LECTURE – 2 CONT. Functional Groups. Outline Water Structure - Review Important properties #4...

LECTURE – 2 CONT.

Functional Groups

Outline

Water Structure - Review Important properties

#4 Solvent properties Carbon

Structure Important properties Functional Groups

#4 – Solvent Properties

Water can disassociate into hydronium and hydroxide ions

2 H2O Hydroxideion (OH)

Hydroniumion (H3O

+)

+

#4 Solvent Properties: Acids & Bases

The dissociation of water molecules has a great effect on organisms

Changes in concentrations of H+ and OH– can drastically affect the chemistry of a cell

#4 Solvent Properties: Acids & Bases

Acid – donates a proton Increases the number of Hydronium Ions in

an aqueous solution Base –

Accepts a proton Reduces the number of Hydronium Ions in

an aqueous solution

#4 – Solvent Properties: The pH scale

pH is a measure of the relative concentration of protons. 0 < pH < 7 is an Acid ([H30+] > 10-7M) 7 < pH < 14 is a Base ([H30+] < 10-7M) pH 7 is neutral ([H30+] = [OH-] = 10-7M)

Figure 3.10pH Scale

Battery acid

Gastric juice, lemon juice

Vinegar, wine,cola

BeerTomato juice

Black coffee

Rainwater

Urine

SalivaPure waterHuman blood, tears

Seawater

Inside of small intestine

Milk of magnesia

Household ammonia

Householdbleach

Oven cleaner

Basicsolution

Neutralsolution

Acidicsolution

0

1

2

3

4

5

6

7

8

9

10

Neutral

[H+] = [OH]In

cre

asin

gly

Basic

[H+]

< [

OH

]

Incre

asin

gly

Acid

ic

[H+]

> [

OH

]

H+ H+

H+

H+H+

H+

H+

H+

OH

OH

H+

OH

H+

OH

OH

OHOH

H+H+

H+

H+

OHOH

OH

OH OHOH

OHH+

11

12

13

14

#4 – Solvent Properties: Buffers

Buffers are substances that minimize changes in concentrations of H+ and OH– in a solution. They resist a change in pH when a small

amount of acid or base is added to a solution.

Most buffers consist of an acid-base pair that reversibly combines with H+

Buffers work within a specific pH range.

#4 – Solvent Properties: Buffers Carbonic Acid – contributes to pH

stability in blood and other biological solutions.

H2CO3 is formed when CO2 reacts with water.

Carbon

Carbon

The backbone of life Living organisms consist

mostly of carbon-based compounds.

Really good at forming large, complex, and diverse molecules.

Proteins, DNA, carbohydrates, and other molecules - all composed of carbon compounds.

Carbon

Electron configuration determines the kinds and number of bonds an atom will form with other atoms

Four valence electrons – Four covalent

Allows for the formation of large, complex molecules

Figure 4.3

Name andComment

MolecularFormula

(a) Methane

(b) Ethane

CH4

Ball-and-Stick Model

Space-FillingModel

(c) Ethene (ethylene)

C2H6

C2H4

StructuralFormula

Carbon bonds determine molecular shape

Diversity of carbon molecules Carbon chains form the skeletons of most organic

molecules Carbon chains vary in length and shapeFigure 4.5

(a) Length

Ethane 1-Butene

(c) Double bond position

2-ButenePropane

(b) Branching (d) Presence of rings

Butane 2-Methylpropane(isobutane)

Cyclohexane Benzene

Valence Electrons

The electron configuration of carbon gives it covalent compatibility with many different elements

The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules

Figure 4.4

Hydrogen(valence 1)

Oxygen(valence 2)

Nitrogen(valence 3)

Carbon(valence 4)

Isomers

Compounds with the same molecular formula but different structures and properties

Structural isomers have different covalent arrangements of their atoms (constitutional)

Cis-trans isomers have the same covalent bonds but differ in spatial arrangements

Enantiomers are isomers that are mirror images of each other (they are chiral)

Isomers – Three typesFigure 4.7 (a) Structural isomers

(b) Cis-trans isomers

(c) Enantiomers

cis isomer: The two Xsare on the same side.

trans isomer: The two Xsare on opposite sides.

CO2HCO2H

CH3

H NH2

L isomer

NH2

CH3

H

D isomer

Isomers - EnatomersFigure 4.8

Drug

Ibuprofen

Albuterol

Condition EffectiveEnantiomer

IneffectiveEnantiomer

Pain;inflammation

Asthma

S-Ibuprofen R-Ibuprofen

R-Albuterol S-Albuterol

http://www.youtube.com/watch?v=L5QbBYj_zVs

Functional Groups

The components of organic molecules that are most commonly involved in chemical reactions

The number and arrangement of functional groups give each molecule its unique properties

The importance of functional groups

CH3

OH

HO

O

CH3

CH3

OH

Estradiol

Testosterone

Female lion

Male lion

7 most biologically important functional groups

Figure 4.9a

STRUCTURE

EXAMPLE

Alcohols(Their specificnames usuallyend in -ol.)

