Cell structure

Modern cell theory

1. Cell is the fundamental unit of structure and function in living organisms
2. Cells arise from pre- existing cells by division
3. Metabolism occurs within cells and It involves biochemical reactions
4. Cells contain hereditary info ( DNA) which is passed from parent cell to daughter cell
during cell division
5. In organisms of similar species, cells are made of similar composition
6. At least 1 cell. – unicellular or multicellular
7. Activity of an organism depends on the total activity od independent cells

Electron microscope allows us to see structures as small as 2nm ( resolution)

Resolution of light microscope is 200nm ( cannot distinguish point that are less than 200nm
apart)

Transmission electon microscopy ( TEM) – thin section of specimen

Scanning electron microsopy ( SEM ) – 3D surface area

Read notes for cell fractionation process- separating the organelles from one another

A typical eukaryotic cell consists of

1. Plasma / cell surface membrane
a. Defines the boundary of a cell and retains its contents
b. Acts as a barrier which controls the movement of substances
2. Nucleus
a. Contains DNA –
b. directs cellular activities by regulating protein synthesis – enzymes ,
structural and regulatory proteins)
3. Cytoplasm
a. Cytosol- semi- fluid jelly like substance – contains ions and organic
compounds eg. Sugars, AA
b. Organelles
c. Cytoskeleton – protein filaments – microtubules , microfilaments and
intermediate filaments - provide support and allows for movement , gives
cells their shape
4. Cell wall
a. In plant cells

Nucleus / nuclear envelope

- Surrounded by a double membrane each of which is a phospholipid bilayer ( nuclear
envelope)
- Envelope has Many small nuclear pores which regulate the passage of substances
into and out of nucleus
From cytoplasm to nucleus : ribosomal proteins , enzymes ( used for transcription
From nucleus to cytoplasm : RNA, ribosomal subunits
Chromosomes/ Chromatin
Chromatin – genetic material ( uncondensed form of chromosomes)
In a cell at interphase
Most of the chromatin is in the loosely coiled, extended and diffused state – active in the
synthesis of RNA through transcription – EUCHROMATIN
Some of chromatin remain tightly coiled – not active in RNA synthesis –
HETEROCHROMATIN – darker

Nucleolus
- Appears as a spherical mass of densely stained granule
- One or more within a nucleus
- Large conc of DNA ribosomal RNA and proteins
- Site of synthesis of rRNA – component of ribosomes
- Site of assembly of rRNA and ribosomal proteins into ribosomal subunits

Ribosomes
Structure
- Spherical , 20nm
- Non membrane bound
- Small subunit and large subunit each made or rRNA and proteins
- Assembled in nucleolus before being exported out of the nucleus into cytoplasm
- Found either
o Freely floating in cytosol
o Attached to RER – for secretion out of the cell – insertion into the membrane
( glycoprotein ) / packaging within organelles ( lysosomes)
Prokaryotes have 70s ribosomes : small (30s) + LARGE ( 60S)
Eukaryotes have 80s ribosomes : small ( 40S) + large ( 60S)
S is rate

Function
- Site of protein synthesis – translation of mRNA to protein

ENDOMEMBRANE SYSTEM
Organelles work together to transport materials into out of and within the cell. this is the
eukaryotic cells endomembrane system.
A manufacturing and material transport network that enables the cell to make, move and
break down cellular products
 cell

organelles plasma
cytoplasm
membrane

non - - cytosol
membraneous
membraneous - cytoskelton

part of not part of - ribosmes

endomembrane endomembrane
system system - centrioles

1.
1. nuclear membrane mitochondrian
2. smooth and rough ER 2. chloroplast
3. golgi
4. lysosomes and various vesicles

Nuclear envelope
- Numerous pores
- Continuous with the ER
- Function : allow regulated passage of substances into or out of the nucleus

Endoplasmic reticulum ( ER )

Structure
- Extensive network of membranous tubules and sacs called cisternae
- ER membrane separates the internal compartment of the ER from the cytosol
RER

