LECTURE 1 - MITOSIS

● Cell division is the process by which cells divide and replicate to make more cells
○ Cell division occurs for reproduction, healing, cell replacement and growth
● In eukaryotes, the cell cycle consists of 4 processes: G1 Phase [which also includes G0
Phase when the cell exits the cell cycle and no longer replicates], S Phase, G2 Phase and
Mitosis
○ G1 Phase is the first gap between a previous mitotic process and DNA synthesis.
Content such as the mitochondria and ribosomes within the cytoplasm increase
○ S Phase is DNA synthesis. All 23 pairs of chromosomes are duplicated in
preparation for replication and division
○ G2 Phase is the second gap between the S Phase and the next mitotic process. The
cell prepares for mitosis to begin
○ Mitosis is the process in which the replicated chromosomes separate into daughter
cells and cytokinesis occurs
○ Interphase​ describes the total time between one mitotic process and the next
[G1 + S + G2]
○ Cells in the G0 Phase are referred to as quiescent
● Mitosis consists of 6 stages: Prophase, prometaphase, metaphase, anaphase, telophase,
and cytokinesis
○ Prophase is the first stage of mitosis. During prophase, the chromatin fibers within
the nuclear envelope condense to form chromosomes. Centrosomes migrate to
opposite poles and radiate microtubules
○ Prometaphase is the second stage of mitosis. During prometaphase, the nuclear
envelope begins to dissolve to release chromosomes and allow them to move
about the cell freely. Microtubules of the mitotic spindle attach to the
chromosomes by connecting to their centromeres. Sister chromatids are attached
at the center via a kinetochore
○ Metaphase is the third stage of mitosis. During metaphase, the chromosomes align
along the center plane of the cell
○ Anaphase is the fourth stage of mitosis. During anaphase, sister chromatids are
pulled apart toward opposite poles to prepare for cytokinesis and the separation
into two daughter cells
○ Telophase is the fifth stage of mitosis. During telophase, chromosomes
decondense back into chromatin fibers and the nuclear envelope redevelops
○ Cytokinesis is the last stage of mitosis. During cytokinesis [in animal cells], a
contractile ring forms between the two new forming cells and fully separates them
into genetically identical daughter cells
● Ploidy levels are the number of sets of chromosomes a cell has. A cell with one complete
set of chromosomes is called a haploid. A cell with two complete sets of chromosomes is
 called a diploid. For example, a gamete [or sex cell] is a haploid. This is because two
gametes fuse together to create a zygote with two complete sets of chromosomes - one
from the mother and one from the father. On the other hand, stem cells are diploids. In
mitosis, chromosomes are duplicated in order to have the genetic material to create two
identical daughter cells

LECTURE 2 - MEIOSIS

● Meiosis is the process by which gametes [reproductive cells] are produced. Meiosis gives
rise to haploid cells, ready to be fused with another haploid cell to give rise to a diploid
zygote with two full sets of homologous chromosomes
● Important things to remember about meiosis are:
○ There is only 1 interphase, much like mitosis
○ Meiosis consists of two different separation events. In the first separation event
[anaphase I], the homologous chromosomes are randomly assorted and separated.
In the second separation event [anaphase II], sister chromatids are separated,
similar to mitosis. This results in the creation of 4 genetically unique daughter
cells
○ As a result of two different separation events, all 4 daughter cells will be haploids

● Major differences between mitosis and meiosis [in human cells]:

○ In mitosis, all 46 chromosomes line up along the centre plane of the cell in
metaphase. In meiosis, 23 pairs of homologous chromosomes line up along the
centre plane of the cell in metaphase I
○ In mitosis, sister chromatids are pulled apart. In meiosis, parent chromosomes are
pulled apart, then sister chromatids are pulled apart
○ In mitosis, no crossing over occurs. In meiosis, recombination occurs between
homologous chromosomes
 ○ In mitosis, mitotic spindles attached to kinetochores are oriented opposite of each
other on both sister chromatids. In meiosis, mitotic spindles are attached to
mono-oriented kinetochores on the sister chromatids
● Meiosis I consists of the separation of homologous chromosomes. Meiosis II consists of
the separation of sister chromatids, much like in mitosis. The difference between mitosis
and meiosis II is that meiosis II produces 4 genetically unique daughter cells that are
haploids, while mitosis produces 2 genetically identical daughter cells that are diploid
● Meiosis I consists of 6 stages: prophase I, prometaphase I, metaphase I, anaphase I,
telophase I, and cytokinesis
○ Prophase I is the first stage of meiosis I. During prophase I, chromosomes become
visible as thin threads - DNA replication has already been completed in the S
Phase of the cell cycle. Homologous chromosomes condense and undergo
synapsis [gene-for-gene pairing]. When synapsis is complete, each pair of
chromosomes creates a bivalent structure. Each chromosome consists of two
sister chromatids. As the chromosomes thicken, the chiasma between homologous
chromosomes becomes apparent

○ Crossing over is the event in which genes are exchanged between homologous
chromosomes at their chiasmas. This results in recombinant chromatids that are
genetically unique from their parent cell
○ Prometaphase I is the second stage of meiosis I. During prometaphase I, spindle
fibers attach to the kinetochores of each chromosome. It is important to note that
in mitosis, the two spindle fibers connect to a single chromosome opposite to each
other in order to pull sister chromatids apart, while in meiosis I, one spindle fiber
connects to each chromosome in order to pull the homologous chromosomes apart
○ Metaphase I is the third stage of meiosis I. During metaphase I, homologous
chromosome pairs line up along the centre plane of the cell to prepare for
anaphase I. The bivalents orient themselves randomly with respect to each other
 ○ Anaphase I is the fourth stage of meiosis I. During anaphase I, homologous
chromosomes are pulled to opposite poles of the cell. That is, the bivalent
structure is pulled apart into two separate chromosomes with each containing a
recombinant variant of a gene. Sister chromatids ​do not s​ eparate in anaphase I
○ Telophase I and cytokinesis are the fifth and sixth stages of meiosis I. The two
daughter cells, which each contain genetically diverse information form
recombination and random assortment, prepare for meiosis II
● Meiosis II consists of 6 stages: prophase II, prometaphase II, metaphase II, anaphase II,
telophase II, and cytokinesis. Meiosis II and mitosis follow closely the same process
○ In prophase II, the nuclear envelope breaks down and the chromosomes condense
○ In prometaphase II, spindle fibers attach to the kinetochores of each chromosome.
It is important to note that in meiosis II, two spindle fibers attach to each of the
chromosomes on opposite sides to prepare for the separation into sister
chromatids
○ In metaphase II, chromosomes line up along the centre plane of the cell
○ In anaphase II, sister chromatids are pulled apart to opposite poles of the cell.
Note that the sister chromatids are genetically diverse as a result from crossing
over
○ In telophase II and cytokinesis, the nuclear envelope redevelops and the two
daughter cells separate into 4 genetically unique haploid cells
● In males, all 4 genetically unique haploid gametes become sperm cells. However, in
females only 1 of the daughter cells becomes an oocyte while the other 3 become polar
bodies

