Bio2 Flashcards
2.1 Explain what
molecular biology
is
Molecular biology explains living processes in
terms of the chemical substances involved.
-living organisms must do many activities to stay
alive, including replicating DNA, cell respiration,
protein synthesis, photosynthesis, etc.
-all of the molecules and reactions involved are
part of the metabolism, the sum total of all
chemical reactions of the organism.
2.1 Explain why life
on Earth is
described as
“carbon based”.
Carbon atoms can form four covalent bonds
allowing a diversity of stable compounds to exist.
Carbon atom has an atomic number of six,
meaning it has six protons, but indirectly it also
means that carbon has six electrons.
Two of these six electrons form the stable inner
shell, and four are found in the second and
unfilled shell. (valence electron)
Hence, it has to share four electrons with other
atoms in order to create a stable configuration of
eight electrons in total.
Each time carbon shares one of its electrons, a
covalent bond is formed, and carbon always
forms four covalent bonds.
2.1 List out and
explain the four
organic compound
types found within
living things.
Carbohydrates
monosaccharides
disaccharides
polysaccharides
-often referred to as sugar (e.g. glucose, sucrose, fructose, etc.)
-function as a source of energy, also a recognition molecule (e.g.
glycoproteins) and as a structural component (part of DNA / RNA)
Proteins
amino acids
dipeptides
polypeptides
-performs a variety of diverse functions (e.g. enzymes, antibodies,
peptide hormones, amino acids.)
-major regulatory molecules involved in catalysis (all enzymes
are proteins)
Lipids
fatty acids
sterols
triglycerides
phospholipids
-fat when a solid, oil when a liquid (e.g. triglycerides,
phospholipids, steroids)
-a major component of cell membranes (phospholipids and cholesterol)
-may be utilised as a long-term energy storage molecule (fats and oils)
-may function as a signalling molecule (steroids)
Nucleic Acids
nucleotides
DNA
RNA
-molecules most often used in genetics
-genetic material of all cells and determines the inherited features of
an organism
-DNA functions as a master code for protein assembly, while RNA plays
an active role in the manufacturing of proteins
2.1 Skill: Identification and
drawings of common
biochemically important
molecules:
alpha-D-glucose
beta-D-glucose
D-ribose
a saturated fatty acid
a generalized amino
acid. glycerol
List out their
chemical formulas.
alpha-D-glucose:
C6H1206
beta-D-glucose:
C6H1206
D-ribose: C5H1005
a saturated fatty acid
a generalized
amino acid:
NH2 + C + H + R
+ COOH
2.1 How does a
saturated fatty
acid attach to
glycerol in a
triglyceride?
Covalent bonding
between C and O
atom and the
process of
anabolism releases
3 water molecules.
A condensation
reaction between the OH and
glycerol group.
2.1 Explain the
process of
metabolism in
an organism.
Metabolism includes all of the reactions in the
cell, with each reaction catalysed by an enzyme.
-provide a source of energy for cellular
processes (growth, reproduction, etc.)
-enable the synthesis and assimilation of new
materials for use within the cell
So, it involves both the formation
macromolecules, and the breakdown of complex
molecules.
Anabolism is the synthesis of complex molecules
from simpler molecules including the formation of
macromolecules from monomers by
condensation reactions.
to build macromolecules, one monomer to
another monomer is bonded and water is
released in this process. (condensation)
Catabolism is the breakdown of complex
molecules into simpler molecules including the
hydrolysis of macromolecules into monomers.
-macromolecules are turned back into monomers
by a reaction type known as hydrolysis.
-water molecule is a reactant during a
hydrolysis reaction.
2.1 Explain the
experiment that
falsified vitalism.
Vitalism is the theory that all
organic compounds come from
living organisms and cannot be
created artificially.
-German scientist Wohler
accidentally created urea using
inorganic compounds.
-urea is produced in the liver
tissue of many animals and
becomes a component of urine.
-urea is an example of a
compound that is produced by
living organisms but can also be
artificially synthesized.
-showed that a vital “life force” in
living organisms was not needed.
21 Skill:
Identification of
biochemicals such
as sugars, lipids or
amino acids from
molecular
diagrams. Explain
how students can
recognize different biochemicals.
sugars: ratio of H
and O atom is 2:1
lipids: has different
amounts of CH2
amino acid:
contains N atom
and R group. Also
has a carboxyl and
amine group at the
two ends.
2.2 Outline and
explain the
hydrogen bonds
between water
molecules.
Water molecules are polar and
hydrogen bonds form between
them.
Hydrogen and oxygen atoms bond
covalently. Due to the higher
electronegativity in oxygen atoms,
the electrons are not shared
equally. Hence, THE OXYGEN END
OF THE MOLECULE BECOMES
SLIGHTLY NEGATIVE AND THE
HYDROGEN END BECOMES
SLIGHTLY POSITIVE causing the
water molecule to be polar.
Water molecules itself is weak, but
when water molecules bond to
itself due to its polar property, it
becomes strong and hard to break.
