B Form and Function

Monday, 29 January 2024

7:40 PM

Organelles B2.2.1
 Discrete subunits of a cell adapted to perform specific functions
o Plasma membrane and ribosomes present in every living cell
o Eukaryotes contain additional membrane-bound organelles that
provide further functionality
Types of organelles
Eukaryotes
 Distinguishing feature is the presence of a nucleus
o Double membrane structure with pores that store the genetic material
of the cell
 Allows eukaryotes to separate the processes of transcription (nucleus) and
translation (cytoplasm)
o Transcription: process by which specific DNA instructions (genes) are
converted into RNA transcripts (mRNA)
o Translation: synthesis of polypeptide chains (proteins) from the RNA
transcripts by ribosomes
Separation of transcription and translation B2.2.2
 Allows for post-transcriptional modification of mRNA before it is translated by
ribosomes
o Help to stabilise the mRNA transcript (via capping and
polyadenylation) amd remove non-coding sequences (introns) via
splicing
o Improves efficiency of protein synthesis and allows for tighter control
of gene expression than in prokaryotic cells
Advantages of compartmentalising cytoplasm into sections B2.2.3
 Also distinguished by membrane bound organelles in cytoplasm
o Enables organelles to maintain an internal chemistry different to the
cytoplasm (suited to its specific function)
o Allows for the concentration of key enzymes and metabolites needed
to optimise function of the organelle
 Lysosomes and phagocytic vacuoles provide evidence for the advantage of
compartmentalising the cytoplasm into discrete sections
 o Organelles contain hydrolytic enzymes responsible for digesting
cellular debris or engulfed pathogenic materials
 Need to be contained or would freely digest the contents of
the cell (autophagy)

B2.3 Cell specialization

Stem Cells B2.3.2

 Unspecialised cells with two key qualities
o Self-renewal (continually divide and replicate)
o Potency (capacity to differentiate into specific cell types
 When a cell differentiates to become specialised, it loses the capacity to form
alternative cell types (meaning stem cell supplies are typically limited)

Different types of stem cells B2.3.4

 Totipotent
o Can form any cell type and develop into entirely new organisms
o Can make embryo and placenta
 Pluripotent
o Can form any cell type arising from the three germ layers
o Can only make embryo
 Multipotent
o Can only form a number of closely related cell types
Totipotent (zygotes) and pluripotent (inner cell mass of blastocyst) stem cells are
considered embryonic, while multipotent stem cells (bone marrow) are considered to
be adult stem cells

Uses of Stem cells

Embryonic and adult stem cells can be used therapeutically to treat diseases by
replacing damaged cells with healthy ones
 Embryonic have a greater potency but there are ethical issues associated with
their use (involves the generation and destruction of an embryo)
 Adult stem cells have less ethical issues and a lower chance of graft rejection,
but have a lower potency and are limited in their potential use

Location and function of stem cell niches in adult humans

B2.3.3
Stem cell niches are sites within the body where adult stem cells are maintained in
preparation for future proliferation and differentiation
 Found in bone marrow, hair follicles, heart, intestines, and brain

Bone Marrow
 Haemopoietic stem cells located within the bone marrow
 Give rise to different types of blood cells
o Erythrocytes
o Leucocytes
o Thrombocytes
 Bone marrow transplants commonly employed to replace the haemopoietic
stem cell niche following chemotherapy form leukemia

Hair Follicles
 Contain a range of epidermal stem cells that are involved in cyclic bouts of
hair growth, skin innervation, vascularisation, and wound repair
 Could potentially be harvested and used to regenerate skin tissue in burn
victims or stimulated to promote hair growth in bald individuals

Differentiation B2.3.1
Differentiation is the process during development whereby newly formed cells
become more specialised and distinct as they mature
 All cells of a multicellular organism share an identical genome
o Each cell contains all the DNA for that organism
 The activation of different genes within a given cell by chemical signals will
cause it to differentiate into different cell types
Embryonic Development
 Following fertilisation, an unspecialised zygote will divide and develop into a
mass of specialised cells (early embryo) via differentiation
 Process driven by release of gene regulating chemicals (transcription factors)
called morphogens
o Impact of the morphogen will be determined by its relative
concentration (decreases as the morphogen diffuses from the source
cell)
o Cells closer to the morphogen source receive higher concentrations,
resulting in more genes activating
o Cells further away receive lower concentration, resulting in less genes
activating

