Little Intro:

- The discovery of the structure of DNA in 1953

- Organic Chemistry: Study of Carbon Compounds
- Biochemistry: study of chemistry in living organisms
Living organism are made of the following organic molecules:
- Carbohydrates, Lipids, Proteins, Nucleic Acids
Most Common Elements in living things:
- Carbon ( C ), Hydrogen (H), Oxygen (O), Nitrogen (N)
Less Common But Present
- Sulful (S), Calcium (Ca), Phosphorus (P), Iron (Fe), Sodium (Na)

Vitalism:
- The theory that the origin and phenomena of life are due to a vital principle, which is
different from purely chemical or physical forces.
- Widely believed that organic compounds in plants and animals could only be made
with the
help of a “vital principle”
Using Urea to Disprove Vitalism:
- Urea was discovered in urine in the 1720s and was assumed to be a product of the
kidneys.
- In 1828 the German chemist Friedrich Wöhler synthesized urea artificially:
- HE USED silver isocyanate and ammonium chloride.
- first organic compound to be synthesized artificially
- no vital principle had been involved in the synthesis
- The obvious deduction was that if urea had been synthesized without a vital principle,
other organic compounds could be as well.
- It is still impossible to make complex proteins such as hemoglobin, for example,
without using ribosomes and other components of cells.
About Urea:
- It is a component of urine and this was where it was first discovered. It is produced
when there is an excess of amino acids in the body, as a means of excreting the
nitrogen from the amino acids.
- A cycle of reactions, catalyzed by enzymes, is used to produce it
- Happens in the liver. Urea is then transported by the bloodstream to the kidneys
where it is filtered out and passes out of the body in the urine.

- Can also be synthesized artificially

- ammonia + carbon dioxide → ammonium carbamate → urea + water

- About 100 million tonnes are produced annually. Most of this is used as a
nitrogen fertilizer on crops.
 - Different reactions from those in the liver and enzymes are not involved
- The urea that is produced is identical.

Carbon Compounds
- Carbon is only the 15th most abundant element on Earth, can be used to make a huge
range of different molecules.
- Carbon atoms form covalent bonds with other atoms. (Strongest Bonds)
- Two adjacent atoms share a pair of electrons, with one electron contributed by
each atom.

- Covalent bonds are the strongest type of bond between atoms so stable
molecules based on carbon can be produced
- Each carbon atom can form up to four covalent bonds
- more than most other atoms, so molecules containing carbon can have
complex structures.
- Elements such a H, O, N,P can bind to carbon atoms
- example*
- The bonds can be with other carbon atoms to make rings or
chains of any length. Fatty acids contain chains of up to 20 carbon
atoms for example

Classification of Carbon Compounds

- Carbs: carbon, hydrogen and oxygen,
- two hydrogen atoms to one oxygen
- Sugars and Starches
- Source of Energy
- (CH2O)n
 - Proteins:
- Composed of one or more chains of amino acids
- All of the amino acids in these chains contain the elements carbon, hydrogen,
oxygen, and nitrogen. Two of the twenty amino acids also contain sulfur.
- 50% of dry weight of cells, regulatory molecules
- Cellular signaling or structural models

- Lipids:
- a broad class of molecules that are insoluble in water
- including steroids, waxes, fatty acids and triglycerides(fats solid at room
temp, or oils if they are liquid at room temp).
- Non polar, hydrophobic
- Major component of cell membranes
- Long term energy storage
- Signaling molecules (steroids)
- Nucleic acids
- chains of subunits called nucleotides (monomers)
- There are two types of nucleic acid: ribonucleic acid (RNA) and deoxyribonucleic
acid (DNA)
- DNA is the master code for proetn assemply, RNA plays an active role in
maufacuritng proteins

Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized
amino acid.
Biologists should be able to draw diagrams of a few of the most important molecules.
Basic Molecules:
More general Instructions:
Each Nucleotide Consists of 3 Components- A Pentose sugar, A nitrogenous base, and a
phosphate group

How to differentiate between organic molecules

- Proteins contain C, H, O and N whereas carbohydrates and lipids contain C, H and O

but not N.

