ap & adv. biology honors needed for class: –3-ring binder (d-rings are best): you might start...

AP & Adv. Biology Honors

• Needed for Class:– 3-Ring Binder (D-Rings are best): You might start with a 2.5” or

a 3.0” binder. At midterm, you will probably need a second binder of similar size.

– Dividers for Binder, labeled• Daily Journal• Class Notes• Homework/Classwork, Study Guides, Labs• Tests/Quizzes

– Pens/Pencils– Colored Pencils Kept in Binder– Highlighter– White Board Markers (optional)

1

Other Items• Logistics:

– Come to class ON TIME– Upon arrival, turn to Daily Journal and answer the day’s question

appropriately. Do not skip any questions.– Remove all items from your desk except binder– No food, snacks, etc.– No cell phones out, in lab, etc. – Keep binder neat and sectioned– Focus: i.e., “Let the dude in the front do your studying”

• Think of YOUR FUTURE. You want to What?__________________• Think College

• How will you succeed there if 90+% of your grade comes from 3-4 Tests?

• If college classes don’t collect homework, then what is the purpose of homework/classwork, etc?

• If there are only 3 tests/Semester, and 12 Chapters are covered per semester, then each test will cover how many chapters?______

• How will you learn that volume of material for the “long-term?”

2

• Grading– Tests = 75%

• Are Cumulative

• Later tests in a Term count more than initial tests in the same term, with each term ending with a “Term Exam”

• When will you do your studying for each test?

• How will you remember the material a year from now (Think College)?

– Labs, Study Guides, Homework, Classwork, Binder = 25%• Are not all equal. Some labs are more complex than others, and count more. Same for all other

work.

• Due dates will be clear, and often, work is due on the day of the exam.

• Study Groups?

• AP vs. Honors Levels– AP receives extra readings, extra study guide questions, extra essay and MC

questions on tests, etc.– Honors receives a grade “boost”

• Extra Lab Time/Extra Help Times– Will be Posted a week in advance.

– Get a pass the day before you plan to come in

3

Other Items

04/21/23 4

Chapter 2: Basic Chemistry Highlites

Essential Elements of LifeAbout 25 of the 92 elements are essential to lifeCarbon, hydrogen, oxygen, and nitrogen make up 96% of living matterMost of the remaining 4% consists of calcium, phosphorus, potassium, and sulfurTrace elements are those required by an organism in minute quantities

CHNOPS

04/21/23 5

Isotopes

• Atoms of an element have the same number of protons but may differ in number of neutrons

• Isotopes are two atoms of an element that differ in number of neutrons• Most isotopes are stable, but some are radioactive, giving off particles

and energy

• Some applications of radioactive isotopes in biological research:– Dating fossils– Tracing atoms through metabolic processes– Diagnosing medical disorders

04/21/23 6

LE 2-7b

Third energy level (shell)

Second energy level (shell)

First energy level (shell)

Atomicnucleus

Energyabsorbed

Energylost

04/21/23 7

LE 2-12

H

O

H

H2O+ +

–

Chapter 3: Water and the Fitness of the Environment

– Water is the biological medium here on Earth– All living organisms require water more than any other substance

• Three-quarters of the Earth’s surface is submerged in water

• The abundance of water is the main reason the Earth is habitable

Figure 3.1

• Concept 3.1: The polarity of water molecules results in hydrogen bonding

• The water molecule is a polar molecule

• The polarity of water molecules

– Allows them to form hydrogen bonds with each other

– Contributes to the various properties water exhibits

Hydrogenbonds

+

+

H

H+

+

–

–

– –

Figure 3.2

Qualities of Water that are caused by its polarity and the biological significance of those qualities

• Water molecules exhibit cohesion: Water attracts to water as it hydrogen bonds to itself

• Biological Significance:

• Water has a high specific heat:

• Biological Significance

– Moderate Temperature

– High Heat of Vaporization

– Ice Floats


Water is a versatile Solvent

• Biological Significance

– Reactions within and outside cells

– Rings of Hydration

– Interacts with Polar Molecules, such as some proteins

– Hydrophilic Materials

– Hydrophobic Materials


• Dissociation of water molecules leads to acidic and basic conditions that affect living organisms