2.2 Essay
Question:
Outline the
thermal,
cohesive and
solvent
properties of
water.
water has a high specific
heat capacity;
a large amount of heat causes a
small increase in temperature;
water has a high latent heat of
vaporization;
a large amount of heat energy is
needed to vaporize/evaporate
water:
hydrogen bonds between water
molecules make them cohesive/
stick together;
this gives water a high surface
tension / explains how water rises
up xylem;
water molecules are polar:
this makes water a good solvent;
2.2 Essay
Question:
Describe the
significance of
each property
of water to
living organisms.
cohesion: surface tension - allows
some organisms (e.g. insects) to move
on water’s surface
polarity / capillarity / adhesion •
helps plants transport water
transparency - allows plants to
photosynthesize in water / allows
animals to see
(excellent) solvent - capable of
dissolving substances for transport in
organisms
(excellent) thermal properties (high
heat of vaporization)
- excellent
coolant (high specific heat capacity)
maintains stable temperature for
aquatic animals
ice floats - lakes / oceans do not
freeze, allowing life under the ice
buoyancy
- supports organisms
structure
- turgor in plant cells /
hydrostatic pressure
2.2 Explain why
substances can
be hydrophilic
or hydrophobic.
The polarity of substances decides if
its hydrophilic or hydrophobic.
Substances that are able to dissolve
in water is hydrophilic and polar.
Polar molecules easily dissolve in
water, because a polar solvent will
dissolve polar solutes.
Substances that do not dissolve in
water are hydrophobic, and non
polar. Organic substances that are
non-polar are typically composed of
just carbons and hydrogens
(hydrocarbons) or have large areas of
the molecule where there are only
carbons and hydrogens (e.g.
methane, triglyceride, lipids,
phospholipids - have long chains of
CH2)
2.2 Application:
Comparison of
the thermal
properties of
water with those
of methane.
Compare water
and methane.
Water is a polar substance,
methane is a non polar
substance.
When methane undergoes a
phase change, because of its
lack of polarity, there are no
hydrogen bonds to increase the
molecular motion needed to
change the state of the
substance.
In water, high temperature is
necessary to create the
relatively high rate of molecular
motion needed to enable the
molecules to ‘escape’ from
each other.
2.2 Application:
Modes of transport
of glucose, amino
acids, cholesterol,
fats, oxygen and
sodium chloride in
blood. Explain how
these substances
are transported in
the blood.
The transport of these substances depends
on their solubility in water.
glucose: it’s polar and can be easily dissolved
in water
amino acid: solubility depends on R group,
generally polar; soluble enough to be
dissolved and transported in blood plasma.
cholesterol: non-polar, hydrophobic, not
soluble; transported through lipoprotein
(hydrophilic phosphate heads face outward,
soluble)
fats: non-polar, hydrophobic, not soluble;
transported through lipoprotein. (hydrophilic
phosphate heads face outward, soluble)
oxygen: small enough to be dissolved in
blood plasma, but easily saturated, not
enough for oxygen transport. Hemoglobin in
red blood cells is present to transport oxygen
instead of just relying on blood plasma.
NaCl: soluble and transported through
blood plasma.
2.2 Application:
Explain how
water is used as
a coolant.
Sweat secretion is
controlled by
hypothalamus, and
released through the
glands of the skin. As water
has a high latent heat of
vaporization, a lot of heat is
required to convert water
from liquid to gas phase.
The heat needed for the
evaporation of water in
sweat is taken from the
tissues of the skin, reducing
their temperature.
2.3 Describe the
relationship
between
monosaccharides,
disaccharides, and
polysaccharides.
List examples for
each of these type
of sugars.
Monosaccharide monomers are
linked together by condensation
reactions to form disaccharides and
polysaccharide polymers.
The combination of monosaccharides
always gives out water. This type of
reaction is called condensation.
The bond created is called glycosidic
linkage.Since this is an anabolic
process, this reaction requires ATP.
Monosaccharide: glucose,
galactose, fructose
Disaccharide: maltose,
lactose, sucrose
Polysaccharides: cellulose,
amylopectin, amylose, glycogen
2.3 Explain the
three types of
fats.
Fatty acids can be saturated,
monounsaturated or polyunsaturated.
Fatty acids are saturated fats because
all possible bonds are taken by single
bonds.
Fatty acids with ONE double bond is
MONOunsaturated, while fatty acids
with MULTIPLE double bonds is
POLYunsaturated.
Unsaturated fatty acids are bent in
structure, originate from plant
sources (i.e. oils) and are typically
liquid at room temperatures
Saturated fatty acids are linear in
structure, originate from animal
sources (i.e. fats) and are typically
solid at room temperatures
2.3 Describe the
two types of
unsaturated
fatty acids, and
its structure.
Unsaturated fatty acids can be cis
or trans isomers.
Cis: The hydrogen atoms attached
to the carbon double bond are on
the same side
Trans: The hydrogen atoms
attached to the carbon double
bond are on different sides
Cis will have a bent shape (H atoms
on a same side) irreqular
formations - lower melting points •
liquid at room temp.
Trans will twist, but remain straight.
These fatty acids do not commonly
occur in nature and are typically
produced by an industrial process
called hydrogenation
2.3 Explain how
triglycerides are
formed.
Triglycerides are formed
when condensation
reactions occur between
one glycerol and three fatty
acids
The hydroxyl groups of
glycerol combine with the
carboxyl groups of the fatty
acids to form an ester
linkage
This condensation reaction
results in the formation of
three molecules of water
2.3 Describe the
structure of
cellulose and
starch in plants
and glycogen in
humans.
cellulose, starch, and glycogen are all polysaccharides.
Cellulose is composed of -glucose subunits, has a
structure of a 1-4 carbon linkage. The glucose subunits in
the chain are oriented alternately upwards and downwards;
hence, making the it straight and rigid.
These long, straight chains are joined by (type of)
hydrogen bonds in order to provide stability and strength
to the molecule.
