U1, T2, Subtopic 2: Structures of proteins and enzyme activity.

2.60
Structure of an amino acid:

-The elements proteins/ amino acids are made of are C, H, O, N, S (in cysteine).
-There are 20 naturally occurring amino acids, the only difference between them is
the nature of the R groups.
-The amino/ amine group is basic, and the carbonyl group is acidic.

The formation of peptide bonds between amino acids:

-A hydroxyl is lost from the carbonyl group of one amino acid while a hydrogen is
lost from the amine group of the other amino acid, resulting in the formation of a
dipeptide, the R groups are not involved.

The four levels of protein structures:

The primary structure of protein:

-The sequence of amino acids that that makes up the polypeptide chain.
-The primary structure determines the folding of a protein as the types and
positions of amino acids determines the type of bonds between R groups. This
ultimately determines the shape and properties of a protein.
-The amino acids are bonded together by peptide bonds.

The secondary structure of protein:

-The arrangement of the polypeptide chain into a regular, repeating 3D structure,
either an alpha-helix or a beta-pleated sheet.
-Hydrogen bonds form between the negativel charged N or O atoms with the
positively charged H atoms.
-Peptide bonds also present.

The tertiary structure of a protein:

-A more compact structure of the bent/ twisted polypeptide chain.
(Conformational)
-Hydrogen bonds between a +H and an electronegative atom, both on R groups.
-Disulphide bonds between two cysteine amino acids.
-Ionic bonds between charged R groups.
-Hydrophobic interactions between non-polar R groups.

The quaternary structure of a protein:

-A 3D structure consists of the combination of two or more tertiary polypeptide
chains.
-All the bonds in a tertiary protein plus non-protein prosthetic groups may be
associated in conjugated proteins.

How does the primary structure of a protein determine its structure and function:
-The primary structure determines the types and sequence of amino acids.
-The types and positions of amino acids determine the types and positions of
disulphite, ionic, hydrogen and hydrophobic bonds.
-This determines the 3D folding of the protein.

Differences between fibrous and globular proteins:

-Fibrous proteins have secondary structures but globular proteins have tertiary or
quaternary structures.
-Fibrous proteins are insoluble but globular proteins are soluble due to the inward
orientation of hydrophobic R groups while the hydrophilic/ polar R groups orientate
themselves towards the aqueous surroundings.
-Fibrous proteins have long, parallel polypeptide chains held together by H-bond
cross-links; globular proteins have spherical shapes with tightly folded polypeptide
chain(s).
-Fibrous proteins have structural functions and globular proteins have physiological
functions.
-Examples of fibrous proteins are collagen, elastin, keratin and fibrin. Examples of
globular proteins are enzymes, HB, fibrinogen, hormones.

Collagen:
-An extremely long fibrous protein that provides tensile strength support to
tendons, ligaments, bones and skins, also forming connective tissues.
-The primary structure is repeating unites of glycine and two other amino acids.
-The secondary structure is an alpha-chain.
-The quaternary structure contains 3 alpha chains arranged in a triple helix, held
together by a lot of H-bonds.
-The H-bonds and covalent bonds hold the triple helix together as fibrils which are
held together forming collagen fibres.

Haemoglobin:
-Contains four polypeptide chains bonded together by disulphide bonds, each
polypeptide chain surrounds an iron-containing haem prosthetic group that each
bind or releases one oxygen molecule.

Enzymes:
-Biological catalysts that speed up the rate of a reaction without being used up or
undergoing a permanent change.
-Enzymes lower the activation energy of a reaction with alternative energy
pathways by bringing reactants together, holding them in the correct orientation
and destabilising the bonds in reactants.
The induced fit model of an enzyme:
-Substrate(s) which has complementary shape to the active site of an enzyme binds
to the active site.
-The ES complex is formed as both the active site and the substrate undergo a
conformational change for an induced fit that allows for an ideal tight bonding.
-Substates have been converted into their products after the reaction.
-Products released and the enzyme carries on binding to another substrate without
being used up.

The effect of temperature on an enzyme catalysed reaction.

