Water and Carbon. BONDS IONIC: between two ions – not as strong – comes apart easily, e.g. soluble in water COVALENT: shared electrons – very strong –

Water and CarbonWater and Carbon

BONDS

•IONIC: between two ions

– not as strong

– comes apart easily, e.g. soluble in water

•COVALENT: shared electrons

– very strong

–most common in biological matter

– can be POLAR or NON POLAR

Polar vs. Nonpolar Bonds

• Polar — charged surface– electrons are shared unevenly– Prefer other polar molecules– Soluble in water, which is also polar

• Nonpolar — no residual charge– electrons are shared evenly– Prefer other nonpolar molecules – Soluble in oils

Molecular Rules of Attraction

• Charged molecules have ionic or polar covalent bonds.

• e.g.: water, salt

• Uncharged molecules have non polar covalent bonds.

• e.g.: oils

CHARGED MOLECULES ARE ATTRACTED TO CHARGED MOLECULES.

• specifically: + charges/polarity is attracted to - charges/polarity

UNCHARGED MOLECULES ARE ATTRACTED TO UNCHARGED MOLECULES.

Water: a molecular view

2H2 + O2 --> 2H2O

Properties of water molecule

• The water molecule is a polar molecule

– Allows formation of hydrogen bonds

– Contributes to the various properties water exhibits

Properties of water

• Cohesion

• Moderation of temperature

• Expansion upon freezing

• Versatile solvent

Frozen water, a.k.a. Ice

• The hydrogen bonds in ice are more “ordered” than in liquid water, making ice less dense and able to float

Versatile solvent

• Polar water molecules interact with:

Ionic compounds other polar molecules

(like proteins)+

+

+

+Cl–

–

-

–

–

Na+

++

+

+

–

––

––

–Na+

Cl–

Dissolving agent = SolventAgent being dissolved = Solute +

–

Hydrophilic and Hydrophobic Substances

• A hydrophilic substance

– Has an affinity for water

• A hydrophobic substance

– Does not have an affinity for water

Dissociation of water

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

• H+ is not stable

H

Hydroniumion (H3O+)

H

Hydroxideion (OH–)

H

H

H

H

H

H

+ –

+

Acids and Bases

• An acid

– Increases the hydrogen ion concentration of a solution (more H3O+)

• A base

– Reduces the hydrogen ion concentration of a solution (more OH-)

The pH Scale• The pH of a solution

– Is determined by the relative concentration of hydrogen ions

– Is low in an acid

– Is high in a base

• pH paper

pH = -log10[H+]

The pH scale

More

Acid

ic[H

+]

> [

OH

– ]M

ore

Basic

[H+]

< [

OH

– ]

Neutral[H+] = [OH–]

Oven cleaner

0

1

2

3

4

5

6

7

8

9

10

11

12

13

14

Battery acidDigestive (stomach) juice, lemon juice

Vinegar, beer, wine, cola

Tomato juice

Black coffeeRainwater

Pure waterHuman blood

Seawater

Milk of magnesia

Household ammonia

Household bleach

Buffers

• Minimize changes in the concentrations of H3O+ and HO- ions

• Consist of an acid-base pair that reversibly combines with hydrogen ions

H2CO3 HCO3- + H+ (H3O+)

More OH-

More H+ (H3O+)

Carbonic acid

Carbon

• The Backbone of Biological Molecules

• All living organisms are made up of chemicals based mostly on the element carbon

• Organic chemistry is the study of carbon compounds

• Organic compounds range from simple molecules to colossal ones

Carbon can covalently bond with four atoms

• Carbon has four valence electrons

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

• Carbon can single, double and triple bond

H O N C

Hydrogen(valence = 1)

Oxygen(valence = 2)

Nitrogen(valence = 3)

Carbon(valence = 4)

Isomers

• Isomers: molecules with the same molecular formula but different structures and properties

Structural Geometric Enantiomers

HHH

HH

H

H

H

HHH

CC

C C CH

H H

X XC C

H H H H HH

H H H H HHC C C C C

H

HX

XC C

H

CO2H

CH3

NH2

C

C

C

CO2H

H

CH3

NH2

C

cis

trans

L-

D-

Enantiomers and Parkinson’s

L-Dopa

(effective against Parkinson’s

disease)