Because it is composed of -glucose, it is indigestible for
most animals (lack the enzyme required to break it down)
Starch: amylopectin and amylose, both are composed of
alpha glucose subunits.
Amylose has a structure of 1-4 carbon linkage, the glucose
molecules orientates to the same side; hence, making it a
helical structure.
Amylopectin is branched, because it can have both 1-4 and
1-6 carbon linkage.
Molecules of both types of starch are hydrophilic but are
too large to be soluble in water.
Glycogen is present only in animals and some fungi and
not plants. It is also composed of alpha glucose subunits.
and can also have a 1-4 and 1-6 carbon linkage, so
therefore is branched.
For all of these it is easy to remove and add glucose
molecules to ir.
2.3 Describe the
function of
cellulose and
starch in plants
and glycogen in
humans.
Cellulose: Cellulose are linked from
bundles called cellulose microfibrils;
together, they have very high tensile
strength to prevent cells from bursting
under high water pressure.
Starch: Starch is stored in plants. In seeds
and storage organs such as potato cells,
glucose is held as starch. It can be also
made as a temporary store in leaf cells
when glucose is being made faster by
photosynthesis than it can be exported to
other parts of the plant.
Glycogen: Glycogen is stored in liver and
some muscles in humans. It is used in cells
where large stores of dissolved glucose
would cause osmotic problems, and
glycogen doesn’t affect osmotic balance.
Glycogen is useful in cells for glucose, and
consequently energy storage.
2.3 Explain the
scientific
evidence for
health risks of
trans fats and
saturated fatty
acids.
Saturated fats and trans fats are proven to be able to
raise blood cholesterol levels, while cis fats can lower
blood cholesterol levels.
Saturated fats increase LDL levels within the body,
raising blood cholesterol levels
Trans fats increase LDL levels and decrease HDL
levels within the body, significantly raising blood
cholesterol levels.
*Low density lipoproteins (LDL) carry cholesterol from
the liver to the rest of the body
Unsaturated (cis) fats increase HDL levels within the
body, lowering blood cholesterol levels
An increase in blood cholesterol levels has a
correlation with an increase in risk of coronary heart
diseases.
When there are high levels of LDL in the bloodstream,
the LDL particles will form deposits in the walls of the
arteries
There is a direct, strong correlation between intake of
trans-fats and saturated fats in food and:
1. all causes of mortality
2. cardiovascular disease
3. coronary heart disease
4. stroke
5. type II diabetes
2.3 Contrast the
function and
advantages of
lipids and
carbohydrates.
SODAS
Lipids:
-storage: acts as long term storage
-osmolarity: less effect on osmolarity
-digestion: less easily digested
-ATP: 6 times more efficient in the amount of
energy that can be stored/ gram of body
mass
-solubility: not water soluble, difficult
to transport
-occupies less space/occupies less
body mass
Carbohydrates:
-short term storage in muscles as glycogen
-osmolarity: more effects on osmotic pressure
(concentration of sugars)
-digestion: more easily digested
-less efficient in energy storage as it also
contains 2g water for /gram of carbs.
-solubility: water soluble, easier to transport.
2.3 Evaluate the
evidence and
the methods
used to obtain
the evidence for
health claims
made about
lipids.
- A positive correlation has been found between the intake
of saturated fats and the incidence of CHD in human
populations
–Counter: Certain populations do not fit this trend (e.g. the
Maasai tribe in Africa have a fat-rich diet but very low rates
of CHD) - Intervention studies have shown that lowering dietary
intakes of saturated fats reduces factors associated with the
development of CHD (e.g. blood cholesterol levels, blood
pressure, etc.)
-Counter: Validity of intervention studies is dependent on
size and composition of cohort, as well as the duration of
the study - In patients who died from CHD, fatty deposits in
diseased arteries were found to contain high
concentrations of trans fats
-Counter: Genetic factors may play a role (e.g. blood
cholesterol levels only show a weak association to dietary
levels)
Evidence Against Health Claims: - Proportion of saturated and trans fats in Western diets
has decreased over the last 50 years, but incidence of CHD
has risen
-Counter: Increased carbohydrate intake may cause
detrimental health effects associated with CD (e.g.
diabetes, obesity)
Counter: Incidence of CHD dependent on a myriad of
factors besides dietary intake (e.g. exercise, access to
health care, etc.)
2.3 State the
formula for the
calculation of
BMI.
weight (kg) /
height (m) ^2
(squared)
2.3 How to
differentiate
ribose to
glucose and
deoxyribose?
Ribose will have
two OH’s on the
bottom facing
downwards, while
glucose will have H
and OH (from left
to right), and
deoxyribose will
have OH and H
(from left to right)
2.4 Explain how
amino acids are
linked together.
Amino acids are linked
together by condensation
to form polypeptides with a
peptide bond formed.
The OH- from the
carboxylic group of one
amino acid, and a hydrogen
from the second amino
acid’s amine group form a
water molecule. A peptide
bond is created between a
carbon of the first amino
acid and the nitrogen of
the second amino.
2.4 Where are
amino acids
synthesized?
Why are there
so many
variations on
polypeptides?
There are 20 different
amino acids in
polypeptides synthesized
on ribosomes. The 20
different amino acids differ
in R group, and can be
linked together in any
sequence giving a huge
range of possible
polypeptides.
For a polypeptide of n
amino acids, there are 20 ^n
possible sequences.
2.4 Describe the
relationship
between genes,
amino acids and
polypeptides.
The amino acid sequence of
polypeptides is coded for by genes.