LECTURE 3 - THE CELL CYCLE

● Cell division cannot occur constantly because uncontrolled division is dangerous and can
lead to cancer
● Progression through the cell cycle is controlled by proteins that appear and disappear in a
cyclical fashion, and by several enzymes that become active and inactive by the presence
or lack of these proteins in cycles. Proteins that appear and disappear cyclically are called
cyclins
● Enzymes called kinases are present throughout the cell cycle. The function of kinase can
be controlled by turning them on or off [presence or absence], activation or deactivation
by phosphorylation or other modifications, its period of function determined by its
half-life and stability as a protein, and co-regulators that bind to the kinases
● The green bars indicate the duration in which proteins that activate the kinases are active.
Each phase has a co-regulator that helps transition between them
● Kinase enzymes are always activated, while the proteins that bind to them will be on for
short periods of time in order to regulate the cell cycle [these co-regulators have a short
half-life]
● Kinase enzymes activate proteins through phosphorylation, which allows the cell cycle to
transition from phase to phase. Therefore, the regulation of the cell cycle is dependent on
the cyclin protein, the cyclin-dependent-kinase enzyme [CDK], and the target protein.
Cyclin-CDK complexes phosphorylate target proteins that promote cell division
● Types of cyclin-CDK complexes involved in the cell cycle are:
○ M-Cyclin-CDK complex helps prepare the cell for mitosis
○ S-Cyclin-CDK complex helps initiate DNA synthesis
○ G1/S-Cyclin-CDK complex prepares the cell for DNA replication
● Cells have many cell-cycle checkpoints, where they can pause the progression if
something is not right. These checkpoints include:
○ DNA replication checkpoint - checks for the presence of unreplicated DNA at the
end of the G2 phase before the cell enters mitosis
○ DNA damage checkpoint - checks for damaged DNA before the cell enters the S
phase and replicated the damaged genetic material
○ Spindle assembly checkpoint - checks for all chromosomes being attached to a
spindle before the cell progresses with mitosis
● What happens through the DNA damage checkpoint?
○ Genes that inhibit the cell cycle are off when the cycle functions normally.
However, when something wrong is detected at the checkpoint, the protein p53
phosphorylates from the activated kinase enzymes. Phosphorylated p53 proteins
act as a transcription factor that turns on genes that inhibit the cell cycle, giving
the cell time to repair the damaged DNA
 ○ Activated p53 proteins target CDK inhibitors, which bind to the active site of
CDK enzymes and prevent the cyclin from activating them
● Oncogenes are cancer-causing genes. Proto-oncogenes are normal genes that have the
potential to become cancer-causing genes through mutation
● Tumour suppressors are genes that will encode proteins whose normal activities will
inhibit cell division. For example, p53 is a tumour suppressor because its normal function
is to inhibit cell division when DNA is damaged

LECTURE 4 - MENDELIAN GENETICS AND PROBABILITY

● Summary of important genetic terms:

○ Gene: an inherited factor encoded in DNA that helps determine a characteristic
○ Allele: one of two or more alternative forms of a gene
○ Locus: a specific place on a chromosome occupied by an allele
○ Genotype: a set of alleles possessed by an individual organism
○ Phenotype: the appearance or manifestation of a characteristic
○ Heterozygote: an individual organism possessing two different alleles at a locus
○ Homozygote: an individual organism possessing two of the same allele at a locus
● The order of generations is: P Generation [parental generation], F1 Generation [first filial
generation], and F2 Generation [second filial generation]
● Mendel’s first law of segregation states that each individual organism possesses two
alleles encoding a trait. In Anaphase I, alleles segregate when gametes are formed and
always segregate in equal proportions
● Mendel’s second law of independent assortment states that alleles at different loci
separate independently
● Rules of probability when calculating the progeny in cross breeding:
○ Multiplicative rule: uses the operative word “and” describing the odds of two
individual events happening in succession or simultaneously in relation to one
another. For example, the multiplicative rule would be applied if the question was
what is the probability that a dice is rolled and you get a four on the first​ ​and
second roll?
○ Additive rule: uses the operative word “or” describing the odds of two individual
events happening that do not overlap. For example, the additive rule would be
applied if the question was ​what is the probability that a dice is rolled and you get
either a 1 ​or a​ 6 on the first roll?
LECTURE 5 & 6- BINOMIAL EQUATION AND DIHYBRID CROSSES

● The possible outcomes of a child being affected in a group of children from the same
parents can be described using the binomial factorial equation:
[n! ÷ x!y!]px q y , where n is the total number of children, x if the number of unaffected
cases, y is the number of affected cases, and p and q are the probabilities of occurrence (p
+ q = 1)

LECTURE 7 - PEDIGREES AND SEX CHROMOSOMES

● Pedigrees trace a specific manifested trait and the people they affect in a family tree
● Autosomal recessive traits appear equally in males and females and tend to skip
generations. Autosomal recessive traits are more likely to appear in progeny of related
parents, and affected offspring are usually born to unaffected parents. When both parents
are heterozygous for the trait, approximately one fourth of the offspring will be affected
● Autosomal dominant traits appear equally in males and females and don’t skip
generations. Affected people have at least 1 affected parent unless they possess a new
mutation and unaffected people will not pass on the trait to their offspring in the next
generation. When one parent is unaffected and the other is heterozygous [affected],
approximately one half of the offspring will be affected
● X-Linked recessive traits are more likely to appear in males than in females. Affected
sons are usually born to unaffected mothers, thus the trait tends to skip generations.
Approximately half of the carrier mother’s sons are affected [the mother has a 50%
chance to pass on either the dominant X-linked trait or the recessive trait]. The trait is
never passed from father to son [fathers must pass on their Y gene to sons] and all
daughters of affected fathers are carriers

LECTURE 8 - DNA STRUCTURE

● DNA consists of three different components: a sugar, a phosphate group, and a base
○ Sugar in DNA exists either as deoxyribose [​DNA]​ or ribose [​RNA]​ . Ribose sugars
have an OH group attached to the 2’-carbon in its chain, while deoxyribose have
an H attached to the 2’-carbon in its chain
○ Bases are divided into two classes: purines [double ring structure] and
pyrimidines [single ring structure]. The purine bases are adenine and guanine, the
pyrimidine bases are cytosine, thymine, and uracil
○ Phosphate groups consist of a phosphate double bonded to an oxygen and three
other oxygens used for binding to other elements. DNA can contain either
 monophosphate bonds [one phosphate bonded to a sugar], diphosphate bonds,
and/or triphosphate bonds.

