bio 121 – molecular cell biology lecture section 1 a.fundamental cell theory and taxonomy b....

BIO 121 – Molecular Cell Biology

Lecture Section 1

A. Fundamental Cell Theory and Taxonomy

B. Species Variability and Cellular Genomics

C. Sources and Regulation of Genetic Change

D. The Role of Cells in Multicellular Organisms

E. Multiple Cell Types in Complex Tissues

A. Fundamental Cell Theory and Taxonomy

1. How do we define ‘alive’?

2. How do we classify living organisms?

3. What are the universal features of cells?

1. What is Life? = What are Cells?

“The basic unit of life on Earth”

“All life is cellular”

“No entity not composed of cells is alive”

OK – So What is Life?(Our current definition of life is descriptive at best)

• Homeostasis: Regulation of the internal environment.

• Organization: Being structurally composed of one or more cells.

• Metabolism: Transformation of energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism).

• Growth: Maintenance of a higher rate of anabolism than catabolism.

• Adaptation: The ability to change over a period of time in response to the environment.

• Response to stimuli: from simple to complex.

• Reproduction: The ability to produce new individual organisms.

Fig. 16-3

Bacterial cell

Phage head

Tail sheath

Tail fiber

DNA

100

nm

1. What is Life?

• Viruses are most often considered replicators rather than forms of life.

• They have been described as "organisms at the edge of life", since they possess genes, evolve by natural selection, and replicate by creating multiple copies of themselves through self-assembly.

• However, viruses do not metabolize and require a host cell to make new products.

• Virus self-assembly within host cells has implications for the study of the origin of life, as it may support the hypothesis that life could have started as self-assembling organic molecules. (Wikipedia, 2010)

1. What is Life?• A prion is an infectious agent that causes bovine

spongiform encephalopathy and Creutzfeldt–Jakob disease.

• Prions are mis-folded proteins that propagate by entering a healthy organism and inducing normal forms of the protein to convert into the rogue form.

• Since the new prions can then go on to convert more proteins themselves, this triggers a chain reaction that produces large amounts of the prion form.

• Evolutionarily, prion replication has been shown to be subject to mutation and natural selection just like other forms of replication. (Wikipedia, 2010)

2. How do we classify living organisms?

• Domains: Archaea, Bacteria, Eukarya

• Old Version: Prokarya and Eukarya

(Kingdoms in Prokarya: Bacteria, Archaea)

• Kingdoms in Eukarya: Animalia, Plantae, Fungi, Protista

Figure 1-21 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

How do we classify living organisms?

• Phyla (Animalia):

Chordata, Echinodermata, Arthropoda, Annelida, Mollusca, Nematoda, Platyhelminthes, Cnidaria, Porifera

• Sub-Phyla (Chordata): Vertebrata, Urochordata, Cephalochordata

• Class (Vertebrata): Mammalia, Amphibia, Reptilia, Osteicthyes, Aves

• Order (Mammalia): Primates, Rodentia, Artiodactyla, Perissodactyla......

• Genus/Species (Primates):

Homo sapiens Pan troglodytes Macaca mulatta........

The closer together the taxa, the more similarities in the cells...

How many cellular species are there?

• Estimates range from 10-100 million species

• Only ~1.8 million have been identified and named

• Vertebrates 62,305

• Invertebrates 1,305,250

• Plants 321,212

• Fungi 100,000

• Estimated 5–10 million bacteria

3. The universal features of cells

a. Basic features of all cells

Plasma membrane: Selectively permeable lipid bilayer

Cytosol: Variably viscous internal fluid

Double-stranded DNA, RNA and proteins

Require an external source of energy

Metabolism: Build-up and break-down of molecules

Intracellular homeostasis

Ability to sense and respond to the environment

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

• Eukaryotic cells are generally much larger than prokaryotic cells (a few m, 15X larger, 1000X greater in volume)

• Eukaryotic cells are also characterized by having stuff prokaryotes don’t have:

– Membrane-bound organelles

– Compartmentalized function

– Multicellular organisms

– *Extracellular homeostasis

– *Cytoskeleton

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

b. Differences Between Euks and Proks

Prokaryoticexamples ofthese havebegun to blurthe lines!

