Download CH 1& 2 REVISION_2012

BIOMACROMOLECULES,
MEMBRANES AND CELL
ORGANELLES
EL: TO REVISE CH 1& 2
Key Knowledge
• the chemical nature of the cell
– synthesis of biomacromolecules:
polysaccharides, nucleic acids and proteins
– the structure and function of lipids
– the structure and function of DNA and RNA
– the structure and functional diversity of
proteins: the proteome
• the role of organelles and plasma membranes in
the packaging and transport of biomolecules
Type of biomacromolecule
Atoms in molecule
Sub-units
Examples and
Cellular functions
Organelle
Cell membrane
Chloroplasts
Mitochondria
Nucleus
Ribosomes
Endoplasmic reticulum
and Golgi complex
Lysosomes
Cytoskeleton and
extracellular matrix
Structure
Function
Type
Diffusion
Osmosis
Facilitated diffusion –
carrier proteins
Facilitated diffusion –
channel proteins
Active transport
Endo/Exocytosis
Description
Molecules
CELL THEORY
•
All living things are made cells – they are the building blocks from
which living things are made.
•
New cells are produced from existing cells.
Types of cells

Prokaryotic
– Very small: less than
2mm in diameter
– Lack membrane bound
organelles
– Circular DNA (not in a
nucleus)
– Bacteria and
archaeans

Eukaryotic
– Much larger: 10100mm in diameter
– Have membrane
bound organelles
– Linear DNA in a
nucleus
– Animals, plants, fungi
and protists
What is a cell?
A fluid filled compartment containing atoms and
molecules
INTRACELLULAR
AQUEOUS
ENVIRONMENT – CYTOSOL
EXTRACELLULAR
AQUEOUS
ENVIRONMENT
CELL BOUNDARY
(PLASMA MEMBRANE)
WHAT IS A CELL?
A chemical factory
Inputs
(small molecules)
Outputs:reactions
useful
Chemical
Outputs:
useful
products
for
products
for
export
between
inputs
driven
by
export
(biomacromolecules)
(biomacromolecules)
energy
in response to
Output: waste products
external/internal
signals
Signals
CELL STRUCTURE:
MEETING THE NEEDS OF MOLECULES

Molecules need to:
– move in and around cell at a certain rate to reach
sites of specific activity (ie where they will react
with other molecules)
– be in adequate concentrations (ie there needs to be
enough of them) for chemical reactions to occur at
the right rate.

Cell structure therefore needs to facilitate the
movement of molecules and maintain them in
adequate concentrations to maintain cell function
(ie so the cell doesn’t die)
Organelles

Large eukaryotic cells increase
their surface area by having
folded membranes and
internal compartments called
organelles

Organelles also allow
different chemical reactions
to occur at the same time in
different places without
interfering with each other

Organelles maintain the
concentration of molecules
at levels that ensure they will
react with each other at
optimum rates
What are cells made of?
Six
atoms make up most of the matter
in living organisms
 Carbon, hydrogen, nitrogen, oxygen, sulfur and
phosphorus
These
atoms can combine to form large
molecules
Molecules
Non-polar molecules
Molecules that have no overall charge are
called non-polar.
They are not attracted to water molecules
and are described as hydrophobic (water
fearing)
Polar molecules
Molecules that have regions of positive
and/or negative charge are called polar.
They are attracted to other polar
molecules, like water, and are described as
hydrophillic (water loving)
Water molecules
Cells contain the molecule water – H2O
 Water is called a polar molecule

 The oxygen atom attracts the electrons it shares with
the hydrogen atoms more strongly
 This makes the oxygen atom slightly negative (d-)
and the hydrogen atoms slightly positive (d+)
d+
d-
d+
water molecules
The d-
oxygen atom of one water
molecule attracts the d+ hydrogen atom
of another water molecule - this is called
hydrogen bonding
Carbon molecules

Many molecules contain carbon due to its
ability to form strong stable covalent
bonds with carbon and other atoms

Each carbon atom can form four covalent
bonds – these bonds can be single
(saturated), double or triple
(unsaturated)
Hydrocarbon molecules

Hydrocarbons are made of carbon
and hydrogen atoms (eg methane –
CH4)

Hydrocarbons are non-polar
Hydrocarbon molecules

Other groups can be substituted for a H,
giving it a new chemical character (eg
methanol – CH3OH)

These functional groups can make a
hydrocarbon polar and explain many of the
molecular interactions in a cell

