CHAPTER 3
Structure & Function
of the Cell
Cell /Plasma Membrane
Structure:
phospholipid bilayer = two layers of phospholipids
Arranged tail to tail with ‘heads’ on the extreme outer &
inner edges of the membrane and tails pointing to the inside
of the membrane
Cholesterol makes up about 1/3 of the lipids in the membrane
Membrane contains embedded proteins which move freely
throughout the membrane
This arrangement is known as the Fluid Mosaic Model
In the Fluid Mosaic Model the individual proteins float
freely in the lipid layer like rubber balls in a tub of water
Hydrophilic
head
Lipid
bilayer
Hydrophobic
tails
Membrane Proteins
Integral proteins penetrate both sides of the membrane
Peripheral proteins attach to inside OR outside of membrane
Channel proteins integral proteins that form a channel
through the membrane. These are SELECTIVE – only some
molecules can pass through them
Factors governing whether a specific ion/molecule might
fit in the channel include:
Shape
Size
Charge
Remember, proteins are intricately
folded polymers. The ‘ribbon’ here
shows the folding. The green ‘blob’
approximates the space taken up by
this protein
While this image doesn’t show this
many of these channels are actually
several individual proteins – pie slices
May be passively open
much of the time
Open channel in response
to an extracellular signal
such as a neurotransmitter
Many uses such as:
Recognition of ‘self’
vs. ‘non-self’
(immunity)
Cytoplasm
The cellular material inside the cell membrane NOT
including the nucleus
This includes:
Cytosol
Organelles
Cytosol – the fluid part of the cell (excluding the organelles)
about 80% water. Includes dissolved solids such as ions,
proteins, other molecules
Cytoskeleton
An internal framework which supports the cell and anchors
many of the organelles in place. Made up of:
Actin (microfilaments) – 8nm diameter fibrils which form
bundles, networks and layers inside the cell. These adjust
cell shape and are responsible for cell movements
Tubulin – hollow tubes about 25nm in diameter. These form
internal scaffolding within the cell.
Intermediate filaments – about 10nm in diameter. Add
strength to cellular projections (e.g. inside of nerve axons)
Cytoplasmic Inclusions
‘Things inside a cell’
Oil/fat droplets – for energy storage
Glycogen grains (animal starch) for energy storage
Organelles – ‘cellular organs’
Organelles… (so we begin)
Ribosomes – the ‘protein factories’ of the cell
Made up of rRNA and Protein
There are two subunits
a large 60S subunit and
a small 40S subunit
Together then form an 80S ribosome
S = refers to their sedimentation rate not their size
so you don’t add the numbers
Endoplasmic Reticulum
abbreviated ER
Vast network of tubes and chambers throughout the cell
This region may be studded with ribosomes, if so it is called
Rough Endoplasmic Reticulum or RER
Since ribosomes produce proteins, RER is a major site of
protein synthesis. Proteins collect on the inside of RER
as they are synthesized.
Finished proteins will be packaged in vesicles which are
small bubbles of membrane for transport to storage
Golgi Apparatus
These ‘pancake-like’ stacks of membrane sacks (think of
a stack of ziplock bags) are storage locations.
Cisterna are individual storage chambers within the Golgi
Complex.
Small secretory (release) vesicles leave Golgi carrying
cell products off for use. Often these fuse with the cell
membrane and release them to the outside in a process
known as exocytosis (cell spitting)
Lysosomes
Vesicles containing enzymes designed to digest.
These hydrolytic enzymes will break down nucleic acids,
proteins, lipids and polysaccharides.
Food particles, invading bacteria, damaged organelles all
can be merged with lysosomes to be broken down and
digested into useable components.
