unit 1 -chemistry of life topic 2 – molecular biology

Unit 1 -Chemistry of Life

Topic 2 – Molecular Biology

2.1 – Molecules to metabolism2.2 – Water2.3 – Carbohydrates and lipids2.4 – Proteins2.5 – Enzymes2.6 – DNA and RNA2.7 – DNA replication, transcription, translation2.8 – Cell respiration2.9 – Photosynthesis

2.1 – MOLECULES TO METABOLISM

Most frequently occurring chemical elements in living things

• Carbon - Forms 4 covalent bonds Ex. CH4

• Hydrogen – Forms 1 covalent bond, Ex. : H2

• Oxygen – Forms 2 covalent bonds, Ex. CO2

• Nitrogen – Forms 3 covalent bonds, Ex. NH3

2.1 – Molecules to metabolism

Elements needed by living organisms

• Sulfur• Calcium• Phosphorus• Potassium &

Sodium • Iron

One role for each of the elements

•Sulfur: Found in certain amino acids (cysteine and methionine), allowing proteins to form disulphide bonds

•Calcium: Found in bones and teeth, also involved in neurotransmitter release in synapses •Phosphorus: Component of nucleic acids and cell membranes

•Sodium and potassium: essential ions in neuron membrane potential, required for nerve impulse transmission

•Iron: Found in hemoglobin (animals), allowing for oxygen transport


Organic vs. inorganic compounds

• Organic: compounds containing carbon that are found in living organisms– exceptions: carbonates (e.g. CaCO3), hydrogen

carbonates (e.g. HCO3), and oxides of carbon (e.g. CO, CO2)

• all other compounds are regarded as inorganic


Types of metabolic reactions

• Metabolism: web of ALL the enzyme-catalyzed reactions in a cell or organism

– Anabolism: SYNTHESIS of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.

– Catabolism: BREAKDOWN of complex molecules into simpler molecules including hydrolysis of macromolecules into monomers

DRAWING


Glucose: C6H12O6

Hexose sugar (six carbons) most commonly found in this ring structure.– product of photosynthesis or

the substrate molecule for respiration.

– polymer as starch, glycogen or cellulose.

– All bonds are covalent.– Is a reducing sugar and will give

positive (Brick red) precipitate in a Benedicts test.

– metabolically active compound– soluble and has osmotic effects

when in solution


• Ribose: Pentose (5 carbon sugar). – Part of one the important organic

molecules in photosynthesis, ribulose bisphosphate. (RUBP)

– A modified version of ribose, deoxyribose is perhaps best known for its role in Deoxyribonucleic acid or DNA where it forms part of the sugar phosphate backbone. The chemical properties of deoxyribose are very different from the properties of ribulose

– Both Ribose and Glucose will attract water molecules (hydrogen bonding) to form solutions.


Fatty Acid• Basis of triglycerides and many other types of lipid. These molecules are

also the basis of the phospholipid molecules that form the bilayer of the cell membrane.

Saturated fatty acid = (no double bonds)• Chain is the formed from a series of covalently bonded carbons saturated

with hydrogens. • The chain is non-polar and hydrophobic • The carbonyl group is polar making this ends of the molecule hydrophilic. • Animals fats have saturated fatty acids which are straight molecules and

very compact. This is gives them a higher melting point than the plant oils


Amino acid• There are 20 common amino

acids • Amino acids are monomers

which combine to form the larger polypeptides. In turn polypeptides combine to form proteins.

• Proteins molecules are the basis of enzymes and many cellular and extra cellular components.

• Each of the common amino acids has the same structure as the one shown except that the R group is different.