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

(may be written HO—)

Ethanol

• Is polar as a resultof the electronsspending moretime near theelectronegativeoxygen atom.

• Can form hydrogenbonds with watermolecules, helpingdissolve organiccompounds suchas sugars.

Hydroxyl

Figure 4.9b

Carbonyl

STRUCTURE

EXAMPLE

Ketones if the carbonylgroup is within acarbon skeleton

NAME OFCOMPOUND


Aldehydes if the carbonylgroup is at the end of thecarbon skeleton

• A ketone and analdehyde may bestructural isomerswith different properties,as is the case foracetone and propanal.

Acetone

Propanal

• Ketone and aldehydegroups are also foundin sugars, giving riseto two major groupsof sugars: ketoses(containing ketonegroups) and aldoses(containing aldehydegroups).

Carboxyl

STRUCTURE

EXAMPLE

Carboxylic acids, or organicacids

NAME OFCOMPOUND


Acetic acid

Polar; can form H-bonds

Weak acids; reversible dissociation in H2O

• Found in cells in the ionizedform with a charge of 1– andcalled a carboxylate ion.

Nonionized Ionized

Figure 4.9c

Amino

Amines

Glycine

STRUCTURE

EXAMPLE • Acts as a base; canpick up an H+ from thesurrounding solution(water, in livingorganisms):

NAME OFCOMPOUND


• Found in cells in theionized form with acharge of 1.

Nonionized Ionized

Figure 4.9d

Sulfhydryl

Thiols

(may bewritten HS—)

STRUCTURE

EXAMPLE • Two sulfhydryl groups canreact, forming a covalentbond. This “cross-linking”helps stabilize proteinstructure.

NAME OFCOMPOUND


• Cross-linking of cysteinesin hair proteins maintainsthe curliness or straightnessof hair. Straight hair can be“permanently” curled byshaping it around curlersand then breaking andre-forming the cross-linkingbonds.

Cysteine

Figure 4.9e

Figure 4.9f

Phosphate

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


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.

Figure 4.9g

Methyl

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Methylated compounds

5-Methyl cytidine

• Addition of a methyl groupto DNA, or to moleculesbound to DNA, affects theexpression of genes.

• Arrangement of methylgroups in male and femalesex hormones affects theirshape and function.

LECTURE - 3

Biological Macromolecules

Outline

Monomers & Polymers Four basic classes of biological

macromolecules Carbohydrates Lipids Proteins Nucleic Acids

Form follows function

Polymers

Polymer is a large molecule build from similar building blocks Legos!

Building blocks are monomers Carbohydrates, Proteins, Nucleic acids

are polymers

Polymer Synthesis

Usually, monomers are joined via a dehydration reaction.

Broken apart via hydrolysis.

Polymer Diversity

Thousands of different macromolecules

They vary Cell to cell Individuals Species…

Can build an immense variety of polymers with a small set of monomers legos

4 Classes of Macromolecules1. Carbohydrates2. Lipids3. Nucleic Acids4. Proteins

#1 Carbohydrates

#1 Carbohydrates

Fuel & building blocks Monosaccharides

Single sugars One carbon ring

Polysaccharides Polymers built from many sugar building

blocks

#1 Carbohydrates: Simple Sugars

General Characteristics of Sugars Generally have some multiple of CH2O Have a carbonyl group (C=O) Multiple hydroxyl groups (-OH) Aldoses & Ketoses Trioses (C3H6O3), Pentoses (C5H10O5) &

Hexoses (C6H12O6)

(Fischer Projections)

Glyceraldehyde

Ribose

Glucose


Aldoses vs. Ketoses Aldoses – Carbonyl group at the end of carbon

skeleton (aldehyde sugar) Ketoses – Carbonyl group within the carbon skeleton

(ketones)

Figure 5.3a

Aldose (Aldehyde Sugar)Ketose (Ketone Sugar)

Glyceraldehyde

Trioses: 3-carbon sugars (C3H6O3)

Dihydroxyacetone


Most sugars exist as ring structures.Figure 5.4

(a) Linear and ring forms

(b) Abbreviated ring structure

12

3

4

5

6

6

5

4

32

1 1

23

4

5

6

123

456

Glucose

#1 Carbohydrates: Glucose vs. Fructose

Glucose

Fructose

#1 Carbohydrates: Disaccharide

2 monosaccarides joined by a glycosidic linkageFigure 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

(important for making beer)

(Table sugar)

#1 Carbohydrates: Polysaccarides

Hundreds to 1000s of monosaccarides held together via glycosidic linkages.

#1 Carbohydrates: Polysaccarides

Storage and structural roles Storage - Carbohydrate “bank” - stored

sugars can later by released by hydrolysis for use in metabolism.