● DNA forms a double stranded helix due to the bonding between complementary bases.
○ Adenine and thymine bond with a double hydrogen bond, while guanine and
cytosine bond with a triple hydrogen bond. Adenine will only bond with thymine
and guanine will only bond with cytosine
○ Because G-C bonds contain 3 hydrogen bonds while A-T bonds only contain 2,
G-C rich DNA tends to be much stronger and A-T rich DNA
● DNA strands run antiparallel to each other
● RNA forms a single stranded helix much smaller than that of DNA due to RNA being a
transcriptor for a specific gene. Additionally, RNA consists of triphosphate bonds rather
than monophosphate bonds and thymine is replaced with uracil that bonds with adenine
● One full turn of a DNA helix is about 3.4nm in length, approximately 10 base-pairs long.
The space between two base-pairs is approximately 0.34nm in length. The width of the
strand of DNA is approximately 2nm wide
● The amount of DNA in a haploid chromosome is about 3.1 billion base-pairs, and 6.2
billion in diploid chromosomes
○ Therefore, the total distance of DNA in a single haploid cell is approximately 2m,
and 4m in a diploid cell
● DNA wraps around nucleosomes and histone proteins that form 10nm structures in
diameter. Histones then wrap around each other to form 30nm diameter chromatin fibers.
Condensed chromatids preparing for mitosis or meiosis are about 1400nm in diameter
LECTURE 9 - DNA MUTATIONS

● Mutations are inherited alterations in the DNA sequence. They are responsible for all
genetic variation and diversity, the backbone of evolution. However, they may also cause
great suffering in the forms of disease and death
● Types of genetic mutations include: base substitutions, insertions and deletions,
expanding nucleotide repeats
○ Base substitutions are a type of mutation where a nucleotide base in a strand of
DNA is substituted with another base. There are two types of substitutions:
transversion and transitions. ​Transversion [​ non-like] is the conversion of a purine
to a pyrimidine or a pyrimidine to a purine. ​Transition​ [like to like] is the
conversion of a purine to another purine or a pyrimidine to another pyrimidine

○ Expanding nucleotide repeats are a type of mutation where the range of codon
repeats in a strand of DNA are significantly increased. This happens when
polymerase slippage causes a “hairpin” to occur in the replicating DNA. There
are enough G-C hydrogen bonds to keep the hairpin from repairing itself, and thus
extra DNA is synthesized to make up for the lack in the original strand

○ Insertions and deletions (called ​indels)​ are a type of mutation where a base
nucleotide in a codon is deleted or an extra is inserted during the process of
 replication. This causes a frameshift, in which the spot where the nucleotide was
inserted or deleted must be replaced with the next nearest base or shifted over to
make room for the insertion
● Phenotypic effects of mutations include: forward mutation, reverse mutation, missense
mutation, nonsense mutation, silent mutation, and neutral mutation
○ Forward mutation is the phenotypic effect where the wild type variant becomes a
mutant type
○ Reverse mutation is the phenotypic effect where the mutant type variant becomes
the wild type
○ Missense mutation is the phenotypic effect where a coded amino acid becomes a
different amino acid. It will still be functional, thus a missense mutation can also
be a neutral mutation
○ Nonsense mutation is the phenotypic effect where a sense codon becomes a
nonsense codon through the introduction of an early stop codon. The protein is
therefore much shorter than it should be, and is nonfunctional
○ Silent mutation is the phenotypic effect where a mutated codon is synonymous
with an already existing, functional codon
○ Neutral mutation is the phenotypic effect where there is a change in the amino
acid but there is no change in its normal function

● Suppressor mutations are mutations that occur that suppress an original mutation that
would have changed the phenotype of the organism. That is, the suppressor mutation
masks the mutation that would cause a change in the phenotype from the wild type to
mutant
○ Suppressor mutations occur at a site different than that of the mutation it
suppresses. It results in the individual having both the original mutation and the
suppressor mutation, but the phenotype of that it would have had without the
original mutation
● Loss of function mutations cause a partial or complete loss of function. Gain of function
mutations cause the appearance of a new trait, or causes the appearance of a trait at an
inappropriate tissue or time
● Mutations are caused by a number of different factors:
 ○ Spontaneous replication errors that result in unequal crossing over - if
homologous chromosomes misalign while crossing over, one crossover product
contains an insertion and the other has a deletion
○ Chemically induced mutations - examples of chemicals that induce mutations are
alkylating agents [donate an alkyl group], nitrous acid [cause deamination], and
hydroxylamine [add a hydroxyl group]
○ Radiation greatly increases mutation rates in all organisms
○ Spontaneous chemical changes that result in deamination

LECTURE 10 - ALLELE VARIATION

● Genes may (and usually) have more than 2 allele variants encoding a trait. Different
alleles may affect the phenotype in different ways. A single gene may control several
traits, while multiple genes may control a single trait
● The most common allele is called the wild type because it is usually the most abundant in
nature.
○ The wild type allele is designated by a superscript +
○ Other variants of the allele are considered mutants
○ Any allele found at appreciable frequencies among a population (at least 1%) is
considered to be a polymorphism
● Different mutations in a gene can cause the same disorder. Different mutations in a gene
can cause different phenotypes
● What makes an allele dominant over recessive?
○ The allele is dominant when the one good copy of a gene is sufficient to make the
protein required for the biological process to occur. Recessive mutations almost
always involve a mutation in a gene that results in at least some loss of protein
function
● Mutations can be of different types:
○ Complete loss of function (null allele)
○ Partial loss of function (hypomorphic allele)
● Additional factors at a single locus can affect the results of genetic crosses. There are
different types of dominance that will affect the phenotype of the progeny
○ Complete dominance - the heterozygous dominant has the same phenotype as the
homozygous dominant
○ Incomplete dominance - the heterozygous phenotype can be differentiated from
those of the two homozygotes and falls between them. Thus, the dominance is
incomplete. The phenotypic ratio for incomplete dominance is 1:2:1, different
from the classic dominance 3:1
 ○ Codominance - the heterozygous phenotype will exhibit both the phenotype of
both homozygotes simultaneously
● Penetrance is the percent of individuals having a particular genotype that expresses the
expected phenotype [​complete = 100%, incomplete = <100%​]. Similarly, expressivity is
the degree to which a character is expressed

LECTURE 11 - TRANSCRIPTION

● Lethal alleles cause premature death early in development, and so some genotypes may
not appear in the progeny. This affects the progeny ratio