D-Dopa

(biologically inactive)

Functional groups• Functional groups are the parts of molecules

involved in chemical reactions

• Six functional groups are important in the chemistry of life

Hydroxyl Carbonyl Carboxyl

Amino Sulfhydryl Phosphate

(may be written HO )

OH

C

O O

C

OH

NH

H(may be written HS )

SHO P

O

OH

OH

Biological moleculesBiological molecules

Macromolecules

• Large molecules composed of smaller molecules

• Most macromolecules are polymers

• A polymer is a long molecule consisting of many similar building blocks called monomers

monomers polymers

Types of macromolecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Synthesis of Polymers

Monomers form larger molecules by dehydration reactions

HO H1 2 3 HO

HO H1 2 3 4

H

H2O

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a water molecule

Breakdown of Polymers

• Polymers can disassemble by hydrolysis

HO 1 2 3 H

HO H1 2 3 4

H2O

HHO

Carbohydrates

• Carbohydrates =

sugars (Monosaccharides or Disaccharides

sugar polymers (Polysaccharides)

• Monosaccharides can be used for fuel

• Polysaccharides

– Are polymers of sugars

– Serve many roles in organisms

Monosaccharides

H C OH

H C OH

H

H

C

O

Glucose

H C OH

H C OH

H C OH

H C OH

H

HO C H

H

C

O

C O

H C OH

H C OH

H C OHH

HO C H

H C OH

H

Glyceraldehyde

HO C H

H C OH

H C OH

H

H

C

O

HO C H

H C OH

Galactose

Fructose

Triose: C3H6O3Hexose: C3H12O6

Monosaccharides are linear or form rings

H

HO C H

H C OH

OC

H

12

3

4

5

6

H

OH

4C

6CH2OH 6CH2OH

5C

HOH

C

H OH

H2 C

1CH

O

H

OH

4C

5C

3 C

H

HOH

OH

H2C

1 C

OH

H

3

O H O

H C OH

H C OH

H C OH

Disaccharides are formed by dehydration

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

O H

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 4

Glucose

Glucose Glucose

Fructose

Maltose

Sucrose

OH

H

H

Polysaccharides functions

• Storage polysaccharides

Glycogen Starch

CH2OH

O

OH

OH

HO41

O

CH2OH

O

OH

OH

O

CH2OH

O

OH

OH

CH2OH

O

OH

OH

O O1 4 41 1

Polysaccharides functions

• Structural polysaccharides: cellulose

CH2OH

CH2OH

OH

OHO

OOHO

CH2OHO

OOH

OCH2OH OH

OH OHO

O

CH2OH

OO

OH

CH2OH

OO

OHO

O

CH2OHOH

CH2OHOHOOH OH OH OH

O

OH OH

CH2OH

CH2OH

OHO

OH CH2OH

OO

OH CH2OH

OH

O

O

O

O

O

O

OH

OH

O

OOH

4

CH2OH

OOH

OH

HO

O1

OH

OOH

CH2OH

O

CH2OH

OOH

OH

OOH

O

CH2OH

O

OH

Lipids

• Are not polymers

• Classes:

– Fats

– Phospholipids

– Steroids

Fats

• Formed from glycerol + Fatty acidH H

H HHH

H HH

H H HH

HH

HOH O HC

C

C

H

H OH

OH

H

HH

HH

HH

HH

HH

HH

HH

H

HCCCC

CC

CCC

CC

CC

CC C

Glycerol

Fatty acid(palmitic acid)

HO

HH

H

H

H H HH

HH

HH

HH

H HH

HH H

HHHHHHHHHHHHHHHH

H

HH H H H H H H H H H H H H H

H

HHHHHHHHHHHHHH

H H H H H H H H H H H H H H HH

HHHHHHHHHHHHHHH

OO

O

OC

C

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

C

CCCCCCCCCCCCCCCC

C C C C C C C C C C C C C C CO

O

dehydration

Ester

Saturated and Unsaturated fats

•Saturated fatty acids

– Max single bonds

– Solid at room temp

•Unsaturated fatty acids

– Contain double bonds

– Liquid at room temp

HH H

HHHO

H H H H H H

CC

CC

CC

CHO H

HH H

HHO

H H H H H

CC

CC

CC

CHO H

Phospholipids• Have only two fatty acids and a Phosphate

group

• Hydrophilic head (phosphate), hydrophobic tail (hydrocarbon)