Structure
- Single membrane with attached ribosomes
- Interconnected fluid filled cisternae
- Cisternae more flattened than SER
Function
- Proteins synthesized by bound ribosomes enter the cisternal space and fold into
their native 3D confirmation
- carbohydrate may be added to the proteins (glycosylation) to form glycoproteins
catalyzed by enzymes found within the membrane of the RER
- transport of protein - transport vesicles bud off from the RER carrying the proteins to
their next destination which is usually the golgi apparatus
- proteins synthesized by bound ribosomes are meant for
 o secretion out of the cell eg, digestive enzymes, insulin
o insertion into the plasma membrane
o packaging into organelles (hydrolytic enzymes in lysosomes
- ER grows by adding membrane proteins synthesized by rough ER and phospholipids
synthesized by smooth ER to its own membrane. the ER membrane is transferred in
the form of transport vesicles to other components of the endomembrane system

Smooth ER
- single membrane
- Cisternae appear more tubular

Function
- SER contains many embedded enzymes that catalyzes the synthesis of a variety of
carbohydrates and lipids
- in liver cells smooth ER enables glycogen that is stored as granules on the external
surface of the smooth ER to be broken down to glucose
- synthesize lipids eg. Phospholipids, cholesterol and steroid hormones
- in liver : detoxify drugs poison and alcohol
- SER in muscle cells called sarcoplasmic reticulum store ca2+ ions

Determination of location of ribosome

1. certain proteins have a stretch of polypeptides coded in their respective genes called
the signal peptide when such proteins are being synthesized by the ribosomes the
signal peptide is the first stretch of polypeptide that is synthesized before the rest of
the protein
2. the signal peptide is recognized by a signal recognition particle in the cytoplasm
which binds to a receptor protein in the rough ER bringing the ribosome to the rough
ER
3. the growing polypeptide is translocated into the rough ER lumen
4. hence it is to signal peptide in proteins that determine if ribosomes are free or
bound to the rough ER

golgi apparatus

structure
- single membrane
- consists of flattened membrane bound sacs called cisternae and golgi vesicles
- convex ‘cis’ face where vesicles from the ER fuse to add new cisternae to the golgi
- concave “trans” face where vesicles pinch off and travel to other sites

function:
- modifying sorting and packaging macromolecule for cell secretion or use within the
cell
- add short sugar chains (glycosylation) to proteins and lipids to form glycoproteins
and glycolipids
- modify existing glycoprotein and glycolipid made in the ER by cleaving a sugar
molecule from their sugar chain or modifying their sugar
 - formation of lysosome – pinch off trans face
- produces polysaccharides (eg. Pectin) which are secreted from the transmembrane
of the golgi
- sorts and targets completed materials to different parts of the cell for secretion out
of the cell. ( exocytosis)
lysosome
- small soherical vesicle
- single membrane
- Contains hydrolytic enzymes (proteases lipases nucleases )used to digest
macromolecules
- contents are acidic enzymes have optimal pH in the acidic range- maintained by
proton pump – h+ions
- lysosomal Membrane and hydrolytic enzymes are made by bound ribosomes on the
rough ER
- transported via vesicles to golgi apparatus for further processing
- proteins on the inner surface of the lysosomal membrane and digestive enzymes
within them are not hydrolyzed as the 3D shape of these proteins shield vulnerable
bonds enzymatic attack

fucntions
- Digestion of material taken in by endocytosis
o lysosome fuses with the vesicle vacuole formed by endocytosis to digest the
contents within
o contents include food materials foreign particles like bacteria
o the useful products of hydrolysis are absorbed and assimilated into the
cytoplasm. the unwanted products are released into the external medium by
exocytosis
- autophagy
o breakdown of unwanted structures within the cell eg. Old organelles
o the organic products from the breakdown processes are returned to the
cytoplasm for reuse
- Release of enzymes outside of the cell by exocytosis
o breakdown of extracellular content
o eg. sperm releases hydrolytic enzymes by exocytosis to digest the sheath of
nutrient cells surrounding the ovum
- autolysis
o Contents of many lysosomes released within the cell simultaneously creating
an acidic environment
o cell undergoes self digestion