● Temperature sensitive alleles are alleles whose product is only functional only at a certain
temperature
● The central dogma of molecular biology is described as the transcription from DNA to
RNA and the translation from RNA to protein. There are several types of RNA with
different functions, which include:
○ Ribosomal RNA [​rRNA​] - found in the cytoplasm of eukaryotic and prokaryotic
cells that are the structural and functional components of the ribosome
○ Messenger RNA [​mRNA​] - found in the nucleus and cytoplasm of eukaryotic and
prokaryotic cells that carries the genetic code for proteins
○ Transfer RNA [​tRNA​] - found in the cytoplasm of eukaryotic and prokaryotic
cells that help incorporate amino acids into polypeptide chains
● The synthesis of RNA consists of a template strand that exists in the DNA. The template
strand is transcribed by polymerase and follows a transcription unit: a promoter,
RNA-coding sequence, and a terminator
● Only one of the DNA strands will be the template for RNA
 ○ The template strand is in the 3’ → 5’ orientation and RNA is synthesized in the 5’
→ 3’ direction. The RNA strand will be complementary to the template DNA
strand and uracil is substituted for thymine
○ The template strand is read (or transcribed) by polymerase
● Not all genes are turned on at the same time. The initiation of a transcription for a
particular gene is activated by promoter regions. Transcription factors recruit the
polymerase to initiate transcription
○ RNA polymerase II is the enzyme responsible for generating the majority of RNA
for making proteins

LECTURE 12 - TRANSLATION

● To translate the RNA transcript we need:

○ A sequence for the ribosome to initiate translation
○ A genetic code that will specify which amino acid will be incorporated
○ A termination sequence so the ribosome knows when to stop
● Translation begins at AUG (a start codon) and terminates at UAA UAG or UGA
● Properties of the genetic code
○ There is no space between codons, they are adjacent
○ The genetic code is non-overlapping, each nucleotide is part of one codon
○ The genetic code is degenerate, most amino acids are specified by more than one
codon
○ The genetic code is ordered, amino acids with similar properties are specified by
related codons
○ The genetic code is nearly universal, with minor exceptions, each triplet/codon
has the same meaning in all organisms
● Methionine is the only codon that is not degenerate, that is, it can only be produced with
the codon AUG. All proteins start with methionine, it is the start codon for the production
of protein
● The process of creating a polypeptide chain is a repeating event where charged transfers
attached to an amino acid are bound to a ribosome unit. The amino acid bonds with the
existing chain and the uncharged transfer on the opposite end is released. The transfers
move one spot over to allow room for another charged transfer to bond
LECTURE 13 - CELL BASICS - FINAL EXAM

● What does it take to make a cell?

○ Information - to create a cell, there must be DNA to code the genetic information
in order to build the primary machinery of the cell and for the cell to pass on the
information to its progeny. The information must be dynamic, that is, the
information can be drawn on and changed. DNA is not static information that
cannot be altered
○ Chemistry - chemicals that come together to form the structure of the cell and are
important for managing the energy of the cell. Chemistry in the general sense is
matter and energy together forming life
○ Compartment - the cell must be a vessel in which these chemical reactions occur
and DNA is contained. Usually defined by a lipid membrane layer. Fundamental
roles of compartments include: establishing physical boundaries that enable the
cell to carry out different metabolic activities, generating micro-environments that
spatially and temporally regulate biological processes, and having selective
permeability. This allows for homeostasis to occur [controlled, regulated, and in
balance]
● Spontaneous generation is a biological theory stating that cells are formed spontaneously
through the combination of chemicals and energy
● The cell theory describes the function and purpose of all cells
○ 1 - The cell is the structural unit of life. That is, the smallest component of all
living beings is a cell
○ 2 - All living organisms are composed of one or more cell types
○ 3 - Cells can only arise through the division of a pre-existing cell [mitosis,
meiosis]
● Basic properties of cells
○ 1 - Cells are highly complex and organized
○ 2 - Activity is controlled by a genetic program; built on DNA
○ 3 - Can reproduce; can make copies of themselves
○ 4 - Can assimilate and utilize energy in a certain way to construct a cell
○ 5 - Can carry out chemical reactions; enzymes
○ 6 - Engage in mechanical activities
○ 7 - Can respond to stimuli
○ 8 - Capable of self-regulation
○ 9 - Cells evolve over the course of time
● The difference between prokaryotic cells and eukaryotic cells is an important distinction
among groups of organisms
○ Prokaryotes were the only form of life on Earth for millions of years until more
complex eukaryotic cells came into being through evolution
 ● Similarities between prokaryotic and eukaryotic cells
○ Both have a plasma membrane that creates a compartment for chemical reactions
to occur. Both cells have cytoplasm and must be able to build proteins

LECTURE 14 - CELL DIVERSITY, VIRUSES, AND MEMBRANES

● Viruses are not cells. They are macromolecular packages that can function and reproduce
only within other living cells. Outside of living cells they exist as virions, or inanimate
particles
○ A virion is made out of a small amount of DNA and RNA. The protein capsule is
called a capsid
○ Viruses are very small and diverse. They can infect plants, animals, and bacteria
● Viruses bind to cell surfaces via specific proteins and then enter the cell. The host range
is determined by how the virus interacts with cells
○ A narrow host range describes viruses that only infect particular organisms in
order to reproduce and in those organisms, only certain types of cells can be
infected
○ A wide host range describes viruses that interact with many different types of
cells and organisms
● Once a virus has entered a cell it hijacks the cellular mechanisms to synthesize nucleic
acids and proteins to assemble new virus particles. The two main types of viral infections
are:
○ Lytic: in which the production of virus particles ruptures and kills the cell (ex.
influenza)
○ Non-lytic / integrative / lysogenic: in which viral DNA is inserted into the host’s
genome [​provirus​]. That is, when the host cell divides, the virus is also divided in
the process. This results in a cell that can survive, but often with impaired
function (ex. HIV)
● The virus life cycle consists of the penetration into a host cell, the uncoating of the
protein capsule to release its genome, hijacking the apparatus for creating regular DNA
and RNA, resulting finally either in a lytic cell ready to rupture and release more copies
of the virus, or a lysogenic cell that reproduces to create more cells containing the virus
● Enveloped viruses are viruses which have protein membranes encapsulating them. These
protein membranes come from replicated virus genomes escaping their host cell and
pushing out of the membrane

● Functions of biological membranes:

○ Plasma membranes form cell boundaries and define/enclose compartments for
metabolic processes to occur within the cell
○ Control the movement of material into or out of the cell
 ○ Allow response to external stimuli and enable interactions between cells
○ Provide scaffold for biochemical activities including energy transduction

LECTURE 15 - MEMBRANE DYNAMICS (FLUID MOSAIC MODEL)