Phospholipid symbol

CH2

O

PO O

O

CH2CHCH2

OO

C O C O

Phosphate

Glycerol

Fatty acids

–

CH2 Choline+N(CH3)3

Hyd

rop

hi lic

h

ead

Hyd

rop

hob

ic t

ai ls

Phospholipids are major component of cell membranes

Hydrophilicheads

WATER

WATERHydrophobictails

Steroids• Contain a carbon skeleton consisting of four

six-membered rings

• Cholesterol is a prime example– Essential for cell membrane fluidity

– Precursor for some hormones

HO

CH3

CH3

H3C CH3

CH3

Proteins: the cell’s workhorse

• Have many roles inside the cell

Structuralproteins

Storageprotein

s

Transportproteins

Hormonalproteins

Motorproteins

Enzymes

Defenseproteins

Receptorproteins

Enzymes• Proteins that accelerate chemical

reactions• Names always end in “-ase”• Chemical reactions occur in the active

site Substrate(sucrose)

Enzyme (sucrase)

Glucose

OH

H O

H2O

Fructose

Active site

Polypeptides and amino acids

• Proteins consist of one or more polypeptides

• Polypeptides = polymers of amino acids

• Amino acids

– Contain an amino group and a carboxyl group (acid)

– Have 20 different side chains (R groups); 20 amino acids make up proteins

C

H

R

COOHH3N

Amino acids

O

O–

CH3CH2

CH

C

H

H3N+

C

CH2H2

CH2

NC

CH2

H

C

Isoleucine (Ile)

Proline (Pro)

H3C O

O–

SH

CH2

C

H

H3N+

CO

O–

H3N+

C C

CH2

OH

H

O

O–

Cysteine (Cys)

Tyrosine(Tyr)

O– OCCH

2

C CH3N

+

H

O

O–

CH2

CH2CH2

CH2

NH3+

CH2

C CH3N

+

H

O

O–

Glutamic acid (Glu)

Lysine (Lys)

Amino Acid are linked by peptide bonds

• Peptide bonds

DESMOSOMES

OH

OH

CH2

C

N

H

C

H O

H OH OH

peptidebond

H H

HH

HN N

SH

OO

CH2 CH2

C CC C

OH

OH

OHH

H

H

H

H H

H

NN N

SHSide

chains

O O O

CH2 CH2 CH2

C C C C C C

_______

amino end(N-terminus)

Backbone

carboxy end(C-terminus)

H2O

Protein Conformation and Function

• A protein’s specific structure determines how it functions

Ribbon model Space-filling model

Four Levels of Protein Structure

• Primary structure

• Secondary structure

• Tertiary structure

• Quaternary structure+H3N

Amino end

Amino acidsubunits

helix

1˚ 2˚ 3˚ 4˚

Primary Structure

Is the unique sequence of amino acids in a polypeptide

TrpGly

Thr

LeuMet

MetTrp

Trp

Trp

Ala

Ala

Ala

AlaCys Cys

Gly Thr

Leu

Thr

ThrThr

ThrThr

Thr

amino terminus(NH3

+) carboxy terminus(CO2

-)