- Many proteins contain sulphur (S) but carbohydrates and lipids do not.

- Carbohydrates contain hydrogen and oxygen atoms in a ratio of 2:1, for example
glucose is C6 H12O6 and sucrose (the sugar commonly used in baking) is C12H22O11

- Lipids contain relatively less oxygen than carbohydrates, for example oleic acid (an
unsaturated fatty acid) is C18H34O2 and the steroid testosterone is C19H28O2
Metabolism

- Metabolism is the web of all the enzyme catalyzed reactions in a cell or organism.
- Set of all life sustaining chemical reactions within the cells of an organism
- Most of them happen in the cytoplasm of cells but some are extracellular,
- Transporting of substances into and between cells
- Sum of all chemical reactions that occur in living things

Anabolism:

The synthesis of complex molecules from simpler molecules including the formation of
macromolecules from monomers by condensation reactions
- If you forget, remember Anabolic Steroids to BUILD up muscle
- Anabolic reaction require energy usually in the for of ATP
Examples:
● Protein synthesis using ribosomes.
● DNA synthesis during replication.
● Photosynthesis, including production of glucose from carbon dioxide and water.
● Synthesis of complex carbohydrates including starch, cellulose and glycogen.

Catabolism:

Catabolism is the breakdown of complex molecules into simpler molecules including the
hydrolysis of macromolecules into monomers.
Larger molecules are broken down into smaller ones. Catabolic reactions release energy and in
some cases this energy is captured in the form of ATP, which can then be used in the cell.
Examples:

● Digestion of food in the mouth, stomach and small intestine.

● Cell respiration in which glucose or lipids are oxidized to carbon dioxide and water.
● Digestion of complex carbon compounds in dead organic matter by decomposers.
Energy is Need it contract bonds (ATP) - Endergonic
Energy is Released when bonds are broken- Exergonic

2.2 Water
Water:
- Covers 70% of earth
- All living things are composed of water
- Three states: solid, liquid, gas
- Odorless, colorless, tasteless,
- Density: 1g/cm^3
Water molecules are polar and hydrogen bonds form between them

❖ A water molecule is formed by covalent bonds between an oxygen atom and two
hydrogen atoms.
❖ The bond between hydrogen and oxygen involves unequal sharing of electrons
➢ POLAR COVALENT BOND
■ The nucleus of the oxygen atom is more attractive to electrons than the
nuclei of the hydrogen atoms
■ Oxygen has a higher electronegativity

← Example of a Dipole Molecule

The unequal sharing of electrons in water molecules causes the hydrogen atoms to have a
partial positive charge and oxygen has a partial negative charge.

- water molecules are bent rather than linear

- the two hydrogen atoms are on the same side of the molecule an
- form one pole and the oxygen forms the opposite pole.

- Positively charged particles (positive ions) and negatively charged particles (negative
ions) attract each other and form an ionic bond.
 - The attraction between water molecules is HYDROGEN BOND
- It is an intermolecular force rather than a bond.
- hydrogen atom in one polar molecule is attracted to a slightly negative
atom of another polar covalent molecule
This structure of water gives it its UNIQUE PROPERTIES THAT MAKE IT VITAL TO LIFE
Properties of Water:
Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent
properties of water.
Cohesive Properties
- Binding together of two molecules of the same type, in this case water
- Water molecules cohere which means they stick to each other
- This is due to the hydrogen bonding that is described above.
- Helps transport water to the top of the tallest trees
- Surface tension also is a result of this

Adhesion:
Hydrogen bonds can form between water and other polar molecules, causing water to stick to
them.
This is called adhesion. This property is useful in leaves, where water adheres to cellulose
molecules in cell walls. If water evaporates from the cell walls and is lost from the leaf via the
network of air spaces, adhesive forces cause water to be drawn out of the nearest xylem
vessel. This keeps the walls moist so they can absorb carbon dioxide needed for
photosynthesis.

