water Balance of Cells Without Walls

• Tonicity is the ability of a surrounding solution to cause a cell to gain or lose water

• Isotonic solution: Solute concentration is the same as that inside the cell; no net water movement across the plasma membrane

• Hypertonic solution: Solute concentration is greater than that inside the cell; cell loses water

• Hypotonic solution: Solute concentration is less than that inside the cell; cell gains water


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

• Hypertonic or hypotonic environments create osmotic problems for organisms

• Osmoregulation, the control of solute concentrations and water balance, is a necessary adaptation for life in such environments

• The protist Paramecium, which is hypertonic to its pond water environment, has a contractile vacuole that acts as a pump


Figure 7.16

Contractile vacuole50 m

Video

http://wps.aw.com/bc_campbell_biology_9_msa_ap/169/43515/11140082.cw/index.html

Water Balance of Cells with Walls

• Cell walls help maintain water balance• A plant cell in a hypotonic solution swells until

the wall opposes uptake; the cell is now turgid (firm)

• If a plant cell and its surroundings are isotonic, there is no net movement of water into the cell; the cell becomes flaccid (limp), and the plant may wilt


• In a hypertonic environment, plant cells lose water; eventually, the membrane pulls away from the wall, a usually lethal effect called plasmolysis


Video

http://wps.aw.com/bc_campbell_biology_9_msa_ap/169/43515/11140082.cw/index.html


Animation: Osmosis Right-click slide / select “Play”

Short-Distance Transport of Water Across Plasma

Membranes• To survive, plants must balance water uptake and

loss• Osmosis determines the net uptake or water loss

by a cell and is affected by solute concentration and pressure


• Water potential is a measurement that combines the effects of solute concentration and pressure

• Water potential determines the direction of movement of water

• Water flows from regions of higher water potential to regions of lower water potential

• Potential refers to water’s capacity to perform work


• Water potential is abbreviated as Ψ and measured in a unit of pressure called the megapascal (MPa)

• Ψ = 0 MPa for pure water at sea level and at room temperature


How Solutes and Pressure Affect Water Potential

• Both pressure and solute concentration affect water potential

• This is expressed by the water potential equation: Ψ ΨS ΨP

• The solute potential (ΨS) of a solution is directly proportional to its molarity

• Solute potential is also called osmotic potential


• Pressure potential (ΨP) is the physical pressure on a solution

• Turgor pressure is the pressure exerted by the plasma membrane against the cell wall, and the cell wall against the protoplast

• The protoplast is the living part of the cell, which also includes the plasma membrane


Figure 36.8

Solutes have a negative effect on by bindingwater molecules.

Pure water at equilibrium

H2O

Adding solutes to theright arm makes lowerthere, resulting in netmovement of water tothe right arm:

H2O

Pure water

Membrane Solutes

Positive pressure has a positive effect on by pushing water.


H2O

H2O

Positivepressure

Applying positivepressure to the right armmakes higher there,resulting in net movementof water to the left arm:

Solutes and positivepressure have opposingeffects on watermovement.


H2O

H2O

Positivepressure

Solutes

In this example, the effectof adding solutes isoffset by positivepressure, resulting in nonet movement of water:

Negative pressure(tension) has a negativeeffect on by pullingwater.


H2O

H2O

Negativepressure

Applying negativepressure to the right armmakes lower there,resulting in net movementof water to the right arm:

• Water potential affects uptake and loss of water by plant cells

• If a flaccid cell is placed in an environment with a higher solute concentration, the cell will lose water and undergo plasmolysis

• Plasmolysis occurs when the protoplast shrinks and pulls away from the cell wall


Water Movement Across Plant Cell Membranes

Figure 36.9

Plasmolyzedcell at osmoticequilibrium withits surroundings

0.4 M sucrose solution:

Initial flaccid cell:

Pure water:

Turgid cellat osmoticequilibrium withits surroundings

(a) Initial conditions: cellular environmental (b) Initial conditions: cellular environmental

P 0

P 0

S

P0

S

P 0.7

S0.9

0.9 MPa

S0.9

0.9 MPa

0.7 MPaS

0.7P

0

0 0 MPa

0.7

0 MPa

• If a flaccid cell is placed in a solution with a lower solute concentration, the cell will gain water and become turgid

• Turgor loss in plants causes wilting, which can be reversed when the plant is watered


LO 2.12 The student is able to use representations and models to analyze situations or solve problems qualitatively and quantitatively to investigate whether dynamic homeostasis is maintained by the active movement of molecules across membranes. [See SP 1.4]

Enduring understanding 3.A: Heritable information provides for continuity of life.

