D1.

1 DNA Replication
How does DNA represent continuity and change:
-​ Continuity
-​ Hereditary material, contains genes that is passed on the offspring
-​ The structure- double membrane
-​ Change
-​ Base pairing
-​ Gene expression
-​ Evolution
-​ Mutation

Step for DNA replication

Complementary base pairing ensures that the DNA stays the same after being replicated.
Replication must proceed mitosis to then cell division. Cell division is important for growth, repair
and replace.
DNA Replication steps:
1)​ The enzyme Helicase unwinds the double helix and separates the two strands by breaking the
hydrogen bonds, this creates a replication fork. The enzyme breaks the hydrogen bonds that
are formed between the complimentary nitrogenous bases
2)​ DNA polymerase links nucleotides together to form a new strand, using the pre-existing
strand as a template. This makes two separate strands from one. The DNA polymerase gets
the new nitrogenous bases from around, they are freely floating around. The two strands are
exact replicas of each other being completely identical. All thanks to the complimentary base
pairing
3)​ You refer to the original one as the template strand and then the new one as the new strand

Two molecules are created each consisting of half of the parent template and half newly synthesised
DNA. This is called semi-conservative replication. Semiconservative replication is the process where
a DNA double helix unwinds, and each original strand serves as a template for a new, complementary
strand. This results in two identical DNA molecules, with each new molecule containing one old
(parental) strand and one new strand. This mechanism ensures that each daughter cell receives a
complete set of genetic information.

D1.2 Protein Synthesis

Transcription
Transcription is the process of copying genes. Genes are specific sequences that code for a protein
(trait). You need to maintain the same nucleic acids, and copy the same DNA. Transcription produces
mRNA, where a single strand is produced. The enzyme that produces the mRNA is RNA polymerase.
It copies complementary base pairs into a strand of mRNA.
This process is located in the nucleus of the cell, due to DNA not traveling outside of it. At the end of
the process you get an RNA fragment. Only the RNA can leave the nucleus, so at the end of this
process a single strand of RNA is free to leave. The RNA strand will be grouped into three bases, this
is called codons. Only one from the two strands get copied.

Replication turns DNA into DNA, it transcription turns DNA into mRNA

Translation
mRNA is translated to a protein. This is located in the cytoplasm, 80s ribosome. Ribosomes have two
parts: a large subunit and a small one and come together as a sandwich, and the mRNA is the fillings.
The sequence "AUG" is the start codon in messenger RNA (mRNA), and it serves as the signal to
begin protein synthesis, this is important for the ribosome to know where to start. The complementary
base pairs called the anti codon attach to the mRNA, thanks to tRNA. tRNA, or transfer RNA, is a
small RNA molecule that acts as an "adaptor" in protein synthesis by carrying specific amino acids to
the ribosome. It matches an mRNA codon with the correct amino acid using its anticodon, which
binds to the complementary codon on the mRNA, ensuring the correct sequence of amino acids is
added to the growing protein chain. At the end of the tRNA there is an amino acid that corresponds to
the red codon.
There are a total of 64 codons and 20 amino acids. There are always two tRNA , and both of them
find corresponding amino acids. These two amino acids link together through condensation reaction
and form a peptide bond. This can continue and make very complicated proteins. Once the peptide
bond happens the tRNA leaves, and then a new one replaces it. The stop codon is the end of the
translation
D 1.3 Mutation
Mutation affects the DNA→ mRNA→ Amino Acid→ Protein
Point mutation is the point where mutation occurs in the genome when a single base pair is added,
deleted or changed. Results can range from no charge to complete changing of the protein structure,
which will in turn affect function
A genome is an organism's complete set of genetic instructions, made of DNA. It contains all the
information needed to build and maintain that organism, and in humans, a copy is found in almost
every cell.
Radiation or the environment can affect the amount of radiation, but under normal conditions there
should be a consistent amount of mutations in animals and plants.
An example of mutation is the:
-​ Sickle cell anemia
-​ It is an inherited blood disease that affects 100 000 people in the United States and 8
million people worldwide. It is a genetic disease
-​ In sickle cell anemia, there is a base substitution mutation (when one base changes to
something else)
-​ In the six codon of DNA, CTC changes to CAC
-​ This results in the mRNA to change from GAG to GUG
-​ The amino acid changes from Glutamic Acid to Valine
-​ Sickle cells cannot manoeuvre easily through the capillaries therefore having a higher
likelihood to get blocked
Mutation creates variations in protein-coding portions of genes that can affect the protein itself. But
even more often, it creates variations in the "switches" that control when and where a protein is active
and how much protein is made.
Radiation, chemicals, byproducts of cellular metabolism, free radicals, ultraviolet rays from the
sun—these agents damage thousands of nucleotides in each of our cells every day. They affect the
nucleotides themselves: converting one base to another, knocking a base off its backbone, or even
causing a break in the DNA strand.
To prevent DNA mutations, DNA repair machines are constantly at work in our cells, fixing
mismatched nucleotides and splicing broken DNA strands back together. Yet some DNA changes
remain. If a cell accumulates too many changes—if its DNA is so damaged that repair machinery
cannot fix it—it either stops dividing or it self-destructs. If any of these processes go wrong, the cell
could become cancerous.