Nucleoid

Plasma membrane

Cell wallBacterialchromosome

Prokaryotes: Cytoplasm bound by plasma membrane, no organelles No nucleus, DNA in an unbound region called the nucleoid

The plasma membrane is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell

Smooth ERRough ER

CYTOSKELETON:

Microfilaments

Intermediatefilaments

Microtubules

MitochondrionLysosome

Golgiapparatus

Plasma membrane

Nuclearenvelope

Typicalanimal

cell

Fig. 6-9b

Nuclear envelope Rough endoplasmic reticulum

Smooth endoplasmic reticulum

Central vacuole

Microfilaments

Intermediate filaments

Microtubules

CYTO-SKELETON

Chloroplast

PlasmodesmataWall of adjacent cell

Cell wall

Plasma membrane

Mitochondrion

Golgiapparatus

Plant and animal cells have most of the same organelles

Same for fungiand protists.....

B. Species Variability and Cellular Genomics

1. The Existing Genomes in the World Today

2. Non-Nuclear Contributions to the Genome

3. Gene Conservation and Model Organisms

All cells store their hereditary info in double-stranded DNA, use RNA as an intermediate and protein as the principle functional molecules.

genome = a species’ DNA sequence

genotype = an individual within a species DNA sequence

• Nearly all of the cells in an individual have exactly the same DNA, only the sex cells are different by being randomly assorted haploids

traditional genetic phenotype = variations in visible ‘characters’

molecular phenotype = variations in protein sequence and function

cellular phenotype = cell specialization in multicellular organisms resulting from expression of a subset of the inherited genotype

1. The Existing Genomes in the World

a. The number of bases and the complexity of their organization vary far more than the number of genes

b. The conservation of critical functions and the base sequence of the genes that code for them show that all cells are related

c. These close structure and function relationships allow us to gain information about ourselves from a wide variety of organisms

a. Life’s genetic complexity is less than you think.

• The smallest genome: Mycoplasma genitalia has 477 genes (580,070 bases)

• The largest animal genome: The waterflea, Daphnia pulex, has 31,000 genes (200M bases)

• Arguably, the most complex: Homo sapiens has ~24,000 genes and ~3 billion bases in our 46 chromosomes.

• There is a fundamental ‘core’ of genes shared by ALL organisms of about 60 genes

• 477 genes compared to 31,000 = ~65X

• 580K bases compared to 3B = ~5,000X

• We have only a 40 fold increase in gene number over Mycoplasma genitalia!

• The big difference between eukarya and prokarya is in non-coding sequence

Figure 1-14a Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

Mycoplasma genitalia

Mycoplasma genitalium: 477 genes, 580,070 basepairs

37 code for non-messenger RNAs

297 of the 440 that code for protein are ‘known’

153 processing of DNA, RNA, protein 71 involved in metabolism 33 involved in nutrient transport 29 involved in surface membrane 11 involved in cell division

143 remain unidentified

Prokaryotic cells

DNA is a single, circular double helix containing 106-107 base pairs and 1,000-6,000 genes

Eukaryotic cells

Chromosomes are linear DNA molecules (fruit flies have 10, we have 46, dogs 78, etc.)

Smallest chromosome in humans is 2 million bases, total DNA is 3.2 x 109 base pairs

As animals become more complex, not just more DNA in the nucleus, embedded controls become more complex

Our chromosomes are 50% protein!!

Plants have greater tendency to have [DNA] change

2. Eukaryotes also have genes from their mitochondria and/or chloroplasts

• Our mitochondria have a genome of 16,569 base pairs which codes for:

– 13 proteins

– 2 ribosomal RNA components

– 22 transfer RNAs

– The rest of the functional DNA components for mitochondrial function reside in the nucleus

Human Mitochondrial Genome

Several neuromusculardiseases are associatedwith mitochondrial mutations

Chloroplast Genome

Usually 110-120 genes

Some as high as 200

3. Gene Conservation and Model Organisms

1. If the function is essential and unchanged, the structure (sequence) must be unchanged - because you’d die if you lost an essential function.