mitochondrion

structure
- spherical , rod
- double membrane – each is phospholipid bilayer
- inner membrane is highly folded to form numerous cristae
o provides large SA for attachment of proteins and enzymes ( ATP synthase)
 - In a membrane divides the mitochondria into two internal compartments
o the intermembrane space between the outer and inner membrane
o the matrix enclosed by the inner membrane
- Fluid matrix containing 70S ribosomes, circular DNA ( own genes – transcription-
mRNA – form proteins ) and various enzymes
Function
- Site of aerobic respiration.
o carry out metabolic processes that generate ATP through oxidation of sugar
fats and other fuels

chloroplast
- Lens shaped
- double membrane , each a phospholipid bilayer
- space between each membrane is known as intermembrane space
- membrane system within the chloroplast – thylakoids – interconnected sacs
- Some regions form stacks of thylakoids = grana
- The grana are joined by intergranal lamellae
o Extensive folding of thylakoid increases the surface area for attachment of
chlorophyll, other pigments , proteins, enzymes
- Fluid outside the thylakoid is the stroma. Contains circular DNA, ribosomes, enzymes
and starch grains

Function :
- Site of photosynthesis. Absorb sunlight and convert solar energy to chemical energy
by using solar energy to drive the synthesis of organic compounds such as sugar from
water and carbon dioxide

vacuole

structure
- Large vesicles derived from the ER and golgi
- fluid filled SAC bound by a single membrane
- plant cells - large central vacuole surrounded by membrane called the tonoplast and
contains the cells app
function
animal
- Food vacuoles formed by phagocytosis enclose materials for digestion by lysosome
- Freshwater org have contractile vacuoles that pump excess water out of the cell
maintaining a suitable ion and molecule concentration in the cell – water potential
Plant
- concentrated cell SAP draws water into vacuole - helps to maintain turgor pressure
for support
- during cell growth as a cell increases in size the vacuole can also enlarge with
minimal increase in cytoplasm
- storage of waste products
- food storage
microtubules
one type of protein fiber found in the cytoskeleton
- Hollow rods ( 25 nm)
- Wall is made of globular protein called tubulin
- Each tubulin is a dimer – 2 subunits
- Grow in length by addition of tubulin subunits and decrease in length by dissembling
units ( A- B tubulin )
- Growth can be inhibited by chemicals
- Stiff and tun a straight course in cytoplasm

Function
- Maintain the shape of cells
o found beneath plasma membrane providing rigidity to parts of the cell where
they occur
- intercellular transport
o serve as tracks along which organelles equipped with motor proteins can
move (movement of golgi vesicles and lysosomes)
- chromosome movement in cell division
o spindle fibers composed of microtubules help in the movement of
chromosomes to opposite poles in nuclear division
- form structural components of centrioles, Cilia and flagella

centrioles

structure
- pair of Cylindrical rod like structures positioned at right angles to each other
- each contain nine triplets of microtubules arranged in a ring
- found within the centrosome
- located close to the nucleus
- not present in most plant cells
function
- During cell division the centrioles replicate and move to opposite ends of the cell
- play a role in nuclear division in animal cells by helping to organize the formation of
spindle fibers – needed for the separation of chromosomes during division

microtubules – organising center.

Structure from which Microtubules emerge

Functions
- Organization of eukaryotic flagella and cilia
- Organization Of the mitotic and meiosis spindle apparatus

Prokaryote vs eukaryote

Feature Eukaryotic cell Prokaryotic cell

Nucleus & membrane Linear DNA within nucleus No true nucleus. Circular
bound organelle Membrane bound DNA in nucleoid region.
 organelles are present Membrane bound organelle
present
Ribosome 80s ribosome 70s ribosome
Cell wall Plant cell have animal dont Peptidoglycan cell wall in
have bacteria
Size and organization Larger. Multicellular Smaller . unicellular
Plasmids No Extrachromosomal DNA in
the form of plasmids
Both have a plasma membrane

CELL MEMBRANE

All membrane made of phospholipid bilayer ( 7.5nm thick ) 10^-9

Components of cell membrane

1. Phospholipid – hydrophilic phosphate head and 2 hydrophobic hydrocarbon tails
- Amphipathic molecule – both hydrophobic and hydrophilic
- Form bilayers/ micelle in aqueous medium
- Micelle is a circle with head on the outside and tail on the inside
- Phospholipids are held together by weak hydrophobic interactions and van der waal
forces
- Able to drift laterally within the plane of the membrane therefore giving rise to
fluidity of membrane
- When temperature decreases, become less active( less k.e) and settle in a closely
pack arrangement. – membrane solidifies
- Since each layer moves independently, if the gaps coincide small non polar
molecules may be able to move across