(Thermal Properties)
Specific Heat Capacity:
- Hydrogen bonds restrict the motion of water molecules and increases the temperature
of water required hydrogen bonds to be broken

- the amount of energy needed to raise the temperature of water is relatively large.
- To cool down, water must lose relatively large amounts of energy.
- Water’s temperature remains relatively stable in comparison to air or land, so it
is a thermally stable habitat for aquatic organisms
- Chemical reactions to occur that are optimal at a certain temperature

High Latent heat of Vaporization:

- First: When a molecule evaporates it separates from other molecules in a liquid and
becomes a vapor molecule
- heat needed to do this is called the latent heat of Water vaporization.
- This causes the evaporation of water to have a cooling effect.
- Considerable amounts of heat are needed to evaporate water, because
hydrogen bonds have to be broken.
- Evaporative coolant example: sweat
- High specific heat heat capacity makes it absorb a lot of heat
energy from the skin before it evaporates

High Boiling Point:

In the liquid state water can be between 0-100 degrees celsius.
This temperature is found in most habitats on earth.

Solvent Properties:
- The polar nature of the water molecule means that it forms shells around charged and
polar molecules
 -
- Na+ , K+ , Cl-
- preventing them from clumping together and keeping them in solution.
- Water forms hydrogen bonds with polar molecules.
- Its partially negative oxygen pole is attracted to positively charged ions and its partially
positive hydrogen pole is attracted to negatively charged ions, so both dissolve. (see
above)
- Cytoplasm is a complex mixture of dissolved substances where chemical
reactions occur.

Hydrophilic and Hydrophobic

- Hydrophilic: used to describe substances that are chemically attracted to water
- All substances that can dissolve in water
- polar molecules such as glucose
- particles with positive or negative charges such as sodium and chloride
ions.
- Substances that water adheres to ex. cellulose

- Hydrophobic: Some substances are insoluble in water although they dissolve in other
solvents such as acetone
- hydrophobic molecules are molecules that do not have a charge, meaning they
are non-polar.
- All lipids are hydrophobic, fat, oils

Explanation of figure:
- If a nonpolar molecule is surrounded by water molecules, hydrogen bonds form
between the water molecules, but not between the nonpolar molecule and the water
molecules.
 - The two nonpolar molecules are attracted to each other
- Slight attraction but more significant than attraction to water molecules
- It is simply because water molecules are more attracted to each other than to the
nonpolar molecules.
- The forces that cause nonpolar molecules to join together into
groups in water are known as hydrophobic interactions.

APPLICATION : COMPARING WATER AND METHANE

Methane:
- Methane is a waste product of anaerobic respiration in certain prokaryotes that live in
habitats where oxygen is lacking.
- Contributes to the greenhouse effect
- Methanogenic prokaryotes live in swamps and other wetlands and in the guts of
animals, including termites, cattle and sheep. And waste dumps.

Water and methane are both small molecules with atoms linked by single covalent bonds.
- water molecules are polar and can form hydrogen bonds
- methane molecules are nonpolar and do not form hydrogen bonds.
- Have different physical properties

