living organisms. living systems are separated from other chemical systems by; the capacity for...

Living Organisms

Living systems are separated from other chemical systems by;

• The capacity for replication;

• The presence of enzymes and other complex molecules;

• A membrane that separates the internal chemicals from the external chemical environment.

Terms applied to cells • Heterotrophs (other-feeder): an organism that

obtains its energy from another organism. Animals, fungi, bacteria, and many protistans are heterotrophs.

• Autotrophs (self-feeder): an organism that makes its own food, it converts energy from an inorganic source in one of two ways

• Photosynthesis is the conversion of sunlight energy into C-C covalent bonds of a carbohydrates. This led to the oxidative metabolism

• Chemosynthesis is the capture of energy released by certain inorganic chemical reactions.

Time scale of Evolution

• Life emerged at least 3.8 billion years ago.

• Simple organic molecules could form and spontaneously polymerize into macromolecules.

• No free oxygen but consists CO2 and N2.. Also small amount of H2, H2S and CO.

• RNA world-self replicating RNA molecules.

Evolution of cells

From the Cell, A Molecular Approach2nd edition; Cooper; ASM Press & Snauer

• Below is a list of the most common units of length biologists use (metric)

4.2 Cell sizes vary with their function

Table 4.2

• Cell size and shape relate to function

Figure 4.2

Why cell size vary?

• Smallest cells:– Mycoplasmas; they have the smallest genome

• Bulkiest cells:– Bird eggs, young need a lot of food

• Longest cells:– Nerve cells, can transmit signals over long

ranges

What limits cell size?

• Lower limits– What does the cell need to contain?

• Must house DNA, proteins, and organelles (in eukaryotes).

• Upper limits– It must have enough surface area, why?

• Must be able to obtain enough nutrients from the environment.

Prokaryotic Cells

• Archaebacteria• Eubacteria

• They have plasma membrane• They have nucleoid• They have cytoplasm with

ribosomes

Prokaryote (pro=before, karyo=nucleus)

From Life: The Science of Biology,

4th Edition Sinauer & WH Freeman

Prokaryotic cells

• Very diverse in their metabolic capabilities.

• Some archae are found in hot springs• Some of them are photosynthetic.• Some are able to oxidize inorganic ions

to obtain energy• prokaryotes are asexual, meaning their

offspring nearly always bear the exact characterisics of the parent cell. Division is by binary fission.

Prokaryotic cells

• Prokaryotic DNA is organized as a circular chromosome.

• DNA is supercoiled• Most of DNA is protein coding

Prokaryotes• In Greek pro means before and karyon refers to

nucleus.• Nucleoid(=nucleus like), coiled DNA of a prokaryote.• No organelles in prokaryotes.• Ribosomes (that assemble amino acids) are free in

cytoplasm.• Cell membrane surrounds the cell; cell wall protects

the cell. In some, there is a sticky coat called a capsule (works like a glu).

• Pili and flagella are for attachment and movement.

Procaryote sizes and structures

From Molecular Biology of the Cell

Third edition; Alberts; Garland

Schematic diagram of a typical prokaryotic cell.

Specialized features of some prokaryotes-1

• Cell wall: Outside the PM. Supports the cell and determines the shape.

• It contains peptidoglycan.

• It is not a barrier and some toxins can cause disease

From Life: The Science of Biology,

4th Edition Sinauer & WH Freeman

Specialized features of some prokaryotes-2

• Capsule: • It encloses cell

wall and outer membrane.

• It may protect from WBC

• It is not necessary for living

Specialized features of some prokaryotes-3

• Mesosome:• It is formed by

infolding of the PM

• It may aid the movement in & out of the cell of materials. It may also aid the replication of DNA and cell division.

Specialized features of some prokaryotes-4

• Flagella•Bacterium

moves with its help

• It is anchored to the PM and cell wall

Specialized features of some prokaryotes-5

• Pili•projected

from the surface

•helps to adhere to another bacteria

•shorter than flagella

From the Cell, A Molecular Approach2nd edition; Cooper; ASM Press & Snauer

Structures of animal cells

From the Cell, A Molecular Approach2nd edition; Cooper; ASM Press & Snauer

Eukaryotic Cells:

• Plasma membrane: to define its boundary and retain its content

• Membranous subcompartments (organelles): various cellular functions are localized

• Nucleus: to house the DNA• Cytoplasm: • Plant cells also have a cell wall outside

the PM• Animal cells are usually surrounded by an

extracellular matrix.