DNA (genes) codes for making
proteins by having its instructors
transcribed into mRNA, and the
ribosomes then translate the mRNA
codes into polypeptide sequences in
the process of synthesis.
Ribosomes are present in cytoplasm
and the rER.
A protein may consist of a single or
any number of polypeptides. The key
is that the function only begins when
the correct polypeptides combine
together.
protein: a molecule that has function.
2.4 Describe the
relationship
between the
structure and
function of
proteins.
The amino acid sequence determines
the three-dimensional conformation
of a protein.
The specific structure of amino acids
forms polypeptides, and their
properties determine how a
polypeptide folds up into a protein.
primary structure: a sequence of
amino acids.
secondary structure: in 2 possible
stable sequences of alpha helices or
beta pleated sheets and are held
together due to hydrogen bonds.
tertiary structure: the alpha helices or
beta pleated sheets fold up due to
interactions in the R group.
quaternary structure: found in
proteins that consist of more than
one polypeptide chain linked
together.
2.4 Why do
living organisms
synthesize
proteins?
Provide some
examples.
Living organisms synthesize many different
proteins with a wide range of functions. Rubisco,
insulin, immunoglobulins, rhodopsin, collagen and
spider silk as examples of the range of protein
functions.
S Structure: proteins of more complex structure
can provide tensile strength, which are a
component on some parts of the body: collagen,
spider silk.
H Hormones: chemically diverse regulatory
substance used to regulate body reactions:
insulin
I Immunity: make huge numbers of antibodies that
helps fight viruses and bacteria: immunoglobins
T Transport: transports molecules around the
body: haemoglobins
S Sensation: acts as receptors, act as binding sites
in membranes: rhodopsin, Sodium Potassium
pump
M Movement: muscle contractions used in
locomotion and transport around the body: actin,
myosin
E Enzymes: catalyses specific chemical reactions:
rhodopsin, needed in photosynthesis.
2.4 Describe the
relationship
between
genome and
proteome.
Each individual organism
has unique DNA. This
explains why humans are
all a little different from
each other; as DNA is the
genetic code for
proteins. It makes sense
that if every organism has
unique DNA, then every
organism also has a
unique set of proteins as
well.
2.4 Explain how
proteins can be
denatured.
Denaturation of proteins by heat or by deviation
of pH from the optimum.
Temperature
-heat disrupts the hydrogen and covalent bonds
between molecules
-as these bonds are broken, the protein will begin
to unfold and lose its capacity to function as
intended
-therefore disrupts the structure and function of
the protein.
-temperatures at which proteins denature may
vary, but most human proteins function optimally
at body temperature (~37°C)
pH
-amino acids are posesses both negatively
(COO-) and positively (NH3+) charged regions
-changing the pH will alter the charge of the
protein, which in turn will alter protein solubility
and overall shape
-all proteins have an optimal pH which is
dependent on the environment in which it
functions
(e.g. stomach proteins require an acidic
environment to operate, whereas blood proteins
function best at a neutral pH)
2.5 Outline the
stages of enzyme
activity.
Enzymes have an active site to which specific
substrates bind.
Most enzyme reactions occur when the substrates
are dissolved in water with random motion and
each molecule moving separately.
1. Specificity: only a substrate is capable of
binding to a particular enzyme’s active site as they
complement each other in therms of both shape
and chemical properties.
2. Needs to collide with enough energy (needs to
have enough thermal energy to create activation
energy)
3. Chemical properties/charges of active site
attract the substrate
4. Active site change into different chemical
substances through a conformational change.
(induced fit model, some can catalyze multiple
reactions)
5. Products separate from the active site; leaving
it vacant for substrates to bind to it again.
2.5 Explain the
factors that affect
the rate of activity
of enzymes
Temperature, pH and substrate concentration
affect the rate of activity of enzymes.
pH: all enzymes have an optimal pH value; when
pH value is beyond optimal range, it can change
the charges on R groups, breaking ionic bonds
within the enzyme and causing a change in shape,
leading to denaturation. temperature: a low temperature consists of a less
kinetic energy, which the chance of the substrate
binding to the enzyme decrease. an increase in
thermal energy can increase collision; however,
temperature beyond optimal range of enzyme
will disrupt the bonds in enzymes, hence changing
the shape and lead to denaturing
substrate concentration: an increase in substrate
concentration can increase enzyme activity as
each active site of each enzyme is saturated and
is thus working as fast as is possible. however, it
will eventually plateau, because it reaches its
maximum rate.
2.5 Explain how
enzymes can be
denatured.
Enzymes can be denatured when the structure it
changes, and it directly impacts its function,
causing inability to function properly. Enzymes
can be denatured through an extreme
temperature or pH.
Temperature:
a high thermal energy can disrupt and destroy the
hydrogen bonds in between enzymes, causing it
to be denatured
pH:
changing the pH will alter the charge of the
enzyme, which in turn will alter protein solubility
and overall shape; changing the shape or charge
of the active site will diminish its ability to bind the
substrate, abrogating enzyme function
2.5 List industries
that use
commercially useful
enzymes.
Detergents: contain proteases and lipase to help
breakdown protein and fat stains.
Textiles: in industry is being polished by enzymes.
Food industry: fructose is used as a sweetener.
2.5 Application:
Explain methods of
production of
lactose-free milk
and its advantages.
Lactase can be immobilized (attached to
something so movement is restricted) in alginate
beads and experiments can then be carried out in
which the lactose in milk is hydrolysed.
