chapters 4 & 5

Chapters 4 & 5

Carbon

Macromolecules

CARBON

Atomic #: 6

1st level: 22nd Level: 4# of bonds able to form – 4- allows the formation of numerous different compounds- compounds that contain carbon are called ORGANIC except for a few very common ones such as CO and CO2

• 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

Name and Comments

Figure 4.3 A-C

• The electron configuration of carbon

– Gives it covalent compatibility with many different elements

H O N C

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)

Figure 4.4

BOND TYPES

Covalent

• single - hydrogen, carbon, nitrogen and hydroxyl

• double - oxygen, carbon, nitrogen

• triple - carbon, nitrogen

• C-H - hydrocarbon - non-polar

• C-O - polar

• C-N- slightly polar

Molecular Diversity Arising from Carbon Skeleton Variation

• Carbon chains

– Form the skeletons of most organic molecules

– Vary in length and shape

H H HH H

HH H H H

H HH H

H H H H

HHHH H

C C C C C

C C C C C C C

CCCCCCCC

(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

Carbon: Base of All Biological MoleculesDifference between biological molecules

• 1) Structure:

• Isomers: same chemical formula but different structure

• Structual: C4H10

• Butane

• Isobutane (2-methylpropane)

• Geometric: Ethene - cis and trans

• - cis and trans:

• L vs. D.

• - left verses Right

• Three types of isomers are

– Structural

– Geometric

– Enantiomers

H H H H HH

C C C C C

C C C C

(a) Structural isomers

(b) Geometric isomers

(c) Enantiomers

Figure 4.7 A-C

• Enantiomers

– Are important in the pharmaceutical industry

L-Dopa

(effective against Parkinson’s disease)

D-Dopa

(biologically inactive)Figure 4.8

2) Functional Groups• - different chemical attachments on hydrocarbons that

change the reactivity• TYPES PAGE 54

• a. Hydroxyl - OH - not hydroxide

• alcohols

• ethane vs. ethanol

• b. Carbonyl - C=O

• aldehydes - on end

• keytones - in middle of chain

• c. Carboxyl - -COOH

• carboxylic acid

• - weak acids

• d. Amino - -NH2

• nitrogen containing

• amino acids

• e. Sufhydryl Group - SHthiols

• stabilize proteins – disulfide bridges• f. Phosphate - PO4

– Give organic molecules distinctive chemical properties

Estradiol

Testosterone

Female lion

Male lionFigure 4.9

• Some important functional groups of organic compounds

FUNCTIONALGROUP

STRUCTURE

(may be written HO )

HYDROXYL CARBONYL CARBOXYL

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).

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

C C OH

HC C H

Figure 4.10

FUNCTIONALPROPERTIES

Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).

A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.

Has acidic properties because it is a source of hydrogen ions.The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example,

In cells, found in the ionic form, which is called a carboxylate group.

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).

Figure 4.10

Monomers Vs. Polymersmost biological molecules are polymers

Monomer - one part

Polymer - many repeating part

Macromolecules - combination of polymers

BUILDING of POLYMERS• Polymerization reaction: 2 units form one larger unit

• KEY EX: Protein synthesis

Condensation Reaction or Dehydration Synthesis

• bond is formed by the removal of a water

• two hydroxyl groups - one molecule loses OH and one loses an H

• results in a bond based on the remaining O and the H and the OH combine to form water

• Requires energy and a catalyst

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

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a watermolecule, forming a new bond

Figure 5.2A

BREAKING UP IS HARD TO DO• Hydrolysis Reaction - addition of water to break a

polymer chain

• Also requires energy and enzymes - but generally gives off more energy than it uses

• Polymers can disassemble by Hydrolysis

(b) Hydrolysis of a polymer

HO 1 2 3 H

HO H1 2 3 4

Hydrolysis adds a watermolecule, breaking a bond

Figure 5.2B

Dehydration Synthesis and HydrolysisBuild - anabolic - requires energy

• Break - catabolic - releases energy

• NOTE: COMBINATION OF MONOMERS IN DIFFERENT QUANTITIES AND PATTERNS RESULTS IN A WIDE VARIETY OF MOLECULES

• eg. Alphabet

Four Major Biological Molecules1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic Acids

CARBOHYDRATESElements: CHO and sometimes N

• FUNCTION:

• Energy

• Structure

• Protection

• Storage

Types of Carbohydrates1. Sugars: simplest

Monomers: monosaccharides

Most common glucose : C6H12O6

• Classification:

• Monosaccharides: one sugar unit

• Ex. Glucose - storage of solar energy via photosynthesis• Characteristics:

• Two types of carbonyls:

