Exam I

Cell

Small, membrane bound units, filled with particles in a concentrated solution of chemicals and endowed with the ability to create copies of themselves by growing and dividing

Cell Theory (Schleiden & Schwann)

1) All living things are a cell or are made up of cells

2) All cells arise from preexisting cells

3) The cell is the basic living unit for all organisms

1st Living Cells

Around 3.6 Billion Years ago

1st Eukaryotic Cells

Around 1.6 Billion years ago

1st Photosynthetic Cells

Around 3.6 Billion Years Ago

1st Multicellular plants and animals

Around .6 Billion years ago

The Cell Theory: all cells arise from division of pre-existing cells

1) a central principle of all biology

2) Foundation of genetics

3) Foundation of evolution

Leeuwenhoek

1674 builds microscope and sees cells

Homunculus

Female is a sterile incubator for babies delivered by sperm cells

Theories fo Uniparental Inheritance

Ancient times- 1860's (Mendel)

1st- Female already has babies inside her, male provides spark.

2nd female is a sterile incubator for babies delivered by sperm cells

How Cells differ

1) Size: bcterium ~2um, animals 20 um

2) shape spherical, rod-shaped, spiral

3) function

4) specialization

Unicellualr vs Multicellular

Unicellular eukaryotes are highly diverse. Plasma membrane versus cell walls, external armor, sensory bristles, photodetectors, leg-like cilia, cell mouths for eating, stinging darts for protection, etc.

Energy Transducing Strategy

Organic Chemistry is the chemistry of life

all life is about acquiring reduced carbon

autotrophic or heterotrophic

Archaea

Only discovered in the last 309 yrs

extremophiles

resemble bacteria in several ways (both are prokaryotes)

Similar to eukaryotes in other ways (mostly related details of DNA replication, transcription, RNA processing, and translation (protein synthesis)

Many gene sequences arte more similar to eukaryotes

Domain: Bacteria

An incomparably successful cell domain

only cells on earth for the first 2billion years

Extreme metabolic diversity

occur everywhere

a minority cause disease

mostly unicellular

Eukarya

Eukaryotic cells contain organelles, prokaryotes do not

Oirganelle

any membrane bound compartment within a cell

Evidence that all cell are related

All cells have the same basic chemistry

DNA synthesis (replication), nucleotides, RNA synthesis (transcription)

protein synthesis (translation)

amino acids

Differences that do exist can be explained by altered instruction, or different application of similar machinery

Comparison of prokaryotes and eukaryotes

Size: 1-3um vs 5-200um

genome: 1 circular DNA molecule vs several linear DNA molecules

Ribosome: both have

No nucleus vs nucleus

no organelles vs organelles

no cytoskeleton vs cytoskeleton

minimal RNA processing vs extensive RNA processing

Similarity of all cells- basic conserved mechanisms of life

1) surrounded by a phospholipid bilayermembrane

2) genetic code written in the same language- DNA the genetic material

3) Same basic chemical machinery required for replicating and reading DNA (gene expression) DNA->RNA->Protein

4) Use ATP as a primary carrier of chemical energy

The first time atoms in a molecule have been imaged

Pentacene imaged with an atomic force microscope

made up of 22 carbon atoms and 14 hydrogen atoms

.14 nanometers between carbon rings.

performed at -268 C

Atomic Force Microscope

uses sharp metal tip that acts as a tuning fork to measure forces between the tip and molecule. The detuning varies from above the moleculeand the molecule it lies on. The measured detuning is converted to an image. The tip is stabilized by a single carbon monoxide molecule.

2009 Nobel Prize Winner

awarded for the detailed mapping of the ribosome, the cell's own protein factory. Mapped at the atomic level, the ribosome reads messenger RNA translating to protein.

3 different classical biological disciplines

Biochemistry, Cytology, and Genetics

Limits of Cytology

Many of the cells and structures we study are too small to be seen by the naked eye. The practical limit of resolution of light microscopy is ~200 nm. The practical limit of electron microscopy is 2 nm.

Plant Cell= 20X30 um. Animal cell= 20um. bacterium = 2X1 um

Cell Part Sizes

Bacterial ribosome= 25nm. Microtubule = 25 nm. Microfilament = 7nm. typical membrane = 7-8 nm thick. DNA helix= 2 nm thick.

2 basic kinds of microscopy

light microscopy: uses visible light source and glass lenses.

electron microscopy: uses a beam of electrons emitted by a tungsten filament and focused by electromagnetic lenses.

