Cellular Form and Function:

The parts of a cell

Bio 130 Part 2

Jennifer Mitchell
Figure 1-30 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
 Bio130 Part 1

DNA
mRNA mRNA
protein

Figure 1-30 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
 Membrane
structure and
transport

Organelles

Cytoskeleton
Junctions, adhesion
and ECM

The cell cycle

Figure 1-30 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
By the end of Bio 130 you should be
able to:
1. Identify the different parts of a eukaryotic cell.

2. Match the processes that take place inside the cell

with the parts of the cell.

3. Place these processes in context of how the whole

cell functions.

4. Recognise the techniques used in different types of

experiments discussed in lectures.
 Asking questions about lecture material

• Tutorial sessions after Thursday’s lecture.

– Clicker questions.
– Open Q & A.

• Blackboard discussion board:

– On Friday afternoon Prof Mitchell will respond to
questions.
 Saccharomyces cerevisiae

Budding yeast: a single-celled eukaryote

Has a cell wall, organelles like mitochondria

Figure 1-42 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
Multicellular organisms are composed
of many different cell types
200 distinct cell types
skin cells
epithelial cells
alveolar lung cells
All have the same
features - mitochon-
dria, nuclei, etc.
 “Typical” Animal Cell
= animal cell specific

determines cell adhesion,

shape, development

degrades cellular
components no longer
needed

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 “Typical” Plant Cell
= plant specific

• Nucleus
• Endoplasmic
reticulum
• Golgi apparatus
• Peroxisome more than 1/3 of cell volume

• Mitochondria
• Plasma
membrane
Vacuole: one type is like animal
lysosome; second storage of small molecules and proteins;
help maintain rigidity of the cell
thylokoids inside chloroplast
Tonoplast is the vacuole membrane
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1 2 3

1. Cytoplasm
 Contents of cell outside the nucleus - all except nucleus

2. Cytosol
 Aqueous part of the cytoplasm - no organelles or nucleus, includes protein structures like
cytoskeleton and ribosomes

3. Lumen
 The inside of organelles

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Membrane Structure

Reading: Alberts p617-624

 Many Cellular Functions Occur at Membranes
1. Compartmentalization

2. Scaffold for
biochemical
activities

3. Selectively H20
permeable barrier
6. Interactions
4. Transporting solutes between cells

5. Responding to external signals

12
 Cell Membranes
- divides cell into compartments
- control movement of molecules
• lipid bilayer
 basic unit

 fluid structure

• membrane proteins
 mobile in lipid layer
 E.g. receptors, channels

The fluid mosaic model of the membrane

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 Lipid Bilayer
Polar head
Lipids are a broad group of hydrophobic groups
molecules which include fat, wax, sterol,
fat-soluble vitamins (K, E, D, A), mono-
glycerides, diglycerides, phospholipids, } Hydrophobic
and others tails

Polar head
groups
Leaflet
 Amphiphilic:
 hydrophilic or polar head group (water loving)

hydrophobic nonpolar tail (water fearing)

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 Lipid Bilayer continued
• Phospholipids
• polar head group
• two hydrophobic tails
Figure 10-2

• In an aqueous environment
 spontaneously self-
associates into a
bilayer

Figure 10-7

15
  Artificial lipid bilayers:
liposomes

exposed to water
Uses:
1) To study lipid properties

naturally curls in 2) Membrane protein properties

3) Delivery into cells (drugs, DNA)

Liposome
Cross-section view

Figure 10-8 Molecular Biology of the Cell (© Garland Science 2008)

Figure 10-9b Molecular Biology of the Cell (© Garland Science 2008)
 Lipid Components—Phospholipids
1) Phospholipids
 most abundant part of bilayer

• E.g. phosphatidylcholine,
sphingomyelin
- Hydrocarbon tails: (fatty acid) (A)

 Around 14-24 carbons in length

 can be saturated or unsaturated (single or
double or triple bonds)

Kink indicates that the tail is unsaturated,

phosphatidylcholine
Contains a cis-double bond

17
 Lipid Components—Steroids
2) Steroids a very hydrophobic molecule!

- animals: cholesterol
- plants: plant steroids, some
cholesterol
- up to 1:1 ratio of cholesterol
and phospholipids
 Cholesterol decreases mobility of
phospholipid tails

 Also make plasma membranes

less permeable to water and other
polar substances

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 Lipid Components—Glycolipids
outside of cell

3) glycolipids: Galactose

 sugar groups attached to lipid

molecules

(have sugar added to them) (inside organelles)

Lipids are glycosylated in the lumen
of the Golgi apparatus
- many different types; any sugar can be added there

Glycolipids are found mainly: inside cell

 inof the outer leaflet of the plasma membrane, the outside

the bilayer
 in the inner leaflet
not

 found in some organelles

protects outside of the cell

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A membrane can be deformed without causing damage

• Technique :Live cell imaging

 Laser tweezers are used to
manipulate the membrane

http://www.dnatube.com/video/4161/Fluidity-of-the-Lipid-Bilayer

Reference:
Essential Cell Biology, 3rd Edition Alberts, Bray,
Hopkin, Johnson
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 Cell Membranes - fluid

Phospholipids rapidly:
 diffuse laterally w/in each leaflet

Phospholipids rarely:
 move from one layer to the other (flip-flop) without the help
of a specific protein phospholipid translocator

21
 Membrane fluidity
• Temperature Temp decrease
At lower temperatures, lipid
Phase transition
bilayers become rigid (gel)

• Phospholipid saturation:
The presence of cis-double bonds allows
the membrane to remain fluid at lower
temperatures - the kinks allow them to
move around a lot more, more room
• Length of phospholipid tails
Shorter hydrocarbon tails increase fluidity
at lower temperatures (lipid tails interact
less)