Membranes in eukaryotic cells

• It consists of phospholipids and proteins organized into two layers (Phospholipid bilayer)

• It has a polar (hydrophilic) head and two nonpolar (hydrophobic) tails.

Diagram of a phospholipid bilayer

From: Life 4th Edition,

by Sinauer Associates

• Membranes organize the chemical reactions making up metabolism

5.10 Membranes organize the chemical activities of cellsMEMBRANE STRUCTURE AND FUNCTION

Cytoplasm

Figure 5.10

Biological membranes:

• To regulate molecular traffic from one side to another

• To restrict the passage of materials, especially polar ones, since its hydrophobicity of its interior.

• To allow interactions amongst the cells. (i.e. recognition of WBC).

• To provide energy (mitochondria and choloroplast)

• Phospholipids are the main structural components of membranes

• They each have a hydrophilic head and two hydrophobic tails

5.11 Membrane phospholipids form a bilayer

Head

Symbol

TailsFigure 5.11A

• In water, phospholipids form a stable bilayer

Figure 5.11B

Hydrophilicheads

Hydrophobictails

Water

Water

– The heads face outward and the tails face inward

• The plasma membrane of an animal cell

Fibers of the extracellular matrix

Figure 5.12

Glycoprotein Carbohydrate (of glycoprotein)

Microfilaments of the cytoskeleton

Phospholipid

Cholesterol

Proteins

CYTOPLASM

Glycolipid

Biological membranes:

From http://www.biosci.uga.edu/almanac/bio_103/notes/may_15.html.

Structure of an animal cell

From http://www.biosci.uga.edu/almanac/bio_103/notes/may_15.html.

Nucleus

• Nuclear envelope: Inner and outer nuclear membranes

• Nuclear pores• Nucleolus

From: Life 4th Edition,

by Sinauer Associates

Liver Cell Nucleus

From: www.DennisKunkel.com

Nuclear envelope and nuclear pores

From: www.DennisKunkel.com

From: Life 4th Edition,

by Sinauer Associates

Nucleus

• Chromatin: DNA associated with proteins, forms long fibers.

• Each fiber constitutes a chromosome.

• Chromosomes condense during mitosis/meiosis.

• Chromosomes are enclosed within a nuclear envelope, a double membrane with pores.

• Nucleolus consists of parts of the chromatin DNA combined with RNA and proteins (components of ribosomes are made).

Cytoplasm

• Organelles• cytoskeleton: maintain the shape

of the cell as well as anchoring organelles, moving the cell and controlling internal movement of structures

• Microtubules • Actin• Intermediate filaments

• The endomembrane system is a collection of membranous organelles– These organelles manufacture and distribute cell

products– The endomembrane system divides the cell into

compartments– Endoplasmic reticulum (ER) is part of the

endomembrane system

Many cell organelles are related through the endomembrane system

Endomembrane System

• Contains • Rough ER (makes membrane and proteins)

• Smooth ER (makes lipids, destroys toxins, stores calcium

• Golgi

• Lysosomes

• Vacuoles

• Nuclear envelope

Rough ER• Contains ribosomes.• It makes membrane when necessary.• Some proteins made by RE are inserted into the

ER membrane.• Phospholipids are made by ER enzymes.• ER membrane enlarges.• Makes proteins secreted by the cell.

– Secretory proteins, e.g., antibody, a defensive molecule. Ribosomes synthesize the proteins of the antibody, they are assembled in the ER. Short chains of sugars are linked (glycoprotein), are transported in the transport vesicle, that buds off.

• The rough ER manufactures membranes• Ribosomes on its surface produce proteins

4.8 Rough endoplasmic reticulum makes membrane and proteins

1 2

3

4Transport vesiclebuds off

Ribosome

Sugarchain

Glycoprotein

Secretory(glyco-) proteininside transportvesicle

ROUGH ER

PolypeptideFigure 4.8

Ribosomes

From: Life 4th Edition,

by Sinauer Associates

From: www.DennisKunkel.com

Smooth ER• Continuous with RE, and lack ribosomes.• It has enzymes within the membrane.• Synthesize lipids (fatty acids, phospholipids,

steroids) depending on the type of the cell.• Regulate the amount of sugar released from liver

cells into the bloodstream.• Other enzymes break drugs, detoxify.• SER increase by exposure to drugs and produce

tolerance. Sometimes it can not distinguish between drugs, so tolerance to a wide range of drugs occurs. (Barbiturate, a sedative, may decrease the effectiveness of antibiotics.