Cell Size B2.3.6

 Cells need to produce chemical energy to survive - requires exchange of
materials with the environment
o Rate of metabolism of a cell is a function of its mass/volume (larger
cells need more energy to sustain essential functions)
o Rate of material exchange is a function of its surface area (large
membrane surface equates to more material movement)
 As a cell grows, volume increases faster than surface area, leading to a
decreased SA:Vol ratio
o If metabolic rate exceeds the rate of exchange of vital materials and
wastes, the cell will die
 o Growing cells tend to dived and remain small in order to maintain a
high SA:Vol ratio suitable for survival
o Cell size also depends in order to optimise the specific function of a
cell (B2.3.5)
 Red blood cells are really small
 Human ovum one of the largest

B2.1 Membranes and membrane transport

Cell membranes function to enclose the contents of the cell, separating the
intracellular components from the external environment (extracellular)
 This allows for the control of internal conditions within the cell and the
maintenance of homeostasis (condition of optimal functioning of a cell)
Cell membranes have two key qualities for homeostasis
 Semi-permeability - only certain materials can freely cross the plasma
membrane
 Selectivity - the cell can control the passage of any material that cant freely
pass through the membrane
Components
 Phospholipid bilayer
o Phospholipids form a bilayer that acts as a semi-permeable barrier
o Hydrocarbon chains that form the core are hydrophobic and have low
permeability to large and charged substances
 Large compounds and hydrophilic particles (ions and polar
molecules) cannot cross the bilayer
 Membrane proteins
 o Embedded within the phospholipid bilayer and may act as points of
transport for large and charged substances
 Makes the lipid bilayer a selective barrier as the membrane
proteins van coordinate the transport of hydrophilic materials
according to need
Phospholipids (B1.1.12)
 Structure
o Polar head (hydrophilic) composed of glycerol and phosphate
molecule
o Two non - polar tails (hydrophobic) composed of fatty acid
(hydrocarbon) chains
o Classed as amphipathic bc of both hydrophilic (love water) and
lipophilic (love fat) regions
 Arrangement
o Spontaneously arrange into a bilayer (two parallel layers of
phospholipids)
o The hydrophobic tail regions face inwards and are shield from
surrounding polar fields
o The two hydrophilic head regions face outwards and associate with
the cytosolic and extracellular fluids respectively
 Properties of the bilayer
o Held together by weak hydrophobic interactions between the tails
o The presence of hydrophilic and hydrophobic layers restrict the
passage of many substances
o Individual phospholipids can move within the bilayer, allowing for
membrane fluidity and flexibility
 Allows for the spontaneous break and reforming of
membranes (endo/exocytosis)

Membrane Proteins
Phospholipid bilayers are embedded with proteins, which may be either permanently
or temporarily attached to the membrane

Integral proteins
 Penetrate the phospholipid bilayer to remain permanently attached to the
membrane
 Cannot be readily isolated without disrupting the bilayer (ie. via detergents)
o Examples include: glycoproteins, ion channels, carrier proteins, and
protein pumps
Peripheral Proteins
 Only temporarily associated with one side of a membrane (can be removed by
polar solvents)
 Eather attached to integral proteins, linked to the polar heads of the bilayer,
or held in place by the cytoskeleton or extracellular matrix
o Examples include: receptor complexes involved in cell signalling (G
proteins)

The composition of a membrane protein is determined by its function within the cell
 Non polar amino acids (hydrophobic) will associate with the lipid bilayer,
while polar amino acids (hydrophilic) will face the aqueous solutions
 The inner surface of a protein channel will be lined with polar amino acids to
facilitate the passage of specific polar or charged molecules