Temp at which membrane solidifies depends on

- Ratio of saturated to unsaturated hydrocarbon chains
o Freeze at lower temp if there is a higher proportion of unsaturated. Kinks at
c=c bond of unsaturated prevent close packing of phospholipids .
o More unsaturated – more kinks – cannot pack closely – More fluid- harder to
solidify - solidify at lower temp. – found in organisms in lower climate
- Relative amount of cholesterol
- Length of hydrocarbon chain
o Longer chain – stronger hydrophobic interactions – less fluid

2. Cholesterol

- 4 ring structure and largely hydrophobic

- Amphipathic , hydrophilic OH group and hydrophobic ring of structure.
- Hydroxyl (OH) group of cholesterol aligns with the phosphate heads if the
phospholipids while the remaining portion is tucked into the hydrophobic core.
Regulates membrane fluidity
- Prevents from being overly fluid at high temp as cholesterol restricts phospholipid
movement through its interactions with the phospholipid
 - the ring structure of cholesterol is rigid and it stabilizes the lipid layer through the
van der wall interactions ( where the hydrocarbon chain is closest to the charged
head )
- prevents the membrane from being overly firm at lower temperatures as cholesterol
prevents the close packing of phospholipids and hence hinders the solidification of
the bilayer
importance of fluidity
- affects the permeability of the membrane and thus its ability to serve as an effective
Barrier.
- It also allows for the transportation of membrane proteins to specific regions of the
membrane where they are needed to carry out vital cellular activities

3. Proteins
- Determine most of the membranes specific functions
- Plasma membrane and membranes of the various organelles have unique collections
of proteins
- proteins can be classified into
o integral/ intrinsic proteins
o peripheral/ extrinsic proteins
integral/ intrinsic
- When folded have the exposed hydrophobic and hydrophilic regions – amphipathic
- hydrophilic regions- amino acid with polar or charged R groups
- hydrophobic regions- amino acid with non polar R group
- Hydrophobic regions of integral proteins lie in the hydrophobic core of the
phospholipid bilayer
- Hydrophilic parts are exposed to the aqueous medium on both or either side of the
membrane
- hydrophobic and hydrophilic interactions between the proteins and phospholipids
stabilize the membrane structure
- integral proteins can be either
o unilateral ( extend until half the membrane )
o transmembrane ( across the thickness of the mbrane )

Peripheral / extrinsic
- Not embedded into the bilayer but loosely attached to the surface of the membrane
or to integral proteins through weak ionic and hydrogen bonds
 - On the cytoplasmic side of the plasma membrane proteins may be held by filaments
of the cytoskeleton
- attachment of proteins to the cytoskeleton and the extracellular matrix of the cell
membrane helps to maintain cell shape and fix the location for some proteins
- - drift slower than phospholipids as proteins larger, anchored to one another / to the
cytoskeleton .

4) glycoproteins and glycolipids (carbohydrate compounds)

- carbohydrates tend to be covalently bonded to either lipids or proteins forming

glycolipid / glycoprotein
- 4 human blood groups reflect the variation in the oligosaccharides on the surface of
the RBC membrane
- Always found projecting out of the extracellular matrix

Functions
1. Cell- cell recognition
a. The ability of a cell to determine if other cells it encounters are alike or
different from itself
b. A-b branching gives rise to diversity
c. Good cell markers that can differentiate one cell type from another.
d. crucial in the functioning of an Organism. Basis for
i. sorting out animal embryo cells into tissues and organs- same cells
come together to form tissues
ii. rejection of foreign cells by the immune system
2. cell receptors
a. as receptors for hormone in cell signaling
b. receptors for viruses bacteria and toxins providing a point of attachment so
that pathogens and toxins can gain entry into the cell
c. receptors for white blood cell recognition
i. when under attack cells will express some glycoproteins that are
presented on their cell surface so that they will are recognized as
infected by white blood cells
ii. the immune system will usually respond by destroying the infected
cell thus preventing further spread of infection