Transport in blood plasma

Methods of transport of glucose, amino acids, cholesterol, fats, oxygen and sodium chloride in
blood in relation to their solubility in water.
- Blood transports a wide variety of substances
Sodium chloride is an ionic compound that is freely soluble in water, dissolving to form sodium
ions (Na+) and chloride ions (Cl-), which are carried in blood plasma.
Amino acids have both negative and positive charges. Because of this they are soluble in
water but their solubility varies depending on the R group
- some of which are hydrophilic while others are hydrophobic. All amino acids are soluble
enough to be carried dissolved in blood plasma.
Glucose is a polar molecule. It is freely soluble in water and is carried dissolved in blood
plasma.
Oxygen is a nonpolar molecule.
- Because of the small size of the molecule it dissolves in water but only sparingly and
water becomes saturated with oxygen at relatively low concentrations.
- Also, as the temperature of water rises, the solubility of oxygen decreases, so blood
plasma at 37 °C can hold much less dissolved oxygen than water at 20 °C or lower.
- The amount of oxygen that blood plasma can transport around the body is not enough
to provide for aerobic cell respiration.
- This problem is overcome by the use of hemoglobin in red blood cells.
- Fats: entirely nonpolar, are larger than oxygen and are insoluble in water.
- carried in blood inside lipoprotein complexes.
- groups of molecules with a single layer of phospholipid on the outside and fats
inside.
- hydrophilic phosphate heads of the phospholipids face outwards and are in
contact with water in the blood plasma.
- Cholesterol: hydrophobic, apart from a small hydrophilic region at one end.
- This wont make them dissolve in water,
- transported with fats in lipoprotein complexes
-

2.3 Carbohydrates and Lipids

Carbohydrates
Monosaccharide monomers are linked together by condensation reactions to form
disaccharides and polysaccharide polymers

2.4 Proteins

- Proteins Are- Large biological molecules, or macromolecules, consisting of one or more

long chains of amino acids

- Perform a vast array of functions within living organisms

- including catalyzing metabolic reactions,
- replicating DNA
- responding to stimuli
- transporting

Amino acids are linked together by condensation to form polypeptides.

- Some proteins contain one polypeptide and other proteins contain two or more.
- Polypeptides are chains of amino acids that are made by linking together amino
acids by condensation reactions
- happens on ribosomes by a process called translation (2.7)
- Polypeptides: main component of proteins and in many proteins they are the
only component.

The condensation reactions that links the proteins

a bond is formed between the two amino acids, called a peptide bond.
- A dipeptide is a molecule consisting of two amino acids linked by a peptide bond
- Polypeptides can contain any number of amino acids, though chains of fewer than 20
amino acids are usually referred to as oligopeptides

Drawing peptide bonds

• General structure of any of 20 naturally occurring amino acids
- Each of the 20 amino acids contains a different, specific molecular structure in
the place of the R group (variable)
- Makes them chemically diverse
- condensation reaction between the amine group of one amino acid and the carboxyl
group of the other (see figure above)

More about Amino Acids:

- Identical structural features:
- a carbon atom in the center of the molecule is bonded to an amine group, a
carboxyl group and a hydrogen atom.
- The carbon atom is also bonded to an R group, which is different in each amino
acid.
- Some proteins contain amino acids that are not in the basic repertoire of twenty.
- In most cases this is due to one of the twenty being modified after a
polypeptide has been synthesized
- Example
- modification of amino acids in collagen
- a structural protein used to provide tensile strength in tendons,
ligaments, skin and blood vessel walls.
- Collagen polypeptides made by ribosomes contain proline
at many positions, but at some of these positions it is
converted to hydroxyproline, which makes the collagen
more stable.
Theories on the origin:
 - These 20 amino acids were the ones produced by chemical processes on Earth before
the origin of life, so all organisms used them and have continued to use them. There
could be other ones if they were available

- They are the ideal 20 amino acids for making a wide range of proteins, so natural
selection will always favor organisms that use them and do not use other amino acids.

- All life has evolved from a single ancestral species, which used these 20 amino acids.

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

The amino acid sequence of polypeptides is coded for by genes.

- The amino acid sequence of each polypeptide is stored in a coded form in the base
sequence of a gene; the genetic code
▲ Table 3 Example of proteins with different numbers of polypeptides
Look at protein Power Point

- POLAR AND NON-POLAR AMINO ACIDS IN CELL MEMBRANE

Polar amino acids allow the positioning of proteins on the external and internal surface of a
cell membrane.

- Non-polar amino acids allow the same protein to site within the phospholipid bilayer.

- The lining of the channel itself will be of polar amino acids to allow the diffusion of
charged molecules and ions.