• Amino acids are soluble


APPLICATION AND SKILLSAPPLICATION 1: Urea as an example of a compound

that is produced by living organisms but can also be artificially synthesized

SKILL 1 : Need to know how to draw molecular diagrams of glucose, ribose, a saturated fatty acid and generalized amino acid

SKILL 2: Identification of biochemicals such as sugars, lipids, or amino acids from molecular diagrams


2.2 - WATER

Water molecules bonding

2.2 - Water

Structure• Water (H2O) is made up of two hydrogen atoms covalently bound to an

oxygen atom• While this bonding involves the sharing of electrons, they are not shared

equally • The oxygen atom, having more protons (+ve), attract the electrons (-ve)

more strongly (i.e. the oxygen has a higher electronegativity)• Thus the oxygen atom becomes slightly negative and the hydrogen atoms

become slightly positive

H-Bonding

• Covalently bonded molecules that have a slight potential charge are said to be polar

• The slightly charged regions of the water molecule can attract other polar or charged compounds

• Water molecules can associate via weak hydrogen bonds (F/O/N bonding with H)

• Water polarity https://www.youtube.com/watch?v=ASLUY2U1M-8

2.2 - Water

https://www.youtube.com/watch?v=ASLUY2U1M-8

https://www.youtube.com/watch?v=ASLUY2U1M-8

Properties of water

Thermal - hydrogen bonds between polar water molecules cause water to resist change

• Water has a high specific heat capacity (the measure of energy required to raise the temperature of 1 g of substance by 1°C)

• Water has a high heat of vaporization (amount of energy absorbed per gram as it changes from a liquid to a gas / vapor)

• Water has a high heat of fusion (amount of energy required to be lost to change 1 g of liquid to 1 g of solid at 0°C)

• These properties occur as a result of the extensive hydrogen bonding between water molecules - this allows water to absorb considerable amounts of energy with little change in form (H-bonds need to be broken first)

2.2 - Water

Cohesive • Water molecules are strongly cohesive (they

tend to stick to one another)• Water molecules will also tend to stick to

other molecules that are charged or polar (adhesion)

• These properties occur as a result of the polarity of a water molecule and its ability to form hydrogen bonds with appropriate molecules

2.2 - Water

Adhesive– hydrogen bonds between polar water molecules and other

substances– Meniscus formation in graduated cylinders– Capillary action (along with cohesion)

Solvent• Water can dissolve many organic and inorganic substances that

contain electronegative atoms (such as sodium, fluorine, oxygen and nitrogen)

• This occurs because the polar attraction of large quantities of water molecules can sufficiently weaken intramolecular forces (such as ionic bonds) and result in the dissociation of the atoms

2.2 - Water

Coolant • Both plants and animals use the evaporation

of water from the surfaces of their bodies to facilitate cooling (sweating and panting in animals, transpiration from leaves in plants)

• Water can be used to carry heat to cooler places in our bodies (countercurrent exchange of thermal energy)

2.2 - Water

Medium for metabolic reactions • Cytoplasm is primarily water, providing a polar

medium in which other polar or charged molecules dissolve

• Water can also absorb thermal energy released as a by-product of many chemical reactions

2.2 - Water

Transport medium • Hydrogen bonds between polar water molecules cause

them to cohere • The forces of attraction between water molecules help

facilitate the transport of water up the xylem of plants• Water is an effective transport medium for dissolved

substances (in plants, minerals from the soil and sugars from the leaves can be transported in water through the xylem and phloem respectively; while in animals, water in the blood is used to transport oxygen, glucose and urea)

2.2 - Water

• APPLICATION 1:– Compare the thermal properties of water with

that of methane (non-polar molecule)• APPLICATION 2:– Use of water as a coolant in sweat

• APPLICATION 3:– Modes of transport of glucose, amino acids,

cholesterol, fats, oxygen, and sodium chloride in blood in relation to their solubility in water

2.2 - Water

APPLICATIONS AND SKILLS

2.3 CARBOHYDRATES AND LIPIDS

CARBOHYDRATES

2.3 – Carbohydrates and Lipids

Condensation Synthesis and Hydrolysis Review

• Condensation (dehydration) reactions occur when molecules are covalently joined together and water is formed as a by-product– In carbohydrates, the bond that is formed is

called a glycosidic linkage• Hydrolysis is the opposite of a

condensation reaction and requires a water molecule to break a covalent bond between two subunits

• Monosaccharides are single monomers that are joined to form disaccharides, while sugars containing multiple subunits (more than 10) are called polysaccharides


http://www.cengage.com/biology/discipline_content/animations/reaction_types.html



• Formation of a disaccharide


Polysaccharide Formation• The chain of glucose molecules

represent the polysaccharide formed by many glucose monomers joining together to form this polysaccharide called amylose.

