A Picture of the Big Picture

Stefanie Kautz, PhD

Bi 211 Chapter 7 Inside the Cell

https://www.khanacademy.org/partner-content/crash-
course1/partner-topic-crash-course-bio-ecology/crash-
course-biology/v/crash-course-biology-104

http://www.bozemanscience.com/a-tour-of-the-cell/
Objectives
1. Describe structure and function of prokaroytic and
eukaryotic cells
2. Describe structure and function organelles, and how this
varies in specialized cells
3. Describe molecular “zip codes” in protein transport.
4. Interpret experiments in protein movement
5. Describe cytoskeletal filaments and motor proteins.
Structure and Function at the Whole-Cell Level
 Cell size and organelles
correlates with function
 Cells are dynamic living
things
– Have interacting parts
– Contain constantly
moving molecules

All cells have

1. Nucleic acids: store and transmit information
2. Proteins: perform most of the cell’s functions
3. Carbohydrates: chemical energy, carbon, support, identity
4. Plasma membrane: selectively permeable membrane
barrier
How are these things organized in the cell to make a
functional living unit?
Grouping Cells
According to morphology, there are two broad groupings of life:
1. Prokaryotes: Lack a membrane-bound nucleus
2. Eukaryotes: Have a nucleus
The three domains according to phylogeny, or evolutionary
history, are
1. Bacteria: prokaryotic
2. Archaea: prokaryotic
3. Eukarya: eukaryotic
Eukarya and archaea are more closely related to one
another than either is to bacteria

https://kaiserscience.wordpress.com/biology-the-living-environment/cells/test/
Prokaryotic Cells: Structural Overview
 All prokaryotes lack a
membrane-bound nucleus
 Bacterial cells vary greatly in
size and shape
 Most bacteria contain several
structural similarities
– Plasma membrane
– A single chromosome
– Ribosomes, which
synthesize proteins
– Stiff cell wall
Most prokaryotic species have one supercoiled circular
chromosome In the nucleoid region of the cell

The chromosome contains a long

strand of DNA, a few supportive
proteins
 The DNA double helix coils on
itself with the aid of enzymes to
form a compact, “supercoiled”
structure
In addition, many bacteria contain E. Coli treated to release DNA
plasmids
 Small, supercoiled, circular DNA
molecules
 Usually contain genes that help
the cell adapt to unusual
environmental conditions
 Are physically independent of the
cellular chromosome
Prokaryotic Cells: Internal Structure
 Other structures contained
within the cytoplasm
 Ribosomes: Consist of RNA
molecules and protein
– Used for protein synthesis

 Many prokaryotes have internal

photosynthetic membranes

 Cytoskeleton: The inside of the

cell is supported by a network of
long, thin protein filaments
Bacterial Organelles: Recently, internal compartments in
many bacterial species were discovered
Bacterial organelles perform an
array of tasks
1. Store [Ca2+] and other key
molecules
2. Holding crystals of the
mineral magnetite which
function like a compass, to aid
swimming in a directed way
3. Organizing enzymes
4. Synthesize complex carbon
compounds from carbon dioxide
5. Sequester enzymes
6. Generate chemical energy
from ammonium ions
Prokaryotic Cells: External Structure
 The cell wall forms a
protective “exoskeleton”
 Most prokaryotes have a cell
wall
 Bacterial and archaeal cell
walls
– Composed of a tough,
fibrous layer
– Surrounds the plasma
membrane
 Many species have an
additional layer:
– Outside the cell wall
– Composed of glycolipids
Prokaryotic Cells: External Structure
Some prokaryotes have tail-like flagella embedded in the
plasma membrane
– spins long, helical filament
– Propels cells through water
Fimbriae (singular: fimbria): Are needlelike projections which
promote attachment to other cells or surfaces
– Extend from the plasma membrane of some bacteria
An Introduction to Eukaryotes
 Range in size from very small
to very large: microscopic
algae to 100-meter-tall
redwood trees
 Many multicellular, some
unicellular
 Large size makes molecules
diffusion across the entire cell
difficult, partially solved by
breaking up the large cell
volume into several smaller
membrane-bound organelles
The compartmentalization of eukaryotic cells
offers two primary advantages:
1. Separation of incompatible chemical reactions
2. Increasing the efficiency of chemical reactions
Eukaryotic cells are partitioned into
functional compartments
The four major life processes in eukaryotic
cells & their organelles
1. Manufacturing: nucleus, ribosomes,
endoplasmic reticulum, and Golgi
apparatus
2. Breakdown of molecules: lysosomes,
vacuoles, and peroxisomes
3. Energy processing: mitochondria in
animal cells and chloroplasts in plant
cells
4. Structural support, movement, and
communication: cytoskeleton, plasma
membrane, and cell wall
Animal cells vs Plant cells
– Lysosomes and centrioles are not found in
plant cells
– Plant cells have a rigid cell wall,
chloroplasts, and a central vacuole
http://www.bozemanscienc
e.com/043-cellular-
organelles
The nucleus is large and highly organized
structure
 Surrounded by a double-
membrane nuclear envelope
 The nuclear envelope is
studded with pore-like
openings
 The nucleus has a distinct
region called the nucleolus
(where ribosomal RNA is
made)
 Function: Information storage
and processing
– Contains the cell’s
chromosomes
– RNA synthesis
Proteins destined for the nucleus have a have 17-amino-acid-
long nuclear localization signal (NLS) which marks them for
transport to the nucleus