Common functional groups are OH, COOH,
NH2 and HS
BIOMACROMOLECULES
Large molecules that are integral to the structure and
function of cells are called biomacromolecules. There
are four types:
Carbohydrates
Lipids
Proteins
Nucleic acids
BIOMACROMOLECULES
Cells
make biomacromolecules from
smaller subunits, calles monomers
Each
kind of biomacromolecule has
characteristics or properties that
make it effective for carrying out its
particular function
Making a BIOMACROMOLECULE
 Biomacromolecules
are synthesised inside cells. This
involves linking smaller sub-units to form large
chains.
 Carbohydrates,
proteins and nucleic acids are formed
when sub-units called monomers link to form a
polymer in a condensation polymerisation
reaction
 Lipids
are not polymers as they are composed of
distinct chemical groups of atoms that don’t undergo
a condensation reaction
Condensation polymerisation
reaction

The OH groups on adjacent
monomers can react, eliminating a
water molecule.
Nucleic acids
Phosphate
group (-ve)
5’-carbon
Nitrogen
base
O
C 5’
4’
1’
3’
2’
H
OH
Phosphate
group (-ve)
Nitrogen
base
O
C 5’
4’
1’
2’
H
3’
OH
3’-carbon
LIPIDS AND MEMBRANES
Lipids

Made of C, H and O atoms

Subunits are fatty acids or glycerol

Insoluble in water due to non-polar HC regions

Three important cellular functions
– Chemical energy storage (store two times as much
energy as carbohydrates)
– Structural
– Chemical signal
Lipids
Type
Function
Fatty acids (eg stearic acid, oleic
acid)
Energy source
Subunit of other lipids
Triglycerides
Energy storage
Phospholipids
Structural component of plasma membranes
Glycolipids
Recognition sites on plasma membranes
Steroids (eg cholesterol, sex
hormones)
Component of plasma membranes (regulates
fluidity)
Signaling molecule
Terpenes (eg Vitamin A)
Antioxidant
Lipids

Saturated
– single covalent
bonds between
atoms
– Straight molecule
– Solid at room
temperature

Unsaturated
– Double or triple
covalent bonds
between molecules
– Bent molecule
– Liquid at room
temperature
Glycerol – a fatty alcohol

Glycerol has three OH groups that bond
with three fatty acids
◦ When the fatty acid group reacts with the
alcohol group, water is formed and is therefore
a condensation reaction
◦ However, there are no repetative linkages: so
lipid not a polymer
phospholipids

Phospholipids have:
– a hydrophopic tail of two fatty acids
attached to a glycerol
– A hydrophillic phosphate head replaces
the third fatty acid tail
The Surface area conundrum

Cells need to maximise their surface area
to ensure the rapid movement of
molecules

Problem:
– As volume increases, surface area
decreases!
– How do cells deal with this?
Membranes
Cell membrane - structure
A plasma membrane is an ultra thin and pliable layer
with an average thickness of less than 0.01 μm
Cell membrane - structure

Called fluid mosaic model

Lipids are the fluid part of the membrane

Proteins are the mosaic part of the membrane – what
are some functions of these proteins?
Cell membrane - functions

Define cell boundary

Provide permeability barrier (acts like a sieve)

Provide sites for specific functions

Regulate transport of solutes

Detect electrical and chemical signals

Assists in cell to cell communication
1. Diffusion
The movement of molecules from areas of
high solute concentration to area of low
solute concentration.
i.e.. Down the concentration gradient.
No energy is involved!
Ways to increase
diffusion
Increasing
concentration
Increasing
temperature
Increasing
surface area
Permeable membrane
Concentration Gradients
Diffusion
High concentration
Low concentration
Equilibrium
Once diffusion is complete the
molecules keep moving but the
overall distribution remains
constant
Partially Permeable
Membrane
If the membrane is partially permeable, the
solvent can move through but the solute
cannot.
Concentration Gradients
Partially permeable membrane
High concentration
Low concentration
2. Osmosis
A special type of diffusion!
Solute
Water
molecules
The Add
solute
cannot cross the membrane. To try and
Solute
balance the concentrations, the water molecules
move to dilute the solution.
Highsolute
concentration
concentration
The
cannot cross theLow
membrane.
To try and
solute
balance
the concentrations, the solute
water molecules
move to dilute the most concentrated solution.
Osmotic Gradient
Concentrated solute
Dilute solute
The pressure that makes the water move is
called the osmotic pressure.
Hypotonic =
extracellular fluid
lower
concentration
than intracellular
fluid and water will
diffuse into cell
making it turgid
Isotonic = extra
and
intracellular
fluid are same
concentration
and there will
be no net
movement of
water
Hypertonic =
extracellular
fluid higher
concentration
than
intracellular
fluid and water
will diffuse out
of cells making
it flaccid
3. Facilitated Diffusion