• Amylose is a polymer of glucose.• Intramolecular hydrogen bonding

causes the chain molecule to twist into a helical shape.

• Amylose is one of two molecules found in starch, the other being a branching polymer of glucose called amylopectin.


• Starch: Starch is composed of two polysaccharides, Amylose and amylopectin

• Starch is metabolically un-reactive and insoluble and hence an excellent storage carbohydrate.


Examples of monosaccharides, disaccharides and polysaccharides


Carb functions in animals vs. plants• Animals• Glucose: A source of energy which can be broken down to form ATP via cellular

respiration• Lactose: A sugar found in the milk of mammals, providing energy for suckling

infants• Glycogen: Used by animals for short term energy storage (between meals) in

the liver

• Plants• Fructose: Found in honey and onions, it is very sweet and a good source of

energy• Sucrose: Used primarily as a transportable energy form (e.g. sugar beets and

sugar cane)• Cellulose: Used by plant cells as a strengthening component of the cell wall


LIPIDS


Formation of a triglyceride (lipid with three fatty acids):• A condensation reaction occurs between the three hydroxyl groups of glycerol and the

carboxyl groups of three fatty acids• This reaction forms a triglyceride (and three molecules of water)• The bond between the glycerol and the fatty acids is an ester linkage• When one of the fatty acids is replaced by a phosphate group and phospholipid is formed• Hydrolysis reactions will, in the presence of water, break these molecules down into their

constituent subunits


• Saturated fatty acids= NO double bonds, max # of H atoms

• Monounsaturated Fatty Acid = 1 double bond

• Polyunsaturated Fatty Acid = many double bonds


• Cis or Trans fats?


• Ted-ed video - http://www.youtube.com/watch?v=QhUrc4BnPgg


http://www.youtube.com/watch?v=QhUrc4BnPgg

http://www.youtube.com/watch?v=QhUrc4BnPgg

APPLICATION AND SKILLS

• APPLICATION 1: structure and function of cellulose, starch in plants and glycogen in humans



• APPLICATION 2:Scientific evidence for health risks of trans fats and saturated fatty acids



• APPLICATION 3: Lipids are more suitable for long-term energy storage in humans than carbohydrates.



• APPLICATION 4: Evaluation of evidence and the methods used to obtain the evidence for health claims made about lipids



• SKILL 1: Use of molecular visualization software to compare cellulose, starch and glycogen (App to download molecules)



• SKILL 2: Determination of body mass index by calculation or use of a nomogram


2.4 - PROTEINS

• Proteins are large organic compounds made of amino acids arranged in a linear chain

• The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code

2.4 - Proteins

Formation of polypeptide• A condensation reaction occurs between the amino group (NH2) of one amino

acid and the carboxylic acid group (COOH) of another amino acid• This reaction forms a dipeptide (plus a molecule of water) that is held

together by a peptide bond• Multiple amino acids can be joined together to form a polypeptide chain• In the presence of water, polypeptides can be broken down into individual

amino acids via hydrolysis reactions

2.4 - Proteins

20 amino acids

2.4 - Proteins

DNA proteins

• Genes encode for amino acids

• Amino acids can be linked together in any sequence giving a huge range of possible polypeptides

2.4 - Proteins

2.4 - Proteins

• Protein formation -https://www.youtube.com/watch?v=iaHHgEoa2c8

2.5 - ENZYMES

Enzyme:– globular proteins – catalysts which speed up

biological reactions – unchanged by the reaction – specific to their substrate

Active Site:– position on the enzyme

occupied by the substrate – affected by temperature and

pH

2.5 - Enzymes

Enzyme–substrate specificity• Lock and key model: • Active site and substrate complement each other in terms of both shape and

chemical properties (e.g. opposite charges)• Binding to the active site brings the substrate into close physical proximity,

creating an enzyme-substrate complex• The enzyme catalyses the conversion of the substrate into a product (or

products), creating an enzyme-product complex• As the enzyme is not consumed in the reaction, it can continue to work once the

product dissociates (hence only low concentrations are needed)– Lock = enzyme’s active site– Key = substrate– Enzymes and substrates are specific for each other