• aldehyde - carbonyl on end

• ex. Glucose

• ketone - carbonyl in middle

• ex. fructose• carbonyl affects ring formation

• placement of hydroxyl groups give different properties

• Glucose and fructose

• Examples of monosaccharidesTriose sugars

(C3H6O3)Pentose sugars

(C5H10O5)Hexose sugars

(C6H12O6)

H C OH

HO C H

H C OH

HO C H

H C OH

C OC O

H C OH

HO C H

H C OH

H H H H

C C C COOOO

Glyceraldehyde

RiboseGlucose Galactose

Dihydroxyacetone

Ribulose

FructoseFigure 5.3

• Monosaccharides

– May be linear

– Can form ringsH

H C OH

HO C H

H C OH

6CH2OH 6CH2OH

(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.

O H OO

Figure 5.4

Glucose + Fructose = Sucrose

Dissacharides

formation of a 2 sugar unit by dehydration synthesis

• glu + glu = maltose

• glu + galac = lactose

• glu + fruc = sucrose

• 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.

O HCH2OH

CH2OH HO

1 41– 4

glycosidiclinkage

1–2glycosidic

linkage

Glucose

Glucose Glucose

Fructose

Maltose

Sucrose

Figure 5.5

Polysaccharides: many sugar units

• Chains of glucose

• Type of polysaccharide dependent on the type of glucose

• alpha glucose

• beta glucose

– differ in orientation of the hydroxyl group on the number 1 carbon

alpha - down position

beta - up position

• STORAGE POLYSACCHARIDES• 1. Starch - storage in plants - as granuals in organelles

called plastids

glucose monomers

linked together a alpha 1-4 glucosidic linkages

two forms of starch

• amalose - unbranched chains

• amylopectin - branched - branches from the sixth carbon• - branches about every 30 units• 2. Glycogen - storage in animals - storage in liver and

muscle cells

• alpha 1-4 linkage• extensivly branched• about every 10 units

Starch– Is the major storage form of glucose in plants

Chloroplast Starch

Amylose Amylopectin

(a) Starch: a plant polysaccharideFigure 5.6

• Glycogen

– Consists of glucose monomers

– Is the major storage form of glucose in animalsMitochondria Giycogen

granules

(b) Glycogen: an animal polysaccharide

Glycogen

Figure 5.6

Structural Polysaccharides

provide protection and support

1. Cellulose - long unbranched, straight chains beta 1-4 linkages

makes for alternating bonds

makes for a very rigid structure

makes up cell walls

enzymes that break alpha bonds can't break beta bonds

Cellulose vs. Starch– Cellulose has different glycosidic linkages than

starch

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

HO4 OH

CH2OH O

OH OHO

CH2OH O

(a) and glucose ring structures

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

glucose glucose

1 4 41 1

Figure 5.7 A–C

Cellulose

Plant cells

Cell walls

Cellulose microfibrils in a plant cell wall

Microfibril

OHOCH2OH

CH2OH OH

OH OHO

CH2OHO

CH2OHOH

CH2OHOHOOH OH OH OH

OH CH2OH

Glucose monomer

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.

Cellulosemolecules

Figure 5.8

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

• Cellulose is difficult to digest

– Cows have microbes in their stomachs to facilitate this process – mutualism

Figure 5.9

Structural Polysaccharides

2. Chitin - structure of arthropod exoskeletons and cell walls of fungus

differs: glucose with a nitrogen compound attached

• Chitin, another important structural polysaccharide

– Is found in the exoskeleton of arthropods

– Can be used as surgical thread

(a) The structure of the chitin monomer.

OHHH OH

HNHCCH3

(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.

Figure 5.10 A–C

LIPIDS

• CHOP - mostly HYDROPHOBIC

• - MOSTLY hydrocarbons

• NET affect - NON-POLAR

• Types: fats, phospholipids, steroids, waxes

• Function: energy storage, structure, chemical commumication, repel water

FATS AND OILSStructure - two parts

1. glycerol - three carbon chain with three hydroxyls

2. fatty acid - long chain of hydrocabons with a carboxyl head

• carboxyl head combines with hydroxyl of glycerol by dehydration synthesis so 3 fatty acids combine with the glycerols = triglycerol or triglyceride

• The massive amounts of hydrocarbons in the tail make fats NONPOLAR

Fats and Oils

Constructed from a glycerol and three fatty acids

Result = TRIGLYCERIDE

FATS vs. OILS

• FATS - animal derived - solid at room temp

• OILS - mostly plant derived - liquid at room temp

• crucial difference?

