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Option C
C1.1 Explain the four levels of protein structure, indicating the significance of each level.
[Quaternary structure may involve the binding of a prosthetic grojup to form a
conjugated protein]
Primary structure:
This is the amino acid sequence. There are 20 different amino acids used
by life, differing in their "R groups" Remember how a peptide bond forms, via a
condensation reaction. These structures are formed on the ribosomes of eukaryotic cells
and prokaryotic cells.
Secondary structure:
This is the beta pleated sheets and alpha helix formed by interactions
between double bonded oxygen and hydronium groups of the amino acids. They are weak
hydrogen bonds.
Tertiary structure:
The beta pleated sheets and alpha helixes are then folded into each other
using both weak hydrogen bonds, and covalent bonds between sulfur groups of Cysteine.
Hydrophobic and hydrophilic properties of the amino acids also affect the folding.
In many proteins, this is the final structure of the protein.
Quaternary structure:
More than one polypeptide is used to make the final protein. Often other
ions are added like Fe+ and Mg+. Hemoglobin has 4 strands and Fe+
C1.2 Outline the difference between fibrous and globular proteins, with reference to two
examples of each protein type.
Fibrous proteins tend to be structural and are best exemplified by actin and
myosin of muscles. Other examples would be collagen in skin , and fibrin in the blood.
Globular proteins are usually enzymes, pumps or signal proteins. DNA
polymerase, RNA polymerase, ligase, pepsin, amylase, the Na and K pump are examples.
C1.3 Explain the significance of polar and non-polar amino acids.
The "R" group of the amino acid is polar if it has either a negative or positive
charge. These amino acids form weak bonds with water and are hydrophyllic.
Examples are serine, threonine, cysteine, tyrosine, asparagine, and glutamine
If the "R" group is not charged, it will be repelled by water and is hyrdrophobic.
Examples are glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine,
typtophan, and proline.
C 1.4 State four functions of proteins giving a named example of each
[ Membrane proteins should not be included]
Structural proteins- collagen, elastin, keratin
Transport proteins- hemoglobin
Hormonal proteins- insulin
Contractile proteins- actin and myosin
Defensive proteins- antibodies
Enzymatic proteins- pepsin, amylase, protease
Enzymes
C2.1 State that metabolic pathways consist of chains and cycles of enzyme-catalysed
reactions
C 2.2 Describe the induced fit model
{ This is an extension of the lock and key model its importance in accounting for
the ability of some enzymes to bind to several substrates should be mentioned]
We are finding that more and more enzymes have a very flexible shape and active
site. The active site conforms to the shape of the substrate after the substrate binds. This
allows an enzyme to operate on more than one substrate.The enzyme undergoes a
conformational change
Related to this : Remember how allosteric enzymes work. They have both an activator
site and a deactivator site. The enzyme oscillates between the active state and inactive
state based upon the relative concentration of the activators and inhibitors.
C2.3 Explain that enzymes lower the activation energy of the chemical reactions that they
catalyse.
This is done by either stressing the bonds of a molecule to be broken by having
the enzyme pull at it ( catabolism), or by moving two substrates closer together as they
both align within an enzyme ( anabolism)
Catabolism is the breaking of chemical bonds- hydration reactions
Anabolism is the making of chemical bonds- condensation reactions
Together they comprise metabolism
C2.4 Explain the difference between competitive and non-competitive inhibition, with
reference to one example of each.
Competitive inhibitors have similar shapes to the target substrate and can bind in
the active site. They can be overcome by adding more substrate.
Example: the enzyme dihydropteroate synthetase ( an enzyme found only in
bacteria )normally has the substrate para-aminobenzoate, but sulfadiazine ( an antibiotic)
competitively inhibits it.
Non-competitive inhibitors bind to the enzyme somewhere other than the active
site and cause a conformational change in the enzyme, inhibiting its function.
Example: the enzyme phosphofructokinase ( part of glycolysis) normally has the
substrate fructose-6 phosphate, but xylitol-5 phosphate is a non-competitive inhibitor
C 2.5 Explain the control of metabolic pathways by end-product inhibition, including the
role of allosteric sites.
Most chemical processes have lots of steps along the way. Glycolysis involves 10
enzymes and steps. Allosteric interactions can control the operation of a pathway. The
final product of a pathway can inhibit an initial reaction in the pathway and thus control
the amount produced, If there is enough product, some of it diffuses to enzymes near the
beginning of the pathway and bind allosterically, inhibiting the enzyme. Once the final
product is used up, the one binding to the enzyme also diffuses away, initiating the
pathway to produce more product.
C3 Cell respiration
C3.1 State that oxidation involves the loss of electrons from an element, whereas
reduction involves a gain of electrons; and that oxidation frequently involves gaining
oxygen or losing hydrogen, whereas reduction frequently involves losing oxygen or
gaining hydrogen.