1. Concentration of substrate can be increased
manually to increase the rate of reaction.
2. Recycled enzymes can be used repeatedly and
are easy to separate from the reaction mixture
3. Separation of products is straight forward (can
also be stopped at the right time)
Advantages of lactose free products:
1. Suitable for lactose intolerant groups
2. prevents crystallisations in ice creams
3. faster production in yogurts and cheeses
(bacteria ferments monossacharide more readily)
4. increases sweetness in the absence of artificial
sweeteners (monosaccharides are sweeter
tasting)
2.6 Outline the parts
of a nucleic acid.
Nucleic acids are the genetic material of the cell,
it is composed of nucleotides.
Nucleotides are always composed of:
1. A phosphate backbone
2. Nitrogenous base
3. 5 carbon pentose sugar
-phosphate is in the left
-pentose sugar is in the middle
-nitrogenous base is on the right.
-to link nucleotides together into a chain
-covalent bonds are formed between the
phosphate of one nucleotide and pentose sugar
of the next nucleotide, which should be either on
the top or the bottom of the phosphate, forming a
strong phosphate backbone.
-covalent bonds also attach the parts within a
nucleotide.
2.6 List out the
differences
between DNA and
RNA
DNA differs from RNA in the number of strands
present, the base composition, and the type of
pentose.
- RNA is constructed by ribose, while DNA is
constructed by deoxyribose. The difference
between these two is that RNA have one extra
oxygen. - DNA and RNA both have 4 nitrogenous bases,
the only difference is that DNA has thymine, while
RNA has Uracil. - DNA has the structure of a double helix
(connected by H bonds between bases), while
RNA is single stranded (one strand of nucleotide)
2.6 Describe the
structure of DNA
DNA is a double helix made of two antiparallel
strands of nucleotides linked by hydrogen
bonding between complementary base pairs.
1. The two strands of the DNA are both a chain of
nucleotides.
-the phosphate group of one nucleotide attaches
to the sugar of another nucleotide (at the 3’
hydroxyl (-OH) group)
-results in a phosphodiester bond forming
between the two nucleotides (and water is
produced as a by-product)
-successive condensation reactions result in the formation of long polynucleotide strands
2. DNA has a double helix shape. This is because
there are two strands and each is in a spiral form.
-in order for the bases to be facing each other
and thus able to pair, the strands must be running
in opposite directions
-the two strands of DNA are described as being
antiparallel
-the two strands of DNA are antiparallel because
they occur in opposite directions.
-on one strand the number 5 carbon is on top. On
the other strand the number 3 carbon is on top
-as the antiparallel chains lengthen, the atoms will
organise themselves into the most stable energv
configuration
-this atomic arrangement results in the double-
stranded DNA forming a double helix (~10 - 15
bases per twist)
3. The nitrogenous base of the nucleotides stick
out side ways, in which Hydrogen bonds occur
between complementary bases, wounding the
two strands together into a double helix.
**A and T are complementary bases and are
connected by two hydrogen bonds. C and G are
complementarv bases and are connected by three hydrogen bonds
2.6 Application: Describe
how Crick and Watson’s
model elucidated the
structure of DNA
Their model showed:
1. A double helix, and the strands are antiparallel.
2. Pair via complementary base pairing.
3. The outer edges of bases remain exposed (allows access to replicative &
transcriptional proteins)
2.6 Explain the Rosalind
Franklin controversy.
The final construction of a correct DNA molecule owed heavily to the X-ray
crystallisation data provided by Rosalind Franklin, which was shared without
permission.
Her data confirmed arrangement of DNA strands into helical structure, and she
is now recognized as a key contributor to the elucidation of DNA structure.
2.6 Skill: Drawing simple
diagrams of the structure of
single nucleotides of DNA
and RNA.
**Use circles, pentagons and rectangles to represent phosphates, pentoses and
bases
2.6 Skill: Draw the structure
of DNA
*Nitrogenous bases face inside
Oxygen molecule points upward on the left, and downward on the right.
*Phosphate backbone faces outside
Note the two strands have carbons numbered in the opposite direction. Also
note the hydrogen bonds between complementary bases. All other bonds in
this molecule are covalent bonds
In diagrams of DNA structure, the helical shape does not need to be shown, but
the two strands should be shown antiparallel. Adenine should be shown paired
with thymine and guanine with cytosine, but the relative lengths of the purine
and pyrimidine bases do not need to be recalled, nor the numbers of hydrogen bonds between the base pairs.
2.7 State the phrase used to
describe the process of DNA
replication, and explain why
it is necessary.
The replication of DNA is semi-conservative and depends on complementary
base pairing.
Semi-conservative means that each of the two molecules of DNA formed in
replication has one strand of the original DNA molecule. The other strand of the
new DNA molecule is new. This new strand is formed from free nucleotides in
the nucleus.
The two strands of DNA are chemically bound by hydrogen bonds between
adenine (A) and thymine (T), and between cytosine (C) and guanine (G).
Semi-conservative is necessary because it is important to include the parental
strand in order to minimize mistakes in DNA replication
2.7 Describe the process of
DNA replication.
- Helicase unwinds the original DNA strand by breaking the hydrogen bonds
the middle between the complementary base pairs.
-the two strands of the parent DNA molecule must separate so that each can
serve as a template for the new DNA strands that are being built. - After the unzipping of DNA, the complementary base pairs of the two strands
are exposed, in which DNA polymerase comes in to link new nucleotides to the
existing template.