• Smooth ER synthesizes lipids

• In some cells, it regulates carbohydrate metabolism and breaks down toxins and drugs

4.9 Smooth endoplasmic reticulum has a variety of functions

SMOOTH ER

ROUGHER

Nuclearenvelope

Ribosomes

SMOOTH ER ROUGH ER

Figure 4.9

Endoplasmic Reticulum

From: Life 4th Edition,

by Sinauer Associates

From: www.DennisKunkel.com

• The Golgi apparatus consists of stacks of membranous sacs – These receive and modify ER products, then send

them on to other organelles or to the cell membrane

4.10 The Golgi apparatus finishes, sorts, and ships cell products

Golgi Apparatus

• Flattened sacs looking like a stack of pitabread.

• Sacs are not interconnected.

• A cell may contain a few or a lot of them, depending on its activity.

• It serves as a molecular warehouse and finishing factory through modification of substances manufactured by ER.

Golgi Apparatus

• One side of the Golgi receives the molecule within the transport vesicle for modification.

• It marks and sorts the molecules into different batches for different destinations.

• Molecules move from sac to sac in transport vesicles (they are shipped).

• At the shipping site, they are stored, the finished products are exported (to membrane, lysosome, etc.)

Golgi Apparatus

From: Life 4th Edition,

by Sinauer Associates

Golgi Apparatus

From: www.DennisKunkel.com

• The Golgi apparatus

Golgiapparatus

“Receiving” side ofGolgi apparatus

Transportvesiclefrom ER

Newvesicleforming

Transport vesiclefrom the Golgi

Golgi apparatus

“Shipping”side of Golgiapparatus Figure 4.10

• Lysosomes are sacs of digestive enzymes budded off the Golgi

Lysosomes digest the cell’s food and wastes

LYSOSOME

Nucleus

Figure 4.11A

Lysosomes

• Is produced by the RER and Golgi.

• Lysosome means breakdown body, so they contain digestive enzymes in a membrane.

• RER puts the enzymes and membranes together, then Golgi chemically modifies them, and releases mature lysosomes.

Lysosomes

• Food vacuoles engulf nutrients, lysosomes fuse with the food vacuoles to digest them. Upon digestion, amino acids are released and reused.

• Lysosomes destroy harmful bacteria, such that white blood cells ingest bacteria, later to be emptied into lysosome.

• Recycling centers for damaged organelles.

Lysosomes

From: Life 4th Edition,

by Sinauer Associates

• Lysosomal enzymes

– digest food– destroy bacteria– recycle damaged organelles– function in embryonic development in animals

Figure 4.11B

Rough ER

Transport vesicle(containing inactivehydrolytic enzymes)

Golgiapparatus

Plasmamembrane

LYSOSOMES

“Food”

Engulfmentof particle

Foodvacuole

Digestion

Lysosomeengulfingdamagedorganelle

• Lysosomal storage diseases are hereditary– They interfere with other cellular functions– Examples: Pompe’s disease, Tay-Sachs disease

Abnormal lysosomes can cause fatal diseases

Lysosomal Diseases

• Lysosomal storage diseases in which a person lacks a hydrolytic enzyme of the lysosome. Lysosomes become fat with indigestable substances.

• They are fatal in childhood.– Pompe’s disease, harmful amounts of glycogen accumulate in

liver cells (lack lysosomal alpha glucosidase).

– Tay-Sachs disease affects the nervous system because lysosomes lack a lipid digesting enzyme, nerve cells accumulate excessive lipid molecules.

• Plant cells contain a large central vacuole– The vacuole has

lysosomal and storage functions

Vacuoles function in the general maintenance of the cell

Centralvacuole

Nucleus

Figure 4.13A

Vacuoles

• Different types

• Food vacuoles work with lysosomes.

• Plant cells have vacuoles that can serve as a large lysosome, absorbs water allowing cell to grow.