● The cell membrane is made up of a trilaminar structure, which is made up of

phospholipid bilayers embedded with proteins
● The fluid mosaic model is a term that describes a map of various phospholipids and a
wide assortment of proteins. ​Fluid ​means that each individual lipid molecule moves
about the membrane freely, and ​mosaic​ describes the diverse particles that penetrate the
lipid layer. The model includes:
○ Bilayer of amphipathic [​having both hydrophobic non-polar and hydrophilic
polar regions]​ lipids
○ Proteins - integral transmembrane, peripheral, lipid-anchored
● Biological membranes are dynamic. Lipids move easily, laterally, within the leaflet [​one
layer in the bilayer​]. Lipid movement to other leaflets is slow
○ Membrane proteins diffuse within the bilayer - the movement of proteins is
restricted spatially and thus long range diffusion is slow. Biochemical
modification can alter protein mobility in the membrane (important for signal
transduction)
● The phospholipid matrix is composed of a hydrated lipid bilayer that contains
amphipathic molecules. That is, the molecule has polar regions [​phosphate head that is
hydrophilic​] and nonpolar regions [​hydrocarbon tails that are hydrophobic]​
○ One hydrocarbon tail will be saturated [​all carbons are occupied by a hydrogen​],
and the other will be unsaturated [​there is a double bond between carbons]​
● Differential membrane structures
○ Mitochondria - the inner membrane contains a very high concentration of protein.
This is because the inner membrane carries out biochemical functions such as
electron transport chains which require large amount of protein to complete
○ Neuron - the myelin sheath contains very low amounts of protein. The myelin
sheath consists of layers of plasma membrane , forming insulation around the
nerve axon
● There are three classes of membrane proteins: integral, peripheral, and lipid-anchored
○ Integral proteins (or transmembrane proteins) have various functions which
include transport, cell-cell communication, and attachment
● Biological membranes are asymmetrical - two leaflets have a distinct lipid composition
○ Generally, the outer leaflet contains glycolipids and glycoproteins [​lipids and
proteins with carbohydrates attached]​
 ● Fluidity is an important feature of biological membranes. Fluidity can be altered in a
number of ways:
○ Raising the temperature increases fluidity. The extreme case of fluids in high
temperature is liquid crystals. Lowering the temperature decreases fluidity. The
extreme case of fluids in low temperature is crystalline gel
○ Membrane fluidity is determined by the nature of the lipids in the membrane.
Unsaturated fats increase fluidity, and saturated fats decrease fluidity
● Membrane fluidity is crucial to cell function and must be maintained. In response to
changes in temperature, lipid composition of membranes can be changed by either the
desaturation of lipids or the exchange of lipid chains [​cutting out a chain and replacing it
with an appropriate chain]​
● Cholesterol modulates membrane fluidity by:
○ Altering the packing and flexibility of lipids
○ If added to crystalline gel, fluidity will increase
○ If added to liquid crystal, fluidity will decrease

LECTURE 16 - MOVEMENT ACROSS MEMBRANES

● Integral membrane proteins have diverse roles. Recall that proteins are long strings of
amino acids with an N terminus on one end [​amino terminus]​ and a C terminus on the
other [​carboxyl terminus]​
○ Integral transmembrane proteins must possess a stretch of amino acids that are
hydrophobic - this is to allow the protein to embed itself in the membrane layer.
This area of hydrophobic amino acids in an alpha helical shape is called a
transmembrane domain
● The movement of substances through the membrane is allowed by dynamic transport
proteins in the fluid
○ Small, uncharged molecules [​i.e oxygen, carbon dioxide, nitrous oxide, water etc.​]
cross membranes relatively easily
○ Many molecules do not pass freely through lipid bilayers. For example, large,
polar, and charged molecules cannot cross through the lipid bilayers
○ Specific mechanisms are required for the controlled transport of many substances
across membranes. For each type of molecule there are certain types of
transporters
● Four basic mechanisms for moving molecules across membranes are: simple diffusion,
diffusion through a channel, carrier-mediated diffusion, and active transport
○ In simple diffusion, molecules do not need transport proteins in order to diffuse
across a biological membrane [​ex. Oxygen, water]​
 ○ In channel diffusion, molecules follow a channel created by a specific
transmembrane protein through the lipid bilayer. It allows certain types of
molecules such as ions to cross the membrane [​ex. Na+​ ​]
○ In carrier-mediated diffusion, molecules must interact with the transporter
proteins in order to cross the lipid bilayer. That is, the diffusion is mediated by the
protein [​ex. Glucose]​
○ In active transport, molecules may be diffused from areas of lower concentration
to higher concentration. This requires energy to complete - ATP: adenosine
triphosphate [​ex. Na+​ K ​ pump​]
​ +​

● Passive transport refers to the diffusion of molecules from a region of high concentration
to low concentration only and does not require energy to complete. This creates a
concentration gradient, where there are areas of high concentration and areas of low
concentration
○ Molecules move down a concentration gradient [​‘downhill’​]
● Ion channels are “gated” - they can be opened or closed. Ion channels are found
predominantly in nerve cells. There are two types of gated channels:
○ Voltage gated channels are channels that respond to changes in charge across
membranes. The gate will open when the correct charge stimulates the protein
○ Ligand-gated channels are channels that respond to the binding of a specific
molecule [​a ligand]​ . The binding of a ligand causes a conformational change in
the structure of the receptor/channel

LECTURE 17 - SIGNAL TRANSDUCTION, ECM, AND MITOCHONDRIA

● Membrane proteins are important for signal transduction. Ligands [​small molecules that
bind to receptors​] change the conformation of the receptor proteins. Note that the ligand
does not enter the cell
○ The cytosolic side of the receptor protein is affected by the conformational
change. The changes cause other proteins to become activated [​ex. Epinephrine
activates conversion of glycogen to glucose​]
● Membrane proteins are important for interacting with components in the extracellular
matrix [​ECM]​ . Multicellular organisms are composed of tissues and organs consisting or
communities of cells. These cells work together to perform a function
○ The ECM is a highly organised network of material produced and secreted by
cells
○ Cells of bacteria, fungi, and plants all have cell walls. Plant cell walls function as
the extracellular matrix and allow the organism to thrive. For example, the ECM
of a plant cell is composed of cellulose, hemicellulose, pectin, and proteins and
provides structural support to the cell and the organism as a whole [​i.e skeleton​].
Additionally, it protects the cell from mechanical damage and pathogen attack
● In animal cells, mitochondria are responsible for the production of ATP [​adenosine
triphosphate​]. In plant cells, chloroplasts are responsible for the production of ATP
through photosynthesis