• Water can dissociate into hydronium ions (H3O)+ and hydroxide ions (OH-)

• Changes in the concentration of these ions can have a great affect on living organisms

H

Hydroniumion (H3O+)

H

Hydroxideion (OH–)

H

H

H

H

H

H

+ –

+

Figure on p. 53 of water dissociating

Results in free H+ ions


• Acids:

• Bases:

• The pH Scale

• Biological Significance of Acids and Bases

– Transport of hormones in plants

– Alteration of protein structures for

• Activation

• Denaturing


• If acids and bases are potentially harmful to cells and living things, what prevents harm? Why can a person drink a quart of orange juice without sustaining a lethal change in blood pH?

– The Answer

– Applications

• Swansea Dam

• Lungs and Small Intestine

Chapter 4

Carbon and the Molecular Diversity of Life

• Overview: Carbon—The Backbone of Biological Molecules

• All living organisms

– Are made up of chemicals based mostly on the element carbon

Figure 4.1

• Concept 4.1: Organic chemistry is the study of carbon compounds

• Organic compounds

– Range from simple molecules to colossal ones

• The concept of vitalism– Is the idea that organic compounds arise only within living

organisms– Was disproved when chemists synthesized the compounds in the

laboratory

In 1953, Stanley Miller simulated what were thought to be environmental conditions on the lifeless, primordial Earth. As shown in this recreation, Miller used electrical discharges (simulated lightning) to trigger reactions in a primitive “atmosphere” of H2O, H2, NH3 (ammonia), and CH4 (methane)—some of the gases released by volcanoes.

A variety of organic compounds that play key roles in living cells were synthesized in Miller’s apparatus.

EXPERIMENT

RESULTS

CONCLUSIONOrganic compounds may have been synthesized abiotically on the early Earth, setting the stage for the origin of life. (We will explore this hypothesis in more detail in Chapter 26.)Figure 4.2

• Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms

• Carbon has four valence electrons

• This allows it to form four covalent bonds with a variety of atoms

• The bonding versatility of carbon– Allows it to form many diverse molecules,

including carbon skeletons

(a) Methane

(b) Ethane

(c) Ethene (ethylene)

Molecular Formula

Structural Formula

Ball-and-Stick Model

Space-Filling Model

H

H

H

H

H

H

H

H

H

H

H H

HH

C

C C

C C

CH4

C2H6

C2H4

Name and Comments

Figure 4.3 A-C

• The electron configuration of carbon– Gives it covalent compatibility with many

different elements: i.e., it can bond covalently with many other kinds of atoms.

H O N C

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)

Figure 4.4

Molecular Diversity Arising from Carbon Skeleton Variation

• Carbon chains– Form the skeletons of most organic molecules– Vary in length and shape

HHH

HH

H H H

HH

H

H H H

H H HH H

H

H

H

H

H

H

HH

HH H H H

H HH 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

CC

C

C

CCC

CC

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

H H H HH

Figure 4.5 A-D

Hydrocarbons

• Hydrocarbons Are molecules consisting of only carbon and hydrogen– Are found as parts of many of life’s vital organic molecules

(a) A fat molecule (b) Mammalian adipose cells

100 µm

Fat droplets (stained red)

Figure 4.6 A, B

Concept 4.3: Functional groups are the parts of molecules involved in chemical reactions

– Are the chemically reactive groups of atoms within an organic molecule– Give organic molecules distinct properties.

CH3

OH

HO

O

CH3

CH3

OH

Estradiol

Testosterone

Female lion

Male lionFigure 4.9

• Some important functional groups of organic compounds

FUNCTIONALGROUP

STRUCTURE

(may be written HO )

HYDROXYL CARBONYL CARBOXYL

OH

In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.)

When an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (—COOH).

C

O O

C

OH

Figure 4.10

The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond.