Membrane Protein Functions

 Junctions - serve to connect and join to cells together
 Enzymes - fixing to membranes localises metabolic pathways
 Transport - responsible for facilitated diffusion and active transport
 Recognition - may function as markers for cellular identification
 Anchorage - attachment points for cytoskeleton and extracellular matrix
 Transduction - function as receptors for peptide hormones
Glycosylation
 Phospholipids and membrane proteins can have carbohydrate chains
attached by a process called glycosylation
o Glycosylation of a phospholipid results in a glycolipid while
glycosylation of a membrane protein produces a glycoprotein
 The carbohydrate chains are located on the extracellular side and play
important roles in adhesion and recognition
o Surface carbohydrates can serve as an attachment point for other cells
 Eg sperm binding to an egg is mediated by glycoproteins
o Can also act as a point of recognition between cells
 Eg the ABO blood group antigens are glycolipids
 Glycoproteins and glycolipids also play an important role in maintaining the
structural integrity of the extracellular matrix
o The extracellular matrix is a network for external molecules that
provide structure and biochemical support to surrounding cells
o The carbohydrate chains can link these extracellular molecules
together to help make the matrix a cohesive network

Fluid Mosaic Model

Cell membranes are represented according to a fluid-mosaic model, due to them
being bith
 Fluid - is viscous and individual phospholipids can move position
 Mosaic - embedded with proteins, resulting in a mosaic of components
When drawing, remember:
 Phospholipids should be arranged in a bilayer, with the polar and non-polar
regions identified
 Glycoproteins and glycolipids should be facing the extracellular side of the
membrane
 Integral proteins should be embedded within the bilayer, while peripheral
proteins should be anchored to one side (either intra or extracellular)
 Cholesterol may be included in animal cell membranes (it will be interspersed
between the fatty acid tails)
Transport Types
Passive Transport
 Involves the movement of material along a concentration gradient (high conc.
--> low conc.)
 Does not require the expenditure of energy (ATP hydrolysis) bc its going
down a concentration gradient'
 Three main types
o Simple diffusion
 Movement of small or lipophilic molecules that can freely cross
the bilayer
o Osmosis
 Movement of water molecules across the bilayer (depended on
solute concentrations)
o Facilitated diffusion
 Movement of large or charged molecules via transmembrane
proteins
Active Transport
 Involves the movement of materials against a concentration gradient (low
conc. ---> high conc.)
 Does require energy expenditure (ATP) bc its going against the concentration
gradient
 Two main types
o Primary
  A molecule is moved against its concentration gradient using
energy from the hydrolysis ATP
o Secondary
 A molecule is moved against its gradient couple to another
molecule moving down an electrochemical gradient
(cotransport)

Diffusion
 Net movement of molecules from a region of high concentration to a region
of low concentration
o The movement is passive and will continue until molecules become
evenly dispersed (equilibrium)
 Rate of diffusion can be influenced by many factors, such as:
 Temperature - affects kinetic energy of particles in solution
 Molecular size - larger particles are subjected to greater resistance
within a fluid medium
 Steepness of gradient - rate of diff. will be greater with a higher
concentration gradient

Simple Diffusion
 Occurs when small and lipophilic molecules pass between phospholipids to
freely cross the bilayer
o Small, non-polar gases (such as oxygen and CO2) will cross the plasma
membrane via simple diffusion
o Lipophilic molecules (such as oestradiol and testosterone) can freely
cross the bilayer
 Large and charged molecules (such as ions and polar molecules) cannot cross
the membrane via simple diffusion
Facilitated Diffusion
 Passive movement of molecules across the cell membrane via the aid of a
membrane protein
 o Utilised by molecules that are unable to freely cross the phospholipid
bilayer (large, polar molecules, and ions)
o Mediated by two distinct types of transport proteins - channel and
carrier proteins
Channel Proteins
 Integral lipoproteins which contain a hydrophilic pore via which ions may
cross from one side of a membrane to the other
 ion-selective and may be gated to regulate the passage of ions in response to
certain stimuli
 only move molecules along a concentration gradient (i.e. are not used in
active transport)
 have a much faster rate of transport than carrier proteins
Carrier Proteins
 Integral glycoproteins which bind a solute and undergo a conformational
change to translocate the solute across the membrane
 only bind a specific molecule via an attachment similar to an enzyme-
substrate interaction
 When a carrier protein moves material against the gradient (using ATP
hydrolysis) it is called a protein pump
 much slower rate of transport than channel proteins (by an order of ~1,000
molecules per second)
Active Transport
 Uses energy to move molecules against a concentration gradient
 This energy may either be generated by:
o The direct hydrolysis of ATP (primary active transport)
o Indirectly coupling transport with another molecule that is moving
along its gradient (secondary active transport)
 Active transport involves the use of membrane proteins (called protein
pumps due to their use of energy)
o A specific solute will bind to the protein pump on one side of the
membrane
o The hydrolysis of ATP (to ADP + Pi) causes a conformational change in
the protein pump
o The solute molecule is consequently translocated across the
membrane (against the gradient) and released