• Ex. Lactase breaks down lactose

2.5 - Enzymes

• Activation Energy: minimum amount of energy needed for a reaction to take place– Catalysts reduce the activation energy needed for

a reaction to occur

2.5 - Enzymes

Effects of temperature, pH and substrate concentration on enzyme activity

• Temperature– Higher temperature higher

kinetic energy more movement of molecules

– Increases reaction rate as temperature increases up to a limit

– Limit based on temperature that enzyme begins to lose 3D shape due to intramolecular bonds being stressed and broken denaturation

2.5 - Enzymes

• pH– pH is dependent of number of hydrogen ions (H+) compared to (OH-) in a

solution– The negative/positive areas of a substrate must match the opposite charge

when in the active site of enz– Too acidic too many H+ ions can bond with the negative charges of enz or

substrate and not allow for proper matching.– Same goes with OH- except with positive enz or substrate

• Human body pH– Most reactions are active in pH near 7– Exception – pepsin (enzyme) in the stomach. Most active in a highly acidic env.

(a)– pepsin activity(b)- salivary

amylase activity

2.5 - Enzymes

• Substrate Concentration– If constant amount of enzyme and substrate

increases• Rate of reaction increases

– Limit – enzymes have a max rate at which they can work

2.5 - Enzymes

Videos

• Enzyme basics - http://www.youtube.com/watch?v=CZD5xsOKres

• Factors affecting enzyme functioning http://www.youtube.com/watch?v=D2j2KGwJXJc&feature=plcp

• Lucy example - http://www.youtube.com/watch?v=8NPzLBSBzPI

• Ted-Ed pain relievers - http://ed.ted.com/lessons/how-do-pain-relievers-work

2.5 - Enzymes

http://www.youtube.com/watch?v=CZD5xsOKres

http://www.youtube.com/watch?v=D2j2KGwJXJc&feature=plcp

http://www.youtube.com/watch?v=D2j2KGwJXJc&feature=plcp

http://www.youtube.com/watch?v=8NPzLBSBzPI

http://ed.ted.com/lessons/how-do-pain-relievers-work

http://ed.ted.com/lessons/how-do-pain-relievers-work

• Denaturation - structural change in a protein that results in the loss (usually permanent) of its biological properties.

2.5 - Enzymes

Use of lactase in the production of lactose-free milk.

• Lactose is a disaccharide of glucose and galactose which can be broken down by the enzyme lactase

• Historically, mammals exhibit a marked decrease in lactase production after weaning - leading to lactose intolerance (incidence is particularly high in Asian / African / Native American / Aboriginal populations)

2.5 - Enzymes

• Lactose-free milk can be produced by purifying lactase (e.g. from yeast or bacteria) and binding it to an inert substance (such as alginate beads)

• Milk passed over this immobilised enzyme will become lactose-free

• The generation of lactose-free milk can be used in a number of ways:– As a source of milk for lactose-intolerant

individuals– As a means to increase the sweetness of

milk (glucose and galactose are sweeter in flavour), thus negating the need for artificial sweeteners

– As a way of reducing the crystallisation of ice-creams (glucose and galactose are more soluble than lactose)

– As a means of shortening the production time for yogurts or cheese (bacteria ferment glucose and galactose more readily than lactose)

2.5 - Enzymes

2.6 – STRUCTURE OF DNA AND RNA

Nucleotide

2.6 – Structure of DNA and RNA

Nitrogen bases

• Adenine and guanine are purines (double ring bases)• Thymine and cytosine are pyrimidines (single ring bases)

Adenine Guanine Thymine Cytosine


DNA structure

**What are the 5’ and 3’ referring to?**Where are the phosphodiester bonds?


Formation of DNA strand

• Nucleotides a linked into a single strand via a condensation reaction

• The phosphate group (attached to the 5'-C of the sugar) joins with the hydroxyl (OH) group attached to the 3'-C of the sugar

• This results in a phosphodiester bond between the two nucleotides and the formation of a water molecule

• Successive condensation reactions between nucleotides results in the formation of a long single strand


DNA structureDNA is a double-helix made of two anti-parallel strands of nucleotides linked by

hydrogen bonding between complementary base pairs.