Structure – Strong structural components are built from polysaccharides.

Structure and function are determined by its sugar monomers and the positions of glycosidic linkages

#1 Carbohydrates: Polysaccarides; Storage - Starch

Starch – Plants version of storage polysaccharides Consists entirely of glucose monomers Plants store surplus starch as granules within

chloroplasts and other plastids

Most starches are built from 1-4 linkages – more complex starches can be linked differently

amylose


Starches are stored in plasteds Animals have enzymes that can

hydrolyze starches Major sources:

Potatoes Grains

Wheat Maize Corn Rice

Chloroplast Starch granules

1 m

#1 Carbohydrates: Polysaccarides; Storage - Glycogen

Animals store glucose as a polysaccharide called glycogen. Made up of glucose

monomers – like Amylopectin but more extensively branched.

In vertebrates it is mostly stored in the liver and muscle cells.

Glycogen stores don’t last long.

MitochondriaGlycogen granules

0.5 m

#1 Carbohydrates: Polysaccarides; Structure

Cellulose is a major component of the tough wall of plant cells

Cellulose is a polymer of glucose. The glycosidic linkages differ from

starch. The difference is based on two ring

forms for glucose: alpha () and beta ()

Figure 5.7a

(a) and glucose ring structures

Glucose Glucose

4 1 4 1

Figure 5.7b

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

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

41

41

Cell wall

Microfibril

Cellulosemicrofibrils in aplant cell wall

Cellulosemolecules

Glucosemonomer

10 m

0.5 m

Figure 5.8


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


Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods

Chitin also provides structural support for the cell walls of many fungi

Figure 5.9a

Chitin forms the exoskeletonof arthropods.

#2 Lipids

Lipids - do not form polymers Lipids is having little or no affinity for

water Hydrophobic

Consist mostly of hydrocarbons (nonpolar covalent bonds)

Fats, phospholipids, and steroids

#2 Lipids - Fats

Constructed from two types of smaller molecules: glycerol and fatty acids

Glycerol -a three-carbon alcohol with a hydroxyl group attached to each carbon

A fatty acid consists of a carboxyl group attached to a long carbon skeleton

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

#2 Lipids – Fats; Saturated vs Unsaturated

Saturated fatty acids (saturated fats) solid at room temperature Most animal fats are saturated

Unsaturated fatty acids (unsaturated fats, or oils) liquid at room temperature Plant fats and fish fats are usually

unsaturated

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.

#2 Lipids – Fats; Saturated vs Unsaturated

Saturated fats – Not so good for you The “tails” lack double bonds so they are

more flexible Flexibility allows them to clump together May contribute to cardiovascular disease

through plaque deposits

#2 Lipids – Fats; Trans fats

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

#2 Lipids – Fats; Unsaturated Fats

Certain unsaturated fatty acids are not synthesized in the human body. Essential fatty acids

Must be supplied in the diet Include omega-3 fatty acids Required for normal growth, thought

to provide protection against cardiovascular disease

#2 Lipids – Fats – what are they for?

The major function of fats is energy storage

Humans and other mammals store their fat in adipose cells

Adipose tissue also cushions vital organs and insulates the body

#2 Lipids – Phospholipids

Two fatty acids and a phosphate group are attached to glycerol.

The two fatty acid tails are hydrophobic; the phosphate group and its attachments form a hydrophilic head

Figure 5.12

Choline

Phosphate

Glycerol

Fatty acids

Hydrophilichead

Hydrophobictails

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

Hyd

rop

hilic

head

Hyd

rop

hob

ic t

ails

Figure 5.13

Hydrophilichead

Hydrophobictail

WATER

WATER

#2 Lipids – Steroids

Lipids characterized by a carbon skeleton consisting of four fused rings

#2 Lipids – Steroids; Cholesterol

An a component in animal cell membranes Plays a roll in cell/cell signaling and helps

maintain membrane integrity Essential in animals High levels in the blood may contribute to

cardiovascular disease

#3 Nucleic Acids

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

Figure 5.25-1

Synthesis ofmRNA

mRNA

DNA

NUCLEUSCYTOPLASM

1

Figure 5.25-2

Synthesis ofmRNA

mRNA

DNA

NUCLEUSCYTOPLASM

mRNAMovement ofmRNA intocytoplasm

1

2

Figure 5.25-3

Synthesis ofmRNA

mRNA

DNA

NUCLEUSCYTOPLASM

mRNA

Ribosome

AminoacidsPolypeptide

Movement ofmRNA intocytoplasm

Synthesisof protein

1

2

3

#3 Nucleic Acids

Polymers called polynucleotides Made of monomers called nucleotides

Nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups

The portion of a nucleotide without the phosphate group is called a nucleoside

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

LECTURE – 2 CONT. Functional Groups. Outline Water Structure - Review Important properties #4...

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