Resolution

Limits microscopy, controlled by physics.

limited by wavelength or other EM spectrum used,

the refractive index of whatever is between the specimen and lens, and the angle of light capture.

R = .6 * wavelength/ (the refractive index * sin( angle))

Phase Contrast Light Microscopy

One of a few ways to increase contrast in light microscopy in LM, not resolution

Electron Microsopy

SEM & TEM

Cathode (tungsten filament)-> anode-> first condenser lens-> second condenser lens-> specimen-> specimen stage-> objective lens-> intermediate lens-> projector lens-> detector

required advent of excellent fixatives. Can only look at dead cells

Scanning Electron Microscopy (SEM)

High resolution surface structures

scans the surface with a beam of electrons; deflected electrons generate a picture

these cells are fixed (dead) and coated with a thin layer of metal!

Transmission Electron Microscopy (TEM)

High resolution visualization of internal cell structure

requires cells be fixed and sliced into very thin sections

How do we "see" the molecular structure of DNA

We can only determine molecular structure using X-ray crystallography

X-ray Crystallography

x-rays diffracted by a DNA fiber produce a diffraction pattern on a photogrphic plate or other detector

the resulting diffraction pattern is analyzed mathematically

The three dimensional structure is deduced

Fluorescent Microscopy

molecule specific fluorescent stains (specific binding to proteins, DNA other intracellular molecules)

Antibodies against proteins in the cell can be used to "label" cellular structures (immunofluorescence microscopy)

How do we study cells?

Cytology- microscopic observations of cellular structure, specific staining for cell components. even staining for enzymatic or other biochemical reactions.

Biochemistry- investigation of cellular chemical reactions and the structure function of biological molecules

Genetics- study of how genes function in cells, and how they are transmitted to offspring cells (heredity)

Biochemistry

Isolate and purify specific cell components (e.g. organelles, an enzyme) and study their properties in vitro

Individual molecules can also be purified by column chromatography

Gel Electrophoresis

separation (purification) of specific cell macromolecules by differential mobility in an electric field

Commonly used for nucleic acids and proteins

Cell Genetics

break a function (gene) in living cells to determine its function

Yeast

general name for unicellular fungi

cell division used as a classic example to discover all genes involved in eukaryotic cell cycle regulation (cdc genes)

Saccharomyces Cervisae

is an important 'domesticated' fungus, known as '"budding yeast" or "bakers yeast"

1st discovered by Pasteur in the 1850's

Now perhaps the best known eukaryotic cell- the model eukaryote

The most important, fundamental contribution to date in cancer biology came from studying how bakers yeast divides

2001 Nobel Prize

to Hartwell, Hunt, and Nurse for their discoveries of key regulators of the cell cycle

yeast cell division mutants were created and used to find all genes that directly regulate progression through the eukaryotic cell division cycle

Used the basic genetic method- break a function and see what happens

break= mutate, function = gene

Hartwell's Method

He used the basic genetic method- break a function and see what happens

He used Conditional mutants that were temperature sensitive.

By producing a colony from a single cell where the mutagenized cells grow into colonies at 23 C, he could isolate temperature sensitive mutants by replicating on two identical plates and storing at 35 C and 23 C. THe one that died at 35 C was still alive on the 23 C plate, thus isolating the temperature sensitive one.

Budding yeast advantages

fast, inexpensive growth on liquid or solid medium

haploids make mutant isolation easier

buds simple observation of the position within the cell cycle

model organisms

Hartwell and others used collection of well defined mutants to discover:

virtually all genes that regulate progression through the cell cycle (cdc family of genes)- highly conserved.

molecular pathways for how this regulation works

identified cdc 28 as the gene controlling START, the first CDK gene (cyclindependent kinase), a major discovery that formed the basis for enormous advances in cancer biology

discovered genes that code for proteins critical to "checkpoints" in the cell cycle

How do you find the gene responsible for a mutant phenotype?

cross cdc 28ts cells individually with the wild type bakers yeast gene X, gene Y, and cdc28. The X & Y will exhibit no colony formation. The cdc28 will produce cells in colony at various cell-cycle stages and Isolate plasmid cdc28

Cell membrane

Defines cell and organelle boundaries

regulates movements of molecules into and out of the cell and organelles

organelles

membrane bound intracellular bodies in which various functions are localized

Cytosol

largest compartment in most cell types (only compartment in prokaryotes)

contains water and a variety of molecules essential for cell function

including: ions, amino acids, proteins (enzymes and structural), polysaccharides

high concentration of proteins causes the cytosol to behave more like a fluid gel than a liquid

contains the ribosomes and the cytoskeleton and most enzymes for intermediary metabolism- glycolysis and production amino acids, nucleotides, and other basic building blocks