Most molecules are too large or too polar to
cross membrane by simple diffusion

Protein assisted movement down a
concentration gradient – facilitated diffusion
can occur in a few different ways
HIGH
CONCENTRATION
GRADIENT
LOW
Facilitated Diffusion
Special channels in the membrane help the diffusion.
This channel or carrier mediated movement is selective
and can become saturated. This may inhibit the
movement of another molecule. No energy is used.
Facilitated diffusion: carrier protein
The molecule binds to its carrier protein,
potentially changing its shape, and is
carried to the other side
Carrier proteins
Facilitated diffusion: channel protein
Channel proteins form pores in the membrane
that fill with water and dissolve hydrophillic
molecules.
4. Active transport
When the cell spends energy to
move molecules against the
concentration gradient.
Concentration Gradients
Active transport
High concentration
Low concentration
Against the concentration gradient!
Extracellular fluid
Example: SodiumPotassium Pumps
Na+
Na+
The sodiumpotassium pump
in nerve cells is a
protein in the
membrane that
exchanges sodium
ions (Na+) for
potassium ions (K+)
across the
membrane.
K+
Na+
Plasma
membran
e
Carrier
protein
K+
ATP
Na+
Na+ moves to
its binding site
Cell cytoplasm
K+
5. Cytosis
When the cell spends energy to
move LARGE molecules.
Moving large molecules

Sometimes, large molecules need to be
moved around in the cell, stored within, or
moved outside the cell

To do this, cells make very small containers
or sacs called vesicles from the plasma
membrane

Transporting out of the cell: exocytosis

Transporting into of the cell: endocytosis
Phagocytosis
During endocytosis the
plasma membrane
invaginates (folds in)
around the molecules to
be transported into the
cell.
Solid particle
CDC
Endocytosis
Pinocytosis
Membranebound vesicle
Endocytosis
1
Materials that are to be
collected and brought into the
cell are engulfed by an
invagination of the plasma
membrane.
2
Plasma
membrane
Vesicle buds off from
the plasma
membrane.
3
Cell cytoplasm
The vesicle carries molecules
into the cell. The contents may
then be digested by enzymes
delivered to the vacuole by
lysosomes.
Example:
Phagocytosis
Food particle
(cell eating)
Amoeba
pseudopod
The particles are contained
within a membrane enclosed
sac (a vacuole).
Digestion of the particles
occur when the vacuole fuses
with a lysosome containing
digestive enzymes.
Engulfed
bacterium
Exocytosis
Exocytosis releases
molecules from the inside of
the cell to outside of the cell.
Exocytosis occurs by fusion of
a vesicle membrane with the
plasma membrane. The
vesicle contents are then
released to the outside of the
cell.
Transport
vesicle
Cross section through the plasma
membrane of cardiac muscle showing
the presence of transport vesicles.
TEM X 162,000
Exocytosis
3
2
1
Vesicle carrying molecules
for export moves to the
perimeter of the cell.
The contents of the vesicle are
expelled into the intercellular space
(which may be into the bloodstream).
Vesicle fuses with
the plasma
membrane.
Summary
There are two types of transport in
a cell.
1. Passive (not requiring energy)
diffusion and facilitated diffusion
Osmosis
Facilitated diffusion
2. Active or energy requiring
Active transport
Cytosis (exocytosis, endocytosis etc)
SUMMARY
Summary: crossing the cell membrane
Type
Description
Molecules
Simple diffusion
Unassisted (passive) movement of solutes down a
concentration gradient (ie from area of high solute
concentration to area of low solute concentration)
Lipophillic molecules and
Small polar or non polar
molecules, eg
oxygen, carbon dioxide
Osmosis
Simple diffusion of water from an area of low solute
concentration to an area of high solute concentration
Water
Facilitated
diffusion – carrier
proteins
Protein assisted movement down a concentration gradient molecule binds to its carrier protein, potentially changing its
shape, and is carried to the other side
Larger molecules –
usually hydrophobic
Facilitated
diffusion – channel
proteins
Protein assisted movement down a concentration gradient Channel proteins form pores in the membrane that fill with
water and dissolve hydrophillic molecules
Molecules that dissolve in
water eg ions
Active transport
Protein assisted movement up (ie from low concentration to
high concentration) a concentration gradient, requiring
energy input
Nutrients, glucose, waste
products
Endo/Exocytosis
Movement of large molecules into (endocytosis) or out of
(exocytosis) the cell
Large molecules or
groups of macromolecules
(eg hormones, mucus)
CARBOHYDRATES –
CHLOROPLASTS AND
MITOCHONDRIA
carbohydrates