• Essential knowledge 3.A.1: DNA, and in some cases RNA, is the primary source of heritable information.

• a. Genetic information is transmitted from one generation to the next through DNA or RNA. 1. Genetic information is stored in and passed to subsequent generations through DNA molecules and, in some cases, RNA molecules.

2. Noneukaryotic organisms have circular chromosomes, while eukaryotic organisms have multiple linear chromosomes, although in biology there are exceptions to this rule.

3. Prokaryotes, viruses and eukaryotes can contain plasmids, which are small extra-chromosomal, double-stranded circular DNA molecules.

4. The proof that DNA is the carrier of genetic information involved a number of important historical experiments. These include:

• i. Contributions of Watson, Crick, Wilkins, and Franklin on• the structure of DNA• ii. Avery-MacLeod-McCarty experiments• iii. Hershey-Chase experiment

b. DNA and RNA molecules have structural similarities and differences that define function. [See also 4.A.1]

• 1. Both have three components — sugar, phosphate and a nitrogenous base — which form nucleotide units that are connected by covalent bonds to form a linear molecule with 3‘ and 5' ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone.

• 2. The basic structural differences include:i. DNA contains deoxyribose (RNA contains ribose).ii. RNA contains uracil in lieu of thymine in DNA.iii. DNA is usually double stranded, RNA is usually single stranded.iv. The two DNA strands in double-stranded DNA are antiparallel in

directionality.• 3. Both DNA and RNA exhibit specific nucleotide base pairing that is conserved

through evolution: adenine pairs with thymine or uracil (A-T or A-U) and cytosine pairs with guanine (C-G).

i. Purines (G and A) have a double ring structure.ii. Pyrimidines (C, T and U) have a single ring structure.

• 4. The sequence of the RNA bases, together with the structure of the RNA molecule, determines RNA function.

i. mRNA carries information from the DNA to the ribosome.ii. tRNA molecules bind specific amino acids and allow information in the

mRNA to be translated to a linear peptide sequence.iii. rRNA molecules are functional building blocks of ribosomes.iv. The role of RNAi includes regulation of gene expression at the level of

mRNA transcription.

• c. Genetic information flows from a sequence of nucleotides in a gene to a sequence of amino acids in a protein.

• 1. The enzyme RNA-polymerase reads the DNA molecule in the 3' to 5' direction and synthesizes complementary mRNA molecules that determine the order of amino acids in the polypeptide.

• 2. In eukaryotic cells the mRNA transcript undergoes a series of enzyme-regulated modifications.

• Addition of a poly-A tail• Addition of a GTP cap• Excision of introns

• 3. Translation of the mRNA occurs in the cytoplasm on the ribosome.• 4. In prokaryotic organisms, transcription is coupled to translation of the

message. Translation involves energy and many steps, including initiation, elongation and termination.The salient features include:

i. The mRNA interacts with the rRNA of the ribosome to initiate translation at the (start) codon.

ii. The sequence of nucleotides on the mRNA is read in triplets called codons.

iii. Each codon encodes a specific amino acid, which can be deduced by using a genetic code chart. Many amino acids have more than one codon.

3.A.1 Learning Objectives• LO 3.1 The student is able to construct scientific explanations that use the

structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information. [See SP 6.5]

• LO 3.2 The student is able to justify the selection of data from historical investigations that support the claim that DNA is the source of heritable information. [See SP 4.1]

• LO 3.3 The student is able to describe representations and models that illustrate how genetic information is copied for transmission between generations. [See SP 1.2]

• LO 3.4 The student is able to describe representations and models illustrating how genetic information is translated into polypeptides. [See SP 1.2]

• LO 3.5 The student can justify the claim that humans can manipulate heritable information by identifying at least two commonly used technologies. [See SP 6.4]

• LO 3.6 The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression. [See SP 6.4]

Concept 5.1: Macromolecules are polymers, built from monomers• A polymer is a long molecule consisting of

many similar building blocks • These small building-block molecules are

called monomers• Three of the four classes of life’s organic

molecules are polymers– Carbohydrates– Proteins– Nucleic acids



Animation: Polymers

Right-click slide / select “Play”

X

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

Figure 5.2b

(b) Hydrolysis: breaking down a polymer

Hydrolysis addsa water molecule,breaking a bond.