Different types of Mutations

Inherited Mutations
-​ Mutations that are inherited from a parent by offspring
-​ All of the offsprings cells will carry these mutations, including those form the germline
-​ The term "germline" is a synonym for gamete cells (egg and sperm cell)
-​ These mutations can be passed onto subsequent generations
-​ Examples of this
-​ Cystic Fibrosis
-​ Huntington disease

New Mutations in the Germline

-​ Mutation that happens during the germline production (egg and sperm cell)
 -​ Offspring may inherit the mutation from an unaffected parent
-​ Example of this
-​ Autism

Somatic Cell Mutations In Development

-​ Mutations that occur in somatic cells relatively early in an individual's life can affect the
development of specific tissues and organs

Somatic Cell Mutations Later in Life

-​ Mutations that occur in somatic cells later in life don't typically affect the individual, but can
lead to cancer

Causes for Mutations

Frameshift
-​ mutation is a genetic error caused by the insertion or deletion of nucleotides in a DNA
sequence in numbers that are not multiples of three.
Insertion
-​ During an insertion mutation, the replicating strand "slips" or forms a wrinkle, which causes
the extra nucleotide to be incorporated
Deletion
-​ In a deletion mutation, a wrinkle forms on the DNA template strand, which causes a
nucleotide to be omitted from the replicated strand.
Mutagens
-​ These are chemicals or other agents in the environment that can cause the structure of DNA to
change and thus mutations to occur
-​ Examples of these include UV radiation, nuclear radiation, and certain chemicals (known as
carcinogens - such as those present in cigarette smoke).

Outcome of Mutations
Disease Resistance/ Cystic Fibrosis
Cystic fibrosis (CF) is a genetic disorder that causes the body to produce thick, sticky mucus, which
can block the lungs, pancreas, and other organs, leading to breathing problems, digestive issues, and
infections. The affected protein is the CFTR that helps maintain chloride ions across cell membranes.
In the lung and intestine, CFTR affects the fluidity of airway mucus and digestive juices. CFTR also
helps immune cells attach to and ingests certain types of bacteria
Variations in the CFTR gene change the amino acid sequence. The protein can't fold properly, and it's
broken down by the cell.
Toxins from bacteria over-activate CFTR channels, causing salt imbalance and water loss through
diarrhea. Because people with disease resistance make half the normal amount of CFTR protein, they
are less susceptible to dehydration.
People with cystic fibrosis (CF) have no CFTR protein. Salt transport doesn't happen properly, and the
fluid around cells thickens, clogging the lungs and other organs
D2.1 Cell and nuclear division