• Pigment vacuoles in the petals of a flower.

• Contractile vacuoles, wheels with spikes. Spikes collect water, and hubs expel it.

• Protists may have contractile vacuoles

Figure 4.13B

Nucleus

Contractilevacuoles

– These pump out excess water

• The various organelles of the endomembrane system are interconnected structurally and functionally

A review of the endomembrane system

Transport vesiclefrom ER

Rough ER

Transport vesiclefrom Golgi

Plasmamembrane

Vacuole

LysosomeGolgiapparatusNuclear

envelope

Smooth ER

Nucleus

Figure 4.14

• Mitochondria carry out cellular respiration– This process uses the chemical energy in food to

make ATP for cellular work

4.16 Mitochondria harvest chemical energy from food

Mitochondria

• Mitochondria contain their own DNA (termed mDNA)

• They function as the sites of energy release (following glycolysis in the cytoplasm) and ATP formation (by chemiosmosis).

• Mitochondria are bounded by two membranes. The inner membrane folds into a series of cristae, which are the surfaces on which ATP is generated.

Mitochondria

From: Life 4th Edition,

by Sinauer Associates

From: www.DennisKunkel.com

• Chloroplasts are found in plants and some protists

• Chloroplasts convert solar energy to chemical energy in sugars

Chloroplasts convert solar energy to chemical energy

Chloroplast Stroma

Inner and outer membranes

Granum

IntermembranespaceFigure 4.15

Chloroplast• Photosynthesizing organelles of plants and

protists.

• Internal membranes partition the chloroplast into three major components.– Intermembrane space between outer and inner

membranes.– Stroma and network of tubules, and interconnected

hollow discs (grana).– The space inside the tubules and discs.

Mitochondria

• Convert energy from one chemical form to another, making ATP.

• Two compartments– Intermembrane space, a liquid filled compartment.– In the intermembrane the mitochondrial matrix, in

which cellular respiration takes place.• Highly folded, enzymes that make ATP are embedded,

folds are called cristae (increase membrane surface area).

Figure 4.16

Outermembrane

MITOCHONDRION

Intermembranespace

Innermembrane

Cristae

Matrix

• When the bond joining a phosphate group to the rest of an ATP molecule is broken by hydrolysis, the reaction supplies energy for cellular work

Figure 5.4A

Phosphategroups

Adenine

Ribose

Adenosine triphosphate

Hydrolysis

Adenosine diphosphate(ADP)

Energy

• How ATP powers cellular work

Figure 5.4B

Reactants

Po

ten

tia

l en

erg

y o

f m

ole

cule

s

Products

Protein Work

What happens to old, worn-out mitochondria?

Mitochondrial numbers are controlled by autophagy. This is a process by which lysosomes are involved in controlling cell constituents. This Figure shows the process; it is taken from Fawcett, A Textbook of Histology, Chapman and Hall, 12th edition, 1994.

• A network of protein fibers makes up the cytoskeleton

THE CYTOSKELETON AND RELATED STRUCTURES

Figure 4.17A

• Microfilaments of actin enable cells to change shape and move

• Intermediate filaments reinforce the cell and anchor certain organelles

• Microtubules – give the cell rigidity– provide anchors for organelles– act as tracks for organelle movement

Microfilaments (e.g., actin)• provides mechanical strength to the cell

• links transmembrane proteins (e.g., cell surface receptors) to cytoplasmic proteins

• Used in mitosis

• interact with myosin ("thick") filaments in skeletal muscle fibers to provide the force of muscular contraction

Intermediate filaments• These cytoplasmic fibers average 10 nm in

diameter (and thus are "intermediate" in size between actin filaments (8 nm) and microtubules (25 nm).

• Examples:– keratins are found in epithelial cells and also form

hair and nails; – nuclear lamins form a meshwork that stabilizes the

inner membrane of the nuclear envelope;

Microtubules• Microtubules are straight, hollow cylinders have

a diameter of about 25 nm

• are variable in length but can grow 1000 times as long as they are thick

• are built by the assembly of dimers of alpha tubulin and beta tubulin.

