Andres Rangel

Unit 2: Molecular Biology Notes

2.1

Molecular biology explains living processes in terms of the chemical substances involved
Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to
exist
Despite being only the 15th most abundant element on the planet, carbon forms the
backbone of every single organic molecule
Covalent bonds are the strongest type of bond between atoms. Stable molecules can be
formed
Carbon atoms contain four electrons in their outer shell allowing them to form four
covalent bonds with potential four other different atoms
The result of these properties is an almost infinite number of different possible molecules
involving carbon
Organic compounds contain carbon and are found in living things
They usually contain C-H or C-C bonds
Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic
acid

Carbohydrates:

Contain carbon, hydrogen, and oxygen

Organic compounds consisting of one or more simple sugars
Monomers follow the general basic formula of (CH2O)x
Monomers are commonly ring shaped molecules
Lipids:
Lipids are a group of organic molecules that are insoluble in water but soluble in nonpolar organic solvents
Common lipids include triglycerides (fats--solid at room temperature and oils--liquid at
room temperature), phospholipids and steroids

Proteins:

Contain carbon, hydrogen, oxygen, and nitrogen (additionally sulfur is common

component, but it is not present in all proteins)
Proteins are large organic compounds made of amino acids arranged into one or more
linear chains

Nucleic acids:

Contain carbon, hydrogen, oxygen, nitrogen and phosphorus

Chains of sub-units called nucleotides
Nucleotides consist of base, sugar and phosphate groups covalently bonded together
If the sugar is ribose then the nucleic acid formed is RNA if the sugar is deoxyribose then
DNA is formed

Metabolism

Metabolism: web of all enzyme catalyzed reactions in a cell or organism. Pathways in

which one type of molecule is transformed into another steps/cycles
Anabolism: synthesis of complex molecules from simpler molecules (condensation)
Catabolism: breakdown of complex molecules into simpler molecules (hydrolysis)
Condensation makes bonds, releasing water
Hydrolysis breaks bonds, splitting water
Monosaccharides are the monomers of polysaccharides
Catabolism is the breakdown of complex molecules into simpler molecules including the
hydrolysis of macromolecules
Urea is an example of a compound that is produced by living organisms but can also be
artificially synthesized

2.2
Water:

Lubricate lungs to exhale

Kidneys remove wastes
Lubricate joints and allow smooth movement
High specific heat capacity
High heat vaporization

Water molecules:

Formed by a polar covalent bond between an atom oxygen atom and two hydrogen atoms
Attraction between water molecules: hydrogen bonds

Cohesion:

Hydrogen bonds between polar water molecules cause them to cohere

Allowing for transpiration in plants moving water against gravity
Allowing for animals such as water striders to walk over the surface of ponds even
though they are denser than water

Thermal properties:

Hydrogen bonds between polar water molecules cause water to resist change

High specific heat capacity

High vaporization
High heat of fusion
Thus, water produces a stable environment for aquatic organisms
Substances can be hydrophilic or hydrophobic

Hydrophilic:

All substances that dissolve in water are hydrophilic, including polar molecules such as
glucose, and particles with positive or negative charges such as sodium and chloride ions
Substances that water adheres to, cellulose for example, are also hydrophilic

Hydrophobic

Molecules are hydrophobic if they do not have negative or positive charges and are
nonpolar
All lipids are hydrophobic, including fats and oils
Hydrophobic molecules dissolve in other solvents such as propanone

Solvent properties:

The polarity of water attracts, or dissolves, any other polar or charged particles by
forming hydrogen bonds with them
Amino acids, glucose, ions, oxygen are soluble in water because they are hydrophilic or
have charges
Fat molecules and cholesterols are not soluble in water and are transported via lipoprotein
Modes of transport of glucose, amino acids, cholesterol, fats, oxygen, and sodium
chloride in blood in relation to their solubility in water

Amino acids:

Positive and negative charges (due to amine and acids groups) therefore soluble in water
R group varies, can be polar, nonpolar or charged
R group determines the degree of solubility
Carried by the blood plasma

Oxygen:

Nonpolar molecule
Due to the small size of an oxygen molecule it is soluble in water, but only just
Water becomes saturated with oxygen at relatively low concentrations
As temperature increases the solubility of oxygen decreases
At body temperature (37 C) very little oxygen can be carried by the plasma, too little to
support aerobic respiration
Hemoglobin in red blood cells carry the majority of oxygen

Hemoglobin has 4 binding sites for oxygen

Water as a coolant:

High temperatures damage tissues and denature proteins--causing enzymes to cease to

work
Takes a lot of energy for water to change temperature
This means that it will heat and cool more slowly than air or land
This is useful to animals in hot climates--who can use water or mud to cool off in the hot day
When water evaporates, it removes a lot of energy from the system
This is felt as a cooling sensation--excess energy is removed from the body
The skin and their blood vessels are cooled
This also helps aquatic habitats remain at fairly constant temperatures in hot summers
TOK: Claims about the memory of water have been categorized as pseudoscientific.
What are the criteria that can be used to distinguish scientific claims from pseudoscientific
claims?
The criteria that can be used to distinguish scientific claims from pseudoscientific is the way the
study was conducted. Scientists need to make sure that this was done using the scientific method,
with a hypothesis and, controlled and changing variables. They can also analyze the standard
deviation of the test and see if it supports the claim.

2.3

Polysaccharides are polymers more than two molecules

They are often very long and may be branched
Glycosidic bonds can be 1-4 or 1.6
Monosaccharides are small, easily absorbed sugars--fast releases for respiration
Disaccharides are quickly digested into their monosaccharides
Lactose is found in milk--ideal for nursing young
Insoluble storage molecule: excess sugars converted by insulin for storage in the liver

Starch

Starch is made by linking together a-glucose molecules

Condensation reactions link carbon atom 1 to carbon atom 4 on the next a-glucose
All the glucose molecules in starch can be oriented in the same way
The consequence of this is that the starch molecule is curved, rather than straight
Size of the molecule is not fixed

Lipids:

Condensation of three fatty acids and glycerol

Saturated (single bond)

Unsaturated (double bond)
Monounsaturated (one double bond)
Polyunsaturated (many double bonds)
Unsaturated fats can be trans/cis isomers
Cis: liquid at room temperatures (oil)
Trans: solid at room temperature (margarine)
There are potential health risks for trans-unsaturated and saturated fats
Glycogen is the medium-term energy storage molecule in animals
Stored in the liver and muscles
The energy stored in glycogen is more readily available than the energy stored in fat
Glucose in the bloodstream is for immediate use and will either be used in respiration to
yield ATP or converted to glycogen or fat

TOK: There are conflicting views as to the harms and benefits of fats in diets. How
Do we decide between competing views?
We decide by finding how impacting the competing views are through research. Studies have
proved that there is a positive correlation between rates of CHD and saturated fatty acid intake.
There are populations that dont apply to the correlation, the Maasai of Kenya. This group has a
diet that is based on meat, fat, blood and milk, but no CHD. Diets that involve olive oil, which
contains cis-monounsaturated fatty acids, are eaten in countries around the Mediterranean. These
diets have low CHD rates. Genetic factors in these populations could be the reason for this data.
There is also a positive correlation between amounts of trans-fat consumed and rates of CHD.
Many other factors were tested to see if they impacted these studies, but none did. Therefore,
trans-fats probably do cause CHD. In patients who had died from CHD, fatty deposits in the
diseased arteries have been found that contain high concentrations of trans-fats, which is much
more evidence to support this point.