• Two polynucleotide chains of DNA are held together by hydrogen bonds between complementary base pairs

• Adenine pairs with thymine (A=T) via two hydrogen bonds• Guanine pairs with cytosine (G=C) via three hydrogen bonds

Adenine Thymine GuanineCytosine


• In order for bases to be facing each other and thus able to pair, the two strands must run in opposite directions (i.e. they are anti-parallel)

• As the polynucleotide chain lengthens, the atoms that make up the molecule will arrange themselves in an optimal energy configuration

• This position of least resistance results in the double-stranded DNA twisting to form a double helix with approximately 10 - 15 bases per twist


DNA vs. RNA

DNA RNAStrands 2 1Bases A, T, G, C A, U, G, CPentose Deoxyribose RiboseLocation Nucleus Nucleus,

cytoplasm



• APPLICATION 1: Functions of rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk

• APPLICATION 2: Denaturation of proteins by heat or deviation of pH from the optimum.

• SKILL 1: Drawing molecular diagrams to show the formation of a peptide bond.

2.4 - Proteins


• APPLICATION 1: METHODS OF PRODUCTION OF LACTOSE-FREE MILK AND ITS ADVANTAGES

• SKILL 1: DESIGN EXPERIMENTS TO TEST THE EFFECT OF TEMPERATURE, pH, AND SUBSTRATE CONCENTRATION ON THE ACTIVITY OF ENZYMES (know the graphs!!)

• SKILL 2: EXPERIMENTAL INVESTIGATION OF A FACTOR AFFECTING ENZYME ACTIVITY

2.5 - Enzymes


• APPLICATION 1: Watson and Crick’s elucidation of the structure of DNA using model making.

• SKILL 1: Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using circles, pentagons and rectangles to represent phosphates, pentoses and bases.


2.7 – DNA REPLICATION, TRANSCRIPTION AND TRANSLATION

DNA replication overview• Process where multiple copies of DNA are

made from template DNA (semi-conservative replication)

• Performed during the S phase (synthesis) phase of mitosis and meiosis

• Occurs in the nucleus

2.7 – DNA Replication, transcription and translation

DNA replication steps

1. Helicase (enzyme) breaks the hydrogen bonds between complementary base pairs. This unzips the double helix at a position called the replication fork.

2. RNA Primase binds to DNA in the initiation point of the 3'-5' parent chain. It attracts RNA nucleotides which are the primers (starters) for the binding of DNA nucleotides.

3. DNA polymerase III adds DNA nucleotides to the RNA primer in a 5’-3’ direction on the leading strand

4. On the lagging strand, RNA Primase adds more RNA Primers. DNA polymerase III reads the template and lengthens the DNA. The DNA fragments created are called "Okazaki Fragments".

5. All RNA primers have to be removed and DNA polymerase I fills in the gaps.

6. Okazaki fragments are joined together with DNA ligase (‘glues’ them together)


Enzymes involved with replication

Helicase• Unwinds the DNA and separates the two polynucleotide strands by

breaking the hydrogen bonds between complementary base pairs• The two separated polynucleotide strands act as templates for the

synthesis of new polynucleotide strands

DNA Polymerase• Synthesizes new strands from the two parental template strands• Free deoxynucleoside triphosphates (nucleotides with three phosphate

groups) are aligned opposite their complementary base partner and are covalently bonded together by DNA polymerase to form a complementary nucleotide chain

• The energy for this reaction comes from the cleavage of the two extra phosphate groups


Complementary base pairing• Each of the nitrogenous bases can only pair

with its complementary partner (A=T ; G=C)• Consequently, when DNA is replicated by the

combined action of helicase and DNA polymerase:– The new strands formed will be identical to the

original strands separated from the template– The two DNA molecules formed will be identical to

the original molecule


Semi-conservative process:• DNA replication is a semi-conservative process because

when a new double-stranded DNA molecule is formed:• One strand will be from the original molecule• One strand will be newly synthesized • How did we figure this out? Meselson and Stahl

experiment - http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120076/bio22.swf::Meselson+and+Stahl+Experiment


http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120076/bio22.swf::Meselson+and+Stahl+Experiment



Polymerase Chain Reaction

• PCR is a way of producing large quantities of a specific target sequence of DNA• It is useful when only a small amount of DNA is available for testing • E.g. crime scene samples of blood, semen, tissue, hair, etc.