Also made of C, H & O atoms in a 1:2:1 ratio

Subunits are simple sugars called
monosaccharides and disaccharides

Solubility in water – depends on size and polarity

Three important cellular functions
– Chemical energy storage
– Component of other important molecules (eg
DNA)
– Structural (esp. in plants)
carbohydrates
Type
Simple
carbohydrates
Monosaccharides (single
sugar unit)
General formula: (CH2O)n
Disaccharides
(two sugar units)
Complex
carbohydrates
Polysaccharides
(many sugar units)
Example
Function
Glucose
Energy source
Fructose
Energy source
Ribose
Component of DNA
Sucrose
Transport sugar in vascular
plants
Lactose
Component of milk
Maltose
Obtained in breakdown of
starch
Starch
Storage molecule in plants
Glycogen
Storage molecule in
animals
Cellulose
Component of plant cell
wall
Chitin
Component of insect and
crustacean exoskeleton
Organelles for energy:
chloroplasts

Chloroplasts are found in green plant cells and
some protists and are the site of
photosynthesis

Have an inner and outer membrane

The inner membrane extends to form a system
of membranous sacs called lamella or
thylakoids. When several of these stack
together they form grana.

Enclosed by the inner membrane is the
stroma – a gel-like enzyme-rich matrix

Have own genetic material: DNA and RNA
and ribosomes.
Organelles for energy:
mitochondria

Small, cigar-shaped organelles found in
cytosol

Consists of smooth outer membrane and
highly folded inner membrane (the folds
are called cristae)

Fluid filled intermembrane space,
filled with protein-rich fluid called
matrix

Have own genetic material: mtDNA
and RNA and ribosomes. This allows
them to undergo division.
NUCLEIC ACIDS AND THE
NUCLEUS
Nucleic acids – DNA & RNA

Subunits are called nucleotides and are
composed of:
– A five carbon (pentose) sugar
 Ribose in RNA
 Deoxyribose in DNA
– A negatively charged phosphate group
– An organic nitrogen containing compound called a
base
 Purines: Adenine (A) and Guanine (G)
 Pyrimidines: Thymine (T) and Cytosine in DNA or Uracil
in RNA
Nucleic acids
Double
ring
Single
ring
PURINES
Adenine
Guanine
PYRAMIDINES
Thymine
Cytosine
Uracil (in RNA)
Nucleic acids

5’-Sugar molecule of one
nucleotide binds to the
phosphate group of the next
in a condensation
polymerisation reaction

A phosphodiester bond is
formed between the
nucleotides creating a
polynucleotide strand

Polynucleotide strand extends
in a 5’-> 3’ direction – said
to have directionality
Nucleic acids
5’-carbon
3’-carbon
3’-carbon
5’-carbon
 DNA
is made of two
polynucleotide
strands that are held
together by
hydrogen bonding
between the
complementary base
pairs
 The
two strands are
anti-parallel
Nucleic acids

Found within nucleus

Store information in a chemical code
called a gene that directs cells to make
proteins

Differences between DNA & RNA
DNA
RNA
Double stranded
Single stranded
Deoxyribose sugar (one less Ribose sugar
O atom)
Thymine base
Uracil base
Nucleus

Information and control centre of the cell - Controls
production of all proteins via DNA in chromosomes

Nucleus contained within double membraned nuclear
envelope, which:
– is continuous with the endoplasmic reticulum (helps
distribute materials through cell)
– Contains numerous openings, called nuclear pores,
channels for moving water soluble

Nuceoli in the nucleus synthesise ribosomal RNA (rRNA)
and ribosomes
Nucleus
PROTEINS
RIBOSOMES, ENDOPLASMIC
RETICULUM AND GOLGI
Proteins

Subunits are amino
acids composed of:
– Central carbon atom
attached to:





Hydrogen atom
Carboxyl (COOH) group
Amine group (NH2)
R group
Type of R group:
– Distinguishes an amino acid and
gives it particular properties
– Gives protein molecule polar and
non-polar regions
Protein structure

Each protein molecule has a characteristic 3D
shape

The function of the protein depends on the
shape of the molecule

Protein structure can be explained by four
levels
Protein structure

Primary:
– Sequence of amino acids
peptide bonded through
condensation
polymerisation reaction into
polypeptide chain