Figure: Chemical reactions for respiration and photosynthesis

● Mitochondria structure is highly complex, consisting of an outer and inner membrane and
an aqueous compartment in-between
○ The outer mitochondrial membrane [​OMM​] contains many enzymes with diverse
metabolic functions and porins. Porins are large channels that control the
permeability of the membrane
○ The inner mitochondrial membrane [​IMM]​ has a high protein : lipid ratio [​3:1​].
Double layered folds form what is known as the cristae, which increase the
surface area of the membrane and contain machinery for aerobic respiration and
ATP formation. The IMM is rich in the phospholipid cardiolipin
○ The aqueous compartments of the mitochondria consist of an intermembrane
space and a matrix. Within the matrix is a high concentration of proteins,
mitochondrial ribosomes, and mitochondrial DNA [​mtDNA​] which encodes
polypeptides that are integrated into the IMM, ribosomes, and tRNA
● Oxidative phosphorylation is the process of ATP synthesis in mitochondria
○ Step 1​ - Electron transport and proton pumping, generating an electrochemical
gradient. High energy electrons pass from coenzymes [​NADH and FADH2​ ​] in the
matrix to electron carriers in the IMM. The series of electron carriers create the
electron transport chain. Energy transfer at each complex is used to pump protons
from the matrix into the intermembrane space. Ultimately, low energy electrons
are transferred to terminal electron acceptors [​O​2​] so water is produced
○ Step 2 - P​ roton [​H+​ ]​ movement down the electrochemical gradient powers ATP
synthesis. This is the controlled movement of protons back across the IMM via
ATP synthase. Potential energy in the electrochemical gradient across the IMM is
converted to ATP in the matrix
LECTURE 18 - CHLOROPLASTS, APOPTOSIS, AND ENDOMEMBRANES

● The big leap in evolution was the development of an energy supply. Energy can be
obtained and generated through the process of aerobic respiration in animal cells and
photosynthesis in plant cells
○ Aerobic respiration converts energy stored in food molecules [​i.e glucose]​ into
chemical energy stored in ATP. This process consumes oxygen and produces
carbon dioxide as a by-product [​waste]​
○ Photosynthesis is the process of building carbohydrates using energy from
photons in sunlight and CO​2
● Chloroplasts are a specialized organelle in plant cells whose primary function is to
undergo light dependent reactions
○ Light-dependent reactions occur in the thylakoid membrane

○ Light-independent reactions [​i.e Calvin cycle​] occur in the stroma. ATP and
NADPH made in light reactions is used to make formaldehyde
● Mitochondria play an important role in programmed cell death [​apoptosis]​
○ Programmed cell death also occurs in plants. For example, the Madagascar Lace
Plant is an aquatic plant that makes fenestrated leaves. In the course of normal
development, PCD generates leaves with holes in them
● Apoptosis is characterised by several defining features:
○ Shrinkage of the cell
○ Blebbing of the plasma membrane
○ Fragmentation of the DNA and nucleus
○ Loss of attachment to other cells
○ Engulfment by phagocytosis
● The intrinsic pathway of apoptosis is initiated by intracellular stimuli [​i.e genetic damage,
hypoxia, virus​]. Killer ​Bax p​ roteins cause changes in the mitochondria membrane such
that they leak protein by creating pores in the membrane [​i.e cytochrome​]
○ Release of apoptotic mitochondrial proteins omits the cell to apoptosis - causes
the formation of caspases initiators
 ● Caspases play an important role in programmed cell death. Their function includes
destroying lamins, disrupting cell adhesion, breaking down the cytoskeleton, and
activating DNase [​enzyme responsible for genome breakdown]​
● Some diseases are directly associated with aberrant apoptosis. In some cases, the problem
is with ​too little ​apoptosis [​ex. In cancer where malignant cells do not die]​ . In other
cases, the problem is with ​too much a​ poptosis [​ex. In Alzheimer’s and Parkinson’s
disease]​
● Main functions of intracellular compartments:
○ Cytosol - protein synthesis, many metabolic pathways
○ Endoplasmic reticulum - synthesis of lipids, synthesis of proteins
○ Golgi apparatus - protein modification, packaging of proteins and lipids
○ Lysosomes - degradation of cellular material
○ Endosomes - recycling, sorting
● The cytoplasmic endomembrane system reveals membrane bound organelles and vesicles
within the cytoplasm, and an extensive network of membranous canals and stacks of sacs
[​i.e cisternae​]
● Technique:​ using GFP to track cell components
○ The green fluorescent protein from jellyfish can be fused with cellular protein.
This fusion protein can be expressed in cells. It fluoresces and can be visualized
under a microscope
○ Observation of the fusion protein provides information about the endogenous
protein [​ex. Where it is located within the cell or organism]​
● Vesicular trafficking is the transport of materials between compartments. It utilizes
transport vesicles [​about 50 - 70 nm in size]​ which are small, spherical,
membrane-enclosed organelles that bud off donor compartments and fuse with acceptor
or recipient compartments
○ Movement is targeted. The cytoskeleton and motor proteins are used and
receptors recognize sorting signals

LECTURE 19 - ER, TRAFFICKING, AND CO-TRANSLATIONAL IMPORT

● Vesicular transport or trafficking is the movement of vesicles to and from a compartment:

○ 1: this movement uses the cytoskeleton and motor proteins
○ 2: vesicles are tethered to compartments via proteins called Rabs and tethering
proteins
○ 3: vesicles are docked to target compartments using proteins called SNAREs
○ 4: vesicles are fused into the target membrane
● Exocytosis is the process of transporting a vesicle from an organelle to the plasma
membrane. Endocytosis is the process of transporting a vesicle from the plasma
membrane to a target organelle
● The endoplasmic reticulum [​ER]​ is an organelle responsible for the synthesis of important
components of the cell
○ The smooth ER’s main functions include synthesis of lipids, production of steroid
hormones [​ex. Glucocorticoids, androgens, estrogens - endocrine cells]​ ,
detoxification [​i.e liver cells, oxygenases, cytochrome P450​] by which enzymes
modify foreign compounds, and sequestration [​storage of calcium​]
○ The rough ER’s main functions include synthesis of membrane phospholipids,
glycosylation [​addition of carbohydrate chains]​ of specific proteins, protein
folding and quality control [​involving the activity of molecular chaperones]​ , and
protein synthesis, modification, and transport
● All protein translation begins on free ribosomes. Translation is completed in 1 of 2 ways:
○ Translation completed on free ribosomes create cytosolic proteins, peripheral
membrane proteins, and proteins targeted to the nucleus, mitochondria,
peroxisomes, and chloroplasts [​in plant cells]​
○ Translation completed on ribosomes associated to the endoplasmic reticulum
create secreted proteins, integral membrane proteins, and soluble proteins
associated with the inside of the endomembrane system [​i.e proteins that function
within the ER, golgi apparatus, and lysosomes​]
● Ribosomes are targeted to the ER membrane by a signal sequence. Proteins that contain
this signal sequence have it at their amino N-terminus which have several consecutive
hydrophobic amino acids
○ This signal sequence directs synthesis of the protein to the ER via a channel. This
process is called ​co-translational import
● Co-translational import defining steps:
○ 1: Signal recognition particle [​SRP]​ binds to signal sequence - translation of the
protein stops
○ 2: Targeting of translation complex to the ER, SRP binds to SRP receptors
○ 3: SRP is released and ribosome binds to the translocon - protein synthesis
resumes
○ 4: Polypeptide enters the ER through the translocon as it is being translated - the
signal sequence is cleaved off and chaperons fold the protein
LECTURE 20 - TRANSMEMBRANE PROTEINS AND GOLGI