how do membrane proteins get embedded in the plasma membrane

1. synthesis of membrane proteins and lipids occur in the endoplasmic reticulum. the
proteins are embedded in the membrane as a result. glycosylation adds
carbohydrates to the proteins making them glycoproteins
2. inside the golgi the glycoproteins undergo further modification and lipids become
glycolipids
3. membrane glycoproteins and glycolipids are transported in vesicle to the plasma
membrane
4. vesicles fuse with the membrane and glycoproteins and glycolipids are presented on
the outside of the plasma membrane
 5. other transmembrane proteins such as channel proteins and carrier proteins are
embedded in the same way

fluid mosaic model

1. fluid
a. compromises of phospholipids and proteins which are free to move laterally
in a layer.
b. Phospholipids are able to ‘flip-flop’ from one layer to another, but this is rare
i. Rare because charged phosphate head will have to pass through the
hydrophobic core of the bilayer. – energetically unfavorable (needs
ATP) – facilitated by enzyme.
2. Mosaic
a. Random arrangement of proteins embedded amongst the phospholipid
molecules resemble a mosaic pattern

Functions of the membranes

1. Regulate movement of substances across the membrane ( surface and internal )
a. Permeable
b. Nonpolar / uncharged molecules are able to dissolve and diffuse through the
hydrophobic of the phospholipid bilayer
c. hydrophobic core repels charged and most polar molecules such as ions.
Must be transported across the membrane by transport protein
2. compartmentalization (internal)
a. formation of unique environment for highly specialized activities
i. eg. lysosomes maintain an acidic environment to allow its enzyme to
work at its optimal pH
ii. if the lysosomes were to burst the hydrolytic enzymes would not work
in the neutral environment of the cytosol
b. accumulation of charged ions and formation of chemicall gradients across
membranes
c. storage of food sauce
3. localisation of proteins of a related function along the membrane (mostly internal)
a. functionally related proteins grouped together. – biochemical processes
facilitated.
4. Increases surface area for chemical reactions (internal)
a. Highly folded cristae of mitochondria increase the surface area to hold more
ATP synthase complexes
5. Cell- cell recognition and adhesion ( surface)
a. Glycoproteins and glycolipids are involved in cell cell recognition
b. glycoprotein of a cell recognizes a glycoprotein of second cell as they are
complementary in shape and charge
c. responsible for the unique surface topography present on the surface of cells
d. (Adhesion ) Membrane proteins of adjacent cells may hook together to form
various kinds of junctions – form tissues and organs
6. Signal transduction ( mostly surface)
 a. Some transmembrane proteins serve as cell surface receptors to transfer
information from the environment into the cell on specific molecules (ligand)
Bind to them
i. Glucagon binds to the Glucagon receptor in the membrane which
triggers chemical reactions leading to the hydrolysis of glycogen to
glucose. cannot enter the cell because of its large size
ii. Pass signal from outside to inside of cell
iii. The formation of the ligand-receptor complex will initiate an
intracellular signaling cascade for signal transduction;
iv.

How substances move across membrane

Importance of movement of substances

1. To excrete substances
2. To obtain nutrients
3. Secrete useful substances
4. Ionic gradient for muscular, nervous activity
5. Maintain suitable pH within cell for enzymatic activity