1 2 3 4

1 2 3

Enduring understanding 4.A: Interactions withinbiological systems lead to complex properties.

• Essential knowledge 4.A.1: The subcomponents of biological molecules and their sequence determine the properties of that molecule.

1. In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate and a nitrogen base (adenine, thymine, guanine, cytosine or uracil). DNA and RNA differ in function and differ slightly in structure, and these structural differences account for the differing functions. [See also 1.D.1, 2.A.3, 3.A.1]

Concept 5.5: Nucleic acids store, transmit, and help express

hereditary information• The amino acid sequence of a polypeptide is

programmed by a unit of inheritance called a gene

• Genes are made of DNA, a nucleic acid made of monomers called nucleotides


The Roles of Nucleic Acids• There are two types of nucleic acids

– Deoxyribonucleic acid (DNA)

– Ribonucleic acid (RNA)

• DNA provides directions for its own replication

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

• Protein synthesis occurs on ribosomes


Figure 5.25-3

Synthesis ofmRNA

mRNA

DNA

NUCLEUSCYTOPLASM

mRNA

Ribosome

AminoacidsPolypeptide

Movement ofmRNA intocytoplasm

Synthesisof protein

1

2

3

Figure 5.26

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

Nitrogenous bases

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

Adenine (A) Guanine (G)

Sugars

Deoxyribose (in DNA) Ribose (in RNA)

(c) Nucleoside components

Pyrimidines

Purines

The Structures of DNA and RNA Molecules

• RNA molecules usually exist as single polypeptide chains

• DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix

• In the DNA double helix, the two backbones run in opposite 5→ 3 directions from each other, an arrangement referred to as antiparallel

• One DNA molecule includes many genes


• The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)

• Called complementary base pairing• Complementary pairing can also occur between

two RNA molecules or between parts of the same molecule

• In RNA, thymine is replaced by uracil (U) so A and U pair


Figure 5.27

Sugar-phosphatebackbones

Hydrogen bonds

Base pair joinedby hydrogen bonding

Base pair joinedby hydrogen

bonding

(b) Transfer RNA(a) DNA

5 3

53

G and C linked by 3 hydrogen bonds, A and T by only 2

DNA and Proteins as Tape Measures of Evolution

• The linear sequences of nucleotides in DNA molecules are passed from parents to offspring

• Two closely related species are more similar in DNA than are more distantly related species

• Molecular biology can be used to assess evolutionary kinship


Proteins

• 2. In proteins, the specific order of amino acids in a polypeptide (primary structure) interacts with the environment to determine the overall shape of the protein, which also involves secondary tertiary and quaternary structure and, thus, its function. The R group of an amino acid can be categorized by chemical properties (hydrophobic, hydrophilic and ionic), and the interactions of these R groups determine structure and function of that region of the protein. [See also 1.D.1, 2.A.3, 2.B.1]

Figure 5.15-a

Enzymatic proteins Defensive proteins

Storage proteins Transport proteins

Enzyme Virus

Antibodies

Bacterium

Ovalbumin Amino acidsfor embryo

Transportprotein

Cell membrane

Function: Selective acceleration of chemical reactions

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

Function: Protection against disease

Example: Antibodies inactivate and help destroyviruses and bacteria.

Function: Storage of amino acids Function: Transport of substances

Examples: 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.

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

Figure 5.15-b

Hormonal proteins

Function: Coordination of an organism’s activities

Example: Insulin, a hormone secreted by thepancreas, causes other tissues to take up glucose,thus regulating blood sugar concentration

Highblood sugar

Normalblood sugar

Insulinsecreted

Signalingmolecules

Receptorprotein

Muscle tissue

Actin Myosin

100 m 60 m

Collagen

Connectivetissue

Receptor proteins

Function: Response of cell to chemical stimuli

Example: Receptors built into the membrane of anerve cell detect signaling molecules released byother nerve cells.

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.

Structural proteins

Function: Support

Examples: 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.