DENATURATION OF PROTEINS
A structural change in a protein (i.e. chemical bonds are broken) that results in a loss (usually
permanent) of its biological properties

What can cause this : pH, temperature, solubility, ionic bond strength
Hydrogen bonds are easily disrupted by increasing temperature or pH, and this in turn
disrupts the shape of the enzyme. The result is an abnormal, dysfunctional or non-functional
protein.

The change in these agents results in bonds to break between molecules, destroying the
original shape of the protein

HEAT- AND pH-TOLERANT PROTEINS

- DNA Taq Polymerase

- Enzyme in extreme prokaryotes that live in volcanic springs or hot water
geothermal q
- Can tolerate extremely high temperatures (800C)
- Used in Biotech

- Pepsin
- enzyme existing in the stomach
- tolerates extreme pH
- works best at pH1.5-2
- helps in food digestion

PROTEIN FUNCTIONS:
⦿ Catalysis, ex. Rubisco enzyme
⦿ Muscle contraction
⦿ Cytoskeleton, ex. actin and myosin
⦿ Tensile strengthening, ex. collagen, spider silk
⦿ Blood clotting
⦿ Transport of nutrients and gases
⦿ Cell adhesion
⦿ Membrane transport
⦿ Hormones, ex. insulin
⦿ Receptors, ex. rhodopsin
⦿ Packing of DNA
⦿ Immunity, ex. immunoglobulin

Proteome:
The total of proteins produced by a cell, a tissue, or an organism
- Is variable according to cell activities
Everyone has a unique proteome

2.5 Enzymes

An enzyme is a PROTEIN

- Proteins with globular shape; the folding of their tertiary and quaternary structure is
important for their function

- Biological catalysts: made by living organisms and influence the rate of chemical
reactions by lowering the activation energy of the reaction

- They are not changed or consumed by the reactions they catalyze and thus can
be re-used

- Commonly have “ase” in the end

⬆️ The shape of the active site and substrate fit or complement each other
- Hence only a specific substrate is capable of binding to a particular enzyme’s active
site; (enzyme-substrate specific

Theory:
Lock and Key
- The exact fit is called the lock and key model and was introduced by E. Fischer in 1890
- Random movements bring any of the substrate molecules close to the active site with
the correct orientation so that binding to the active site is accomplished

-
- Not entirely true

Induced Fit Model:

Koshland 1959

Factors affecting Enzymatic Activity: TEMP

- Each enzyme has an optimal temperature at which it works fastest, ex. mammalian
enzymes about 40°C
- Rate increases because both the enzyme and substrate molecules have more
kinetic energy so they collide more often.
Factors affecting enzymatic activity: Ph
- Most enzymes have an optimal pH and are active only over a narrow pH range.
- Many work best at around pH 7 but proteases in stomach have optimal pH of 2

- Many enzymes become inactive and usually irreversibly denatured when the medium is
made very acidic or very basic

Factors affecting enzymatic activity: SUBSTRATE CONCENTRATION

- Rate of an enzymatic reaction is proportional to the concentration of substrate present,

up to a limiting value then it levels off, because all the active sites are filled up (enzyme
is saturated
Immobilized enzyme
- Most commonly used in industry
- Can be immobilized with several ways, such as attaching to a glass surface, trapping in
gel, bonding them to form enzyme aggregat

- Advantages include:
- Easy separation of enzyme from products to avoid contamination
- Recycling of enzymes, especially expensive ones
- Better stability and tolerance of enzymes to extreme conditions (pH,
temperature) to avoid degradation
- Can bind to more substrate speeding up reaction rate

Lactose intolerance

Lactose: Disaccharide(glucose +galactose) → milk sugar

- People with lactose intolerance must drink lactose free milk
- People who are lactose intolerant lack the enzyme “lactase” which will break down
lactose in glucose and galactose.
- Not only used for lactose intolerant people but also food industry
- galactose and glucose are sweeter than lactose so less sugar is added to
milk products
- galactose and glucose are more soluble than lactose so give a smoother
texture , ex. ice cream
- bacteria ferment glucose and galactose more quickly than lactose, so
production of yogurt and cottage cheese is f
2.6 DNA AND RNA STRUCTURE
● DNA IS A DOUBLE HELIX
DNA is a double-stranded helix
◦ James Watson and Francis Crick worked out the 3-dimensional structure of DNA, based on
work by Rosalind Franklin