Secondary structure• Is the folding or coiling of the polypeptide

into a repeating configuration

• Includes the alpha helix and the Beta sheet

R R

O C Alpha helix

Beta sheet

Amino acidsubunits NC

H

C

O

C N

H

CO H

R

C NH

C

O H

C

RN

HH

R C

O

R

CH

NH

C

O H

NCO

R

CH

NH

H

C

R

C

O

C

O

C

NH

H

R

CC

ON

HH

C

R

C

O

NH

R

CH C

ON

H H

C

R

C

O

NH

R

CH C

ON

H H

C

R

C

O

N H

H C RN H

O

O C N

C

CH O

CHR

N HO C

RC

H

N H

O CH C R

N H

CC

N H

O C

H C R

N H

O C

RC

H

H

C

RN

H

CO

C

NH

R

CH C

ON

H

C

H H

Tertiary structure

• 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 bonds

Polypeptide

backbone

Hydrogen bond

ionic bond

CH2

disulfide bridge

Quaternary structure

• Aggregation of two or more polypeptide subunits for overall structure

Polypeptidechain

Collagen

Chains

Chains

Hemoglobin

IronHeme

Sickle-Cell Disease: results from a single amino acid change

• Glutamate to Valine change in hemoglobin

ß subunit

Protein folding in the cell

• Chaperones assist in the proper folding of other proteins

Hollo

w

cylin

der

Cap

Correctlyfoldedprotein

Polypeptide

Nucleic acids• Deoxyribonucleic acid (DNA) Hydrogen at 2’

C

– Stores information (blueprint)

– Directs DNA synthesis and protein synthesis through RNA

• Ribonucleic acid (RNA) OH at 2’ C

– Working copy

– Used directly in protein synthesis

• The Central Dogma

DNA RNA protein

The Structure of Nucleic Acids

• Nucleic acids exist as polymers = polynucleotides

3’C

5’ end

5’C

3’C

5’C

3’ endOH

O

O

O

O

NitrogenousBase

O

O

O

O P CH2

5’C

3’CPhosphate

group_________

sugar

O

Monomer = nucleotide

Structural difference between DNA and RNA

Ribose (in RNA)

OHOCH2

H

H H

OH

H

OHOCH2

HH H

OH

H

Pentose sugars

Deoxyribose (in DNA)Ribose (in RNA)OHOH

4’

5”

3’OH H

2’

1’

5”

4’

3’2’

1’Base

Nucleoside

O

O

O

O P CH2

5’C

3’CPhosphate

group Pentosesugar

O

The nitrogenous bases

O H

N

N

O

H

SugarUracil (U)

________

N HN

N

N

N

Sugar

Adenine (A)

N

N

N

N

Sugar

O H N

NH

N OH

H

N

Sugar

Guanine (G) Cytosine (C)

H

O CH3

N

N

O

H

SugarThymine (T)

H__________

________

Forming the DNA double helix

3’C

5’ end

5’C

3’C

5’C

3’ endOH

O

O

O

O

3’ end

5’ end

OH

Base-pairing of nitrogenous bases

O H

N

N

O

H

SugarUracil (U)

N HN

N

N

N

Sugar

Adenine (A)

N

N

N

N

Sugar

O H N

NH

N OH

H

N

Sugar

Guanine (G) Cytosine (C)

H

O CH3

N

N

O

H

SugarThymine (T)

H

A TG CA U

The DNA double helix

Base pair

3’ end

Phosphatebackbone

3’ end5’ end

3’ end

5’ end

5’ end

Base pair

3’ end

Cell membranes

Cell Theory

All living things are composed of one or more cells.

All cells come from preexisting cells

Animal Cells

- Boundaries:- Boundaries: membranesmembranes

- Movement: - Movement: cytoskeletoncytoskeleton

- Energy:- Energy: mitochondriamitochondria

- Protein synthesis and transport:- Protein synthesis and transport: nucleus, ribosomes, ER, Golgi, vesiclesnucleus, ribosomes, ER, Golgi, vesicles

- Waste:- Waste: lysosomeslysosomes

- Communication:- Communication: junctionsjunctions

CellsCellsCellsCells

NucleusNucleusNucleusNucleus

Plasma membranePlasma membranePlasma membranePlasma membrane

CytoplasmCytoplasmCytoplasmCytoplasm

Lipid bilayers

Phospholipids form membranes as lipid bilayers.

HydrophobicHydrophobicHydrophilicHydrophilic OUTOUT

ININ

HydrophobicHydrophobicHydrophilicHydrophilic OUTOUT

ININ

Plasma Membrane (aka Cell Membrane)

OUTSIDEOUTSIDE

INSIDEINSIDE

OligosaccharidesOligosaccharides Membrane ProteinsMembrane Proteins

CholesterolCholesterol

OuterOuterSurfaceSurface

Fluid Mosaic Modelof Membrane Structure

Membranes

How do substances get across membranes?Diffusion

How does diffusion work?