C3.2 Outline the process of glycolysis, including phosphorylation lysis, oxidation and
ATP formation
[ In the cytoplasm, one hexose sugar in converted into two three-carbon atom
compounds ( pyruvate) with a net gain of two ATP and two NADH + H+]
Glycolysis
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means "splitting of sugar"
takes place in the cytoplasm, so it can occur in prokaryotes and
eukaryotes
6-carbon glucose is split into two 3-carbon pyruvate molecules
( this is what they mean by lysis)
Initially, 2 ATP have to be added
The yield is 4 ATP and 2 NADH and 2 pyruvate molecules and
Net gain is 2 ATP and 2 NADH + H+
ATP is formed by substrate level phosphorylation ( by an enzyme)
Oxidation is the losing of electrons, which glucose does… the
electrons move to NAD+, which is reduced to NADH+ H+ This
gives up its energy in the electron transport chain if oxygen is
present.
Remember: no gasses are involved at all in glycolysis
C3.3 Draw and label a diagram showing the structure of a mitochondrion as seen in
electron micrographs.
C3.4 Explain aerobic respiration, including the link reaction, the Krebs cycle, the role of
NADH+ + H+, the electron transport chain and the role of oxygen.
[ In aerobic respiration( in mitochondria in eukaryotes), each pyruate is
decarboxylated ( CO2 removed). The remaining two-carbon molecule ( acetyl group)
reacts with reduced coenzyme A, and, at the same time, one NADH+ H+ is formed. This
is known as the Link reaction.
In the Krebs cycle, each acteyl group (CH3CO) formed in the link reaction yields
two CO2. The names of the intermediate compounds in the cycle are ot required. Thus it
would be acceptable to note: C2 + C4= C6 and so on.]
Link reaction
Pyruvate is decarboxylated ( CO2 is removed) The remaining two-carbon
molecule (acetyl group) reacts with reduced coenzyme A, and, at the same time, one
NADH + H+ is formed.
Krebs cycle…..in mitochondrial matrix, releases CO2
yields 6 NADH, 2 FADH2, 2 CO2, and 2ATP from
substrate level phosphorylation
Follow the carbons:
C2 + C4= C6 + CO2 = C5 + CO2= C4
Kreb's Cycle… takes place in the mitochondrial matrix
3 carbon pyruvate is converted to 2 carbon Acetyl CoA releasing CO2 The
pyruvate is decarboxlylated… the carboxyl group is removed from the pyruvate.
Each turn of the Kreb's cycle, 2 carbons enter as Acetyl CoA, 2 carbons leave as CO2.
3 NADH, 1 FADH2 and 1 ATP are produced.
A glucose provides two turns of the cycle. ( 2 pyruvates from glycolysis)
Note that most energy from the Kreb's cycle resides in the NADH and FADH2
Electron transport chain
Electron transport chain is where the ATP is mostly produced.
A series of enzymes are imbedded in the cristae, or inner membrane of the mitochondria.
Many of these enzymes, cytochromes, incorporate iron, like hemoglobin does.
The movement of the energetic electrons ( from NADH and FADH) powers the pumping
of H+ into the inner membrane, these hydrogen ions are allowed to diffuse back out
through ATP synthetase, which phosphorylates ADP
C 3.5 Explain oxidative phosphorylation in terms of chemiosmosis
(See Electron transport chain above)
It is called oxidative phosphorylation because oxygen is the ultimate acceptor of
the electrons being passed down the electron transport chain. It is called chemiosmosis
because the H+ ions diffuse through the inner membrane down their concentration
gradient and power the phosphorylation of ADP to ATP
C 3.6 Explain the relationship between the structure of the mitochondrion and its
function
The cristae provide lots of surface area for the electron transport proteins to be
imbedded in. In order for one protein to pass electrons sequentially to the next, each
protein has to be closely aligned within a membrane. It doesn't work if the proteins are
floating randomly around in the cytoplasm
C 3.7 Analyse data relating to respiration
C4 Photosynthesis
C 4.1 Draw and label a diagram showing the structure of a chloroplast as seen in electron
micrographs
C4.2 State that photosynthesis consists of light-dependent and light-independent reactions
[ These should not be called light and dark reactions]
C4.3 Explain the light-dependent reactions.
[ Include the photactivation of photsystem II, photolysis of water, electron
transport, cyclic and noncyclic photophosphorylation, photoactivation of photosystem I,
and reduction of NADP+]
C4.4 Explain photphosphorylation in terms of chemiosmosis
C4.5 Explain the light- independent reactions
[ Include theroles of ribulose biphosphate( RuBP), carboxylase, reduction of
glycerate 3- phosphate ( GP) to triose phosphate ( TP), NADPH+ H+, ATP, regeneration
of RIBP, and subsequent synthesis of more complex carbohydrates]
C4.6 Explain the relationship between the structure of the chloroplast and its function
[ Limit this to the large surface area of thylakoids for light absorption, the small
space inside thylakoids for the accumulation of protons, and the fluid stroma for the
enzymes of the Calvin cycle.]
C4.7 Explain the relaitionship between the action spctrum and the absorption spectrum of
photosynthetic pigments in green plants
C4.8 Explain the concept oflimiting factors in photosynthesis, with reference to light
intensity, temperature and concentration of carbon dioxide.
C 4.9 Analyse datat relating to photosynthesis.