Acetic acid, which gives vinegar

its sour tatste

NAME OF

COMPOUNDS

Alcohols (their specific

names usually end in -ol)

Ketones if the carbonyl group is

within a carbon skeleton

Aldehydes if the carbonyl

group is at the end of the

carbon skeleton

Carboxylic acids, or organic

acids

EXAMPLE

Propanal, an aldehyde

Acetone, the simplest ketone

Ethanol, the alcohol

present in alcoholic

beverages

H

H

H

H H

C C OH

H

H

H

HH

H

H

C C H

C

C C

C C C

O

H OH

O

H

H

H H

H O

H

Figure 4.10


The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton.

AMINO SULFHYDRYL PHOSPHATE

(may be written HS )

The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape.

In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P . The phosphate group (—OPO3

2–) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens).

N

H

H

SH

O P

O

OH

OH

Figure 4.10


Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids.

Glycine EthanethiolGlycerol phosphate

O

C

HO

C

HH

N

H

H

H

C C SH

H

H H

H

H

OH

C C C O P O

OHHH

OH OH

Figure 4.10


Chapter 5

The Structure and Function of Macromolecules

• Macromolecules

– Are large molecules composed of smaller molecules (polymers)

– Are complex in their structures

Figure 5.1

Concept 5.1: Most macromolecules are polymers, built by joining identical or similar monomers into long chains.

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

– Carbohydrates: Sugars, Starch

– Proteins

– Nucleic acids: DNA, RNA

The Synthesis and Breakdown of Polymers• 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

H

H2O

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a watermolecule, forming a new bond

Figure 5.2A

• Polymers can disassemble by– Hydrolysis

(b) Hydrolysis of a polymer

HO 1 2 3 H

HO H1 2 3 4

H2O

HHO

Hydrolysis adds a watermolecule, breaking a bond

Figure 5.2B

Sugars• Monosaccharides

– Are the simplest sugars

– Can be used for fuel

– Can be converted into other organic molecules

– Can be combined into polymers

Triose sugars(C3H6O3)

Pentose sugars(C5H10O5)

Hexose sugars(C6H12O6)

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

HO C H

H C OH

H C OH

H C OH

H C OH

HO C H

HO C H

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

C OC O

H C OH

H C OH

H C OH

HO C H

H C OH

C O

H

H

H

H H H

H

H H H H

H

H H

C C C COOOO

Ald

os

es

Glyceraldehyde

RiboseGlucose Galactose

Dihydroxyacetone

Ribulose

Ke

tos

es

FructoseFigure 5.3

• Monosaccharides– May be linear– Can form rings (about 65% of the time)

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

4C

6CH2OH 6CH2OH

5C

HOH

C

H OH

H

2 C

1C

H

O

H

OH

4C

5C

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

Figure 5.4

• Disaccharides– Consist of two monosaccharides– Are joined by a glycosidic linkage

• Examples of disaccharides Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide.

Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring.

(a)

(b)

H

HO

H

HOH H

OH

O H

OH

CH2OH

H

HO

H

HOH

H

OH

O H

OH

CH2OH

H

O

H

HOH H

OH

O H

OH

CH2OH

H

H2O

H2O

H

H

O

H

HOH

OH

OH

CH2OH

CH2OH HO

OHH

CH2OH

HOH

H

H

HO

OHH

CH2OH

HOH H

O

O H

OHH

CH2OH

HOH H

O

HOH

CH2OH

H HO

O

CH2OH

H

H

OH

O

O

1 2

1 41– 4

glycosidiclinkage

1–2glycosidic

linkage

Glucose

Glucose Glucose

Fructose

Maltose

Sucrose

OH

H

H

Figure 5.5

Polysaccharides• Polysaccharides Are polymers of sugars

– Serve many roles in organisms

• Starch Is a polymer consisting entirely of glucose monomers

– In plants, the starch is amylose or amylopectin, such as in potatoes.

– In animals, the starch is glycogen, stored in the liver and muscles.