Passive processes : simple diffusion , facilitated diffusion , osmosis

Active process : active transport , bulk transport

- ATP needed

1. Simple diffusion
a. Of non polar molecules ( can pass through hydrophobic core )and polar water
molecule ( small molecule )
b. No atp
c. Down conc gradient
d. Factors affecting
i. Temp – increase ke. Of molecule and membrane becomes more fluid-
formation of transient pores
ii. Molecule size
iii. Solubility in lipid bilayer
iv. Conc gradient
v. S.a of cell membrane
vi. Distance
2. Facilitated diffusion
a. Transport proteins are needed as ions or polar molecule cannot diffuse
through the hydrophobic core.
b. Everything else same as simple diffusion
c. Types of transport proteins – each transport protein is specific for a particular
solute
i. Channel proteins
 1. Transmembrane protein. - provides a hydrophilic pore through
which only a particular ion. Polar molecule can diffuse through
readily from one side to other
2. Eg. Water channel proteins ( aquaporins) in cells lining
collecting duct in kidney – allow water molecules to flow very
quickly. – intake Is greater .
3. The exterior of aquaporin channels are made up of amino
acids with hydrophobic R groups that are able to interact with
the hydrophobic core region of the phospholipid
bilayer and therefore penetrate the length of the membrane;
4. Some can be gated- - open with arrival of a chemical
ii. Carrier proteins
1. – usually transmembrane
2. 2 alternate conformations
a. Hydrophilic interior of carrier protein contains a
binding site for solute and is exposed to one side of the
membrane
b. A conformational change in the protein occurs when
the solute binds to binding site
c. Solute is now exposed to other side where it is released
d. Transport depends on chance collision between
transport protein and solutes
3. Osmosis
a. Can be simple diffusion or facilaited diffusion through aquaporins

4. Active transport
a. Active transport is a transport of polar molecules or ions across a membrane
against a concentration gradient with the expenditure of ATP
b. specialized carrier proteins called pumps
c. One Direction only
d. Sodium potassium pump
i. Oscillates between two conformational states in one pumping cycle
ii. Translocate 3 Na+ out of the cell for every 2 K+ into the cell
iii. ATP How was the changes in confirmation by phosphorylating the
transport protein
5. Bulk transport
a. Active process as ATP is used to mobilize the movement of the membrane
b. not considered active transport
types of bulk transport
1. endocytosis
a. Uptake of substances into the cell
b. enfolding of the cell surface membrane to form a vesicle allows the cell to
acquire macromolecules
c. Membrane envelopes the material

3 types of endocytosis in animal cells

- Phagocytosis
 o ‘Cell eating’- material taken up is in solid form
o White blood cells engulfing bacteria by phagocytosis
o filaments in the cytoskeleton are arranged to help form pseudopodia ( with
ATP)
o Pseudopodia at the outward extension of the membrane which wraps around
and engulfs the particle
o the ends of the pseudopodia fuse and vesicle containing the solid matter is
pinched off and moves into the cytoplasm
o After this a lysosome containing hydrolytic enzymes fused with the vacuoles
in the enzyme will hydrolyze the particles into soluble products
o useful products are absorbed into the cytoplasm
o unwanted products within the vacuole can be released to the external
medium via exocytosis
- pinocytosis
o ‘cell drinking ‘ – material taken up is in liquid form
o A small area of the plasma membrane invaginates to form tiny vesicles within
the cell- plasma membrane moves inwards – enclosed in vesicle

Receptor – mediated endocytosis

- specific transport
- protein receptors ( usually glycoprotein) are in bedded in membranes that are
exposed to the extracellular fluid
- extracellular substances that bind to the receptors are called ligands
- Of the membrane occurs to form vesicles containing the liggen receptor complexes
which are then transported within the cell
- the receptor proteins are usually clustered in the regions of the membrane called
quoted pits
- helps cell to acquire large quantities of specific substances even though they may not
be in very high concentration in the extracellular fluid
- eg, Iron transported in blood is complexed to a protein called transferrin. When
receptors encounter molecule of transferrin they bind tightly to it. Then engulfed by
endoctytosis

exocytosis
- secretion of macromolecules ( waste materials , undigested remains) by the fusion of
vesicle with the plasma membrane
- A transport mythical blooded from the golgi moved to the cell surface membrane
- membrane of the vesicle fuses with the cell surface membrane to release contents of
the vesicle to extracellular environment
- often used for the transport of manufactured products. Insulin is manufactured in
the pancreas and directly secreted into blood by exocytosis

diffrences between facilitated diffusion and osmosis

1. Osmosis involves the diffusion of water molecules from a region of higher
water potential to a region of lower water potential. Facilitated diffusion
involves the diffusion of polar, charged molecules or ions, from a region of
higher concentration to a region of lower concentration;
2. Osmosis includes simple diffusion across a selectively permeable membrane
and facilitated diffusion mediated by aquaporin. Facilitated diffusion involves
movement of polar, charged molecules or ions across the membrane via
channel or carrier proteins