2. Example 1: All cells from bacteria to humans have extremely high sequence homology (structure) in the small ribosomal sub-unit because they use the same mechanism to express DNA (function).

3. Example 2: MADS-box family transcription factors have been found in every eukaryotic cell type on Earth.1. MEF-2, agrafens, deficiens, SRF


Conservation of sequence of the small ribosomal subunit

Model Organisms

1. Prokaryotic bacteria: Escherichia coli

2. Eukaryotic yeast: Saccharomyces cerivisiae

3. Eukaryotic protists: Tetrahymena pyriformis

4. Complex plants: Lycopersicon esculentum and Arabidopsis thaliana

5. Nematode worms and fruitflies: Caenorhabditis elegans and Drosophila melanogaster

6. Frogs, fish and birds: Xenopus laevis, Danio rerio, Gallus gallus, Coturnix coturnix

7. Rats and mouse: Rattus norvegicus and Mus musculus

8. Chimpanzees and monkeys: Pan troglodytes, Macaca mulatta (rhesus)

9. Humans: Homo sapiens

Figure 4-83 Molecular Biology of the Cell (© Garland Science 2008)

Figure 1-42a Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

Saccharomycescerevisiae


Arabidopsisthaliana


Caenorhabditis elegans


Drosophilamelanogaster


Xenopustropicalis

Xenopuslaevis

C. Sources and Regulation of Genetic Variability

1. Natural genetic flow

2. Generation of new genes

3. Disruption or loss of existing genes

4. Size of a genome reflects the relative DNA addition and DNA loss

1. Natural Genetic Flow

• Bacteria have multiple mechanisms

– Plasmids can cause horizontal gene transfer across species

– Viruses can cause horizontal gene transfer across species

Independent Assortment of Chromosomes during Meiosis in Sexually Reproducing Organisms

• Homologous pairs of chromosomes orient randomly at metaphase I of meiosis

• In independent assortment, each pair of chromosomes sorts maternal and paternal homologues into daughter cells independently of the other pairs

• The number of combinations possible when chromosomes assort independently into gametes is 2n, where n is the haploid number

• For humans (n = 23), there are more than 8 million (223) possible combinations of chromosomes

Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Fig. 13-12-5Prophase Iof meiosis

Pair ofhomologs

Nonsisterchromatidsheld togetherduring synapsis

Chiasma

Centromere

Anaphase I

Anaphase II

Daughtercells

Recombinant chromosomes

TEM

Crossing over

Random Fertilization

• Random fertilization adds to genetic variation because any sperm can fuse with any ovum (unfertilized egg)

• The fusion of two gametes (each with 8.4 million possible chromosome combinations from independent assortment) produces a zygote with any of about 70 trillion diploid combinations


Crossing Over

• Crossing over produces recombinant chromosomes, which combine genes inherited from each parent

• Crossing over begins very early in prophase I, as homologous chromosomes pair up gene by gene

• In crossing over, homologous portions of two nonsister chromatids trade places

• Crossing over contributes to genetic variation by combining DNA from two parents into a single chromosome


Transposable Elements

• “Parasitic” DNA sequences that colonize genomes and spread within them – many resemble viruses

• Can disrupt gene function, alter regulation

• Can create new genes by integration within and fusion with host gene segments

• Half of all human DNA has homology to known transposons

• 10% of currently occurring mouse mutations are transposon-driven

2. Generation of New Genes: New genes are generated from preexisting genes, no mechanism for new synthesis

a. Gene Duplication - provides an important source of genetic novelty

b. DNA Shuffling - Reassortment during homologous recombination

c. Horizontal Transfer - Genes transferred between organisms, in the lab and in nature

d. Transposable elements

e. Mutation - Accidents/mistakes followed by non-random survival

The evolution of sex has had a big impact on the first three.....