Chloroplast Starch

Amylose Amylopectin

1 m

(a) Starch: a plant polysaccharideFigure 5.6

• Glycogen– Consists of glucose monomers– Is the major storage form of glucose in animals

Mitochondria Glycogen granules

0.5 m

(b) Glycogen: an animal polysaccharide

Glycogen

Figure 5.6

Structural Polysaccharides• Cellulose Is a polymer of beta glucose

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

H O

O

CH2OH

HOH H

H

OH

OHH

H

HO

4

C

C

C

C

C

C

H

H

H

HO

OH

H

OH

OH

OH

H

O

CH2OH

HH

H

OH

OHH

H

HO

4 OH

CH2OH

O

OH

OH

HO41

O

CH2OH

O

OH

OH

O

CH2OH

O

OH

OH

CH2OH

O

OH

OH

O O

CH2OH

O

OH

OH

HO4

O1

OH

O

OH OHO

CH2OH

O

OH

O OH

O

OH

OH

(a) and glucose ring structures

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

1

glucose glucose

CH2OH

CH2OH

1 4 41 1

Figure 5.7 A–C

Plant cells

0.5 m

Cell walls

Cellulose microfibrils in a plant cell wall

Microfibril

CH2OH

CH2OH

OH

OH

OO

OHO

CH2OHO

OOH

OCH2OH OH

OH OHO

O

CH2OH

OO

OH

CH2OH

OO

OH

O

O

CH2OHOH

CH2OHOHOOH OH OH OH

O

OH OH

CH2OH

CH2OH

OHO

OH CH2OH

OO

OH CH2OH

OH

Glucose monomer

O

O

O

O

O

O

Parallel cellulose molecules areheld together by hydrogenbonds between hydroxyl

groups attached to carbonatoms 3 and 6.

About 80 cellulosemolecules associate

to form a microfibril, themain architectural unitof the plant cell wall.

A cellulose moleculeis an unbranched glucose polymer.

OH

OH

O

OOH

Cellulosemolecules

Figure 5.8

– Is a major component of the tough walls that enclose plant cells

• Cellulose is difficult to digest– Cows (and termites) have microbes in their

stomachs to facilitate this process

Figure 5.9

An Animal Structural Polysaccharide

• Chitin, is an important structural polysaccharide in animals– Is found in the exoskeleton of arthropods– Can be used as surgical thread

(a) The structure of the chitin monomer.

O

CH2OH

OHH

H OH

H

NH

CCH3

O

H

H

(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emergingin adult form.

(c) Chitin is used to make a strong and flexible surgical

thread that decomposes after the wound or incision heals.

OH

Figure 5.10 A–C

Carbohydrates Review

Lipids: Fats, Waxes, Oils

• Concept 5.3: Lipids are a diverse group of hydrophobic molecules

• Lipids Are the one class of large biological molecules that do not consist of polymers– Share the common trait of being hydrophobic

• Fats

– Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids

Fats

(b) Fat molecule (triacylglycerol)

H HH H

HHH

HH

HH

HH

HH

HOH O HC

C

C

H

H OH

OH

H

HH

HH

HH

HH

HH

HH

HH

H

HCCC

CC

CC

CC

CC

CC

CC C

Glycerol

Fatty acid(palmitic acid)

H

H

H

H

HH

HH

HH

HH

HH

HH

HH

HH

HHHH

HHHHHHHHHHHH

H

HH

H HH

H HH

HH

HH

HH

HH

HHHHHHHHHHH

HH

H

H H H H H H H H HH

HH H H H

H

HH

HHHHHH

HHHHH

HH

HO

O

O

O

OC

C

C C C C C C C C C C C C C C C C C

C

CCCCCCC

CCCCCCCCC

C C C C C C C C C C C CC

CC

O

O

(a) Dehydration reaction in the synthesis of a fatEster linkage

Figure 5.11

• Fatty acids Vary in the length and number and locations of double bonds they contain

• Saturated fatty acids Have the maximum number of hydrogen atoms possible: Have no double bonds

(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12

• Unsaturated fatty acids Have one or more double bonds– Can be converted to saturated via hydrogenation (pump-in

hydrogens), forming trans-fats, or trans-fatty acids.