• bonding in the fatty acids

Saturation vs. Unsaturation

Saturated - all carbon bonds are single bonded - all possible hydrogens

• straight chains

• atheriosclerosis

Unsaturated - carbons may have double bonds

• - causes a bend in the chain

• - chains can't stack as neatly

• 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

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12

PARTIALLY HYDROGENATED OILS

BAD BAD BAD BAD BAD

ENERGY Content of Fats and Oils

9 Cal/g

• - carbs: 4 Cal/g

• - protein: 4 Cal/g

• - alcohol: 7 Cal/g

• Protection and Insulation

Ex: Blubber

PHOSPHOLIPIDS

• Function: STRUCTURE - cell membranes

• Composition:

• Hydrophyillic head:

• phosphate joined to glycerol

• POLAR

• - joins with other polar molecules - choline

• Hydrophobic tail:

• two chains not three

• Phospholipid structure - amphipathic

– Consists of a hydrophilic “head” and hydrophobic “tails”

OPO OOCH2CHCH2

C O C O

Phosphate

Glycerol

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

Fatty acids

(c) Phospholipid symbol

Hydrophilichead

Hydrophobictails

hea d CH2 Choline

Figure 5.13

N(CH3)3

• Reaction with water

• heads out tails in

• 2 structures

• 1. micelle

• 2. lyposome

• - cell membrane – PHOSPHOLIPID BILAYER

Phospholipids in Water

• The structure of phospholipids

– Results in a bilayer arrangement found in cell membranes

Hydrophilichead

Hydrophobictail

Figure 5.14

Steroids

four fused rings

• examples:

• testosterone

• estrogen

• cholesterol - stabilize cell membranes

• One steroid, cholesterol

– Is found in cell membranes

– Is a precursor for some hormones

H3C CH3

Figure 5.15

PROTEINS: molecular tools of cells

Function: PAGE 68

• support

• storage

• Transport

• Communication

• Movement

• Protection

• *****CATALYST*******

• 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

H2OFructose

3 Substrate is convertedto products.

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

reactant on which the enzyme acts.

Substrate binds toenzyme.

4 Products are released.Figure 5.16

Structure of a ProteinPOLYPEPTIDE - chain of amino acids

• amino acid - monomer

Four parts of amino acid

1. alpha carbon

2. carboxyl group

3. amino group

- carboxyl and amino change with pH of environment

- very acidic: amino and carboxyl have H+

- as increase in pH # of H + decreases so H+ dissociate

- until reaches no H+ on amino or carboxyl

- point in between where amino group is positively charged and carboxyl is negatively charged is called the ZWITTERION

Zwitterion

Amino Acid Structure (cont.)

4. functional group - DISTINGUISHES ONE AA FROM ANOTHER - a.k.a. R group - gives specific chemical properties

- some hydrophilic - can be acidic or basic

- some hydrophobic

• 20 different amino acids make up proteins

H3N+ C C

H3N+ C

CH3 CH3

CH3CH3

H3N+ C

Nonpolar

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

Methionine (Met) Phenylalanine (Phe)

Tryptophan (Trp) Proline (Pro)

Figure 5.17

OH CH3

H O–

H3N+ CO

O–H3N+ C C

NH2 OC

C CH3N+O

Electricallycharged

–O OC

C CH3N+

O– OC

C CH3N+

C NH2+

C CH3N+

Serine (Ser) Threonine (Thr)Cysteine

(Cys)Tyrosine

(Tyr)Asparagine

(Asn)Glutamine

Acidic Basic

Aspartic acid (Asp)

Glutamic acid (Glu)

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

BUILDING A PROTEIN

process called protein synthesis

• AA bond by dehydration synthesis between amino and carboxyl

• FORM A PEPTIDE BOND

• as build get different conformations based on the AA sequence and the interactions of the R groups - resulting structure will determine function

Amino Acid Polymers

• Amino acids

– Are linked by peptide bondsOH

DESMOSOMES

DESMOSOMESDESMOSOMES

H OH OH

Peptidebond

SHSide

chains

CH2 CH2

CH2 CH2 CH2

C C C C C C

C CC C

Peptidebond

Amino end(N-terminus)

Backbone

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

STRUCTURE OF A PROTEIN

• 1. Primary structure: sequence of amino acids - determined by genetic information of DNA - change in one AA can alter function

Four Levels of Protein Structure

• Primary structure

– Is the unique sequence of amino acids in a polypeptide

Figure 5.20–

Amino acid subunits

+H3NAmino

oCarboxyl end

GlyProThrGlyThr

GluSeuLysCysProLeu

MetVal

ValLeu

AspAlaVal ArgGly

SerPro

lleSerProPheHisGluHis

GluValValPheThrAla

AspSer

GlyProArg

ArgTyrThr

lleAla

LeuSer

ProTyrSerTyrSerThrThr

AlaVal

ValThrAsnProLysGlu

ThrLys

SerTyrTrpLysAlaLeu

GluLle Asp

• 2. Secondary structure: alpha helix or pleated sheets

- from interactions of Hydrogen bonds amino and carboxyl groups of AA

• alpha helix - H bonds every 4th AA

• pleated sheets - two regions of the chain lie next to one another

O C helix

pleated sheet

Amino acidsubunits NC

H C RN H O

N HO C

O CH C R

• Secondary structure

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

– Includes the helix and the pleated sheet

Figure 5.20

• 3. Tertiary Structure: interactions that hold the different areas of a protein together