● Co-translational import is how soluble proteins get into the endomembrane system
○ Once in the ER, a protein is part of the biosynthetic/secretory endomembrane
system and may ultimately become part of a compartment or be secreted
● Transmembrane proteins are integrated into the membrane, except for those in
mitochondria and chloroplast membranes
○ Proteins with signal-anchor sequences are threaded through a channel in the ER
membrane until the signal-anchor sequence is encountered. The ER channel then
releases the protein into the membrane, where it remains after translation is
completed
● Transport from the ER to the Golgi complex
○ The golgi apparatus receives proteins and lipids from the ER and sorts them to
other organelles, the plasma membrane, or the cell exterior
○ Material moves from the ER to the Golgi to other compartments and the plasma
membrane in a proximal and distal direction
● The golgi complex is a smooth, flattened, disc-like cisternae ~0.5 - 1 micron in diameter
curved like a shallow bowl
○ Cisternae are biochemically unique and show polarity
○ The membrane is supported by a protein skeleton [​i.e actin, spectrin​]
○ The scaffold is linked to motor proteins that direct movement of vesicles into and
out of the Golgi complex
● The Golgi complex has structural differences
○ CGN acts as a “sorting station” [​i.e sorts whether proteins should continue to the
next Golgi stack or be shipped back to the ER]​
○ TGN sorts protein into different vesicles
○ Proteins are modified “step-wise” as they traverse the Golgi. Different cisternae
of the Golgi contain different enzymes that modify proteins. The differential
staining of the Golgi cisternae reflects their biochemical differences
 ● The Golgi complex is the processing factory of the cell. It is responsible for the synthesis
of polysaccharides, the modification of proteins and lipids [​through glycosylation and
proteolytic modification​], and the transport and sorting of proteins
● Endocytic pathways of protein sorting: fully processed proteins are exported to the
trans-Golgi network [​TGN​] and then sorted and delivered to their final destinations
○ The transfer of of vesicles from the ER to the Golgi and between the Golgi
subcompartments is achieved by coat proteins
○ Coat proteins have 2 functions:
■ Help form the vesicle
■ Help select cargo [​i.e material in the vesicle lumen or inserted in
membrane]​
● Lysosomes are hydrolytic enzymes which are digestive organelles. They have an internal
pH of 4.6 [​due to hydrogen bonded ATPase]​
○ The lysosomal membrane is made up of glycosylated proteins

LECTURE 21 - LYSOSOMES, CYTOSKELETON, AND MICROTUBULES

● The function of lysosomes is to degrade internalized material. This means recycling

plasma membrane components and extracellular material as well as destroying pathogens
in phagocytic cells
○ Autophagy defines “organelle turnover”, or the destruction and recycling of
organelles. To do this, lysosomes fuse with ER-derived autophagic vesicles to
form autolysosomes which enzymatically digest and release its contents
● Vacuoles are plant specialized organelles bound to the membrane and filled with fluid.
They can take up to 90% of the cell’s total volume. The tonoplast is the vacuolar
membrane that contains active transport systems that generate high interior ions
○ The function of vacuoles is intracellular digestion due to low pH and acid
hydrolases, storage of solutes and macromolecules, and mechanical support [​i.e
giving the plant rigidity and supporting soft tissues]​
● The cytoskeleton is a dynamic network of interconnected filaments and tubes that extends
throughout the cytosol of eukaryotes
○ Some functions of the cytoskeleton include: structural support, spatial
organization within the cell, intracellular transport, contractility and mobility
● Microtubules are the largest cytoskeletal element made from a polymer of proteins [​i.e
a-tubulin and B-tubulin]​ . There are 2 major types: i) axonemal MT [​highly organized and
stable, part of structures involved in cell movement]​ and ii) cytoplasmic MT [​loosely
organized and very dynamic, located in the cytosol​]
 ● Microtubule structure is formed by a/B heterodimers forming long protofilaments which
create an array, forming a hollow cylinder. Heterodimers are aligned in the same
direction [​head to tail​] creating structural polarity
○ MTs have a slow growing minus end and a fast growing plus end
○ Structural polarity is important for MT growth/shrinkage and direction of
movement of material along the MT
● Microtubules undergo dynamic assembly and disassembly: in vivo, this leads to rapid
turnover of MTs within the cell - dynamic instability
○ Shrinkage can occur very rapidly at the plus end - termed catastrophe
○ The formation of MTs is regulated and controlled
● The microtubule organizing centre is the site of MT assembly
● Microtubule associated proteins describe several different proteins the MTs bind to which
modulate assembly and function, as well as mediate interactions with other cellular
structures. They stabilize MTs or stimulate assembly
● Two classes of MAPs:
○ 1. Non-motor MAPs control MT organization in the cytosol
○ 2. Motor MAPs use ATP to generate force and can move materials along the MT
track. There are two main types: kinesin and dynein
○ Dynein is minus end directed while kinesin is plus end directed. Kinesin carries
cargo such as vesicles toward the plus end of microtubules