• are found in both animal and plant cells

Microtubule motors

• There are two major groups of microtubule motors: – kinesins– dyneins

cytoskeleton

From: Life 4th Edition,

by Sinauer Associates

MICROFILAMENT

Figure 4.17B

INTERMEDIATEFILAMENT

MICROTUBULE

Actin subunit Fibrous subunitsTubulinsubunit

7 nm 10 nm25 nm

Cytoskeleton

• Meshwork of fine fibers for structural support and cell movement, and transmitting signals.– Microfilaments: made of actin (globular), a twisted double

chain of actin molecules (change shape).

– Intermediate filaments: fibrous proteins with a ropelike structure, work for reinforcement and hold tension.

– Microtubules: straight, hollow tubes composed of tubulins, elongate by adding subunits of tubulin pairs, disassembled.

• Eukaryotic cilia and flagella are locomotor appendages that protrude from certain cells

• A cilia or flagellum is composed of a core of microtubules wrapped in an extension of the plasma membrane

Cilia and flagella move when microtubules bend

Cilia and Flagella

• Used for locomotion.

• Core of microtubules wrapped in an extension of the plasma membrane.

• A ring of nine microtubule doublets surrounds a central pair of microtubules.

• Dynein arms (motors) bends the microtubules.

Figure 4.18A

FLAGELLUM

Outer microtubule doublet

Plasmamembrane

Centralmicrotubules

Outer microtubule doublet

Plasmamembrane

Electron micrograph of sections:

Flagellum

Basal body

Basal body(structurally identical to centriole)

• Clusters of microtubules drive the whipping action of these organelles

Figure 4.18B

Microtubule doublet

Dynein arm Slidingforce

• Cells interact with their environments and each other via their surfaces

• Plant cells are supported by rigid cell walls made largely of cellulose– They connect by plasmodesmata, channels that allow

them to share water, food, and chemical messages

EUKARYOTIC CELL SURFACES AND JUNCTIONS

Figure 4.19A

Vacuole

Layers of one plant cell wall

Walls of two adjacent plant cells

PLASMODESMATA

Cytoplasm

Plasma membrane

• Animal cells are embedded in an extracellular matrix

– It is a sticky layer of glycoproteins– It binds cells together in tissues – It can also have protective and supportive functions

• Tight junctions can bind cells together into leakproof sheets

• Anchoring junctions link animal cells

• Communicating junctions allow substances to flow from cell to cell

TIGHTJUNCTION

ANCHORING JUNCTION

COMMUNICATINGJUNCTION

Plasma membranes ofadjacent cells

ExtracellularmatrixFigure 4.19B

Epithelial cells

• Epithelia are sheets of cells that provide the interface between masses of cells and a cavity or space (a lumen).

• The portion of the cell exposed to the lumen is called its apical surface.

• The rest of the cell (i.e., its sides and base) make up the basolateral surface.

Tight Junctions• They seal epithelial cells• They prevent the passage

of molecules and ions through the space between cells.

• They block the movement of integral membrane proteins (red and green ovals) between the apical and basolateral surfaces of the cell.

Human Lung Epithelia

• The epithelial cells of the human lung express a growth stimulant, called heregulin, on their apical surface and heregulin receptors, called erbB, on the basolateral surface.

• As long as the sheet of cells is intact, there is no stimulation of erbB by heregulin thanks to the seal provided by tight junctions.

• However, if the sheet of cells becomes broken, heregulin can reach its receptors. The result is an autocrine stimulation of mitosis leading to healing of the wound.

Anchoring (Adherence) junctions

• provide strong mechanical attachments between adjacent cells. – They hold cardiac muscle cells tightly together

as the heart expands and contracts.

Adherence junctions

• They are built from: – cadherins —

transmembrane proteins (shown in red) whose extracellular segments bind to each other and whose intracellular segments bind to catenins (yellow). Catenins are connected to actin filaments

Gap Junctions

• are intercellular channels some 1.5 - 2 nm in diameter. These permit the free passage between the cells of ions and small molecules (up to a molecular weight of about 1000 daltons).

• They are constructed from 4 (sometimes 6) copies of one of a family of a transmembrane proteins called connexins.

Desmosomes

• Desmosomes are localized patches that hold two cells tightly together. They are common in epithelia (e.g., the skin). Desmosomes are attached to intermediate filaments of keratin in the cytoplasm.

• Eukaryotic organelles fall into four functional groups

4.20 Eukaryotic organelles comprise four functional categories

Table 4.20

Table 4.20 (continued)