Ribosomes

not organelles, found in all cells, One of the biggest and most complex molecular machines life ever created

1) thousands to millions occur in each cell

2) the site of protein synthesis (translation) in all cells

3) Consist of many proteins and a few special RNA molecules that are the enzymes of protein synthesis

2 basic kinds of ribosomes

1) free or cytosolic ribosomes

2) bound ribosomes- stuck to the outside surface (cytoplasmic face) of the rough ER

each produces proteins destined for different fates in the cell

Free Ribosomes

produce proteins that:

a) are imported to the nucleus

b) are imported into mitochondria

c) remain in the cytosol

Bound Ribosomes

a) are going to be associated with the endomembrane system (vesicles), or the cell membrane.

b) are going to be excreted by the cell (via vesicles)

Nucleus

Eukaryotic cells

contains most of the DNA, also proteins and RNA (RNA exported to the cytoplasm)

surrounded by nuclear envelope (a double membrane)

Nucleolus

a dark area within the nucleus where ribosomal RNA (rRNA) genes are located and where ribosomes are assembled prior to export

Nuclear pores

occur in the nuclear envelope and provide channels for export of RNA into the cytoplasm, and import and export of proteins

Endoplasmic Reticulum (ER)

a highly convoluted membrane, continuous with the outer membrane of nuclear envelope.

estends throughout the cell, inside the ER is a space called the lumen of the ER

Site for production of new membrane

Site for production of membrane associated proteins, and proteins destined for excretion from the cell

Smooth ER

no ribosomes, site for lipid and hormone synthesis

Rough ER

attached ribosomes, site for protein synthesis

Golgi Complex

a stack of flattened vesicles. Vesicles containing proteins bud off from the ER fuse with the Golgi. THe proteins are then packaged together by function.

Similar protein types bud off the Golgi in transport vesicles, with 3 basic fates:

1) to become membrane proteins

2) to become secreted proteins

3) to become enzymes found in lysosomes and peroxisomes (breakdown organelles).

Endomembrane System

A complex, ever moving system comprised of The ER, Golgi, and vesicles

The source of new cell membrane and its associated proteins

source of proteins to be secreted from the cell

highly regulated, proteins with different fates are packaged in the Golgi.

Based on an address system of sugar residues covalently bound to different proteins

Exocytosis

the process of secretion in eukaryotic cells

digestive enzyme secretion by the pancrease

hormone secretion

neurotransmitter molecules from one nerve cell to the next

Lysosomes

organelles for hydolytic cellular digestion, the recyclin center of the cell

contain many hydrolase enzymes

acidic ph (~5)

like secretory proteins, lysosomal hydrolases are synthesized on the rough ER, transported to the Golgi, and then packaged into vesicles that fuse with lysosomes

Autophagy

Peroxisomes

a 2nd kind of breakdown vesicle. Breakdown occurs by oxidation rather than hydrolysis. Abundant in kidney and liver cells.

H2O2 is produced by oxidation of organic carbon, and must be itself broken down using the enzyme catalase

Peroxisomes detoxify reactive compounds, break down unusual substances

Play a role in the oxidative breakdown of long chain fatty acids into shorter lengths that mitochondria can handle

Organelle linked diseases

Heritable diseases caused by mutation of specific organelle proteins either involved in import of some substance into the organelle, or subsequent breakdown of a particular substance

lysosomal disorders

(over 40 different heritable diseases) all involve harmful accumulation of a specific substance (usually lipids or carbohydrate) that would normally be broken down by the lysosomes.

ie tay sachs disease. accumulation of glycolipids in cells. People who are homozygous for this mutation die (dementia, paralysis, blindness, then death)

Peroxisomal disorders

each caused by a defective protein

ie neonatal adrenoleukodystrophy (NALD). the defective gene encodes a protein needed to transport long-chain fatty acids into the peroxisome. Result is buildup of these molecules in cells. Adrenal failure, neurological disorder, death at a young age

Mitochondria

found in virtually all cells

specific site of cellular respiration- reduced carbon is oxidized to drive synthesis of ATP

without mitochondria, eukaryotes would be unable to use oxygen to extract maximum energy from food molecules.

in fact oxygen would be poison rather than essential

Chloroplasts

found in plant and other photosynthetic eukaryotic cells

site of photosynthesis- the energy of sunlight is used to reduce inorganic (oxidzed) carbon to produce organic (reduced) carbon

