Topic 3

The Chemistry of Life

Polarity of Water

• Hydrogen pole is positive• Oxygen pole is negative• This makes water molecules polar

Hydrogen Bonding in Water

• Hydrogen bond: bond that can form between the positive pole of one water molecule and the negative pole of another

• Many bonds form in liquid water which makes it useful for living organisms

The Properties of WaterProperty name Outline Use in living organisms

Cohesion Hydrogen bonds let water molecules stick to each other

Used as a transport medium in plants

Solvent properties Water’s polarity allows it to dissolve many different substances

Water is the medium for metabolic reactions

Heat capacity Large amounts of energy are needed to raise water’s temperature

Water in blood can transfer heat

Boiling point Water has a high boiling point; large amounts of energy are needed to break hydrogen bonds to turn water into a gas

Water is the medium for metabolic reaction when it is a liquid

Cooling effect of evaporation

Water can evaporate at temps below boiling point; heat energy is taken from breaking H bonds

Water can act as a coolant (i.e. sweat)

Elements in Living Organisms

• Four most common elements:1. Carbon

2. Hydrogen

3. Oxygen

4. Nitrogen

• Other important elements:– Sulfur, Calcium, Phosphorus, Iron, Sodium

Organic and Inorganic Compounds

• Organic compounds: containing carbon and found in living organisms

• All compounds that do not contain carbon are inorganic

• Few compounds that do contain carbon are inorganic (Example: Carbon dioxide)

• Living organisms generally have three types of organic compounds:– Carbohydrates– Lipids– Proteins

Subunits of Organic Macromolecules

• Many organic compounds are made up of large molecules called macromolecules

• They are built up using subunits

Condensation Reactions

• Two molecules are joined together and water is also formed in the reaction

• Two amino acids in a condensation reaction create a peptide bond

• Two monosaccharides in a condensation reaction create a disaccharide

• Fatty acids link to glyceral in a condesnation reaction and creates gylcerides

Hydrolysis Reactions

• Hydrolysis: breaks down large molecules into smaller molecules with water

• The reverse of condensation reactions

Examples of Carbohydrates

Name Example In animals In plants

Monosaccharide •Glucose•Fructose•Galactose

Glucose is carried by blood to transport energy

Fructose makes fruit sweet to attract animals to disperse seeds

Disaccharide •Lactose•Maltose•Sucrose

Lactose is the sugar in milk that provides energy

Sucrose transports energy through the phloem

Polysaccharide •Starch•Gycogen•Cullulose

Glycogen is used for short-term energy storage in the liver/muscles

Cellulose makes strong fiber to construct the plant cell wall

Functions of Lipids

• Energy storage– Create fat in humans– Create oil in plants

• Heat insulation– Layer of fat under skin reduces heat loss

• Buoyancy– Lipids are less dense than water so they can

help animals float

Carbohydrates and Lipids in Energy Storage

Advantages of lipids Advantages of carbohydrates

Contain more energy per gram than carbohydrates, making stores lighter

More easily digested than lipids, making energy release faster

Insoluble in water and so do not effect osmosis in cells

Soluble in water and so are easier to transport

Usually used for long term energy storage

Usually used for short term energy storage

Nucleotide Subunits of DNA

• DNA is made of nucleotides• Each nucleotide contains a sugar,

phosphate group, and a base• There are four different bases found in

nucleotides:– Adenine– Thymine– Guanine– Cytosine

Building DNA Molecules

• Two DNA nucleotides can be linked together by a covalent bond – Bond forms between the sugar of one

nucleotide and the phosphate of another

• DNA consists of two strands of nucleotides in a double helix

Complementary Base Pairing

• Certain nucleotide bases will only bond with one other kind of nucleotide base– Adenine bonds with Guanine– Thymine bonds with Cytosine

• This is called complementary base pairing

DNA Replication

• Semi-conservative: each molecule formed by replication contains one strand of the original DNA and one new strand

• Stages of replication:1. DNA uncoils and hydrogen bonds are broken

by the enzyme Helicase

2. Single strand acts as a template upon which free nucleotides bond to; caused by the enzyme Polymerase

3. New strands of DNA form double helix

Differences Between DNA and RNA

DNA RNA

Two strands of nucleotides to form a double helix

One strand only

Deoxyribose sugar Ribose sugar

Use bases Adenine, Guanine, Cytosine, and Thymine

Uses bases Adenine, Guanine, Cytosine, and Uracil (instead of Thymine)