-As temperature increases, the enzyme and its substrate gain more kinetic energy.
-The rate of successful collisions increases.
-More ES complexes are formed.
-The rate of enzyme reaction increases till the optimum temperature.
-At higher temperatures, too much increase in kinetic energy causes hydrogen and
ionic bonds to be broken.
-The enzyme is denaturing as its tertiary 3D structures and active site change shape.
-Substrates can no longer bind to the active site, less ES complexes formed.
-Rate decreases sharply.

The effect of pH on an enzyme catalysed reaction.

-At extremes of pH, charged H+ ions and OH- ions disrupt/ break the ionic and H
bonding in the enzyme.
-This alters the 3D tertiary structure of the enzyme.
-This alters the shape and charge of the active site.
-Substrates can no longer bind to it.
-ES complexes are less likely to form.

The effect of substrate concentration on an enzyme catalysed reaction.

-As the concentration of substrate increases, the number of substate molecules

increases.
-A greater chance of successful collisions between enzymes and substrates.
-More Es complexes forming.
-The rate eventually levels off when all enzymes are saturated.

Why do we measure the initial rate of a reaction:

-To ensure that substrate concentration is not a limiting factor.
-As the reaction proceeds the substate concentration decreases as the substates are
being used up.
The nature of genetic codes:
Non-overlapping:
Each triplet code is discrete, so each codon is read once only.
Degenerate:
The same amino acid is coded by more than 1 triplet code. (This reduces the effect
of mutation as there will be no effect on the resulting protein since the same amino
acid is produced.)

DNA replication process:

-DNA helicase unwinds the double helix by breaking H bonds between
complementary base pairs.
-Both strands act as templates.
-DNA polymerase lines up new nucleotides along the template strands and
catalyses the phosphodiester bonds between the nucleotides.
-The new nucleotides bind with the original nucleotides complementarily, A-T, C-G.
-DNA ligase reforms the H bonds and catalyses the phosphodiester bonds,
annealing the fragments.
-Semi-conservative model.

Transcription process:
-Transcription happens in the nucleus.
-DNA unwinds as RNA polymerase catalyses the breaking of H bonds.
-Mononucleotides line up with complementary bases on the template/ non-
coding/ anti-sense strand of the DNA.
-RNA polymerase then catalyses the formation of phosphodiester bonds between
the nucleotides, a condensation reaction.
-The mRNA detaches from the DNA.
-The mRNA strand leaves the nucleus into the cytoplasm via the nuclear pores.

Translation process:
-Translation happens in the cytoplasm.
-The ribosome first binds to the starting codon (AUG) of an mRNA strand.
-A tRNA with complementary anticodons bind to the codons on the mRNA while
bringing a specific amino acid.
-H bonds between tRNA and mRNA.
-The ribosome moves along the mRNA, bringing together 2 tRNAs.
-The two amino acids are joined together by peptide bonds using an enzyme and
ATP.
-The first tRNA gets released and is free to collect another amino acid.
-When the stop codon is reached, the mRNA strand and the last tRNA detach and
the polypeptide chain is complete.
The role of mRNA in protein synthesis:
-mRNA is a copy of a section of DNA.
-It moves out of nucleus into the cytoplasm to the ribosomes.
-It acts as a template for translation as it carries the genetic information for the
protein being synthesized.

The role of tRNA in protein synthesis:

-Involved in translation as it has anticodons complementary to the codons on the
mRNA.
-Brings its specific amino acid to the ribosome.
-Holds the amino acids in place for the formation of a polypeptide chain.

Differences between tRNA and mRNA:

-tRNA is folded and has a clover leaf shape while mRNA is straight.
-tRNA contains two polynucleotide strands with hydrogen bonds but mRNA
contains only one polynucleotide strand without hydrogen bonds.
-tRNA has anticodons but mRNA has codons.
-tRNA has an amino binding site.
-tRNA has a fixed length but mRNA has variable length.
2.10
Diffusion definition:
The movement of molecules (liquid/ gas) from an area of their higher concentration
to an area of their lower concentration down their concentration gradient until
uniform equilibrium due to the random motion of molecules.
Types of diffusion:

Simple diffusion Facilitated diffusion

Types of Small, non-polar, lipid soluble. Large, polar, charged, water soluble.
molecules The molecules pass through The molecules pass through are specific
are not specific. to their protein carriers.
Examples CO2, O2. H2O, amino acids, ions, glucose.
Mechanisms Through phospholipids. Through protein channels (hydrophilic)
and carrier proteins of specific shape to
the molecules. They don’t require
energy and the process is all passive.
Describe how carrier proteins enable facilitated diffusion:
The molecule whose shape is specific to a particular carrier protein/ channel binds
to the carrier protein passively, this causes a conformational change in the carrier
protein (opens and closes), so the molecule is carried across and released to the
other side of the membrane down its concentration gradient.
Factors affecting diffusion:
Temperature. More kinetic energy so faster movement of molecules.
Concentration gradient. The steeper the concentration gradient, the faster the
rate of diffusion. This is done is the body by immediately
metabolising a substance, chemical changes or take it
away from its location immediately.
Size of particles. The smaller the particles, the faster the rate.
Thickness of exchange The thinner the exchange membrane, the shorter the
membrane. (If present.) diffusion distance, thus the faster the rate.
Surface area to volume The larger the surface area to volume ratio, the more
ratio. particles can be exchanged at one time, the faster the
rate.
The number or density The larger the number, more exchange of particles at.
of protein channels or One time, the higher the rate of facilitated diffusion.
carrier proteins.
Fick’s law of diffusion (for a given temperature):

Understand how the structure of the mammalian lung is adapted for rapid gas
exchange:
-Alveolus has only a thin, single layer of epithelial cell. (One cell thick).
-Capillary consists of a single layer of endothelial cell.
This shortens the diffusion distance for O2 and CO2.
-Lots of alveoli forming a network.
This increases the surface area to volume ratio of the gas exchange membrane.
-A thin layer of firm of water in alveoli.
O2 first dissolve in water as a solution before simple diffusion, this makes diffusion
easier.
-Constant and rapid flow of blood.
Removes O2 and brings CO2 at a high rate to maintain a steep concentration
gradient of O2 and CO2.
2.40
Osmosis definition:
The net movement of free water molecules through a partially permeable
membrane from an area of higher water potential to an area of lower water
potential down a water potential gradient.
(From a dilute solution to a concentrated solution.)
Osmosis in plant cells:

The solution is hypotonic to the cell’s cytoplasm,

meaning the concentration of solutes outside the cell is
lower than inside, which means the water potential
outside is higher than inside.
Water moves into the cell, making the vacuole swell and
pressing the cytoplasm against the cell wall, exerting
turgor pressure, the cell is turgid. The cellulose plant cell
wall prevents the cell from bursting.

The solution is isotonic to the cell’s cytoplasm, meaning

both the concentration of solutes and the water
potential inside and outside the cell are the same.
No net movement of water/ equal volume of water
moves in and out of the cell, the vacuole shrinks and
doesn’t push against the cell wall, the cell loses turgor,
incipient plasmolysis.

The solution is hypertonic to the cell’s cytoplasm,

meaning the concentration of solutes outside the cell is
higher than inside, which means the water potential
outside is lower than inside.
Water moves out of the cell, the vacuole and the
cytoplasm shrink, the cell membrane is pulled away
from the cell wall.
Osmosis in animal cells:

The solution is hypotonic to the cell’s cytoplasm, so water

moves in by osmosis down a water potential gradient, the
cell bursts and is lyses as too much water moves in.

The solution is isotonic to the cell’s cytoplasm, so there’s no

net movement of water, the cell maintains its normal
biconcave shape.

The solution is hypertonic to the cell’s cytoplasm, so water

moves out by osmosis, the cell shrivels and becomes
cremated.

2.50
Active transport definition:
The movement of molecules (large ions and polar) from an area of their lower
concentration to an area of their higher concentration against a concentration
gradient across a membrane using the energy in ATP that has been broken down by
ATPase.

Active transport mechanism:

-Molecule of a specific shape binds to its specific protein carrier.
-ATPase catalyses the hydrolysis of ATP.
-ATP is hydrolysed to ADP and phosphate. The energy released is used to cause a
conformational change/ change in shape of the carrier protein which carries the
molecule across the membrane/ released to the other side.
-Finally, carrier protein returns to its original shape passively to allow more
molecules to enter.
Endocytosis:
Phagocytosis mechanism:
-Membrane protein receptors interact with bacteria.
-Macrophage membrane surrounds the bacteria.
-The field movements of phospholipids allow the membrane that surrounds the
bacteria to fuse.
-Formation of a vesicle that contains the bacteria.