Figure 5.UN01

Side chain (R group)

Aminogroup

Carboxylgroup

carbon

Figure 5.16a

Nonpolar side chains; hydrophobic

Side chain

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)

Figure 5.16b

Polar side chains; hydrophilic

Serine(Ser or S)

Threonine(Thr or T)

Cysteine(Cys or C)

Tyrosine(Tyr or Y)

Asparagine(Asn or N)

Glutamine(Gln or Q)

Figure 5.16c

Electrically charged side chains; hydrophilic

Acidic (negatively charged)

Basic (positively charged)

Aspartic acid(Asp or D)

Glutamic acid(Glu or E)

Lysine(Lys or K)

Arginine(Arg or R)

Histidine(His or H)

Figure 5.17

Peptide bond

New peptidebond forming

Sidechains

Back-bone

Amino end(N-terminus)

Peptidebond

Carboxyl end(C-terminus)

Figure 5.18

(a) A ribbon model (b) A space-filling model

Groove

Groove

Figure 5.19

Antibody protein Protein from flu virus

Figure 5.20aPrimary structure

Aminoacids

Amino end

Carboxyl end

Primary structure of transthyretin


Animation: Primary Protein StructureRight-click slide / select “Play”


Animation: Secondary Protein Structure Right-click slide / select “Play”


Animation: Tertiary Protein StructureRight-click slide / select “Play”

Figure 5.20g

Quaternary structure

Transthyretinprotein

(four identicalpolypeptides)

Figure 5.20h

Collagen

Hemoglobin

Heme

Iron

subunit

subunit

subunit

subunit

Figure 5.20i


Animation: Quaternary Protein Structure Right-click slide / select “Play”

Figure 5.21

PrimaryStructure

Secondaryand TertiaryStructures

QuaternaryStructure Function Red Blood

Cell Shape

subunit

subunit

Exposedhydrophobicregion

Molecules do notassociate with oneanother; each carriesoxygen.

Molecules crystallizeinto a fiber; capacityto carry oxygen isreduced.

Sickle-cellhemoglobin

Normalhemoglobin

10 m

10 m

Sic

kle-

cell

hem

og

lob

inN

orm

al h

emo

glo

bin

1

23

456

7

1

23

456

7

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


Figure 5.22

Normal protein Denatured protein

Den tur t on

Ren t r t on

a a i

a u a i

Figure 5.23

The cap attaches, causingthe cylinder to changeshape in such a way thatit creates a hydrophilicenvironment for thefolding of the polypeptide.

CapPolypeptide

Correctlyfoldedprotein

Chaperonin(fully assembled)

Steps of ChaperoninAction:

An unfolded poly-peptide enters thecylinder fromone end.

Hollowcylinder

The cap comesoff, and theproperly foldedprotein isreleased.

1

2 3

• Scientists use X-ray crystallography to determine a protein’s structure

• Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization

• Bioinformatics uses computer programs to predict protein structure from amino acid sequences


Figure 5.24

DiffractedX-rays

X-raysource X-ray

beam

Crystal Digital detector X-ray diffractionpattern

RNA DNA

RNApolymerase II

EXPERIMENT

RESULTS

Lipids

• 3. In general, lipids are nonpolar; however, phospholipids exhibit structural properties, with polar regions that interact with other polar molecules such as water, and with nonpolar regions where differences in saturation determine the structure and function of lipids. [See also 1.D.1, 2.A.3, 2. B.1]

Concept 5.3: Lipids are a diverse group of hydrophobic molecules

• Lipids are the one class of large biological molecules that do not form polymers

• The unifying feature of lipids is having little or no affinity for water

• Lipids are hydrophobic becausethey consist mostly of hydrocarbons, which form nonpolar covalent bonds

• The most biologically important lipids are fats, phospholipids, and steroids


Figure 5.10a

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

Fatty acid(in this case, palmitic acid)

Glycerol

X

Figure 5.10b

(b) Fat molecule (triacylglycerol)

Ester linkageX

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.

X

• A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits

• Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen

• Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds

• These trans fats may contribute more than saturated fats to cardiovascular disease


X

Choline

Phosphate

Glycerol

Fatty acids

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

Hyd

rop

hil

ic h

ead

Hyd

rop

ho

bic

tai

ls

Figure 5.12a

X

Steroids• Steroids are lipids characterized by a carbon

skeleton consisting of four fused rings• Cholesterol, an important steroid, is a

component in animal cell membranes• Although cholesterol is essential in animals,

high levels in the blood may contribute to cardiovascular disease


X

Figure 5.14

X

Carbs

4. Carbohydrates are composed of sugar monomers whose structures and bonding with each other by dehydration synthesis determine the properties and functions of the molecules. Illustrative examples include: cellulose versus starch.