Mitosis
Haploid: 23 chromosomes
Diploid: 46 chromosomes=somatic cell
Mitosis is a fundamental biological process involving the division of a cell’s nucleus, resulting in the
equal distribution of replicated DNA into two daughter cells. This process ensures genetic consistency
across cell generations by organizing DNA into chromosomes and precisely segregating identical
copies during cell division. This is nuclear division
DNA is stored in chromosomes that are wrapped around the nucleusome. Replicating DNA means to
copy a chromosome. It turns one chromosome into two sister chromatids. These two sisters are
identical. In mitosis you separate the chromatin, so that each cell ends up with one pair of the
chromosomes. The single one is the chromosome and when they are replicated they turn into sister
chromatids. The chromatids have a centromere which are together. Interphase is the normal cell before
anything else happens
Prophrase:
-​ Nuclear membrane and nucleolus begin to break down.
-​ DNA condenses to form visible chromosomes.
-​ Spindle fibers attach to kinetochores on chromosomes.
Metaphase:
-​ Chromosomes are aligned at the cell’s equatorial plane, known as the metaphase plate.
-​ Spindle microtubules ensure chromosomes are properly positioned for separation.
Anaphase:
-​ Spindle Fibres shorten, pulling sister chromatids apart to opposite poles of the cell.
-​ Instead of being sister chromatids they turn back into chromosomes
-​ Unattached spindle fibers elongate, stretching the cell.
Telophase:
-​ Reach the opposite poles
-​ Chromatids, now individual chromosomes, reach the poles.
-​ Nuclear membranes begin to reform.
-​ Nucleoli reappear.
-​ Chromosomes relax and DNA unwinds.
-​ Cytokinesis happens just after telophase where the cells separate into two daughter cells

Mitosis is slightly different in plants than animals due to them having a cell wall the cytokinesis step
is harder to undergo. They have stiff cell walls. Rather than spider fibers
Meiosis
The purpose of meiosis is to produce genetically unique haploid gametes. This is a necessary process
as part of a sexual life cycle as haploid gametes fuse during fertilisation. It produces haploid cells
more specifically gametes. The steps are called the same but have a slight difference. But instead of
having one division in mitosis, meiosis has two divisions, so PMATx2. At the end of the two divisions
you have four haploid cells
Meiosis reduces the chromosome number by half, producing haploid cells from an original diploid
cell. It consists of two successive divisions: Meiosis I and Meiosis II, each with four distinct phases
Homologous chromosomes are pairs of chromosomes in a diploid organism that are similar in size,
shape, and gene arrangement, with one inherited from each parent
A homologous pair contains one chromosome that is maternal (from the mother) and one paternal
form the father. After meiosis it becomes diploid containing two haploids. During meiosis I the
homologous separates so the gametes only have 23 chromosome therefore becoming gametes
Meiosis I: Reduction Division and Genetic Recombination
Before meiosis: Interphase
-​ DNA is copied.
-​ Each chromosome becomes two sister chromatids joined together.
-​ The cell is still diploid (2n).
Prophase I:
-​ Chromatin condenses into X-shaped chromosomes consisting of identical sister chromatids
-​ Each chromosome pairs up with the one from the other parent (same type).
-​ Non-sister chromatids exchange segments of DNA- called crossing over where you mix the
alleles (creating genetic variation.
-​ Nuclear membrane breaks down.
-​ Spindle fibres form.
Metaphase I:
-​ Homologous chromosome pairs align at the cell equator.
-​ They line up randomly The pairs are in a ‘random orientation’ creating variation
-​ Each chromosome attaches to spindle fibers from opposite poles.
Anaphase I:
-​ Spindle fibers pull homologous chromosomes apart to opposite poles.
-​ Sister chromatids remain attached.
-​ Transporting half of the chromosomes to one end and the other to the other
-​ ‘Reduction division’
Telophase I:
-​ Chromosomes reach poles, still composed of sister chromatids.
-​ Nuclear membrane reforms; spindle fibers disappear.
-​ Cytokinesis divides the cell into two haploid cells, each with paired sister chromatids.
-​ Sister chromatids are no longer identical due to crossing over.

Meiosis II – like mitosis, but with haploid cells

-​ There is no DNA copying again.

Why are the gametes all different?

Crossing over (in Prophase I)
-​ Paired chromosomes swap pieces → new combinations of alleles.
Random way the chromosomes line up (in Metaphase I and II)
-​ Different mixes of chromosomes go into each gamete.
Random fertilisation
-​ Any sperm can meet any egg.

Non disjunction is the failure of chromosomes to separate. It leads to the changes in chromosome
number and occurs in anaphase I or II. This error results in daughter cells with an abnormal number of
chromosomes. Non disjunction is an example of a reason for down syndrome.

D2.3 Movement of Water

Water as a Solvent
-​ Water’s polarity enables it to dissolve solutes effectively:
-​ Ionic compounds (e.g., salt): Water molecules form hydration shells around ions, with
partially positive hydrogens surrounding negative ions and partially negative oxygens
surrounding positive ions, preventing ions from recombining.
-​ Polar molecules (e.g., glucose): Water forms hydrogen bonds with polar groups,
facilitating dissolution.