DNA HAS four Nitrogenous Bases

A,T,C,G

DNA AND RNA ARE POLYMERS OF NUCLEOTIDES

Each nucleotide consists of

- A five carbon sugar, deoxyribose or ribose

- A phosphate group PO4
- A nitrogenous base (A,T, G,C, U)

DNA VS RNA
- DNA (deoxyribonucleic acid) is a more stable double stranded form that stores the
genetic blueprint for cells
- RNA (ribonucleic acid) is a more versatile single stranded form that transfers the
genetic information for decoding
 - Both DNA and RNA are polymers of nucleotides, however key differences exist in the
composition of DNA and RNA nucleotides

Structure of the DNA Backbone

Nucleotides are covalently bonded between the phosphate of one nucleotide to the C3 of the
second nucleotide.

- The bond is a phosphodiester bond which indicates that there are two covalent bonds
formed between the -OH and the acidic phosphate group.

DNA STRUCTURE
- Nucleic Acid made of longs chains of nucleotide monomers
- The sugar phosphate backbone provides the stable backbone of one of the helices.
- Each nucleotide on the chain is linked through covalent bonds
- The bases face the center
- At one end there is pentose with 5' ("five prime" ) carbon which is free from bonding.
 - At the other end there is a 3' carbon free from bonding to other nucleotides (good
example above figure)

Double Helix
- Two chains of nucleotides alongside each other
- The strands are antiparallel,i.e.they run in opposite directions thus 5' to 3' is parallel to
3' to 5'.
- The bases that are facing inward attach through hydrogen bonds(weak bonds)
- The base pairs are COMPLEMENTARY
- A to T and C to G

Diagram depiction of the orientation of the chains

Importance of DNA base pairing

- Complementary base pairing is the basis for DNA’s ability to pass on information.
- Replication, Transcription, Translation
- DNA REPLICATION:the DNA molecule passes on the information it carries to the next
generation
- TRANSCRIPTION of mRNA:the messenger RNA copies the message by complementary
base pairing and carries it out of the nucleus to the ribosomes (see later)
- TRANSLATION into protein:the mRNA code is translated into protein again by the
complementary base pairing of the tRNA molecules which carry the amino acids (see
later)

RNA STRUCTURE
- Has ribose instead of Deoxyribose
 - Uracil instead of Thymine base
- Single Strand

2.7 DNA REPLICATION, TRANSCRIPTION & TRANSLATION (this is the biggest pain in the
ass unit )

Replication:
1. Starts with the separation of DNA strands
2. Then enzymes use each strand as a template
3. To assemble new nucleotides into complementary strand
Cute lil diagram:

Because there are two color on the last strand remember SEMI CONSERVATIVE
- When a new double-stranded DNA molecule is formed:
- One strand will be from the original template molecule One strand will be
newly synthesized

- This occurs because each nitrogenous base can only pair with its
complementary partner Adenine (A) pairs with thymine (T) Cytosine (C) pairs
with guanine

Enzymes used:
- when DNA is replicated by the combined action of helicase and DNA Polymerase
- Helicase: Unzips or Untwists the the DNA DOUBLE HELIX by BREAKING the
HYDROGEN BONDS (Replication Fork)
- Remember H in Helicase of Hydrogen bonds broken
- Running through the DNA strand can take a few hours which can make the process of
DNA replication very long
- Bacteria don't face this problem because they have relatively small amount of
DNA
- Eukaryotic organisms accelerate DNA replication by having thousands of
replication forks (or bubbles) along the length of the DNA molecule
Example below!:

- DNA Polymerase:
- because one strand is synthesized continuously (also called the “leading” or
sense strand) using DNA polymerase enzyme, which brings free nucleotides to
the open strand
- the other strand (also called the “lagging” strand or anti-sense strand) is
synthesized as a series of short pieces (called Okazaki fragments), which are
finally connected by DNA ligase enzyme
-

Overall direction of Replication is 5-3 Prime

Theories of Replication: Conservative, Semiconservative, Dispersive

In 1958, Matthew Meselson and Frank Stahl Experiment

Used radioactive isotopes of nitrogen, to convince everyone that the actual mechanism of
replication was semi-conservative as originally proposed by Watson & Crick

Significance of Base Pairing:

- The DNA molecule is copied precisely from one cell generation to the next.
 - In a unicellular organism, this means that the total genome is successfully copied into
each new generatio
- In a multi-cellular organism, all cells contain an exact copy of the total genome (even
though not fully expressed
- Genes (base sequences) are faithfully passed from one generation to the next with as
few mistakes (mutations) as possib
- . The order of bases is maintained and passed on, and carries the instructions for
synthesizing the proteins that will make cells func
Polymerase Chain Reaction (PCR)
- A way to duplicate DNA under laboratory conditions
- PCR will amplify large quantities of a specific DNA sequence, from one single sample.
- A standard PCR machine can create over 1 billion copies of
- The reaction occurs in a thermal cycler and uses variations in temperature to control the
replication process via three steps
- Denaturation – DNA sample is heated (~90ºC) to separate the two strands
- Annealing – Sample is cooled (~55ºC) to allow primers to anneal (primers
designate sequence to be copied)
- Elongation – Sample is heated to the optimal temperature for a heat-tolerant
polymerase (Taq) to function (
PCR uses just one enzyme Taq DNA polymerase to extend the nucleotide chain from the
primers

DNA TRANSCRIPTION
THE FLOW OF GENETIC INFORMATION
DNA → RNA → Protein
- The DNA genotype is expressed as proteins, which provide the molecular basis for
phenotypic traits
- The information constituting an organism’s genotype is carried in its sequence of its
DNA bases
- A particular gene is a linear sequence of many nucleotides – Specifies a polypep
 - The base sequence of an mRNA molecule encodes the production of a polypeptid
- The mRNA sequence is read by the ribosome in triplets of bases called codo
- Each codon codes for one amino acid with a polypeptide chain
- The order of the codons in an mRNA sequence determines the order of amino
acids in a polypeptide chain

- RNA polymerase separates the DNA strands and synthesizes a complementary RNA
copy from one of the DNA strand
- When the DNA strands are separated, free nucleotides align opposite their exposed
complementary base partner
- RNA polymerase removes the additional phosphate groups and uses the energy from
this cleavage to covalently join the nucleotide to the growing sequence
- Once the RNA sequence has been synthesized, RNA polymerase detaches from the
DNA molecule and the double helix reforms

GENE
The sequence of DNA that is transcribed into RNA is called a gene
- The strand that is transcribed is called the antisense strand and is complementary to
the RNA sequence
- The strand that is not transcribed is called the sense strand and is identical to the RNA
sequence (with T instead of U)
- Transcription of genes occurs in the nucleus (where DNA is), before the RNA moves to
the cytoplasm (for translation) where protein synthesis occurs
The Genetic Code
A set of rules by which information encoded within mRNA sequences is converted into amino
acid sequences (polypeptides) by living cell
It identifies the corresponding amino acid for each codon combinations
64 codon possibilities
- Start codon AUG
- UAA, UAG, UGA
Features of Genetic Code
- Detenerage
- AUG- G codes for Methionine and is also a START signal for translati
- UAA, UAG, UGA ALL Codons for STOP