If incorrectly ruptured, lysosomes can destroy the cell
Peroxisomes
Vesicles which contain enzymes which can break down fatty
acids and amino acids into useable components
Hydrogen peroxide is a waste product from these reactions
To help remove hydrogen peroxide these peroxisomes contain
catalase, an enzyme which converts hydrogen peroxide to water
and oxygen
Present in liver and kidney (detox & filtering organs)
Endosymbiotic
Theory
Production of energy for the cell. Synthesize ATP
Enzymes within the matrix are involved in the
production of ATP (energy storage molecule)
Mitochondria have their own DNA & divide on their own
Cilia & Flagella
Movement of material across cell surface OR movement
of the cell itself
Cylindrical structures - two central tubules wrapped by
nine pairs of tubules (see fig 3.26 pg 79)
Flagella tend to be relatively long (55 μm) and only 1 per cell
e.g. sperm cell ‘tail’ is a flagellum. Move in whip-like motion
Cilia – tend to be shorter (10 μm) and occur in large numbers
these beat in a power & return stroke and set up a current across the
surface of the tissue… e.g. respiratory tract, fallopian tubes
motion comes from flexing of
dynein arm – driven by ATP
Centrosome
A special region of cytoplasm which contains:
two centrioles (definition follows)
Centriole – a bundle of microtubules:
Nine groups of three evenly spaced bundles
Used in cell division (they duplicate and then move to
opposite ends of cell … two at each end)
These serve as anchor points for spindle fibers which form
during cell division
Microvillus
‘hair-like’ projections of cell membrane
Supported internally by cytoskeletal filaments
Purpose – to increase surface area, providing better absorption
Cell structures & functions
Be familiar with table 3.1 on page 59 which lists
structure and function for organelles and other cell parts
Sit Down
Be Quiet
Hang On!
This could get messy.
Movement Across Cell Membrane
Diffusion
this is just a list… details of each to follow
Osmosis
Filtration
Mediated (assisted) Mechanisms:
Facilitated Diffusion
Active Transport
Secondary Active Transport
Endocytosis & Pinocytosis
Exocytosis
Shape
Size
Charge
Active Transport
Membrane Protein carries molecule but requires
energy - ATP
Can move molecules against concentration gradient
Example – Na+/K+ pump (sodium/potassium)
Three sodium ions are pumped out of the cell as two
potassium ions are pumped in
Energy cost to cell = 1 ATP
Secondary Active Transport
Uses the flow of one ion along its concentration gradient
to assist the flow of a different molecule
Cotransport -the two can be moving in the same direction
also called Symport (directional word)
Countertransport – the two ions move in opposite direction
also called Antiport (directional word)
Must function through a transport protein
Example: Na+ assisted glucose transport (fig 3.19 p73)
notice – glucose is
being moved against
its concentration gradient
Movement of large
particles & droplets
Endocytosis – engulfing large solids by flowing around them
also called phagocytosis
Pinocytosis – engulfing droplets of fluid by flowing around them
Receptor Mediated Endocytosis – receptors on cell surface
attach specific molecules and when filled are taken in to cell
Exocytosis – release of materials from cell by merging
vesicle with cell membrane (usually cell products released)
Cell Division
Mitosis – division of somatic (body) cells
Results in two cells each of which have the same number
of chromosomes as the parent cell
Prophase
chromatin condenses to form chromosomes
centrioles head to opposite ends of cell
spindle forms & attach to kinetochore
during interphase the
DNA is unpacked, loosely
coiled strands called chromatin
Notice, these are duplicated (double) chromosomes
each half is referred to as a chromatid
Metaphase
chromosomes aligned at equator
Anaphase
Chromatids pulled to
opposite ends
Cytokinesis
cells ‘pinch apart’
Telophase
migration complete new
nuclear membrane forms
spindle disappears
chromosomes begin to
unravel into loose chromatin strands
DNA Replication
Occurs during S Phase of cell cycle
DNA is double-stranded. Replication is the faithful copying of each strand
Since base pairing is specific, each strand can serve as the template for the opposite
One parent molecule of double-stranded DNA gives two daughter molecules
each daughter molecule contains one "original" strand and one newly synthesized strand
this is called semiconservative replication
G C
G C
G C
T A
T A
T A
A T
A T
A T
CG
C G
C G
G C
G C
G C
T A
T A
T A
DNA Replication continued
DNA strands are antiparallel
one strand runs in the 5’ – 3’ direction
the other runs 3’ – 5’
new synthesis occurs in a specific direction (5’-3’)
one new strand is the leading strand synthesizes continuously
(occurring in the 5’-3’ direction)
the other is the lagging strand (cannot synthesize continuously
due to direction of DNA)
This image IS NOT in your book… not to worry, you can get it from Moodle
DNA Polymerase
Leading strand
Helicase
Lagging strand
DNA Ligase
What is a gene?