Cell Structures HL
Nucleus B2.2.6
The nucleus stores the genetic material of the cell as chromatin (DNA + histone
proteins)
 The chromatin is contained within a gel-like solution called the nucleoplasm
(as opposed to the external cytoplasm)
 By housing the cell’s genetic material, the nucleus acts as a control centre
(regulates the expression of genetic instructions)
The nucleus is surrounded by a double membrane called the nuclear envelope, which
is embedded with pores
 The nuclear envelope is a double membrane structure because it is part of the
endomembrane system (it is connected to the ER network)
 This means that proteins synthesised by the ER can access the nucleus
without requiring vesicular transportation
 The nuclear envelope also functions as a barrier to separate the processes of
transcription and translation (prokaryotes lack this separation)
  The presence of pores allows the cell to control the rate at which these
interlinked processes can occur (coordinates gene expression)
A double membrane is also beneficial to the process of mitosis and meiosis
(nuclear division in eukaryotic cells)
 During these processes, the nuclear envelope must be disassembled to allow
the chromosomes to be sorted and separated
 Because it is a double membrane structure, the envelope can break down
into vesicles – these can be reconstituted to reform the nuclear envelope at
the end of the division process

Ribosomes B2.2.7
The ribosome is the site of polypeptide synthesis (protein assembly) within the cell
 It is composed of protein (provides stability) and ribosomal RNA (responsible for
catalytic activity)
 Eukaryotic ribosomes are larger in size (80S) compared to prokaryotic ribosomes
(70S)
Ribosomes are comprised of two distinct subunits:
 The small subunit is responsible for binding to mRNA, while the large subunit binds
to tRNA
 When the two subunits form a complex, translation of an mRNA sequence can occur
In eukaryotes, ribosomes can either be located freely within the cytosol or embedded within
the rough endoplasmic reticulum
 Free ribosomes synthesise proteins for use within the cytosol (i.e. intracellular
proteins)
 Ribosomes embedded within the rough ER synthesise proteins that will be packaged
into vesicles and transported to other organelles
 If the vesicles are transported to the Golgi apparatus, then the proteins will be
secreted from the cell for extracellular use
Mitochondria B2.2.4
Mitochondria are the ‘powerplants’ of the cell – synthesising large amounts of ATP via
aerobic respiration
 All eukaryotic cells possess mitochondria – certain prokaryotes use the cell
membrane to respire aerobically
Mitochondria are thought to have once been independent prokaryotes that were
internalised via endosymbiosis
 They have a double membrane structure (due to vesicular coating as part of the
endocytotic process)
 They have their own DNA (circular and naked) and ribosomes (70S)
 Their metabolic processes are susceptible to certain antibiotics
The structure of the mitochondrion is adapted to the function it performs:
 Outer membrane – the outer membrane contains transport proteins that enable the
shuttling of key materials from the cytosol
 Inner membrane – contains the electron transport chain and ATP synthase (used for
oxidative phosphorylation)
 Cristae – the inner membrane is arranged into folds (cristae) that increase the SA:Vol
ratio (more available surface area)
 Intermembrane space – small space between membranes maximises hydrogen
gradient upon proton accumulation
 Matrix – central cavity that contains appropriate enzymes and a suitable pH for the
Krebs cycle to occur
Chloroplasts B2.2.5
Chloroplasts are the ’solar energy plants’ of a cell – they convert light energy into chemical
energy
 This chemical energy may be either ATP (light dependent) or organic compounds
(light independent)
 Only photosynthetic tissue possess chloroplasts (it is present in the leaves of plants
but not the roots)
Chloroplast are thought to have once been independent prokaryotes that were internalised