2.4

Amino acids are the building blocks of life

Linked together by condensation reaction to form polypeptides
There are 20 different amino acids
Amino acids can be linked together in any sequence give a range of polypeptides
The sequence is coded for by
Single polypeptides or more than one polypeptides linked together
Determines the 3D structure of the protein
Interaction between variable R groups forming
Hydrophobic interaction between nonpolar amino acids
Hydrogen bonds between polar amino acids

Ionic bonds between ionic amino acids

Covalent bonds between sulfur containing amino acids
Each individual has a unique proteome
Protein functions:
Structural: collagen in connective tissue, spider silk
Contractile: actin and myosin in muscle tissue
Hormonal: insulin
Transport: hemoglobin
Protective: antibodies, immunoglobulins
Enzymatic: amylase, rubisco
Pigments: rhodopsin

2.5

Substrate: reactant in a biochemical reaction

Enzyme: globular protein which acts as a catalyst for biochemical reactions
Polar regions of amino acids attract substrate and active site of the enzyme
Active sites: region on the surface of an enzyme to which substrates bind and which
catalyzes the reaction
Once a substrate has been locked into the active site, the reaction is catalyzed
The products are released and the enzyme is used again
Enzyme catalysis involves molecular motion and the collision of substrates with the
active site.
When the substrate approaches the enzyme, there is a conformational change in the active
site
Alters stability of bonds in the substrate
The concentration of the substrate affects the rate of activity of an enzyme
Enzymes can be damaged (denatured) by changes in temperature a pH
All enzymes have an optimum pH
What happens to the enzyme when the pH is not in the optimal range?
All enzymes have an optimum temperature
Immobilized enzymes are used in industry
The enzyme is attached to an inert, insoluble molecule which makes the enzyme more
resistant to changes in temperature or pH
The enzyme is also easily separated from the substrate and can be used again
Enzyme immobilization: to restrict enzyme mobility in a fixed space
Lactose (milk sugar)
Lactose intolerance is the inability to digest lactose, because of a lack of the required
enzyme lactase in the digestive system
Lactase is obtained by artificially culturing a fungus

Biotechnology companies culture the yeast, extract the lactase from the yeast, and purify
it for sale

TOK: Development of some techniques benefits particular human populations more than
others. For example, the development of lactose-free milk available in Europe and North
America would have greater benefit in Africa/Asia where lactose intolerance is more
prevalent. The development of techniques requires financial investment. Should knowledge
be shared when techniques developed in one part of the world are more applicable in
another?
I think that that knowledge should be shared when techniques developed in one part of the world
are more applicable in another many countries, like Africa, would eventually need this
technology because they have a higher number of lactose intolerance populations. Knowledge
should also be shared to find new alternatives for issues that affect a population.
2.8

Cellular respiration: controlled release of energy from organic compounds in cells to form
ATP

Controlled release: enzymes

Organic compounds: carbohydrates, lipids, proteins
Phosphate bond yields high energy
Glycolysis:
Glucose is a 6-carbon molecule broken down by glycolysis into pyruvate (3 carbon
molecule)
Yield: small amounts of ATP
Aerobic respiration occurs in the presence of oxygen
Reactions continue in the mitochondria
Pyruvate diffuses from the cytosol into the mitochondrial matrix
Series of reactions (link reaction, Krebs cycle, electron transport system, oxidative
phosphorylation) oxidizes pyruvate to produce ATP
Anaerobic respiration occurs in the absence of oxygen
Reaction do not continue in the mitochondria
Carbon dioxide and ethanol are produced in yeast (fermentation)
Lactic acid (lactate) is produced in humans and other animals

Aerobic:

Uses oxygen
High yield of ATP
Waste products: CO2 and water
Pyruvate carried to mitochondria

Can metabolize other molecules

Anaerobic:

No oxygen
Low yield of ATP
Waste products: CO2 and ethanol (yeast)
Occurs in cytoplasm only