Osmosis
Defined as the passive movement of water across a semi-permeable membrane toward areas of higher
solute concentration (water follows solute).
-​ Occurs when solutes cannot cross the membrane, leading to water movement to equalize
solute concentrations on both sides.
-​ Osmosis is passive and requires no cellular energy.

Water Movement in Different Solutions:

-​ Hypotonic solution: Water enters the cell (can cause swelling or bursting in animal cells).
-​ Isotonic solution: Water movement is balanced with no net change.
-​ Hypertonic solution: Water exits the cell, causing shrinkage or shriveling.
Membrane Permeability and Aquaporins
-​ Water can pass through the phospholipid bilayer but does so more efficiently through
aquaporins, specialized channel proteins.
 -​ Cells regulate osmosis by altering solute concentrations or the number of aquaporins
embedded in their membranes.

By placing plant tissue (e.g., carrot cells) in solutions of varying solute concentrations, the percentage
change in mass reveals whether the tissue is in a hypo-, iso-, or hypertonic solution:
-​ Gain in mass indicates a hypotonic environment.
-​ Loss in mass indicates a hypertonic environment.
-​ No mass change indicates isotonic conditions, which corresponds to the tissue’s osmolarity.
Controlled variables in such experiments include:
-​ Consistent tissue source and size
-​ Temperature control
-​ Equal exposure times

Animal VS. Plant cells response to osmotic pressure

Aspects Plant Cells Animal Cells

Cell Wall Present provides rigidity and Absent, more prone to bursting
prevents bursting and shrinking

Response to hypotonic Become turgid (swollen but May burst due to excess water
intact) due to cell wall intake
pressure, this is the best
climate for plant cells

Response to isotonic Cells become flaccid (wilting No net water movement, cell
appearance) maintain shape. This is the best
climate for animal cells

Response to hypertonic Undergo ‘plasmolysis’ Shrivel and shrinks

(membrane shrinks from wall)
leads to death of the cell

-​ Plant cell walls create turgor pressure, critical for structural support and upright growth.

Some freshwater unicellular organisms (e.g., Paramecium) use contractile vacuoles to expel excess
water in hypotonic environments, an energy-dependent homeostatic adaptation.
Paramecium is a single-celled eukaryote that regulates water balance via an organelle known as a
contractile vacuole.
The regulation of water balance is known as Osmoregulation and is a key function of Homeostasis.

Practical Applications
Medical relevance of isotonic solutions:
-​ IV saline solutions are isotonic to human cells, preventing cell damage from osmotic
imbalance during rehydration.
-​ Organs for transplantation are bathed in isotonic solutions to maintain cellular integrity.
Water Potential

Ψ = Ψs + Ψp

Water potential describes the energy required to remove water from a cell.
The water potential of pure water is zero. Dissolved salt or other solutes will bind with water
molecules and it will therefore take more energy to remove this water. Thus all cells will have a water
potential of less than zero.

Water always moves from an area of higher water potential ( more hypotonic) to an area of lower
water potential (more hypertonic).
Water potential is denoted by the Greek letter ψ (psi - think Poseidon, god of water) and the units are
usually megapascals (MPa)
Water potential of pure water is 0, as soon as you add solute to the water you lower the solute
potential

Solute Potential Ψs Pressure Potential - Ψp

Solute potential describes the contribution of Pressure Potential describes the effect of
dissolved solute to water potential. The more changes in hydrostatic pressure on water
solutes present, the lower the water potential potential.
will be. The higher the pressure, the more potential
energy water has.

Solute potential
When salt is put into water, the water breaks up the ionic bond making the chloride and sodium
separate. Water then attaches around the elements, the chloride gets the hydrogen side attached (being
protective so attracting) and vice versa for the sodium. When this happens the water separates and
makes spaces within the water/ionic bonds, therefore lowering the water potential.

Pressure Potential
The more water goes into a cell the more positive the pressure gets. In the roots there is a high water
potential due to the solute concentration, and the further it goes up the more negative it is. But
specifically in the roots the higher up the root the higher the pressure potential. Due to transpiration
there is a low water potential at the leaves, therefore the water moves up the plant through adhesion
and cohesion, being attracted to the low water potential.