• PCR occurs in a thermal cycler and involves a repeat procedure of 3 steps:• 1. Denaturation: DNA sample is heated to separate it into two strands• 2. Annealing: DNA primers attach to opposite ends of the target sequence• 3. Elongation: A heat-tolerant DNA polymerase (Taq) copies the strands

• One cycle of PCR yields two identical copies of the DNA sequence• A standard reaction of 30 cycles would yield 1,073,741,826 copies of DNA (230)


PCR


Videos

• http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/

• http://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter3/animation__dna_replication__quiz_3_.html

• Crash course – DNA Structure and Replication

https://www.youtube.com/watch?v=8kK2zwjRV0M


http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/

http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/

http://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter3/animation__dna_replication__quiz_3_.html





Transcription and translation

• 2 steps of protein synthesis. Occurs whenever a cell makes a protein (all the time!)

• Transcription makes an mRNA copy of genetic information in DNA– Occurs in nucleus

• Translation assembles amino acids together based on the mRNA sequence– Occurs in ribosome


Types of RNA• Multiple types of RNA that assist with protein synthesis• Three main types of RNA are predominantly made:

1. Messenger RNA (mRNA): A transcript copy of a gene used to encode a polypeptide

2. Transfer RNA (tRNA): A clover leaf shaped sequence that carries an amino acid

3. Ribosomal RNA (rRNA): A primary component of ribosomes


Transcription• Transcription is the process by which an RNA sequence is produced

from a DNA template:• RNA polymerase separates the DNA strands and synthesises a

complementary RNA copy from one of the DNA strands• It does this by covalently bonding ribonucleoside triphosphates that

align opposite their exposed complementary partner (using the energy from the cleavage of the additional phosphate groups to join them together)

• Once the RNA sequence has been synthesised, RNA polymerase will detach from the DNA molecule and the double helix will reform

• The sequence of DNA that is transcribed into RNA is called a gene• Transcription occurs in the nucleus (where the DNA is) and, once made,

the mRNA moves to the cytoplasm (where translation can occur)


Translation• Translation is the process of protein synthesis in which the genetic

information encoded in mRNA is translated into a sequence of amino acids in a polypeptide chain

• Ribosomes bind to mRNA in the cell's cytoplasm and move along the mRNA molecule in a 5' - 3' direction until it reaches a start codon (AUG)

• Anticodons on tRNA molecules align opposite appropriate codons according to complementary base pairing (e.g. UAC will align with AUG)

• Each tRNA molecule carries a specific amino acid (according to the genetic code)

• Ribosomes catalyse the formation of peptide bonds between adjacent amino acids (via a condensation reaction)

• The ribosome moves along the mRNA molecule synthesising a polypeptide chain until it reaches a stop codon, at this point translation stops and the polypeptide chain is released


Genetic code• The genetic code is the set of rules by which information encoded in

mRNA sequences is converted into proteins (amino acid sequences) by living cells

• Codons are a triplet of bases which encodes a particular amino acid• As there are four bases, there are 64 different codon combinations (4 x

4 x 4 = 64)• The order of the codons determines the amino acid sequence for a

protein • The coding region always starts with a START codon (AUG) and

terminates with a STOP codon• The genetic code has the following features:

– It is universal - every living thing uses the same code (there are only a few rare and minor exceptions)

– It is degenerate - there are only 20 amino acids but 64 codons, so more than one codon may code for the same amino acid (this allows for silent mutations whereby a change in the DNA sequence does not affect the polypeptide sequence)


Animations• Transcription -

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter3/animation__mrna_synthesis__transcription___quiz_1_.html

• Translation - http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter3/animation__mrna_synthesis__transcription___quiz_1_.html

• Entire process- http://www.youtube.com/watch?v=NJxobgkPEAo

• Firefly - http://learn.genetics.utah.edu/content/begin/dna/firefly/

• Song - https://www.youtube.com/watch?v=-CoY7-riEUI








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

http://learn.genetics.utah.edu/content/begin/dna/firefly/

https://www.youtube.com/watch?v=-CoY7-riEUI

2.8 CELL RESPIRATION

• Definition: Cell respiration is the controlled release of energy from organic compounds in cells to form ATP (adenosine triphosphate). ATP from cell respiration is immediately available as a source of energy in the cell.