• Gene Duplication

• DNA Shuffling

• Horizontal Transfer

Gene Duplication

• The idea is that during meiosis in sexually reproducing organisms, crossover mutations can form multiple copies of an exon, a gene, a chromosome or the entire genome.

• The organism survived just fine with one copy so it only repairs damages to one copy, leaving the other to freely mutate.

• Once in a blue moon the mutated copy develops new, advantageous functions.


Gene Duplication


Xenopustropicalis

Xenopuslaevis

Wholegenome

duplication!

DNA Shuffling

• Pieces of different genes can be combined to form new genes with hybrid functions

• Incomplete or partial cross-over events

• Insertion of small numbers of nucleotides may alter the reading frame, producing a frameshift mutation and produce novel gene functions

Gene Families

a. Gene duplications give rise to families of related genes in a single cell

b. More than 200 gene families are common to all three domains

c. The function of a gene can often be deduced from its sequence

Duplication and Divergence Give Rise to Related Genes – Very Common Events!

• 4873 protein-coding gene families have been identified in life on earth

– 264 are designated ‘ancient’ - in all lineages

– 63 are ubiquitous in all genomes analyzed

• Most of the shared ‘ancient’ families perform:

– replication and transcription

– translation and amino acid metabolism


Bacillus subtilis4014 Genes

47% in families

ABC Transporterfamily has 77 members in thissingle bacterium!

Expansion of gene families gives rise to function

• Transcription factors regulate gene expression and, thus, cell diversity and complexity in multicellular organisms

– bHLH TFs: 7 in yeast, 41 in worms, 84 in flies, 131 in humans

• Adhesion and signaling are far more critical in multicellular animals

– 2000 major plasmamembrane proteins in worms not present or in low numbers in yeast

3. Disruption or loss of existing genes

a. DNA Shuffling - Reassortment during homologous recombination

b. Transposable elements

c. Mutation - Accidents/mistakes followed by non-random survival

c. Background on DNA Mutations

1. Mutation rates are extremely low but are an essential component of evolutionary change

2. The most common source of DNA mutation is error during replication

3. Environmental damage to the DNA is independent of DNA mutation but can also be the underlying cause

Potential outcomes in protein expression and phenotype

a. Silent mutations have no effect on the amino acid produced because of redundancy

b. Missense mutations still code for an amino acid, but not necessarily the right amino acid

c. Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein

d. Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation


1. Intragenic Mutation

• Only 1 nucleotide pair per 1,000 is randomly changed in the germline per 1 million years

however.....

• This means that in a population of 10,000 every possible nucleotide substitution will have been tried out ~20 times in a million years

Mutation rates are extremely low but are an essential component of evolutionary change

• Mutations that become part of the multicellular genome must occur in the cells of the germ line

• Somatic mutations may or may not affect the individual but cannot affect the population

• Low rates of mutation can result in high rates of evolution in single-celled organisms

2. The most common source of DNA mutation is error during replication

• There is an average mistake of 1 base pair every 10,000

• Due to proofreading and repair mechanisms this rate declines to 1 every 1,000,000,000

• Inherent in meiosis are assortment and cross-over events that lead to highly significant changes in germ line DNA sequences

c. Single-stranded and double-stranded breaks can result from reactive oxygen species activity

1. ROS are generated by either endogenous metabolic processes or exogenous ionizing radiation (like gamma and X-rays)

2. DNA mutation is the loss or gain of significant amounts of DNA, including chromosomal deletions, additions

3. Potential outcomes range from gene shuffling in or across chromosomes, gene inactivation, altered gene regulation, gene duplication

4. DNA repair system that can remove these mutations

1. ROS are generated by either endogenous metabolic processes or exogenous ionizing radiation (like gamma and X-rays)

c. Size of a genome reflects the relative DNA addition and DNA loss

• Both loss and gain occur constantly

• The relative rates determine size


The Fugu – experienced a long period of low rates of DNA addition accompanied by normal rates of DNA loss