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12

Phospholipids• Phospholipids Have only two fatty acids Have a phosphate group instead of

a third fatty acid

• Phospholipid structure Consists of a hydrophilic “head” and hydrophobic “tails”

CH2

O

PO O

O

CH2CHCH2

OO

C O C O

Phosphate

Glycerol

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

Fatty acids

(c) Phospholipid symbol

Hy

dro

ph

ob

ic t

ail

s

Hydrophilichead

Hydrophobictails

–

Hy

dro

ph

ilic

he

ad CH2 Choline

+

Figure 5.13

N(CH3)3

The structure of phospholipids

– Results in a bilayer arrangement found in cell membranes. They will spontaneously form into this structure when placed in water.

• This happens because water is excluded from the hydrophobic regions and attracted to the hydrophilic.

Hydrophilichead

WATER

WATER

Hydrophobictail

Figure 5.14

Steroids: A type of Lipid (guaranteed answer on this year’s AP Exam!!)

• Steroids Are lipids characterized by a carbon skeleton consisting of four fused rings

• One steroid, cholesterol Is found in cell membranes

– Is a precursor for some hormones

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15

• Concept 5.4: Proteins have many structures, resulting in a wide range of functions– Proteins

• Have many roles inside the cell– Enzymes– Channels, gates, receptors in membranes– Signals (protein kinases)– Transcription Factors– And More!!

• An overview of protein functions

Table 5.1

• Enzymes– Are a type of protein that acts as a catalyst,

speeding up chemical reactions

Substrate(sucrose)

Enzyme (sucrase)

Glucose

OH

H O

H2O

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.

22

4 Products are released.

Figure 5.16

Polypeptides

• Polypeptides Are polymers of amino acids• A protein Consists of one or more polypeptides

• 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

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

Figure 5.17

S

O

O–

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)

Amino Acid Polymers• Amino acids

– Are linked by peptide bondsOH

DESMOSOMES

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

SHSide

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)

Figure 5.18 (b) Carboxyl end(C-terminus)

Determining the Amino Acid Sequence of a Polypeptide

• The amino acid sequences of polypeptides is CRITICAL!!– Were first determined using chemical means– Can now be determined by automated machines

• A protein’s specific conformation

– Determines how it functions

• Two models of protein conformation

(a) A ribbon model

(b) A space-filling model

Groove

Groove

Figure 5.19

Four Levels of Protein Structure

• Primary structure– Is the unique sequence of amino acids in a

polypeptide

Figure 5.20–

Amino acid

subunits

+H3NAmino

end

oCarboxyl end

oc

GlyProThrGlyThr

Gly

GluSeuLysCysProLeu

MetVal

Lys

ValLeu

AspAlaValArgGly

SerPro

Ala

Gly

lleSerProPheHisGluHis

Ala

GluValValPheThrAla

Asn

AspSer

GlyProArg

ArgTyrThr

lleAla

Ala

Leu

LeuSer

ProTyrSerTyrSerThrThr

AlaVal

ValThrAsnProLysGlu

ThrLys

SerTyrTrpLysAlaLeu

GluLleAsp

O C helix

pleated sheet

Amino acidsubunits NC

H

C

O

C N

H

CO H

R

C NH

C

O H

C

R

N

HH

R C

O

R

C

H

NH

C

O H

NCO

R

C

H

NH

H

C

R

C

O

C

O

C

NH

H

R

C

C

O

N

HH

C

R

C

O

NH

R

C

H C

ON

HH

C

R

C

O

NH

R

C

H C

ON

HH

C

R

C

O

N H

H C R

N HO

O C N

C

RC

H O

CHR

N H

O C

RC

H

N H

O CH C R

N H

CC

N

R

H

O C

H C R

N H

O C

RC

H

H

C

RN

H

CO

C

NH

R

C

H C

O

N

H

C

• Secondary structure– Is the folding or coiling of the polypeptide into a

repeating configuration– Includes the helix and the pleated sheet

H H

Figure 5.20

• Tertiary structure

– Is the overall three-dimensional shape of a polypeptide

– Results from interactions between amino acids and R groups

CH2CH

OH

O

CHO

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3

CH3

H3C

H3C

Hydrophobic interactions and van der Waalsinteractions

Polypeptidebackbone

Hyrdogenbond

Ionic bond

CH2

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

But What Holds all this Together??