• hydrogen bonds

• hydrophobic region attracted to one another

• Van der Walls

• Disulfide bridges - bonds between two sulfurs in R groups – Between 2 cysteine AA

• STRONG

• Ionic Bonds between R groups

• Tertiary structure

– Is the overall three-dimensional shape of a polypeptide

– Results from interactions between amino acids and R groups

CH2 NH3+ C-O CH2

CH2SSCH2

Hydrophobic interactions and van der Waalsinteractions

Polypeptidebackbone

Hyrdogenbond

Ionic bond

Disulfide bridge

• 4. Quaternary Structure: putting other proteins together in a cluster

EX: hemoglobin, collagen

• Shaping of the protein aided by CHAPERONE PROTEINS (chaperonins) -direct conformation

• Quaternary structure

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

Polypeptidechain

Collagen Chains

ChainsHemoglobin

IronHeme

• The four levels of protein structure

+H3NAmino end

Amino acidsubunits

Sickle-Cell Disease: A Simple Change in Primary Structure

• Sickle-cell disease

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

• Hemoglobin structure and sickle-cell disease

Fibers of abnormalhemoglobin deform cell into sickle shape.

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin A

Molecules donot associatewith oneanother, eachcarries oxygen.Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen

10 m 10 m

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin S

Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.

subunit subunit

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

Normal hemoglobin Sickle-cell hemoglobin. . .. . .

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

Environmental Effects on Protein Structure

Denaturation - changing the protein so its no longer effective

• pH, salt, temperature - cause protein to unravel by breaking interlinking bonds

Denaturation

Renaturation

Denatured proteinNormal protein

Figure 5.22

• Chaperonins

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

Hollowcylinder

Chaperonin(fully assembled)

Steps of ChaperoninAction: An unfolded polypeptide enters the cylinder from one end.

The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide.

The cap comesoff, and the properlyfolded protein is released.

Correctlyfoldedprotein

Polypeptide

Figure 5.23

NUCLEIC ACIDS• - direct cell function - informational polymers

• DNA – deoxyribonucleic acid

• RNA – ribonucleic acid

• Differences

• DNA -deoxyribose, two chains, adenine, thymine, guanine, cytosine

• RNA - ribose sugar, one chain, uracil instead of thymine

• DNA makes RNA which directs formation of proteins which direct the chemical reactions of the cell

– Directs RNA synthesis

– Directs protein synthesis through RNA

Synthesis of mRNA in the nucleus

Movement of mRNA into cytoplasm

via nuclear pore

Synthesisof protein

NUCLEUSCYTOPLASM

Ribosome

AminoacidsPolypeptide

Figure 5.25

• Nucleic Acid Monomers: NUCLEOTIDES1. sugar: deoxribose or ribose - difference C #2

• 2. phosphate

• 3. nitrogenous base:

• purines (bigger) : adenine and guanine

- 6 C ring + 5 C ring

• pyrimidines (smaller): thymine/uracil, cytosine

- 6 C ring

• Each polynucleotide

– Consists of monomers called nucleotides

Nitrogenousbase

Nucleoside

O P CH2

3’CPhosphategroup Pentose

(b) NucleotideFigure 5.26

Nucleotide Monomers

• Nucleotide monomers

– Are made up of nucleosides and phosphate groups

(c) Nucleoside componentsFigure 5.26

Uracil (in RNA)U

Ribose (in RNA)

Nitrogenous bases Pyrimidines

CytosineC

Thymine (in DNA)T

NH2 ON

NHC NH2

AdenineA

GuanineG

Purines

OHOCH2

Pentose sugars

Deoxyribose (in DNA) Ribose (in RNA)OHOH

Uracil (in RNA)U

3’OH H

3’ 2’

• In DNA Nitrogenous bases link together by hydrogen bonds

• A bonds to T

• G bonds to C

• - must pair purine with pyrimidine – Page 298

• pur with pur to big

• pyr with pyr to small

• - # of correlating H bonds

• Sequence of A, C, T, and G determines genetic info

N H O CH3

Adenine (A) Thymine (T)

Guanine (G) Cytosine (C)Figure 16.8

chapters 4 & 5

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