• Occurs in ALL cells• 2 types

– Anaerobic – Aerobic

2.8– Cell respiration

Anaerobic respiration

• Anaerobic respiration occurs in the absence of a ready supply of oxygen (e.g. during intense physical activity, when oxygen reserves are depleted)

• Main step is glycolysis (“breaking “of glucose molecule) and it occurs in the cytoplasm

• In order to generate the small amounts of energy provided by glycolysis, the end product (pyruvate) must be converted into another substance before more glucose can be used– Glycolysis is the breakdown of one molecule of glucose (6C) into two molecules

of pyruvate (2 x 3C) with a small net yield of ATP (2 molecules of ATP)– This process also results in the reduction of two hydrogen acceptors (NAD+) to

form 2 molecules of NADH + H+

• The conversion of pyruvate replenishes the levels of the hydrogen acceptor (NAD+) needed for glycolysis to occur


• The conversion of pyruvate occurs in the cytoplasm of the cell and the products are:

• Lactate (3C) in animal cells• Ethanol (2C) and carbon dioxide (CO2) in

plants, fungi (e.g. yeast) and bacteria• The conversion of pyruvate into ethanol and

CO2 is also known as fermentation


Anaerobic respiration


Aerobic respiration

• Aerobic respiration occurs in the presence of oxygen and takes place in the mitochondrion

• Pyruvate is broken down into carbon dioxide and water and a large amount of ATP is formed (34 - 36 molecules)

• Although this process begins with glycolysis (to break down glucose into pyruvate), glycolysis does not require oxygen and is an anaerobic process

• Steps of aerobic respiration1) Glycolysis2) Link reaction (intermediate step)3) Kreb’s cycle (aka citric acid cycle)4) Electron transport chain


Chemical reactions

Ethanol + 2 CO2

(in plants)


Aerobic Cell respiration2.8– Cell respiration

2.9 PHOTOSYNTHESIS

Overview• Photosynthesis is the process by which plants synthesize

organic compounds (e.g. glucose) from inorganic compounds (CO2 and H2O) in the presence of sunlight

• Photosynthesis is a two step process: • 1. The light dependent reactions convert the light energy into

chemical energy (ATP)• 2. The light independent reactions use the chemical energy

to synthesize organic compounds (e.g. glucose)• The organic molecules produced in photosynthesis can be

used in cellular respiration to provide the energy needed by the organism

2.9– Photosynthesis

Chlorophyll• Chlorophyll is the main site of light absorption

in the light dependent stage of photosynthesis• There are a number of different chlorophyll

molecules, each with their own distinct absorption spectra (the spectrum of light absorbed by a substance)

• When chlorophyll absorbs light energy, they release electrons which are used to make ATP (chemical energy)

• Chlorophyll and Photosystems


Light• Sunlight is white light, made up of all the

colors of the visible spectrum• Colors are different wavelengths of light and

range from ~ 400 nm - 700 nm• The colors of the visible spectrum are (from

longer to shorter wavelength):• Red Orange Yellow Green Blue

Indigo Violet (R.O.Y.G.B.I.V)


Absorption spectrum

• The main colors of light absorbed by chlorophyll are red and blue light

• The main color of light not absorbed (it is reflected) by chlorophyll is green light

• This explains why leaves are green - excepting when the presence of other pigmented substances (e.g. anthocyanins) produces a different color

• Deciduous trees stop producing high amounts of chlorophyll in the winter (due to insufficient sunlight), allowing other photosynthetic pigments (e.g. xanthophylls, carotenoids) to come out, which changes the color of the leaf


Absorption spectrum

Action spectrum


Limiting factors for photosynthesis

1) Temperature• Primarily affects the light independent reaction (and to a

lesser extent the light dependent reactions)• High temperatures will denature essential enzymes (e.g.

rubisco), whereas insufficient thermal energy will prohibit reactions from occurring