The huntington Gene

-High homology-Perfect exon alignment-Small introns-Little non-coding DNA

D. The Role of Cells in Multicellular Organisms

1. Regulation of Organism Size by Cell Mass

2. Regulation of Extracellular Structure

3. Regulation of Cell Adhesion

4. Regulation of the Internal Aqueous Environment

5. Regulation by Intercellular Communication

6. Regulation by Cell Specialization

1. Regulation of Organism Size by Total Cell Mass

Cell mass determines the size of an organism and is a combination of cell size and number

a. The size of cells varies among organisms

b. Cell number is a balance between cell division and cell death

b. Numbers in a Cell Population

• Cell number is a combination of....

• Cell divisions – Cell deaths (necrotic + programmed)

• Necrosis is premature cell death

– disease, injury, starvation, toxicity, excitotoxicity

• Programmed cell death is death by design

– apoptosis, anoikis, cornification, autophagy

• Same for an organism, system, organ or tissue, and for single cell populations in an ecosystem


We’ve even learned to control it.........

A mutation in a signal molecule that limits muscle cell division has been bred in.

2. Regulation of Extracellular Structure

• These extracellular materials are produced and organized by the cells themselves.

• Extracellular structures keep the organism intact and allow coordinated function

• Mechanical support and defense

• Adhesion for cells and tissues

• Substrate for cell and organismal movement

• Regulation of cell growth and function

• Animal cells secrete an elaborate “ECM”

• Vertebrate four compound ECM

• Exoskeletal carapace in many arthropods

• Plants, fungi and prokaryotes secrete a sugar “cell wall”

• Cellulose cell wall in plant cells

• Chitin in fungi

• (Pseudo-) peptidoglycan in prokaryotes

• Bacterial cells secrete “plaques”

• Extracellular polymeric substance: DNA, protein and polysaccarides (including cellulose)

b. Variations in Animal ECM

• Basic components Vertebrates

• Sugar Ground Substance glycosaminoglycans

• Protein Organizers proteoglycans

• Tensile Strength collagen, fibronectin

• Tissue Flexibility elastic proteins

• Hardening Agents Ca2+-apatite for bone

b. Variations in Animal ECM

• Basic components Arthropods

• Sugar Ground Substance chitin

• Proteinaceous matrix leathery structure

• Hardening Agents Ca2+-carbonate

b. Variations in sugar cell walls

• Plants/Algae Fungi Prokaryotes

cellulose chitin Bacteria

pectin peptidoglycan

crossslinking glycan Archaea

pseudopeptidoglycan

Bacterial Biofilms are ECM for Populations

Cells become: -adherent -differentiated -cooperative

Components: -DNA -proteins -polysaccharides (cellulose)

3. Regulation of Cell Adhesion

• Most of the cells of multicellular organisms must adhere to survive – VERY few are free

• Cells adhere to other cells, the ECM or, quite commonly, to both

• It is also common for cells that lose their appropriate attachments to undergo anoikis

4. The Internal Aqueous Environment

• All multicellular organisms on Earth maintain an aqueous environment

• Most animals have the roughly the same pH and ion concentrations as sea water

• Plants are more dependent on their external environment for these

• Some of us maintain the water temperature, others rely on solar energy

• All plants and animals have water in their cells and in the extracellular matrix

• Some also have water in a vascular system that can exchange that water with tissues

• Animals with a GI or respiratory systems also exchange water with those systems

• Vertebrate animals also have a specialized cerebrospinal and lymphatic fluid systems

5. Regulation by Intercellular Communication

Single celled organisms use intercellular signals to coordinate such things as gene expression, mating, sporulation and cell death in response to population density, nutrients, stress and other cues.

Multicellular organisms use intercellular communications to coordinate the activities of their component cells.

– The overall purpose is to coordinate the activities of multiple cells in response to the needs of the organism and changes in its environment.

• We have evolved very complex cell communications systems to regulate our 100 trillion cells

• These pathways are similar to and likely arose from those that single celled organisms use to molecularly sense their environments.