The two newly formed DNA will be identical, because nucleotides with the
nitrogenous base A always pair with nucleotides with the nitrogenous base T.
The same is true for C and G.
2.7 Skill: Analyze Meselson
and Stahl’s results to obtain
support for the theory of
semi-conservative replication
of DNA
They wanted TOK ow whether the DNA is replicated conservatively, semi-conservatively, or if it’s dispersive.
1. They cultivated E Coli and allowed the first generation to replicate their DNA
in Nitrogen 15 labelled medium.
The DNA was spun down a centrifuge, and it appears that all the DNA consists
of Nitrogen 15.
2. They put the 15N labelled E Coli DNA into 14N (lighter nitrogen) for the
second generation to replicate. The DNA was then spun down the centrifuge
again, and it showed a mixture between 15N and 14N, indicating that one strand
of the DNA was 15N while the other strand was 14N
3. The same DNA was put into 14N to replicate for the third time. After spinning
it down the centifuge, it showed both a mixture of 15N and 14N AND a mixture
of only 14N.
This results indicated that the originally 15N 14N DNA was unzipped, and that
the 14N strand formed a new DNA by creating another 14N strand; while the 15N strand formed a new DNA by creating another 14N strand.
As the process continued, the mixture of 15N and 14N DNA decreased (because
there was only 2 strands of 15N DNA from the first generation), and the 14N and
14N mixture increased (because it was consistently placed in 14N solution for
DNA replication.
15N strand formed a new DNA by creating another 14N strand.
2.7 Define transcription, and
explain the process.
Transcription is the synthesis of mRNA copied from the DNA base sequences
using RNA polymerase.
1. RNA polymerase binds to a site of DNA at the start of the gene.
2. Moves along the gene, separating the DNA into two strands while only
sticking to the sense strand, and starts pairing up RNA nucleotides.
(so in this case uracil is paired up with adenine instead of thymine)
3. RNA polymerase forms covalent bonds between the RNA nucleotides.
4. RNA polymerase separates from DNA and double helix reforms. The DNA is
then transcribed by synthesizing one strand of RNA>
2.7 Define translation, and
explain the process.
Translation is the synthesis of polypeptides on ribosomes, using the transcribed
Original
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RNA
b. messenger/mRNA attaches to ribosome (small unit);
c. many ribosome/polyribosomes bind to same mRNA;
d. (mRNA) carries codons/triplet of bases each coding for one amino acid;
e. transfer/tRNA each have specific anticodon;
f. tRNA carries specific amino acid;
g. tRNA anticodon binds to codon in the mRNA;
h. to corresponding triplet base/codon by complementary base pairing /
OWTTE;
i. a second tRNA (anticodon) binds to next codon;
J. two amino acids bind together / peptide linkage is formed;
k. first tRNA detaches;
I. ribosome moves along mRNA;
m. another tRNA binds to next codon;
n. continues until stop codon is reached;
0. stop codon has no corresponding tRNA (anticodon)/amino acid/causes
release of polypeptide;
Hence, the amino acid sequence of polypeptides is determined by mRNA
according to the genetic code.
Once the polypeptide is produced the mRNA-ribosomal complex breaks apart.
The ribosome is then able to combine with a different mRNA to produce a
totally different polypeptide.
2.7 Describe and explain how
codons work.
Each three-base sequence of nucleotides along an mRNA molecule is called a
codon and codes for a specific amino acid, which is located and transferred by
the tRNA
There are 64 codon possibilities for 20 amino acids, and it is common in almost
all organisms.
2.7 Describe and explain how
anti-codons work in the
translation of mRNA
Translation depends on complementary base pairing between codons on
mRNA and anticodons on tRNA.
Anticodons are a region on the tRNA, which pairs with the complementary
mRNA codon. The difference in tRNA molecules is based on the anticodon
present.
Each tRNA attaches to a specific amino acid, depending on the anti-codon. By
the complementary pairing of bases between codons and anticodons, amino
acids are lined up in the exact sequence called for in the genetic code, allowing the proper polypeptide to be produced.
2.7 Application: Describe the
production of multiple copies
of DNA rapidly.
Taq DNA polymerase is used to produce multiple copies of DNA rapidly by the
polymerase chain reaction (PCR).
1. Denaturation
DNA sample is heated to 95C to break the hydrogen bonds between the two
strands of the DNA.
2. Annealing
DNA sample is cooled immediately to 54C, allowing the primers (short pieces
of DNA that matches a target to be amplified, so that the DNA taq polymerase
only copies that area) attach to the opposite ends of the target sequence.
3. Elongation
Tag polymerase copies the two strands
Tag polymerase is an enzyme isolated from the thermophilic bacterium Thermus
aquatics, and can withstand high temperatures.
2.7 Describe the
production of
insulin using
bacteria.
Because the 64 codons to generate amino acids is
universal, genetic information is transferrable
between species to produce human insulin.
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1. Scientists insert gene from humans that
produces insulin into E Coli.
2. E Coli can then produce human insulin, and can
be harvested, purified, and packaged for human
Use.
-this “recombinant” bacteria will produce the
protein encoded by the human gene because the
genetic code is universal.
-scientists build the human insulin gene in the
laboratory.
-then they remove a plasmid from the bacteria
insert the human insulin gene into the plasmid.
-the “recombinant” plasmid is returned to the
bacteria.
-the “recombinant” bacteria are put in large
fermentation tanks where they repeatedly divides
and use the insulin gene to begin producing
human insulin.