Peptide Bonds

Sulf-hydryl groups form di-sulfide bridges

Hydrogen bonds

Van der Waals forces

Hydrophobic interactions

If you remove all but the peptides, you lose the 2’, 3’, and 4’.

Remove the peptides, lose it all.

Sickle-Cell Disease: A Simple Change in Primary Structure

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. . .. . .

Figure 5.21

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 (notice the improper usage in this phrase? Good to avoid it).

Denaturation

Renaturation

Denatured proteinNormal protein

Figure 5.22

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

Cap

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

2

1

3

Figure 5.23

Some Uses of Proteins

• Antibodies

• Enzymes

• Contractile Proteins

• Gene Regulation

• Receptor Proteins

• Sensory Proteins

• Signal Proteins

• Transport Proteins

• Concept 5.5: 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)

• Stores information for the synthesis of specific proteins

• Directs RNA synthesis• Directs protein synthesis

through RNA– Ribonucleic acid (RNA)

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

Figure 5.25

The Structure of Nucleic Acids

• Nucleic acids Exist as polymers called polynucleotides

(a) Polynucleotide, or nucleic acid

3’C

5’ end

5’C

3’C

5’C

3’ endOH

Figure 5.26

O

O

O

O

•Each polynucleotide Consists of monomers called nucleotides

Nitrogenousbase

Nucleoside

O

O

O

O P CH2

5’C

3’CPhosphate

group Pentosesugar

(b) NucleotideFigure 5.26

O

Nucleotide Monomers• Nucleotide monomers

– Are made up of nucleosides and phosphate groups

(c) Nucleoside componentsFigure 5.26

CHCH

Uracil (in RNA)U

Ribose (in RNA)

Nitrogenous bases Pyrimidines

CN

NC

OH

NH2

CHCH

OC

NH

CH

HNC

O

CCH3

N

HNC

C

HO

O

CytosineC

Thymine (in DNA)T

NHC

N C

CN

C

CH

N

NH2 O

NHC

NHH

CC

N

NH

C NH2

AdenineA

GuanineG

Purines

OHOCH2

H

H H

OH

H

OHOCH2

HH H

OH

H

Pentose sugars

Deoxyribose (in DNA) Ribose (in RNA)OHOH

CH

CH

Uracil (in RNA)U

4’

5”

3’OH H

2’

1’

5”

4’

3’ 2’

1’

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

•Cellular DNA molecules Have two polynucleotides that spiral around an imaginary axis and Forms a double helix

• The DNA double helix

– Consists of two antiparallel nucleotide strands

3’ 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

Itinerary For The Week

• Tues., Wed, Fri. (9/10 – 9/13): Notes: Ch. 2-5

• Thurs-Fri: DO?

• Fri: Thornton Wilder

“It is a far, far better thing that I do, than I have ever done; it is a far, far better rest that I go to than I

have ever known.”

• Readings:– P. 27: Familiarize– 51 – 56– 63 – 66– 68 – 89 (as needed; should be very little)

73

04/21/23 74

Itinerary For The Day

• Sidney Carton, as he comforted a young lady as they both were carted to the guillotine.

• He saved Charles Darnay for Lucy.

• Author????:

Extra Help, Lab Time, Advisory

Date Day of Week Day of Rotation

Times Notes

9/6 Friday 7 9:15 – 1:30

Note: Whenever possible, get a pass the day BEFORE coming, and in ANY case, get a pass. Can’t make one of those times, please see me and we’ll work something out.

Assignments, Tests, and Due Dates

Assignment Due Date

Agar Lab 9/6

Test: Ch. 2-5 ??

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