Gene = the sequence of DNA which contains the information
to make one protein
Gene (DNA) read and copied as Messenger RNA (mRNA)
the writing of mRNA from DNA is called Transcription
This piece of mRNA will then be used to make a protein. The
message is read by a ribosome.
mRNA nucleotides are read in groups of three called codons.
Each codon calls for a specific amino acid
Protein Synthesis
background terminology
tRNA = Transfer RNA – each of the 20 different amino acids has
a specific tRNA which acts as a carrier molecule for the amino acid
One end of the tRNA holds it’s specific amino acid the other end,
called the anticodon is a complimentary match for the mRNA code
which signals for the amino acid
Translation – the process of making a protein: ribosome reads mRNA
tRNAs add amino acids, peptide chain grows
tRNA
Met
This end holds the amino acid
and is specific – it only holds ONE
PARTICULAR amino acid type
This end, called the anticodon, is complimentary
to the codon on the mRNA. (base pair rules)
A
G
C
A
U
G
A
G
C
A
C
G
C
Genetic Code
61 different codons (mRNA)
code for 20 different amino acids
(obviously some repeat)
ONE codon AUG signals START and occurs
at the beginning of every mRNA
It codes for the amino acid methionine, so
every proteins starts with this amino acid
Three codons signals STOP and one of these
will be found at the end of each mRNA
UAA, UAG or UGA
Notice: where different codons code for
the same amino acid, the first two bases
are often the same and the last differs.
Because of this, the third base is often
called the ‘wobble base’. It may help to
protect against mutations in some cases
Let’s Translate A Protein
If our mRNA reads like this…
AAAAGUAUGCGUUGGUGUGGUGGCGAUGCAGUAUGUUACUCAUAACCUAA
Find the START codon (AUG) and break the sequence into codons (3 base sections) from
that point… continue until you reach a STOP codon (UAA, UAG or UGA)
Then read the codons to determine the appropriate amino acid to use next)
AAAAGU AUG CGU UGG UGU GGU GGC GAU GCA GUA UGU UAC UCA UAA CCUAA
Met- Arg- Trp- Cys- Gly- Gly- Asp- Ala- Val- Cys- Tyr- Ser- STOP
Protein Synthesis
an overview
Gene (DNA) is read and copied as Messenger RNA (mRNA)
mRNA (a ‘recipe’ for a protein) leaves the nucleus & enters
the cytoplasm
Ribosome binds to mRNA (at AUG)
Ribosome ‘reads’ mRNA one codon at a time (=3 bases)
Appropriate transfer RNA (tRNA) brings in the correct
amino acid needed for each section of mRNA
Next section of mRNA read, next tRNA brings next amino acid.
Protein gets one amino acid longer… repeat... repeat…repeat…
mRNA Editing
not all portions of gene are used to
make a protein
Introns removed
Exons - translated into protein
WHY?
Among other reasons…
this can allow one gene to code
for multiple versions of a protein
Parts A + B + D = protein X
Parts B+C+E = protein Y
Two ‘slots’ for tRNA on the ribosome
first tRNA (carrying Methionine (Met)
attaches in slot #1
Second tRNA, carrying it’s amino acid
attaches in slot #2
Amino acid from the tRNA in #1
is transferred to the amino acid held
by #2 (peptide bond forms)
First tRNA, having passed off
it’s amino acid falls away. mRNA
clicks one step farther on carrying
the tRNA from slot #2 to slot #1
leaving slot #2 open for the next
tRNA.