via endosymbiosis
 They have a double membrane structure (due to vesicular coating as part of the
endocytotic process)
 They have their own DNA (circular and naked) and ribosomes (70S)
 Their metabolic processes are susceptible to certain antibiotics
The structure of the chloroplast is adapted to the function it performs:
 Thylakoids – flattened discs that have a small internal volume to maximise hydrogen
gradient upon proton accumulation
 Grana – thylakoids are arranged into stacks to increase SA:Vol ratio of the thylakoid
membrane
 Photosystems – pigments organised into photosystems in thylakoid membrane to
maximise light absorption
 Stroma – central cavity that contains appropriate enzymes and a suitable pH for the
Calvin cycle to occur
 Lamellae – connects and separates thylakoid stacks (grana), maximising
photosynthetic efficiency\
Golgi Apparatus B2.2.8
The Golgi apparatus (also known as Golgi complex or Golgi body) is responsible for sorting,
storing, modifying and exporting cellular material
 It is composed of a series of flattened sacs (called cisternae) that are located between
the ER (cis facing) and the plasma membrane (trans facing)
 Proteins (from rough ER) and lipids (from smooth ER) arrive in vesicles at the Golgi
body and are modified into functional molecules
 The different sacs are responsible for specific chemical modifications based on the
enzymes involved (e.g. phosphorylation (adding phosphate), glycosylation (adding
sugar), etc.)
 Secretory proteins, glycoproteins, cell membrane proteins, lysosomal proteins, and
some glycolipids all pass through the Golgi apparatus
 In plant cells, much of the cell wall material passes through the Golgi apparatus as
well
Materials destined for secretion are packaged into vesicles at the Golgi body for extracellular
release (exocytosis)
 can be either released immediately (constitutive secretion) or stored in secretory
vesicles for a sustained release (regulatory secretion)
 Regulatory secretion is triggered by an external chemical signal (ligand) binding to a
specific receptor
Vesicles B2.2.9
Vesicles are membrane-wrapped containers involved in shuttling materials between cellular
compartments
 Most molecules are too large to pass directly through membranes and so are
packaged into vesicles that can fuse with a membrane to deliver the material
Clathrin
 Some vesicles form with the help of a coat protein called clathrin
 Clathrin is a triskelion-shaped molecule that is recruited to a membrane by adaptor
proteins (adaptin)
 The clathrin proteins then link together to form a rounded lattice that pulls the
membrane into a bud
 This bud is then cleaved by another protein (dynamin) to form a vesicle, at which
point the clathrin architecture disassociates

Receptor-Mediated Endocytosis
 While clathrin helps to shape the vesicle, not all vesicles will be formed via the
clathrin coating mechanism
 As clathrin requires recruitment to the membrane, it is commonly used for receptor-
mediated endocytosis
 In this process, a specific ligand binds to a receptor, which then recruits clathrin (via
an adaptor protein)
  The advantage of receptor-mediated endocytosis is that only the specific ligand will
be internalised, allowing greater regulatory control over what materials enter a cell

Cell Adaptations B2.3 HL

Cells that are specialised for material exchange will possess adaptations to increase their
surface area
 Cells that are flat and long (squamous) will have a higher SA:Vol ratio than cells that
are larger or cuboidal in shape
 Tissues lining absorption surfaces will have ruffled projections (villi), while the cells
themselves will possess membranous extensions (microvilli)
Examples of cells that are specialised for material transport include:
 Red blood cells: The cells are thin and flat (biconcave) and have had their nuclei
removed to store more haemoglobin (increases oxygen uptake)
 Tubule cells: The proximal convoluted tubule of the kidney is folded into villi and the
tubule cells possess microvilli to improve selective reabsorption