LECTURE 22 - INTERMEDIATE FILAMENTS, F-ACTIN, MYOSIN AND MOTILITY

● Intermediate filaments are intermediate in size [​10-12 nm in diameter]​ and are exclusive
to multicellular animal cells. They provide structural support and mechanical strength to
the cell and are incredibly stable relative to microtubules or microfilaments
○ Intermediate filaments are made up of fibrous α-helical proteins
○ IFs are ​not p​ olar and thus are not used for transport of vesicles
○ Examples​: keratins, neurofilaments, lamins. Intermediate filaments composed of
keratins in the cytoplasm are stained red. Intermediate filaments composed of
lamins in the nucleus are stained blue
● Microfilaments are the thinnest cytoskeletal element [​~8 nm in diameter]​ made up of a
polymer of actin protein. It is a double helix of actin monomers
○ The polypeptide is 42 kDa [​kilodaltons]​ in molecular weight and binds ATP
■ Monomer microfilaments form globular G-actin
■ Polymer microfilaments form F-actin
● Microfilaments serve many functions within the cell:
○ Maintenance of the cell’s shape
○ Cell movement
 ○ Cytokinesis
○ Endocytosis and phagocytosis
○ Vesicle transport [​especially in plant cells]​
■ Microfilament tracks move vesicles to distant parts of root cells powered
by a MF-specific motor protein ​myosin
● Microfilaments, like microtubules, are dynamic with a plus and minus end. The plus end
assembles quickly and the minus end assembles slowly
● Both G-actin and F-actin have polar structures [​a plus and minus end​]. G-actin
polymerizes reversibly:
○ From the minus end, G-actin undergoes nucleation slowly. G-actin ⟶ Dimers ⟶
Trimers ⟶ Short Filaments
○ From the plus end, G-actin elongates quickly. Monomers add to both ends
● Microfilament assembly by polymerization/depolymerization is regulated by
actin-binding proteins. Filaments can be loose arrays and networks or tight bundles and
cables. Polymerization and branching provides force for directed cell motility
○ The Arp2/3 complex starts polymerization at branch points. F-actin networks are
highly branched
● Directed cell motility is the coordinated activity of actin-binding proteins which controls
microfilament formation in a lamellipodium to allow directed cell movement
● Myosin is a microfilament-associated motor protein. It is the largest family of proteins,
most moving from the minus end of the filament to the plus end. They are divided into
two broad groups:
○ Conventional myosins: type II. Primary motors for muscle contraction
○ Unconventional myosins: types I, III, and IV. Motors for cell motility -
unconventional myosins generate force and contribute to motility in non-muscle
cells
● Microtubule motor proteins and microfilament-based motor proteins cooperate in
intracellular transport
 ● The nucleus has many functions including storage, replication, the repair of genetic
material, and the expression [​transcription and translation]​ of DNA. It is also responsible
for ribosome biosynthesis

LECTURE 23 - NUCLEUS, NUCLEAR IMPORT, NUCLEOLUS

● The nucleus is bound by the nuclear envelope [​the nuclear membrane made of two
parallel phospholipid bilayers​] which contains nuclear pores and the nuclear lamina. The
nucleus has a double membrane structure
○ Within the nucleus is the genetic material of the cell [​chromatin, nucleoplasm,
nucleolus​] and is where transcription takes place
● The outer nuclear membrane [​OMM​] binds ribosomes and is continuous with the rough
endoplasmic reticulum. The inner nuclear membrane [​IMM]​ bears integral proteins and
connects to the nuclear lamina
● Functions of the nuclear envelope include the separation of nuclear content from the
cytoplasm [​i.e the separation of transcription and translation]​ , and acting like a selective
barrier which limits the movement of molecules between the nucleus and the cytoplasm
○ Supported by the nuclear lamina
○ Small ions and molecules can pass through the nuclear envelope but large
molecules and RNA require active transport
● The nuclear lamina is a thin meshwork of filamentous proteins called lamins
[​intermediate filaments]​ in animal cells. The nuclear lamina is bound to the nuclear
envelope by integral membrane proteins. It provides structural support for the nuclear
envelope and act as attachment sites for chromatin
● Nuclear pores act as gateways between the nucleoplasm and the cytoplasm. They occur
where inner and outer membranes fuse and have a complex protein structure called the
nuclear pore complex
○ The NPC is composed of nucleoporins arranged in octagonal symmetry and
projects into the cytoplasm and the nucleoplasm
○ Nuclear pores are a huge supramolecular structure
● The NPC is responsible for the passive diffusion of small molecules [​down the gradient​]
and the slow regulated movement of larger molecules requiring a nuclear localization
signal [​i.e several positively charged amino acids within the protein sequence]​
● The NLS targets proteins to the nucleus by interacting with importin proteins which
create NLS/Importin complexes to carry cargo to its destination
● The nucleolus is an important structure found within the nucleus which is responsible for
the synthesis of ribosomes
○ Ribosome biogenesis includes the synthesis of rRNA, rRNA processing, assembly
of subunits, and export into the cytoplasm
IMPORTANT PROCESSES:

● Signal transduction
○ 1. Epinephrine hormone is created by the adrenal gland
○ 2. Epinephrine binds to receptor proteins on the outer membrane of cells, causing
a conformational change in their shape
○ 3. The change in shape of the transmembrane proteins causes inner proteins to be
“switched on” by the exchange of GDP for GTP
○ 4. The activation of proteins triggers a chain reaction in which glycogen is
converted to glucose

● Co-Translational import
○ 1. Protein synthesis begins on free ribosomes in the cytoplasm
○ 2. The signal sequence of the protein binds to signal receptor proteins which guide
the ribosome to transmembrane proteins embedded in the ER and stops translation
○ 3. The signal receptor proteins bind to signal receptors embedded in the
membrane which allows the ribosome to continue translation
○ 4. The signal sequence of the translating protein is cleaved off and the SRP is
released back into the cytoplasm to continue the cycle
○ 5. The translated protein is folded by chaperones and the ribosome is released
back into the cytoplasm to begin the translation of its next protein

● Co-Translational import of transmembrane proteins

○ 1. Protein synthesis begins on free ribosomes in the cytoplasm
○ 2. Co-translational import begins like normal
○ 3. Hydrophobic sequences are made along the polypeptide chain
○ 4. The hydrophobic regions are embedded into the membrane while the rest of the
protein is translated into the lumen

● Movement of vesicles to and from the Golgi Complex

○ 1. Specific cargo is bound to proteins that stick out of the membrane of the vesicle
○ 2. Coat proteins bind to the vesicle as it separates from the ER [​COPII for
anterograde, COPI for retrograde]​
○ 3. The coat proteins guide the vesicle to the Golgi and release in proximity
○ 4. The vesicle is tethered and SNARE proteins attach to the incoming vesicle to
allow it to fuse to the Golgi

● Apoptosis triggered by the mitochondria

○ 1. The cell undergoes intracellular damage or stimuli
○ 2. ​Bax p​ roteins create lesions or pores in the mitochondria membrane
 ○ 3. Cytochrome leaks out into the cell triggering the creation of apoptosomes
○ 4. Caspases are initiated by the creation of apoptosomes
○ 5. The cell is destroyed by caspases

● Targeting proteins to the nucleus via NLS

○ 1. NLS carrying cargo interacts with an importin protein to create an
NLS/Importin complex
○ 2. Cargo is brought into the nucleus
○ 3. Ran-GTP interacts with the importin protein to dislodge the complex and free
the cargo
○ 4. Ran-GTP is hydrolysed into Ran-GDP which releases both back the importin
and the Ran to continue the cycle

● Oxidative Phosphorylation
○ 1. High energy electrons pass from coenzymes in the matrix to electron carriers in
the IMM
○ 2. The transfer of electrons between complexes generates an electrochemical
gradient allowing the pumping of protons from the matrix into the intermembrane
space
○ 3. Low energy electrons are transferred to electron acceptors [​i.e Oxygen, creating
water​ ​H2​ O ​
​ ]
○ 4. Protons are moved back across the IMM in a controlled way using ATP
synthase
○ 5. Potential energy in the electrochemical gradient is converted into ATP in the
matrix