2) Light intensity• Light is required for the light dependent reactions• Low light intensities results in insufficient

production of ATP and NADPH + H+ (both needed for the light independent reaction)



3) Carbon dioxide concentration• Carbon dioxide is required for the light independent

reaction to occur (carbon fixation by rubisco)• At low levels, carbon fixation will occur very slowly,

whereas at higher levels the rate will peak as all rubsico are being used



• The rate of photosynthesis can be measured by changes in the amounts of inputs (CO2) or outputs (O2 or glucose) of the photosynthesis equation

• Water cannot be measured as it is involved in a number of essential processes besides photosynthesis (e.g. condensation and hydrolysis reactions)


Measuring CO2 Uptake

• CO2 uptake can be measured by placing a plant in an enclosed space with water

• Carbon dioxide interacts with the water molecules, producing bicarbonate and hydrogen ions, which increases the acidity of the resulting solution

• The change in pH can therefore provide a measure of CO2 uptake by a plant (increased CO2 uptake = more alkaline pH)

Measuring rate of photosynthesis2.9– Photosynthesis

Measuring rate of photosynthesis

Measuring O2 Production

• O2 production can be measured by submerging a plant in an enclosed space with water attached to a sealed gas syringe

• Any oxygen gas produced will bubble out of solution and can be measured by a change in water level (via the position of the meniscus)


Measuring Biomass (Indirect)• Glucose production can be indirectly measured by a

change in a plant's biomass (weight)• This requires the plant to be completely dehydrated prior

to weighing to ensure the change in biomass reflects a change in organic matter and not water content

• An alternative method for measuring glucose production is to determine the change in starch levels in a plant (glucose is stored as starch)

• Starch can be identified via iodine staining (resulting solution turns purple) and quantitated using a colorimeter

Measuring rate of photosynthesis2.9– Photosynthesis

Animations

• http://www.mhhe.com/biosci/bio_animations/02_MH_Photosynthesis_Web/index.html

• Song - https://www.youtube.com/watch?feature=player_embedded&v=_IV-E68rh18

• Overview - http://www.youtube.com/watch?v=ARbtnUt15b4

http://www.mhhe.com/biosci/bio_animations/02_MH_Photosynthesis_Web/index.html

http://www.mhhe.com/biosci/bio_animations/02_MH_Photosynthesis_Web/index.html

https://www.youtube.com/watch?feature=player_embedded&v=_IV-E68rh18

https://www.youtube.com/watch?feature=player_embedded&v=_IV-E68rh18

http://www.youtube.com/watch?v=ARbtnUt15b4



APPLICATIONS AND SKILLS*APPLICATION 1: Use of Taq DNA polymerase to produce multiple copies of

DNA rapidly by the PCR (polymerase chain reaction).*APPLICATION 2: production of human insulin in bacteria as an example of

the universality of the genetic code allowing gene transfer between speciesSKILL 1: Use of a table of the genetic code to deduce which codon(s)

corresponds to which amino acid*SKILL 2: Analysis of Meselson and Stahl’s results to obtain support for the

theory of semi-conservative replication of DNA (see semi-conservative replication slide McGraw Hill animation)

SKILL 3: Use a table of mRNA codons and their corresponding amino acids to deduce the sequence of amino acids coded by a short mRNA strand of known base sequence.

*SKILL 4: Deducing the DNA base sequence for the mRNA strand (working backwards)



• APPLICATON 1: use of anaerobic cell respiration in yeasts to produce ethanol and carbon dioxide in baking

• APPLICATION 2: Lactate production in humans when anaerobic respiration is used to maximize the power of muscle contractions

• SKILL 1: Analysis of results from experiments involving measurement of respiration rates in germinating seeds or invertebrates using a respirometer



APPLICATION 1: Changes to the Earth’s atmosphere, oceans, and rock deposition due to photosynthesis

SKILL 1: Drawing an absorption spectrum for chlorophyll and an action spectrum for photosynthesis

SKILL 2: Design of experiments to investigate the effect of limiting factors on photosynthesis

SKILL 3: Separation of photosynthetic pigments by chromatograph


unit 1 -chemistry of life topic 2 – molecular biology

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