Concept 5.2: Carbohydrates serve as fuel and building material

• Carbohydrates include sugars and the polymers of sugars

• The simplest carbohydrates are monosaccharides, or single sugars

• Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks


Sugars• Monosaccharides have molecular formulas

that are usually multiples of CH2O

• Glucose (C6H12O6) is the most common monosaccharide

• Monosaccharides are classified by – The location of the carbonyl group (as aldose

or ketose)

– The number of carbons in the carbon skeleton


Figure 5.4

(a) Linear and ring forms

(b) Abbreviated ring structure

1

2

3

4

5

6

6

5

4

32

1 1

23

4

5

6

1

23

4

5

6

X

Figure 5.5

(a) Dehydration reaction in the synthesis of maltose

(b) Dehydration reaction in the synthesis of sucrose

Glucose Glucose

Glucose

Maltose

Fructose Sucrose

1–4glycosidic

linkage

1–2glycosidic

linkage

1 4

1 2


Animation: DisaccharideRight-click slide / select “Play”

Figure 5.5

(a) Dehydration reaction in the synthesis of maltose

(b) Dehydration reaction in the synthesis of sucrose

Glucose Glucose

Glucose

Maltose

Fructose Sucrose

1–4glycosidic

linkage

1–2glycosidic

linkage

1 4

1 2

Figure 5.6

(a) Starch: a plant polysaccharide

(b) Glycogen: an animal polysaccharide

Chloroplast Starch granules

Mitochondria Glycogen granules

Amylopectin

Amylose

Glycogen

1 m

0.5 m

X


Animation: PolysaccharidesRight-click slide / select “Play”

X

Figure 5.7b

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

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

41

41

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Cell wall

Microfibril

Cellulosemicrofibrils in aplant cell wall

Cellulosemolecules

Glucosemonomer

10 m

0.5 m

Figure 5.8

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• Enzymes that digest starch by hydrolyzing linkages can’t hydrolyze linkages in cellulose

• Cellulose in human food passes through the digestive tract as insoluble fiber

• Some microbes use enzymes to digest cellulose

• Many herbivores, from cows to termites, have symbiotic relationships with these microbes


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.

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b. Directionality influences structure and function of the polymer.

1. Nucleic acids have ends, defined by the 3' and 5' carbons of the sugar in the nucleotide, that determine the direction in which complementary nucleotides are added during DNA synthesis and the direction in which transcription occurs (from 5' to 3'). [See also 3.A.1]

2. Proteins have an amino (NH2) end and a carboxyl (COOH) end, and consist of a linear sequence of amino acids connected by the formation of peptide bonds by dehydration synthesis between the amino and carboxyl groups of adjacent monomers.

3. The nature of the bonding between carbohydrate subunits determines their relative orientation in the carbohydrate, which then determines the secondary structure of the carbohydrate.

4.A.1 Learning Objectives

• LO 4.1 The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. [See SP 7.1]

• LO 4.2 The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. [See SP 1.3]

• LO 4.3 The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecule. [See SP 6.1, 6.4]

L.O. 4.1

Enduring understanding 4.B: Competition andcooperation are important aspects of biological

systems.• Essential knowledge 4.B.1: Interactions between

molecules affect their structure and function.a. Change in the structure of a molecular system may result in a change of the function of the system. [See also 3.D.3]

Learning Objective: LO 4.17 The student is able to analyze data to identify how molecular interactions affect structure and function. [See SP 5.1]

Enduring understanding 4.C: Naturally occurring diversity among and between components within biological systems affects

interactions with the environment.• Essential knowledge 4.C.1: Variation in molecular units

provides cells with a wider range of functions.• a. Variations within molecular classes provide cells and organisms with a wider

range of functions. [See also 2.B.1, 3.A.1, 4.A.1, 4.A.2]

• Different types of phospholipids in cell membranes

• Different types of hemoglobin

• MHC proteins

• Chlorophylls

• Molecular diversity of antibodies in response to an antigen

b. Multiple copies of alleles or genes (gene duplication) may provide new phenotypes. [See also 3.A.4, 3.C.1]

1. A heterozygote may be a more advantageous genotype than a homozygote under particular conditions, since with two different alleles, the organism has two forms of proteins that may provide functional resilience in response to environmental stresses.

Learning Objective: LO 4.22 The student is able to construct explanations based on evidence of how variation in molecular units provides cells with a wider range of functions. [See SP 6.2]

Essential knowledge 1.D.1 There are several hypotheses about the natural origin of life on Earth, each with supporting scientific evidence. a. Scientific.

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