Genes and Polypeptides

• Polypeptides are made up of amino acids• Information for making polypeptides are

stored in a coded form in the genes of the amino acids

• The sequence of bases in a gene codes for the sequence of amino acids in a polypeptide

Transcription

• Transcription: Copying of a base sequence of DNA by making RNA

• Uses complementary base pairing; replacing Thymine with Uracil when bonded to Adenine

• Stages:1. DNA uncoils and separates

2. Free RNA nucleotides assemble using one strand as a template

3. RNA nucleotides link together

4. The RNA strand then separates from DNA; it is now messenger RNA (mRNA)

5. DNA reforms a double helix

Translation• Translation: Translates the RNA genetic code (which

are in groups of codons) into an amino acid chain• Stages:

1. mRNA binds to the small subunit a of ribosome; mRNA contains codons

2. Free transfer RNA (tRNA) molecules have anticodons that are complementary to certain mRNA codons; tRNA also carries amino acids

3. tRNA bonds to the ribosome if it is complementary to the mRNA codon; these codons and anticodons form hydrogen bonds

4. The amino acids carried by the bonding tRNA molecules bond together into peptides

One Gene-One Polypeptide Hypothesis

• There is almost always a single gene to code for a polypeptide that does not code for any other polypeptide

Introducing Enzymes

• Enzymes: globular proteins that catalyze chemical reactions

• By making only certain enzymes, cells can control what chemical reactions take place

• Denaturation: changing the structure of an enzyme so it can no longer carry out its function

• Substrates: the reactants in enzyme reactions

Enzyme-Substrate Specificity• Most enzymes are specific and only catalyze

certain reactions with certain substrates• Substrates bond to active site of an enzyme• Active site: region on the surface of an enzyme

to which substrates bind to catalyze a chemical reaction with the substrate– Only certain substrates can fit

the shape (like a key fitting into

a lock)

Factors Affecting Enzyme Activity

• Temperature– As temp increases, so does enzyme activity– At a certain temp enzyme activity will drop

• pH– Optimum pH is 7– pH levels closest to 7 have highest activity

• Substrate concentration– The greater the amount of substrates available to

bind to, the greater the activity– Enzyme activity eventually plateaus

Lactase and Lactose-Free Milk

• Lactose: natural sugar in milk• Lactase: converts lactose into glucose and

galactose• Biotechnology can extract lactase to

prevent possible negative effects caused by lactose

Energy and Cells

• All living cells need continuous energy• Cell respiration: controlled release of ATP

energy from organic compounds in cells• Can be aerobic (with oxygen) or

anaerobic (without oxygen)

Use of Glucose in Respiration

• Cell respiration often uses glucose• Glucose is broken down into pyruvate (a

simpler ogranic compound)• This produces a small amount of ATP

energy that is released by glucose

Anaerobic Cell Respiration

• If oxygen is unavailable, pyruvate is converted into a waste product– Waste product is either lactate (in humans); or

ethanol or carbon dioxide (in yeast)

• No ATP is produced

Aerobic Cell Respiration

• If oxygen is available, the pyruvate is absorbed into the mitochondria and is broken down into Carbon Dioxide and Water

• ATP is produced

Introducing Photosynthesis

• Photosynthesis: process used by plants to produce organic substances from light energy and inorganic substances

• Light energy is converted to chemical energy

• Chlorophyll is the main pigment that absorbs light

• Some of the absorbed energy makes ATP and other split into water molecules

Measuring Rates of Photosynthesis

• Can measure the rate of photosynthesis with: – Production of Oxygen– Uptake of Carbon Dioxide– Increase in Biomass

Factors Affecting Photosynthesis

• Light intensity– As light intensity increases, the rate of photosynthesis

increases– Eventually plateaus

• Carbon Dioxide– As CO2 concentration increases, the rate of photosynthesis

increases– Eventually plateaus

• Temperature– As temperature increases, the rate of photosynthesis

increases steeply– Reaches an optimum temperature then the rate drops