 Nuclear pores function as doors into and out of the nucleus

 Nuclear proteins are synthesized by ribosomes in the cytosol
 Movement of proteins and other large molecules into and out
of the nucleus is an energy-demanding process
Ribosomes function in protein synthesis
 Ribosomes are non-
membranous
 Are not considered
organelles
 Have large and small
subunits
– Both contain RNA
molecules and protein
– Can be attached to the
rough ER
– Can be free in the
cytosol, the fluid part of
the cytoplasm

https://www.youtube.com/watch?v=MiVqjxi0DfQ
Rough Endoplasmic Reticulum (Rough ER, RER)
Structure: Network of membrane-bound tubes and sacs
studded with ribosomes
– The interior is called the lumen, is continuous with the
nuclear envelope
Function: Synthesis of specific proteins that will be
– Inserted into the plasma membrane
– Secreted to the cell exterior
– Shipped to an organelle
Smooth Endoplasmic Reticulum (Smooth ER,
SER)
Structure: network of membrane-bound tubes and sacs lacking
ribosomes
Function:
– Contains enzymes that catalyze reactions involving lipids which
– Synthesize lipids needed by the organism
– Break down lipids and other molecules that are poisonous
– Detoxifies cell
– Reservoir for Ca2+ ions
Golgi Apparatus
Structure: formed by a series of stacked
flat membranous sacs called cisternae
 Has a distinct polarity, or sidedness
 The cis (“this side”) surface is closest to
the nucleus
 The trans (“across”) surface is oriented
toward the plasma membrane
Function: Processes, sorts, and ships
proteins synthesized in the rough ER
 cis side of a Golgi apparatus receives
products from the rough ER
 trans side ships them out to other
organelles or the cell surface
 Membranous vesicles carry materials
to and from the organelle
 The Endomembrane System (SER, RER, Golgi,
Lysosomes): A system for protein and lipid synthesis
Most of the proteins found in peroxisomes, mitochondria, and chloroplasts are
actively imported from the cytosol.
 Contain special signal sequences that target them to the appropriate
organelles
Proteins intended for secretion out of
cell are synthesized and processed
by the endomembrane system

In the RER lumen, proteins are

folded and glycosylated
(carbohydrates are attached to the
protein)

Proteins are packaged into vesicles

when they move from the RER to the
Golgi apparatus and from the Golgi
apparatus to the cell surface
The Signal Hypothesis
 The signal hypothesis: Proteins bound for the endomembrane
system have a 20-amino-acid-long ER signal sequence which
directs the growing polypeptide to the ER
 The ER signal sequence binds to a signal recognition particle
(SRP)
– That then binds to a receptor in the ER membrane
Moving from ER to Golgi to Plasma Membrane

Cisternal maturation:
Golgi is dynamic
 New cisternae form
at cis face
 Old cisternae exit
from trans face
 Replaced by the
cisternae behind them

https://www.youtube.com/watch?v=rvfvRgk0MfA
How Are Products Shipped from the Golgi?
 Proteins exiting Golgi have molecular tag which places it in a
particular type of transport vesicle which also has a tag
directing it to correct destination
 Exocytosis and Endocytosis
A cell uses two mechanisms for moving
large molecules across membranes

Exocytosis is used to export bulky

molecules, such as proteins or
polysaccharides

Endocytosis is used to import

substances useful to the livelihood of
the cell
– The sequence of events begins
when macromolecules outside the
cell bind to receptors on the
plasma membrane

http://highered.mheducation.com/sites/983409
2339/student_view0/chapter5/endocytosis_and
_exocytosis.html
Lysosomes
Structure: single-membrane-
bound structures
 Contain approximately 40
different digestive enzymes
 Found only in animal cells

Function:
 Digestion
 Waste processing
 Acid hydrolases (break down
polymers via hydrolysis)
http://highered.mheducation.com/si
tes/0072495855/student_view0/cha
pter2/animation__lysosomes.html
 Recycling Material in the Lysosome via Autophagy
and Phagocytosis
Autophagy (literally, “same-eating”): Damaged organelles are enclosed
within an internal membrane and delivered to a lysosome where the
components are digested and recycled
Phagocytosis (“eat-cell-act”): The plasma membrane of a cell surrounds a
smaller cell or food particle and engulfs it forming a structure called a
phagosome
– Is delivered to a lysosome, where it is taken in and digested
 Vacuoles
Structure: large, membrane-bound structures
found in plants and fungi