Adapted from: Figure 10-12 Molecular Biology of the Cell (© Garland Science 2008)
 Lipid movement to the other leaflet
• enzymes in cell membrane - flip lipids from
one leaflet to other
• eg. phospholipids synthesized in cytosolic
leaflet of endoplasmic reticulum
– phospholipid translocators
lumen
 aid in rapid flipping of phospholipids
to non-cytosolic leaflet

Why needed?
Phospholipids synthesised in cytosolic leaflet of
endoplasmic reticulum, need equal number on both sides
cytosol
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 Cytosolic and exoplasmic face

outside of cell, or
inside of lumens

made up of two leaflets

Nucleus and mito. are
different:
- the orange face will face usually inside,
inside of nucleus in inner facing cytosol
nuclear membrane
- similar situation of mito.
cytosolic is facing the matrix
- both have four "leaflets";
double phospholipid

*everything in purple is where the

exoplasmic face faces
 Asymmetry of the Lipid Bilayer
• glycolipids - outer leaflet of plasma membrane
 synthesised of the luminal face of the Golgi apparatus
- interaction of cell with
environment
- protection from
harsh conditions

• specific phospholipids - cytosolic leaflet of PM (plasma membrane)

 bind cytosolic proteins

• eg. Phosphatidylserine - bound by Protein kinase C

(green in diagram -ve)
25
Membrane Proteins

Reading: Alberts p629-640

 Cell Membrane Proteins
• specific functions
• associated with the lipid bilayer in different
ways
outside the cell

inside the cell 7 & 8 are

peripheral proteins
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 Transmembrane proteins
pass through the ENTIRE lipid bilayer
• Amphiphilic
– hydrophilic domains - aqueous
– hydrophobic membrane-spanning domain
hydrophillic
 AA side chains are nonpolar
middle, hydrophobic
• Single-pass
1) single α-helix
• Multipass
2) multiple α-helices hydrophillic

3) rolled-up β-sheet (β-barrel)

 rigid, has an aqueous pore

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 A membrane spanning alpha-helix

Figure 10-21 Molecular Biology of the Cell (© Garland Science 2008)

 Examples of membrane protein functions

1. receptor: proteins stick to the outside, while intracellular portion will signal that protein
2. ion channels: conformational changes regulate permeability
3. some channels in bacteria, mitochondria, chloroplasts (don't undergo conformational changes - always
open)
 Techniques: How are these
structures identified?
• X-ray Crystallography
 determines 3-D structure

• Hydrophobicity plots: portion inside

the bilayer**

 Segments of 20-30 hydrophobic amino

acids can span the lipid bilayer as an
alpha-helix; determines proportion of the
protein located in the bilayer.
The more +, the more hydrophobic;
takes more energy to move it into the
opposite leaflet

Figure 10-22a Molecular Biology of the Cell (© Garland Science 2008)

 Cell membrane proteins on one side
4) proteins anchored on cytosolic face by an
amphiphilic α-helix

Why?
Because it has one side of the helix
facing inward away from water, and
one side outward touching water
only on cytosolic face

32
Lipid-anchored Membrane Proteins
5a) fatty acid chain anchor red-the anchor lipid

– Myristate or palmitate

5b) prenyl anchor

– farnesyl or geranylgeranyl

 Cytosolic enzymes add the anchor

 Directs the protein to the cytosolic face

33
Lipid-anchored Membrane Proteins
6) GPI anchor (glycosylphosphatidylinositol)


synthesised in ER on lumen - exoplastic face!

 end up on cell surface

34
 Non-Covalent Interactions with
other Membrane Proteins
7 & 8) bound on either face

• Peripheral membrane
proteins

• Bound to other proteins on

either face
 non-covalent interactions
These are peripheral membrane proteins, don't insert into the bilayer

35
 Techniques: Extraction of membrane proteins

Peripheral membrane proteins use gentle extraction

gentle extraction

that does not destroy lipid bilayer

Integral membrane proteins:

destroy membrane with
destroy membrane
detergents to extract
the protein
detergents are small amphiphillic molecules

Figure 10-30 Molecular Biology of the Cell (© Garland Science 2008)

 Techniques :Studying the properties of
integral membrane proteins
*standard way to study proteins,
through isolation

Figure 10-31 Molecular Biology of the Cell (© Garland Science 2008)

 Techniques :Lateral Diffusion of
Membrane Proteins
• Lateral diffusion within leaflet
• no flip-flop
2008 Nobel Prize
Study of protein movement
• FRAP: Fluorescence Recovery
After Photobleaching
– protein fused to GFP
(green-fluorescent protein)

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 Lateral Diffusion of Membrane Proteins
• Lateral diffusion within leaflet
• no flip-flop

Study of protein movement

• FRAP: Fluorescence Recovery
After Photobleaching
– protein fused to GFP

– bleach small area by laser beam

 measure GFP-protein movement into bleached area
39
 Technique: Fluorescence Recovery After
Photobleaching

grey: PL-bilayer
green: translipid
proteins

40
 Lateral Diffusion of Membrane
Proteins
• Video
– Molecular Biology of the Cell, 5th Edition
– 10.6 FRAP

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 Mobility of membrane proteins
• Different proteins have different mobility in the
membrane.
• Some proteins have very limited mobility
• Limitation of FRAP
 Measures the mobility of a population of protein molecules, rather
than an individual protein molecule

• Using single molecule tracking

 Seen that proteins are restricted to doamins
 And that removing cytoplasmic portions of the protein increases
mobility
 Next…
• How the lipid bilayer and membrane proteins
regulate the movement of molecules across
membranes.
End