- It is universal
- nearly all organisms use exactly the same genetic code so genetic information is
transferable between species
- ts There are 20 common amino acids; therefore 64 triplets are mapped to 20
amino
Translation 2.7
Synthesis of polypeptides on ribosomes
GENETIC CODE IS UNIVERSAL EXAMPLES:
- Genetically engineered bacteria (ex. E. coli) produce human insulin for diabetics
- This avoids allergy problems caused by extracting insulin from cow and pig
carcasses
- Since then yeast cells (fungus) and safflower (plant) have been engineered to
produce human insulin
- Each of these organisms has been genetically modified by transferring the gene
for making human insulin to it mimicking the process of transcription and
translation in human cells.
Intro to translation
- Translation is the process of protein synthesis in which the genetic information
encoded in mRNA is translated into a sequence of amino acids on a polypeptide chain
- Translation takes place in the cytoplasm of the cell
- A ribosome (rRNA and protein) is attached to the mRNA, and translates its message
into a specific polypeptide aided by tRNA
- tRNA molecules INTERPRET the sequence during translation
- Each tRNA is a folded molecule (clover-shaped
- It bears a based triplet, called anticodon on one end (will bind to mRNA)
Ribosome Structure:
- Where protein synthesis happens
- Has two subunits that hold the tRNA molecule and the mRNA close together during
translation.
- Made out proteins and Ribosomal RNA rRNA

TRANSLATION OVERVIEW
1. The ribosome binds to the mRNA molecule in the cytoplasm and moves along the
molecule in the 5 prime to 3 prime direction until it reaches AUG
2. Anticodons on tRNA molecules align opposite appropriate codons according to
complementary base pairing (ex. AUG = UAC)
a. Each tRNA molecule carries a specific amino acid (according to the genetic code)
3. Enzymes catalyze the formation of peptide bonds between adjacent amino acids (via
condensation reactions)
4. The ribosome moves along the mRNA molecule synthesizing a polypeptide chain until
it reaches a stop codon (UAA/ UAG/UGA)
5. At this point translation ceases and the polypeptide chain is released

STAGES:
- Initiation: A ‘START’ codon marks the start of a mRNA message mRNA, a specific
tRNA, and the ribosomal subunits assemble into a complex
- Elongation: Once initiation is complete, amino acids are added one by one to the
growing polypeptide chain
- Termination: protein synthesis
 Mr. Cat App

2.8 Cell Respiration

ATP or Adenosine triphosphate is the energy currency of the cells and is immediately available
with cell respiration.

It directly fuels the majority of biological activities in cells, such as:

- Biosynthesis of macromolecules (e.g. polymer assembly)
- Active transport (e.g. endocytosis / exocytosis)
- Nerve transmission (e.g. propagation of action potentials)
- Growth and repair (e.g. mitotic division)
- Movement (e.g. muscle contraction)
- Emission of light (e.g. bioluminescence)

• Eukaryotic cells make their own ATP in mitochondria.

How is ATP a source of energy
One molecule of ATP contains three covalently linked phosphate groups
- which store potential energy in their bonds
- When ATP is hydrolyzed or oxidized (to form ADP + Pi)
- the energy stored in the phosphate bond is released to be used by the
cell
- Cell respiration uses energy stored in organic molecules to regenerate ATP from
ADP + Pi (via oxidation)

ANAEROBIC RESPIRATION
- Anaerobic respiration: breaking down of organic molecules without the use of oxygen
to produce energy in the form of ATP (small yield)
- Takes place in the cell cytoplasm of prokaryotes. Also occurs in yeast, plants and
animals.
- Why do we respire ANAEROBICALLY if it creates a small yield of ATP
- When oxygen supplied run out in respiring cells • In oxygen-deficient
environments, ex. waterlogged soils
- Also known as FERMENTATION

- Two types of fermentation: Alcoholic Fermentation, Lactic Acid fermentation

- LACTIC ACID FERMENTATION
- Used by humans during strenuous activity when there is an oxygen debt (i.e. the
demand for oxygen that builds up during a period of anaerobic respiration)
- Muscle cells convert the 3-C pyruvate molecules (from glycolysis) to 3-C lactate
(or lactic acid) GLUCOSE → LACTATE
-