Function:
– Some vacuoles are specialized for
digestion
– Some contain digestive enzymes
– Most are used for storage of water and/or
ions to help the cell maintain its normal
volume
– Inside seeds, they are filled with proteins
– In flower petals or fruits, they are filled
with colorful pigments
– They may be packed with noxious
compounds to protect leaves and stems
from being eaten by predators
 Peroxisomes
Structure:
– Globular organelles bound by a
single membrane
– Originate as buds from the ER

Function:
– Center of oxidation reactions
– Liver cell peroxisomes contain
enzymes that remove electrons from,
or oxidize, the ethanol in alcoholic
beverages
– Specialized peroxisomes in plants,
called glyoxysomes
– Are packed with enzymes
– Oxidize fats to form a compound for
energy storage

https://www.youtube.com/watch?v=I6oANzTflIo
Mitochondria
Structure: two membranes
 The inner one is folded into
a series of sac-like cristae
 The solution inside the
cristae is the mitochondrial
matrix
 Have their own DNA
(mtDNA)
 Manufacture their own
ribosomes

Function: ATP production is

a mitochondrion’s core
function
https://en.wikipedia.org
Chloroplasts: contained in most plant and algal cells
Structure: double membrane
 Chloroplasts contain
membrane-bound, flattened
vesicles called thylakoids
stacked into piles called
grana
 Outside the thylakoids is the
solution called the stroma
 Contain their own DNA
(cpDNA)

Function: Chloroplasts
convert light energy to
chemical energy via
photosynthesis
https://en.wikipedia.org
Cytoskeleton
Structure: Composed of protein fibers
Function:
 Gives the cell shape and structural stability
 organizes all of the organelles and other cellular structures
into a cohesive whole
 Aids cell movement
 Transport of materials within the cell
The Dynamic Cytoskeleton
A dense and complex network of fibers helps maintain cell
shape by providing structural support
Its fibrous proteins move and change to alter the cell’s shape,
shift its content, or move the cell itself

Three types of cytoskeletal elements:

– Actin filaments (microfilaments)
– Intermediate filaments
– Microtubules
Actin Filaments
 Actin filaments the smallest cytoskeletal elements
– Formed by polymerization of individual actin molecules
– Grouped together into long bundles or dense networks
– Usually found just inside the plasma membrane
– Structures that help define the cell’s shape
 The two distinct ends of an actin filament are referred to as plus and
minus ends
 The structural difference results in
– Different rates of assembling new actin subunits
– The plus end growing faster than the minus end
 Actin–Myosin Interactions
 Actin filaments are involved in movement and dependent on the protein
myosin
 Myosin is a motor protein that converts the potential energy in ATP into the
kinetic energy of mechanical work
 Actin–myosin interactions can cause cell movements such as
– Cytoplasmic streaming: is the directed flow of cytosol and organelles
– Cytokinesis: last step of cell division
Cytokinesis (“cell-moving”) is the process of cell
division
 In animals, cytokinesis occurs by the use of actin filaments
connected to the plasma membrane arranged in a ring
around the circumference of the cell
 Myosin causes the filaments to slide past one another, draw
in the membrane and pinch the cell in two
 Intermediate Filaments
Intermediate filaments: Are defined by size rather than composition
– Many types exist, each consisting of a different protein
– Provide structural support for the cell and are not involved in
movement
Examples
Keratin: Includes fingernails, toenails, and hair
Nuclear lamins:
– Form a dense mesh under the nuclear envelope, give the nucleus
its shape and anchor the chromosomes
– Project from the nucleus through the cytoplasm to the plasma
membrane
– Form a flexible skeleton that helps shape the cell surface and hold
the nucleus in place
 Microtubule Structure & Function
 Microtubules: large, hollow tubes made of α-tubulin and β-tubulin
dimers
– Are dynamic and polar, usually growing at their plus ends
– Originate from the microtubule organizing center
 Microtubules: Provide stability, involved in movement, provide a structural
framework for organelles
 Microtubules can act as “railroad tracks” to transport vesicles move
through the cell along these tracks in an energy-dependent process
 Microtubules require ATP and kinesin for vesicle
transport
Kinesin is a motor protein that converts chemical energy in ATP into
mechanical work
 The head region binds to the microtubule
 The tail region binds to the transport vesicle
These domains “walk” along the microtubule using energy from ATP
hydrolysis
The Cell Wall
 Fungi, algae, and plants have a stiff outer cell wall that
protects the cell
 The cell wall in plants and algae: Primary component is
cellulose
 The cell wall in fungi: Primary component is chitin
 Some plants have a secondary cell wall containing lignin
http://www.bozemanscienc
e.com/043-cellular-
organelles

http://www.bozemanscienc
e.com/a-tour-of-the-cell/