-the insulin is then harvested from the bacteria,
purified and used as a medicine for people.
2.7
Skill: Use a table of
the genetic code to
deduce which
codon(s)
corresponds to
which amino acid.
Skill: 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: Deducing the
DNA base
sequence for the
mRNA strand
**Unless otherwise noted, the genetic code table
uses mRNA codons!
If given the mRNA codon and asked to find the
amino acid for which it codes:
-find the mRNA codon in the genetic code table
and the corresponding amino acid.
If given the tRNA anticodon:
-determine the complementary mRNA codon
-then find the mRNA codon in the genetic code
table and the corresponding amino acid.
If given the antisense sequence
-determine the complementary mRNA codon
-find the mRNA codon in the genetic code table
and the corresponding amino acid.
If given the sense sequence:
-determine the mRNA codon
-then find the mRNA codon in the genetic code
table and the corresponding amino acid.
2.8 Define cell respiration,
and describe the different
stages of cell respiration.
Cell respiration is the controlled release of energy from organic compounds to
form ATP through oxidation reactions.
-oxidation process is slow because it breaks down one covalent bond at a time.
-each step in the oxidation reaction of cell respiration is controlled by enzymes.
-the small amounts of energy released are used to produce the ATP molecules.
-slow process ensures that small amount of energy is released at a time.
-important because if a large yield of energy is released at once, there will be
an increase in heat.
-if there is heat then not all energy will be converted into ATP, which is less
efficient.
-the increased heat produced could also very well damage the cell.
ATP is then the molecule which provides the energy for all the life processes of
the cell to occur.
2.8 Explain how ATP is used
in the cell?
ATP is the product of cell respiration, and is the form of energy used by the cell
to carry out the life functions.
-it is immediately available as source of energy after cell respiration.
-consists of three COVALENTLY linked phosphate molecules.
-last two phosphates are bonded by a high energy bond, which cell can easily
break to and release the energy to carry out the necessary functions of the cell.
-this process is called hydrolysis (ATP turns into ADP + Pi).
Cell respiration uses energy stored in organic molecules to regenerate ATP
from ADP + Pi (via oxidation)
2.8 Define anaerobic
respiration and explain its
process
Anaerobic respiration is the generation of energy without the use of oxygen.
-gives only a small yield of ATP from glucose.
-occurs in the cell cytoplasm.
-requires 2 ATP molecules to start the process.
Glycolysis:
1. Enzyme modifies 6 carbon glucose to make it in the state of unstable
2. A series of reactions split glucose into 2 pyruvate (3 carbon compounds)
-the energy from the bonds that are broken in this process are used to generate
4 ATP molecules.
-if no oxygen is present after the first part of anaerobic cell respiration called
glycolysis, a process called fermentation will occur.
-animal:pyruvate stays in the cytoplasm and in humans is converted into lactate which is the removed from the cell.
-yeast: the pyruvate is converted into carbon dioxide and ethanol. In either
case, no ATP is produced in the process AFTER glycolysis.
**Note that if oxygen becomes available in human cells, the lactic acid (lactate)
produced may be changed back to pyruvate and used in aerobic cell
respiration. This is referred to as a reversible reaction.
2.8 Explain the
similarities and
differences in
anaerobic and
aerobic cellular
respiration.
Similarities:
1. Essential to life as it generates ATP and energy/
heat.
2. Both start with glucose.
3. Both start with the process of glycolysis.
4. Both produces pyruvate.
Differences:
1. Aerobic respiration requires oxygen while
anaerobic respiration does not.
2. Aerobic respiration produces a large yield of
ATP over a longer period of time, and anaerobic
respiration produces a small yield of of ATP in a
short time period.
3. Aerobic respiration produces carbon dioxide
and water. Anaerobic respiration produces
lactate (lactic acid) in humans, and ethanol and
carbon dioxide in yeast and plants.
4. Aerobic leads to Kreb’s cycle and anaerobic
leads to fermentation.
5. Anaerobic occurs in cytoplasm while aerobic
occurs in mitochondria (pyruvate is transported to
there).
2.8 Applications:
Describe the role of
yeast in the
brewing, the baking
industry and the
production of dairy
products.
Yeast carries out anaerobic respiration;
Which produces ethanol and carbon dioxide;
From the breakdown of sugars/monosaccharides/
carbohydrates (in the dough/grape juice);
In wine fermentation, ethanol is the essential
product making the juice into wine;
Ethanol concentration rises in the ferment causing
the process to stop/death of yeast;
In bread making, carbon dioxide causes the
dough/bread to rise;
The ethanol evaporates during baking/heating/
cooking;
Yogurt / Cheese - Bacteria produce lactic acid
anaerobically, which modifies milk proteins to
generate yogurts and cheeses
2.8 Applications:
Explain anaerobic
respiration in
humans during
intense exercise.
Lactate production in humans when anaerobic
respiration is used to maximize the power of
muscle contractions.
Lactate production in humans occurs during
intense muscle activity. Due to the intensity of the
activity not enough oxygen can be delivered to
the muscles. The result of this lack of oxygen
delivery is maximum muscle contraction.
However, the lactate produced will seriously limit
the number of maximum muscle contractions, as it
is poisonous. Lactate will be converted back into
pyruvate with the presence of oxygen.
2.8 Skill: Describe a
respirometer set up.
A respirometer is a simple apparatus that can measure the rate of respiration
-measures the consumption of oxygen as an indication of the respiration rate.
-in Tube A, the organism to be tested (or germinating seed) is positioned, and
the tap is closed
-the organism starts respiring, consuming 02 and producing CO2 and H2O.