How do substances get across membranes?Diffusion

How does diffusion work?

Properties of the Lipid Bilayer

Types of PASSIVE Transport Across a Membrane

1. Simple diffusion• down the concentration gradient• no extra energy

2. Facilitated diffusion• down the concentration gradient• no extra energy• uses Channel proteins.

3. Osmosis•Water down the concentration gradient•no extra energy•special membrane, such as plasma

membrane: lets only water go across

Diffusion

1111 2222

3333The direction of movement is

from high concentration to low.

The direction of movement is

from high concentration to low.

DOWN gradientDOWN gradientDOWN gradientDOWN gradient

Diffusion across a membrane

1. SIMPLE DIFFUSION1. SIMPLE DIFFUSION1. SIMPLE DIFFUSION1. SIMPLE DIFFUSION

- no extra energy required- no extra energy required- no extra energy required- no extra energy required

Plasma membranePlasma membranePlasma membranePlasma membrane

Diffusion across a membrane

2. FACILITATED DIFFUSION2. FACILITATED DIFFUSION2. FACILITATED DIFFUSION2. FACILITATED DIFFUSION

- no extra energy- no extra energy- no extra energy- no extra energy

-channel proteins shuttle molecules down the channel proteins shuttle molecules down the -channel proteins shuttle molecules down the channel proteins shuttle molecules down the concentration gradientconcentration gradientconcentration gradientconcentration gradient

Plasma membranePlasma membranePlasma membranePlasma membrane

channelchannelchannelchannel

Diffusion

Molecules are always vibrating

Molecules in gas and liquid move randomly.

If there is a concentration gradient to start with, over time it will become uniform.

Molecules move from [HIGH] to [LOW].

Doesn’t require extra energy

Water across a membraneOSMOSIS: Movement of water

across a membranelipid-soluble molecules

(O2, CO2, H2O)

(extracellular fluid)

(cytoplasm)

Simple diffusion

HYPHYPERERTONICTONICHYPHYPERERTONICTONIC ISOISOTONICTONICISOISOTONICTONIC HYPHYPOOTONICTONICHYPHYPOOTONICTONIC

OSMOSIS – movement of water across a membrane

OSMOSIS: Results

HYPHYPERERTONICTONICHYPHYPERERTONICTONIC ISOISOTONICTONICISOISOTONICTONIC HYPHYPOOTONICTONICHYPHYPOOTONICTONIC

Normal RBCs

Isotonic SolutionIsotonic Solution

Osmosis

Equal movement of waterinto and out of cells

Net movement ofwater out of cells Net movement of

water into cells

Shriveled RBCs

Swollen RBCs

Hypertonic SolutionHypertonic Solution Hypotonic SolutionHypotonic SolutionResult: Into Result: Into Hypertonic Hypertonic solution?solution?

Result: Into Result: Into Hypertonic Hypertonic solution?solution?

Result: Into Result: Into Hypotonic Hypotonic solution?solution?

Result: Into Result: Into Hypotonic Hypotonic solution?solution?

Common theme: REQUIRES NO

EXTRA INPUT OF ENERGY

Common theme: REQUIRES NO

EXTRA INPUT OF ENERGY

PASSIVE Transport Across a Membrane

Transport through the Plasma Membrane

Passive: DOWN gradient Passive: DOWN gradient Passive: DOWN gradient Passive: DOWN gradient

Acitve: UP gradient Acitve: UP gradient Acitve: UP gradient Acitve: UP gradient

Active Transport

UP a concentration gradient

Requires energy (ATP)

Protein PUMPS

Movement

from low concentration to high reauires ENERGY!

Movement

from low concentration to high reauires ENERGY!

UP gradientUP gradientUP gradientUP gradient

Key concepts and words

Plasma membrane includes:Lipid bilayer made of phospholipids (which have hydrophobic and hydrophilic parts)

Integral and peripheral membrane proteinsCholesterol (wedges!)

Transport across a membrane:Passive: simple or facilitated diffusion (channels), down a concentration gradient, no energy.

Active transport (pumps), up a concentration gradient, requires energy.

Osmosis: hypotonic, isotonic, hypertonic