BIOCHEMISTRY

WATER

Chapter 3: Water and Life

maima

(Hebrew) amane (Berber) amanzi (Zulu)

biyo (Somali) mizu

(Japanese)

jo (Warao) shouei (Chinese)

Paani (Hindi)

wasser

(German)

su (Turkish)

dlo (Haitian)

Water

• Cells are 70-90% water• Three-fourths of Earth’s surface is

covered by water• Water is the biological medium for

life on Earth• Water must be present for life (as

we know it)

Hydrogen bonds between water molecules 

Water’s polarity• Polar – opposite ends of molecule have

opposite charges– Opposing charges due to oxygen’s

electronegativity•Oxygen has partial negative•Hydrogens have partial positive

• Water forms H bonds (opposite charges attract)– ~15% water molecules in our body

are bonded to four partners

Four Properties of Water Allowing for Life

1. Cohesion/Adhesion2. Moderation of temperature3. Insulation of bodies of water by

floating ice4. The solvent of life

Trees

Walking on water

Cohesion• Cohesion - H bonding keeps water molecules

close together• Makes water a “structured” liquid• Adhesion – the clinging of one substance to

another– Ex. water sticks to sides of a glass

• Both cohesion and adhesion help water move up from roots to plants to leaves

• Surface tension – measure of how difficult it is to stretch or break the surface of a liquid– Water has a high surface tension due to H

bonds – almost like a thin film on the surface.

Moderation of Temperature• Heat – measure amount of total

kinetic energy (cal, kcal, or J)– 1 cal = amount of heat needed to

raise the temp of 1g of water 1°C– 1000 cal = 1 kcal – 1 cal = 4.184 J

• Temperature – measures the intensity of heat due to average kinetic energy of molecules (°C)

• Specific heat – amount of heat that must be absorbed or lost for 1 g to change its temp by 1 °C – Specific heat of water = 1 cal/g/°C

– Compared to most substances, water’s specific heat is quite high.

– This means water will changes its temp slower when it absorbs or gives off heat.

– Why? H bonds need heat to break and heat is released when bonds are formed.

– High specific heat allows large bodies of water to absorb lots of heat in summer without raising temp too high. In winter, gradual cooling of water helps warm the air.

– High specific heat helps stabilize ocean temp to better support marine life.

• Heat of vaporization – the quantity of heat a liquid must absorb for 1 g to be converted to gaseous state

• Water has a high heat of vaporization – 580 cal of heat needed to evaporate 1 g

water at 25°C because H bonds must be broken before molecules can change to gas.

– Evaporative cooling – as liquid evaporates, the surface cools because the hottest molecules leave as gas and cooler molecules are left behind•Why sweat? Evaporative cooling in

progress!•Why do we sweat more on humid

days?

Insulation of Bodies of Water by Floating Ice

• Water is more dense than ice. At 4°C water is at its most dense state, then as it cools to O°C, the molecules freeze. The H bonds keep the water molecules slightly apart (like a lattice) so air pockets form within ice.

• Lakes, oceans etc. would freeze solid if ice was more dense than water. During the summer, only upper few inches of ocean would thaw making life as we know it impossible (not to mention ice skating and hockey! )

Ice Caps/Glaciers Melting

• Global warming causing ice to melt.– Loss of habitat– Less sunlight reflected into space so

increases temp

The structure of ice

Ice, water, and steam

Floating ice and the fitness of the environment

Floating ice and the fitness of the environment: ice fishing

Ice floats and frozen benzene sinks

The Solvent of Life

• Solvent - dissolving agent in a solution

• Solute – the substance that is dissolved

• Aqueous solution – water is the solvent

• Water can dissolve many substances, but obviously not all!– Hydrophilic – likes water – Hydrophobic – repel water (nonpolar

and nonionic)

A crystal of table salt dissolving in water

A water-soluble protein

• Concentrations– Molecular mass – sum of mass of

atoms (daltons)• Molecular mass of CO2 = 12 + 16(2) = 44

daltons

– 1 mole = 6.02 x 1023 molecules

– 1 mole CO2 = 44 grams

– Molarity (M) = mole/liter

Moles

Chemical reaction: hydrogen bond shift

pH• H+ (protons) occasionally move from

one water molecules to another (disassociation).

• If water loses a H+ then it becomes OH- (hydroxide ion).

• If water gains a H+ then it becomes H3O+ (hydronium ion).