Very ancient events at the base of the eukaryotic innovation

ancestral eucaryotic cell ingested a bacterium which reproduced and became mitochondria then became animal cells

early eucaryotic cells hosting mitochondria that ingested photosynthetic bacterium that later became chloroplasts became plant like eukaryotes

The Endosymbiont Principle of Eukaryotic Evolution

1) Mitochondria and chloroplast have their own genome ( a small circular DNA molecule)

2) divide on their own by fission (the cell cannot manufacture them)

3) are surrounded by 2 different membranes

4) have their own (prokaryotic type) ribosome and their own gene expression machinery

Endosymbiosis

requires horizontal gene transfer

more than 80% of human mitochondrial genes have been transferred to the "host" nucleus

result: all eukaryotes are chimeric organisms

result: the mitochondrion is dependent on the host cell to produce most (but not all) of its required proteins

Cytoskeleton

EM and probes show cytoplasm is filled with filaments

composed of : actin- thin filaments for movement, microtubules- thickest filaments for cell division, and intermediate filaments for mechanical strength

collectively interact

Microtubules

form the mitotic spindle that separates chromosomes during cell divisino, make up structure of eukaryotic flagella (tubulin- dynein motors)

Microfilaments

involved cell movement, dividing the entire cell, and most intracellular movements of organelles (actin-myosin motors)

Intermediate Filaments

more permanent- involved in maintaining the cell structure

Chemicals in Cells

Cabon atomic number 6 atomic weight 12

Hydrogen

C,H,O,N make up 99% of a cell

mostly carbon- hydrogen compounds

depends on reactions that take place in a watery solution

enormously complex compared to nonliving chemistry

cell structure and activities are dominated and coordinated by very large macromolecules, (polymeric molecules)

Reactive

capable of forming a covalent bond

life operates with reactive elements

all elements in cells have unfilled outermost shells and can thus participate in chemical reactions with other atoms

Noncovalent bonds

only less than 1/20 the strength of covalent bonds, but are very important in the chemistry of cells

The most important noncovalent bond in cell chemistry are: 1) hydrogen bonds 2) electrostatic (ionic) interactions 3) hydrophobic interactions

Polar Molecules

Can form hydrogen bonds with other polar or charged molecules

has a positively and negatively charged side due to unequal sharing of electrons between the atoms

Hydrogen Bonds

because they are polarized, two adjacent H2O molecules can form a linkage known as a hydrogen bond. Hydrogen bonds have only about 1/20 the strength of a covalent bond. Strongest when the 3 atoms lie in a straight line

Hydrophilic Molecules

substances that dissolve readily in water. they are composed of ions or polar molecules that attract water molecules through electrical charge effects. Water molecules surround each ion or polar omlecule on the surface of a solid substance and carry it into solution.

Ionic substances dissolve because of ionic attractions

Polar substances dissolve because they form hydrogen bonds with water

Carbon Skeletons

Carbon and hydrogen make stable compounds that are non polar do not form hydrogen bonds, and are generally insoluble in water.

Hydrophobic Molecules

molecules that contain a preponderance of nonpolar bonds are usually insoluble in water and are termed hydrophobic. water molecules are not attracted to such molecules and so have little tendency to surround them and carry them into solution

C-O Compounds

alcohol- hydroxyl group

aldehyde & ketones - carbonyl group (C=O)

carboxylic acid- COOH carboxyl group

esters- combining an alcohol with an acid

C-N Compounds

Amines and amides

amine is N+ 2H

amide is N+ 2C

Non Covalent Chemical Complementarity

Allows specificity in all processes of the Central Dogma (eg Life)

two bases G and C hydrogen bonded in DNA or RNA

specific assembly of macromolecular structures like the ribosome

enzyme substrate specificity

all noncovalent bonds their utility is in their specificity and reversibility (impermanence)

Lumen

Inner space of ER

actually contains the nucleus

Chromatin

Generic term for uncondensed chromosomes

Golgi Apparatus

2 surfaces

cis face and trans face

cristae

convolutions of the inner membrane of mitochondria

Proteins

the most complex molecules

of the thousands of amino acids, 20 used in proteins

peptide bond links amino acids to form proteins. always between a carboxyl group to a nitrogen

always have an amino terminus to a carboxyl terminal

short polymer: peptide

KiloDalton

atomic weight equivalent to 1000 hydrogen atoms

Proline

the alpha helix breaker. the only one that loops the R group back

R- groups

project alternatingly in pleated sheets

Exam I

Biology 3111 with Parrow at University of Charlotte

About this deck

About StudyBlue

Sign up (free) to study this.

About this deck

About StudyBlue