Notice, here… many ribosomes can be reading a single piece
of mRNA. Each ribosome is making a protein.
Meiosis
The production of gametes (sex cells)
Where body cells have two copies of each chromosome – diploid
sex cells have only one copy of each chromosome - haploid
Each gamete has 23 chromosomes:
22 somatic (body) chromosomes and
one sex chromosome (either X or Y)
Oocytes (eggs) always have an X chromosome
Sperm may carry either X or Y
Meiosis Differs From Mitosis
Undergoes two separate divisions
During prophase the two homologous pairs group together
to form a tetrad - Don’t let this disturb you, all the same chromosomes
were here during mitosis they just didn’t pair up this way…
Meiosis proceeds through
Prophase-1
Metaphase-1
Anaphase-1
Telophase-1
Then on to…
Prophase-2
Metaphase-2
Anaphase-2
Telophase-2
Count the chromatids
(duplicate chromosomes)
as we start
Compare this to what we end up with
Crossing Over
When tetrads form during Prophase-1 crossing over may occur
Small pieces of a chromosome may become detached (precisely so)
May exchange a similar region with their partner chromosome
Perhaps the chromosome you inherited from Dad will swap
it’s eye color region with the eye color region from Mom’s
This provides a way for you to make new genetic combinations
of genetic material every time you make a new sex cell.
blue
Make the
bad man
Stop !!!
HELP!
MY HEAD
IS LEAKING!
Metabolism of Glucose
Our Goal:
To retrieve energy (ATP) from glucose
Carbohydrate Catabolism
•Three phases – making a total of 38 ATP for each glucose molecule
•Glycolysis – splits glucose (6-Carbons) in half making two (3-carbon)
•pyruvic acid molecules --- process releases a small amount of energy
•and small amount of NADH
•Krebs Cycle – extracts energy from pyruvic acids (small amount)
•creates lots of NADH and FADH2 for later use in the….
•Electron Transport Chain – extracts lots of energy from NADH
•and FADH2 (Electron carrying molecules)
Glycolysis
occurs in
cytoplasm
Krebs
occurs in
mitochondria
Electron transport
chain occurs in
mitochondria
Glycolysis
Preparatory phase – costs cell energy
Energy conserving phase – produces energy
Cost = 2 ATP
Gain = 4 ATP & 2 NADH (NADH to be used later)
Produces two pyruvic acids to send through Krebs Cycle
Glycolysis occurs in the cytoplasm of eukaryotes
Energy Input - COST
Energy Input - COST
Total cost so far = 2 ATP
Total energy gain = 0
Cost = 0 during this stage
Gain = 4 ATP + 2 NADH (will be used later)
produce 2 pyruvic acid to use in
Krebs Cycle
Krebs Cycle (Plus “the bridge”)
Each cycle of Krebs and “the bridge step” produces
1 ATP
4 NADH
1 FADH2
Since we can run Krebs
twice our total yield is:
2 ATP
8 NADH
2 FADH2
Krebs Cycle – runs once for each pyruvic acid each glucose broken
produces two pyruvic acids so we can run Krebs twice.
The NADH and FADH2 will be used in the next step to recover many
ATPs
Electron Transport Chain
NADH enters at first protein – ejects 2 hydrogen ions (one pair of H+)
from the inner membrane of the mitochondria
Ejects two more pairs of H+ at the next two steps in the chain
A total of 3 pairs of H+ have been ejected when an NADH completes
it’s passage along the chain
Each pair of H+ ions passes through an ATP Synthase molecule
making one ATP as they pass through
FADH2
Also uses the electron transport chain but can’t enter at the first
step
must enter at the second step
Because of this it can only move 2 pairs of H+ and will ultimately
be responsible for production of 2 ATP molecules
Energy Yield
…from Electron Transport Chain
10 NADH = 30 ATP
2 FADH2 = 4 ATP
If you add this to the two we got from Krebs plus the two we
gain from Glycolysis you have a total produced of 38 from the
breakdown of a single glucose molecule
The rest of these…
Are just for fun!
Begin here...