Secondary:
– Parts of the chain undergo
coiling (a-helices) and
folding (b-sheets) due to
hydrogen bonding
between amino acids.
– Other parts form random
loops
Protein structure

Tertiary:
– Hydrophilic and hydrophobic R groups of one
amino acid attract like groups of another amino
acid, making the chain more folded, coiled or
twisted into the protein’s functional shape
– Determines biological functionality

Quarternary:
– Many large protein molecules have two or more
polypeptide chains
Protein function
Function of protein
Example
Structural
Collegen, keratin, fibrin
transport
Haemoglobin, protein carrier, serum
albumin
regulatory
Hormone, enzyme
Protein pathways

Eukaryotic cells have mechanisms to
assemble, package and transport proteins
within a cell
Protein Synthesis Summary
Protein synthesis: Ribosomes

Proteins are synthesised on extremely small
organelles called ribosomes

There are enormous numbers of ribosomes in a cell to
make all the proteins needed

Lack a membrane and are composed of 2 sub-units –
rRNA and protein

mRNA from the nucleus passes through nuclear pores
into the cytosol and is translated by ribosomes into
polypeptide chains, with the help of tRNA
Protein synthesis: Ribosomes
Protein transport: Endoplasmic reticulum

In eukaryotic cells, ribosomes are attached to membranes of the
endoplasmic reticulum (ER).

The ER is a series of
folded membranes and
tubules found in the
cytosol.

Proteins produced by
the ribosomes enter
the tubules and are
transported around
the cell

Proteins may also be
modified in ER
Protein packaging: Golgi

Receives proteins from ER,
where they may undergo
further modification and/or
storage

Proteins are placed in a
vesicle and transported to
other parts of the cell or the
plasma membrane for
exocytosis
OTHER CELL COMPONENTS
AND COMMUNICATION
Cellular recyclers: Lysosomes

Lysosomes are vesicles containing powerful
digestive enzymes

Can break down macromolecules and even
organelles into simpler molecules.

Any material that is not reused inside the cell
is released from the lysosome by exocytosis
into the extracellular fluid

In white blood cells, they also digest
pathogens
Cell movements and connections: cytoskeleton
Cell movements and connections: cytoskeleton

The cytoskeleton consists of a network
of protein fibres
Fibre
Function
Microtubules
Movement of chromosomes, organelles, cilia and
flagella
Intermediate
filaments
Provide tensile strength for the attachment of
cells to each other and their external
environment
Microfilaments
Composed of contractile filaments of actin that,
together with myosin, control muscle
contraction, maintain cell shape and carry out
cellular movements
Cell movements and connections:
extracellular matrix

Most cells have an extracellular matrix
(ECM) that are an integral part of the structure
and function of the cell:
– eg cell wall in plants
– Bone and cartilage in animals are connective
tissues largely made up of ECM

ECM has important role in determining shape
and mechanical properties of tissues and organs
Animal Cells

There are three different types of
junctions in animal cells: occluding,
communicating (gap) and anchoring
(desmosomes) junctions (see figure
2.25).
Anchoring
junctions are
the most
common form of
junction
between
epithelial cells.
Dense plaques
of protein exist
at the junction
between two
cells. Fine fibrils
extend from
each side of
these plaques
and into the
cytosol of the
two cells
involved. This
structure has
great tensile
strength and
acts throughout
a group of cells
because of the
connections
from
one cell to
another.
Occluding junctions involve
cell membranes coming
together in contact with each
other. There is no movement of
material between cells.
Communicating junctions consist of protein-lined pores in the membranes of adjacent cells. The
proteins are aligned rather like a series of rods in a circle with a gap down the centre and permit the
passage of salt ions, sugars, amino acids and other small molecules as well as electrical signals from
one cell to another.
Plant cells

Plants have rigid cell walls. Hence, plant cells have no
need for a structure such as the anchoring junctions of
animal cells.

Secondary walls are laid down in each cell on the
cytosol side of the primary wall so that the structure
across two cells is relatively wide, at least 0.1 μm thick.

The junctions that exist in plant cells to allow
communication between adjacent cells in spite of the
thick wall are plasmodesmata (singular:
plasmodesma)
Plant cells

Because of the way in which plant cell
walls are built up, the gap or pore
between two cells is lined with plasma
membrane so that the plasma membrane
of the two cells is continuous.

A structure that bridges the ‘gap’ is also
continuous with the smooth endoplasmic
reticulum of each cell.