-the alkaline solution at the bottom of Tube A will absorb the CO2
-Tube B is the control where no 02 is used or CO2 produced because no living
organism is present.
-the capillary connecting the two tubes is a manometer.
-he reduction in oxygen in Tube A will reduce the pressure in Tube A
-and will move the coloured liquid in the manometer in the direction of Tube A,
providing an indirect measurement of the oxygen consumed
-allowing the rate (amount of oxygen consumed per time unit) to be calculated
2.9 Define
photosynthesis
Photosynthesis is the production of carbon
compounds in cells using light energy.
2.9 Describe the
spectrum of visible
light regarding its
color and length in
wavelengths.
Visible light ranges from red to violet and 400nm
to 700nm. Violet has the shortest wavelength
(400nm) while red has the longest wavelength
(700nm). The colours with the shortest
wavelengths possess the highest energy
2.9 Explain the
absorption of line
spectrum of the
chlorophyll.
Chlorophyll is a green pigment found in
photosynthetic organisms and they are
responsible for light absorption. This absorbed
light energy in then used to convert carbon
dioxide and water into carbohydrates such as
glucose and oxygen.
Chlorophyll absorbs red and blue light most
effectively. The energy of the red and blue
colors is then used in the production of glucose
Chlorophyll reflects green light more than other
colors.
2.9 Describe what
chromatography is
and explain how it is
used.
Paper chromatography is a technique used to
separate substances in a mixture based on the
movement of the different substances up a piece
of paper by capillary action.
The pigment molecules migrate, or move up the
paper, at different rates because of differences in:
-solubility
-molecular mass
-variable hydrogen bonding with the
chromatography paper.
This is important because plants don’t reply on
only one pigment to absorb light.
Two of the most common techniques for
separating photosynthetic pigments are:
Paper chromatography - uses paper (cellulose) as
the stationary bed
Thin layer chromatography - uses a thin layer of
adsorbent (e.g. silica gel) which runs faster and
has better separation
-a stationary bed (e.g paper) is dipped into
mobile phase, you might use ethanol as the
solvent, or you may use propanone (acetone).
**the mobile phase dissolves pigments, allowing
them to travel up the paper strip.
Varying colors in different areas of the
chromatogram with different Rf values indicate
separate pigments.
Rf = distance travelled by sample/ distance
travelled by solvent
Method of paper chromatography:
1. a leaf is ground in a mortar and pestle, using a
small amount of sand to help grind the sample
and break down the cell walls.
2. a small amount of solvent is added, and the
sample is ground up further to dissolve the
pigments in the solvent.
3. when the solvent is dark green, let the solids
settle and then pour off the solvent (which now
contains the sample of pigments) into a small
beaker or watch glass.
4. this step raises the concentration of the
pigments in the solvent, which makes it easier to
see the separated pigments once the
chromatography is complete.
5. use a toothpick or very small paintbrush to
apply the pigment sample to a spot that is at least
20 mm from the bottom of your paper or TLC
strip.
6. situate the paper or TLC strip in a sample tube;
ensure that the pigment sample is above the
solvent at the beginning of the experiment
2.9 Explain the
process of
photosynthesis
Photosynthesis can be split into 2 stages, light
dependent reaction and light independent
reaction.
Light dependent reaction: Oxygen is produced in
photosynthesis from the photolysis of water.
1. splitting of water to produce oxygen.
Photolysis is the process in which energy from
light is used to split water.
When photolysis occurs oxygen gas is produced.
Most of the oxygen is released into the
atmosphere. Hydrogen is also produced. The
hydrogen is used in later stages of
photosynthesis.
Light independent reaction: Energy is needed to produce carbohydrates and other carbon
compounds from carbon dioxide.
The energy from the absorbed colours of the
visible light spectrum is used to build carbon
compounds which include carbohydrates.
2. H+ combines with CO2 to form complex
organic compounds. (carbs, amino acids, etc)
Hence, the products of photosynthesis are:
-oxygen
-glucose
2.9 Explain the
effects of
photosynthesis.
Earth’s atmosphere:
-amount of plants determine level of CO2 inside
the atmosphere
-which may lead to increase in global
temperature and acidity of the rain
Ocean:
-Earth’s oceans initially had high levels of
dissolved iron (released from the crust by
underwater volcanic vents)
-When iron reacts with oxygen gas it undergoes a
chemical reaction to form an insoluble precipitate
(iron oxide)
-When the iron in the ocean was completely
consumed, oxygen gas started accumulating in
the atmosphere.
In
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Rock deposition:
-The reaction between dissolved iron and oxygen
gas created oceanic deposits called banded iron
formations (BIFs)
-These deposits are not commonly found in
oceanic sedimentary rock younger than 1.8 billion
years old
- This likely reflects the time when oxygen levels
caused the near complete consumption of dissolved iron levels
-As BIF deposition slowed in oceans, iron rich
layers started to form on land due to the rise in
atmospheric 02 levels
dissolved iron levels
2.9 What are some
limiting factors on
the rate of
photosynthesis?
Temperature:
-photosynthesis is controlled by enzymes
-high temperature will cause denaturation
Light intensity:
-more light intensity = more chlorophyll are being
photo activated (increase in reaction)
-will eventually plateau when all chlorophyll are
saturated with light.
CO2 concentration
-more reactant = more product = increase in rate
-cuz CO2 is involved in the fixation of carbon
atoms to form organic molecules.