8.1

Cell respiration involves the oxidation and reduction of electron carriers

Phosphorylation is a reaction where a phosphate group is added to an organic molecule
The phosphorylated molecule is less stable and therefore reacts more easily in the
metabolic pathway
Reactions that would otherwise proceed slowly and require energy into a reaction that
happens quickly releasing energy
The most common hydrogen carrier is NAD
Another less frequently used hydrogen carrier is FAD
Metabolic pathways consist of chains and cycles of enzyme-catalyzed reactions
Enzymes go through steps to facilitate reactions
Multiple enzymes for breaking down glucose
Enzymes lower the activation energy of reaction
Activation energy is the amount of energy that must be up into a reaction to make it occur
An enzyme stresses the bonds in the substrates, reducing the activation energy required
for a reaction to occur
Initially, a lot of energy is needed
Enzymes weaken the bonds, lowering the amount of energy need to make the reaction
occur
Substrate: reactant
Substrate and inhibitor are chemically very similar
Competitive inhibition:
Inhibitor binds to the active site of the enzyme, prevents substrate from binding
Other things besides damaging the enzyme can cause it not to work
Inhibitor binds to the enzyme, so it can't function, fewer enzymes working
Example: bacteria need to create folic acid to survive; anti-biotic is an inhibitor that binds
to the enzyme, preventing the bacteria from creating folic acid
Non-competitive inhibition:
Inhibitor binds to another part of the enzyme, changing the shape of the active site,
preventing the substrate from binding
Competitive: takes up the space; non competitive: binds to the active site

Example: silver: silver forms bonds with the -SH groups of cysteine, the amino acid
which forms covalent disulfide bridges; the disruption of disulfide bridges alter the
tertiary structure of the enzyme, affecting its active site; silver is the inhibitor to any
amino acid from a protein, changing the overall protein structure
Feedback inhibitor: reaction product binds to a different part of the enzyme and changes
the shape

End product inhibition:

When the end product is formed in the excess, the excess products interact with the
enzymes at the beginning of the pathways: decrease enzyme activity
Negative feedback: the rate of the process decreases as the concentration of the product
increases
Example: threonine to isoleucine (amino acids)
This is done to decrease the amount of a certain product being made in your body
Distinguish between different types of inhibition:
Competitive inhibition: more substrate, greater rate of reaction
Non-competitive inhibition: prevents enzyme from binding regardless of substrate
concentration
Non-competitive inhibitor is more effective than a competitive inhibitor; competitive
inhibitor eventually reaches the same maximum, but non-competitive does not
Much substrate overcomes the blockage of competitive inhibitor

8.2 Cell Respiration

Respiration is the controlled release of energy from organic compounds in cells to form
ATP
Cell respiration involves the oxidation and reduction of electron carriers
The electron are used for ATP
The whole goal is to take the electrons to gain energy for ATP
The electrons come from glucose
Phosphorylation is a reaction where a phosphate group is added to an organic molecule
The phosphorylated molecule is less stable and therefore reacts more easily in the
metabolic pathway
Reaction that would otherwise proceed slowly and require energy into a reaction that
happens quickly releasing energy
Cell respiration involves the oxidation and reduction of electron carriers
The most common hydrogen carrier is NAD
Glucose loses on hydrogen and two electron
NAD is the electron carrier molecule that becomes NADH
A second carrier that is not used so much is FAD, another type of electron carrier

Only one hydrogen becomes part of the molecule

8.2.3 Glycosis

Phosphorylation: glucose is reduced with 2 ATP

Lysis: glucose is split into two 3-carbo molecules
Oxidation: glucose is oxidized to pyruvate
ATP formation: energy is released from glucose produces 4 ATP
Occurs in the cytoplasm
Anaerobic respiration
In the absence of oxygen, glycolysis is the only source of ATP for cellular functions
o Glycolysis reduces NAD to NADH + H, depleting the supply of NAD
o Without NAD, glycolysis will stop, so NADH + H must be oxidized back to NAD
Fermentation allows for the oxidation of NADH + H back to NAD. Reduces pyruvate to
lactate humans or ethanol
Link Reaction
Oxidative decarboxylation of pyruvate
Decarboxylation: pyruvate loses 1 C02
Forming a 2-carbon acetol fragment, carried by CoA as acetylcoenzyme
Loses hydrogen, electron, and oxygen
This forms a 2-carbon fragment which is carried by the coenzyme to form the next
reaction
Hydrogen removal is oxidation

TOK: Peter Mitchells chemiosmotic theory encountered years of opposition before it was
finally accepted. For what reasons does falsification not always result in an immediate
acceptance of new theories or a paradigm shift?
Falsification does not always result in an immediate acceptance of new theories because society
might believe that these proposed theories are radical, and scientists at first dont have enough
solid evidence to support their claims. Until, time goes by and more evidence is found to prove
these theories.