• In pure water, the OH- and H+

concentrations are equal.• Acid – increases H+ concentrations• Base – decreases H+ concentrations

•pH = -log [H+] –For neutral water:

• pH = -log 10-7 = -(-7) = 7 –pH decreases as H+ increases–A pH of 3 vs. pH of 6 is a 1000 fold difference (10 fold for each step)

The pH of some aqueous solutions

Buffers

• Buffers – minimize changes in pH by being able to release or take in H+

• Buffers keeps blood between 7 and 7.8• The equation below shifts right to

decrease pH and left to increase pH (bicarbonate buffer)

H2CO3 HCO3- + H+

Carbonic acid

bicarbonate proton

Acid Rain

• Acid precipitation – below 5.6• Caused primarily by increased levels of

sulfur and nitrogen oxides released from the burning of fossil fuels

• Acid precip can damage lakes, streams, and soil.

• Acid can make harmful heavy metals more soluble in water.

The effects of acid precipitation on a forest

Pulp mill

Acid rain damage to statuary, 1908 & 1968

CARBON AND THE MOLECULAR DIVERSITY OF

LIFECHAPTER 4

ISOMERS• Compounds with the same chemical

formula but different structures

Functional Groups See diagram of functional groups

Three types of isomers

Structural isomers

Functional Groups of Organic Compounds

A comparison of functional groups of female (estradiol) and male (testosterone) sex hormones

THE STRUCTURE AND FUNCTION OF LARGE

BIOLOGICAL MOLECULESCHAPTER 5

Macromolecules

• Polymer – long molecule consisting of many similar building blocks connected by covalent bonds

• Monomer – the building blocks

SYNTHESIS AND BREAKDOWN

• Dehydration synthesis (condensation reaction) – removal of water to join 2 compounds (anabolic)

• Hydrolysis – addition of water to break a bond between 2 compounds (catabolic)

The synthesis and breakdown of polymers

CARBOHYDRATES• Monomers are sugars.• Used for energy.• Types of carbohydrates

– Monosaccharides – one sugar•Examples: glucose, fructose, and galactose

– Disaccharides – two sugars joined•Examples: lactose, sucrose and maltose•Joined by glycosidic linkage via dehydration

synthesis– Polysaccharides – many sugars joined

•Examples: starch, glycogen, chitin (exoskeletons of insects), and cellulose (fiber)

The structure and classification of some monosaccharides

Linear and ring forms of glucose

Examples of disaccharide synthesis

Storage polysaccharides

Starch and cellulose structures 

Starch and cellulose structures 

The arrangement of cellulose in plant cell walls

Cellulose digestion: termite and Trichonympha

Cellulose digestion: cow

Chitin, a structural polysaccharide: exoskeleton and surgical thread

LIPIDS• Little or no affinity for water (hydrophobic)• No monomers• Many uses including insulation, store energy,

hormones• Examples: Fat, phospholipids, and steroids• Fats – composed of glycerol (an alcohol) and

fatty acids– Saturated – no double bonds in carbon

chain– Unsaturated – at least one double bond in

carbon chain• Phospholipids – make up plasma membrane• Steroids – consist of 4 carbon rings;

examples include cholesterol, vitamin D, estrogen, and testosterone

Examples of saturated and unsaturated fats and fatty acids 

Saturated and unsaturated fats and fatty acids: butter and oil

The structure of a phospholipid

Two structures formed by self-assembly of phospholipids in aqueous environments   

The synthesis and structure of a fat, or triacylglycerol

Cholesterol, a steroid    

An Overview of Protein Functions

PROTEIN

• Monomers are amino acids.• Many uses including enzymes,

antibodies, receptors, structural, hormones, and transport

• Protein – consists of one or more polypeptides with specific 3-D structure– Polypeptide = polymer of amino acids– Peptide = bond between 2 amino acids

• There are 20 different amino acids differing only by the R group

The 20 amino acids of proteins: nonpolar

The 20 amino acids of proteins: polar and electrically charged

Making a polypeptide chain

• Four levels of protein structure– Primary – sequences of amino acids– Secondary – hydrogen bonds cause coils and

folds•Beta pleated sheet and alpha helix

– Tertiary – irregular contortions due to various weak bonds:•Hydrophobic interactions•Disulfide bridges•Ionic bonds•Van der Waals interactions (weak attractions

from transient partial charges)– Quaternary – two or more polypeptide chains

aggregated into one functional macromolecule•Examples: collagen and hemoglobin

The primary structure of a protein

A single amino acid substitution in a protein causes sickle-cell disease

Sickled cells

The secondary structure of a protein

Examples of interactions contributing to the tertiary structure of a protein

The quaternary structure of proteins

Review: the four levels of protein structure

Protein Structure

• The function of a protein depends on its 4 levels.