• Much of our genetic energy is spent on cell signaling and control.

1. Paracrine signaling

2. Endocrine signaling

3. Synaptic signaling

4. Juxtacrine signalling

5. Cytosolic sharing


“Juxtacrine”

Fig. 6-31

Interior of cell

Interior of cell

0.5 µm Plasmodesmata Plasma membranes

Cell walls

Plasmodesmata in Plant Cells

Gap Junctions in Animal Cells

6. Regulation by Cell Specialization

Cells of an organism share the exact same DNA but they can be very different

a. There are over 200 cell types in adult humans

b. Cell types are determined by differential gene expression

Anatomical Organization in Multicellular Organisms is Based on Cell Functions

Tissues are made up of multiple cell types

Organs are made up of multiple tissue types

Systems are made up of multiple organs

Anatomical Organization in Multicellular Organisms is Based on Cell Functions

• Characteristic Types of Cells

• epithelial vs. mesenchymal

• parenchymal vs. support

• stem cells vs. adult cells

E. Four Types of Vertebrate Tissue

1.Epithelium

2.Connective Tissue

3.Muscle

4.Nervous Tissue

1. Architecture of Epithelium

• Simple, Stratified, Pseudostratified, Transitional

• Squamous, Cuboidal, Columnar

• Ciliated or not

• Examples:

– Small Intestine = Simple Columnar Epithelium

– Trachea = Ciliated Pseudostratified Columnar Epithelium

– Blood Vessel = Simple Squamous Epithelium

– Skin = Stratified Squamous Epithelium

Structure equals Function

– Small Intestine:

Simple Columnar Epithelium = absorption

– Trachea:

Ciliated Pseudostratified Columnar Epithelium = filtering debris

– Blood Vessel:

Simple Squamous Epithelium = gas exchange

– Skin:

Stratified Squamous Epithelium = protective physical barrier

Function: 1. absorption of nutrients2. enzymatic digestion at neutral pH3. multiple defensive mechanisms

Simple,ColumnarEpithelium

4 Cell types in Small Intestine

Small Intestine

Cellular Adhesion in Small Intestine

DesmosomesHemidesmosomesAdherens JunctionsOccluding Junctions

Tracheal Epithelium

Ciliated Pseudostratified

Columnar Epitheliumwith Goblet Cells

1. Mucus traps dust and air-borne microorganisms

2. Ciliar waving gets rid of unwanted material

The Vasculature: Simple, Squamous Epithelium

Gas Exchange Fluid Exchenge

Epidermis of Skin

Stratified Squamous Epithelium

Creates tough,

waterproof barrier

Differentiation and Direction of Movement in Epidermis

Cornification is the over- production

of cytokeratins,

ECM and the

adhesions to a degree that stops

cellular metabolism.

2. Mesenchymal Cell Types and Connective Tissues

The Fibroblast

Loose Connective Tissue

Dense Regular CT

Dense Irregular CT

Elastic Connective Tissue

The dermis is as complex as the epidermis and contributes greatly to skin function

Cartilage and the Chondrocyte

Lacunar Structure of the Hyaline Cartilage

Extremely low blood flow

Lacunar structure of the long bones

Osteoblasts

Cortical Bone vs. Spongy Bone

Marrow of Long Bones has Stem Cells

Cell Types of the Bone

Start out as cartilage models built by chondrocytes

Chondrocytes hypertrophy, calcify and die

Osteoblasts and osteoclasts finish up

The Adipocyte

MesenchymalStem Cells are a

continuous source of

adipocytes


3. Contractile Tissue

Arteries, veinsLymphatic vesselsGastrointestinal tractRespiratory tractUrinary bladderReproductive tractUrinary tractIris of the eyeErector pili of skin

4. Nervous Tissue

Nerve Bundles

bio 121 – molecular cell biology lecture section 1 a.fundamental cell theory and taxonomy b....

Documents

forms of life

origin of life

edge of life

host cells

current definition of

basic unit of life

living organisms

role of cells