Pneumocytes
Pneumocytes (or alveolar cells) are the cells that line the alveoli and comprise of the majority
of the inner surface of the lungs
 There are two types of alveolar cells – type I pneumocytes and type II pneumocytes
Type I Pneumocytes:
 Type I pneumocytes are involved in the process of gas exchange between the alveoli
and the capillaries
  They are squamous (flattened) in shape and extremely thin (~ 0.15µm) – minimising
the diffusion distance for respiratory gases
 The cells are connected by occluding junctions, which prevents the leakage of tissue
fluid into the alveolar air space
Type II Pneumocytes:
 Type II pneumocytes secrete pulmonary surfactant, which reduces surface tension in
the alveoli (making it easier for them to inflate)
 They are cuboidal in shape and possess many granules called lamellar bodies (which
store the surfactant)

Muscles
All muscles contain long protein filaments (myofibrils) which are responsible for muscle
contraction and relaxation – however different types of muscles possess specialised features
according to their function
 Striated muscles connect to the bones of the skeleton and are responsible for
locomotion (voluntary movement)
 Cardiac muscle cells are found within the heart tissue and are responsible for the
rhythmic beating of the heart

Striated Muscle Fibres:

 Skeletal muscles are comprised of long, cylindrical fibres that are formed from the
fusion of individual cells
 The fibres therefore have a single, continuous plasma membrane (sarcolemma) and
are multinucleate
 These long and cylindrical fibres are packed together in unbranching strands
(typically 2–3 cm in length) that collectively form a muscle bundle
 While the muscle fibre operates as a single functional unit, the fact that it was formed
from the fusion of individual muscle cells makes it debatable whether a muscle fibre
can be considered a cell

Cardiac Muscle Cells:

 Cardiac muscle cells are short (~0.1 mm), narrow and fairly rectangular in shape
 Unlike in skeletal muscle, the cardac muscle cells are not fused together and
consequently are mononucleated (one nucleus per cell)
  The individual muscle cells are connected by gap junctions at intercalated discs,
which allow for electrical conduction between the cells
 Cardiac muscle cells are branched, allowing for faster signal propagation and
contraction in three dimensions
 The cells have more mitochondria than striated muscle fibres as they are more reliant
on aerobic respiration for ATP production

Reproductive Gametes
The male and female reproductive gametes (sperm and egg) have specialised structures
which reflect their functions
 The male gamete (sperm) is small and motile and only contributes the male’s haploid
nucleus to the zygote
 The female gamete (egg) is large and non-motile and contributes all the organelles
and cytoplasm to the zygote
Sperm:
 A typical human spermatozoa can be divided into three sections – head, mid-piece
and tail
 The head region contains three structures – a haploid nucleus, an acrosome cap and
paired centrioles
o The haploid nucleus contains the paternal DNA (this will combine with
maternal DNA upon fertilisation)
o The acrosome cap contains hydrolytic enzymes which help the sperm to
penetrate the egg
o The centrioles are needed by a zygote to divide (egg cells expel their
centrioles within their polar bodies)
 The mid-piece contains high numbers of mitochondria which provide the energy
(ATP) needed for the tail to move
 The tail (flagellum) is composed of a microtubule structure called the axoneme, which
bends to facilitate movement
Ovum (Egg):
 A typical egg cell is surrounded by two distinct layers – the zone pellucida (jelly coat)
and corona radiata
o The zona pellucida is a glycoprotein matrix which acts as a barrier to sperm
entry
 o The corona radiata is an external layer of follicular cells which provide the egg
with nourishment
 Within the egg cell are numerous cortical granules, which release their contents upon
fertilisation to prevent polyspermy
 Although diagrams of egg cells commonly include a haploid nucleus, no nucleus will
form within the egg until after fertilisation has occurred
o The egg cell is arrested in metaphase II until it becomes fertilised by a sperm