• Denaturation – the “unraveling of a protein” so that the 2nd, 3rd, and 4th level structures are gone and all that is left is the primary sequence– Loss of structure = loss of

function– Causes of denaturation - High

temp, high or low pH

Denaturation and renaturation of a protein

Spider silk: a structural protein

Silk drawn from the spinnerets at the rear of a spider

NUCLEIC ACIDS

• Monomers are nucleotides.• Nucleotides – are made of sugar,

phosphate, and a N-base• Examples: DNA, ATP, and RNA• We will discuss these in great

detail later in the semester!

The components of nucleic acids

The DNA double helix and its replication

AN INTRODUCTION TO METABOLISM

CHAPTER 8

 Transformations between kinetic and potential energy

Kinetic and potential energy: dam

Kinetic and potential energy: cheetah at rest and running

BIOENERGETICS• Bioenergetics – the study of how energy

flows through living organisms• Catabolic – reactions or pathways where

a larger molecule is broken down into smaller molecules

• Anabolic - reactions or pathways where smaller molecules are joined to build a larger molecule

THERMODYNAMICS

• First Law of Thermodynamics – energy can be transferred and transformed, but not created nor destroyed

• Second Law of Thermodynamics – every energy transfer or transformation makes the universe more disordered (have more entropy)

– Entropy – measure of disorder or randomness

– Most energy transformations involve at least some energy be changed to heat

– Heat is the lowest form of energy– Biological order has increased over

time– Second law requires only that

processes increase the entropy of the universe

– Organisms may decrease entropy but entire universe must increase entropy

Order as a characteristic of life

• Free energy (G) – energy available to do work when temperature is uniform throughout system

G = H – TS

• H = system’s total energy (enthalpy)• T = temp in Kelvin (° C + 273)• S = entropy (measure of disorder)

∆ G = G final state – G starting state

∆ G = ∆ H - T∆ S• For a spontaneous reaction:

–∆ G = negative•So must: give up energy (decrease H) and/or give up order (increase S)

∆ G = 0 at equilibrium• Free energy increases if move away

from equilibrium and decreases if move toward equilibrium

The relationship of free energy to stability, work capacity, and spontaneous change

• Exergonic – ∆ G = negative– Spontaneous– Net release of energy

• Endergonic– ∆ G = positive– NOT spontaneous– Stores free energy in molecules

Energy changes in exergonic and endergonic reactions

• Cells at equilibrium are dead!• Cells can keep disequilibrium by

having products of one reaction not accumulate but instead become reactants of another reaction

• Energy coupling – an exergoinc reaction drives an endergoinc reaction (or a reaction that increase entropy is paired with one that decreases entropy)

Disequilibrium and work in closed and open systems

ATP = ADENOSINE TRIPHOSPHATE

ATP + H2O ADP + Pi∆ G = -7.3kcal/mol

•ADP = adenosine diphosphate• Normally the phosphate is bonded

to an intermediate compound which is then considered phosphorylated

• The reverse reaction is endergonic and requires +7.3 kcal/mol to make ATP from ADP

The structure and hydrolysis of ATP

 Energy coupling by phosphate transfer

The ATP cycle

ENZYMES• Catalytic proteins or enzymes –

change the rate of reaction without being consumed by the reaction

• Activation energy (EA) – energy needed to start a reaction– Energy needed to contort the reactants

so the bonds can change• Enzymes lower activation energy by

enabling reactants to absorb enough energy to reach transition state at moderate temps

• Enzymes are substrate specific• Substrate – the reactant on which

an enzyme works• Active site – area on enzyme where

substrate fits• Induced fit – model of enzyme

activity

Energy profile of an exergonic reaction

The effect of an enzyme on activation

FThe induced fit between an enzyme and its substrate

The catalytic cycle of an enzyme

• Effects of pH and Temp – Optimal temperatures and pH ranges

exist for enzymes– High temperatures can denature an

enzyme– Changes in pH can also denature

enzymes

Environmental factors affecting enzyme activity

• Cofactors – non-protein helpers that bind to active site or substrate (zinc, iron)– Coenzymes – cofactors that are organic

(vitamins)• Enzyme Inhibitors – reduce enzyme activity

– Competitive inhibitors – block substrate from entering active site•Reversible•Overcome by adding more substrate

– Noncompetitive inhibitors – bind to another part of enzyme thereby changing the enzyme’s shape making it inactive•Irreversible•Examples: DDT, sarin gas, and penicillin

Inhibition of enzyme activity

• Allosteric regulation– Allosteric sites – receptors on

enzymes (not the active site) that may either inhibit or stimulate enzyme activity

• Cooperativity – an enzyme with multiple subunits where binding to one active site causes shape changes to rest of subunits which in turn activates those subunits

• Feedback inhibition– End product of a pathway acts as a

inhibitor of an enzyme within the pathway

Allosteric regulation of enzyme activity

Cooperativity

Feedback inhibition