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Cell Biology
Cell Biology, Dr. Das-Bradoo, Spring 2012
107
Biology
Undergraduate 2
01/05/2012

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Term
Cells contain four major families of small organic molecules
Definition
sugars (polysaccharides), fatty acids (fats, lipids, membranes), amino acids (proteins, polypeptides), and nucleotides (nucleic acids)
Term
condensation reactions
Definition
a bond in which a molecule of water is expelled as the bond is formed
Term
hydrolysis
Definition
breaking a bond in which a molecule of water is consumed
Term
amphiphilic
Definition
Molecules such as phospholipids, with both hydrophobic and hydrophilic regions
Term
amino acids
Definition
all possess a carboxylic acid group and an amino group, both linked to a single carbon atom called the alpha-carbon. Their chemical variety comes from the side chain that is also attached to the alpha-carbon. Amino Acids are linked together to form proteins. Exist as optical isomers in D- and L-forms. Only L-forms are found in proteins.
Term
pyrimidines
Definition
Cytosine, Thymine, Uracil - all derive from a six-membered pyrimidine ring
Term
purines
Definition
Adenine, Guanine - have a second, five-membered ring fused to the six-membered ring.
Term
Adenosine Tri-phosphate
Definition
a ribonucleotide transfers energy in hundreds of different cell reactions
Term
Ribose
Definition
A, G, C, U - based on ribose sugar
Term
Deoxyribose
Definition
A, G, C, T - hydroxyl at the 2' position of the ribose carbon ring is replaced by a hydrogen
Term
Glycosidic bonds
Definition
condensation reactions that bond monomers of sugars to form polysaccharides
Term
Examples of polysaccharides
Definition
starch and glycogen
cellulose and chitin
glycoproteins (oligosaccharide bound to proteins) and glycolipids (oligosaccharides bound to lipids)
Term
pK of an amino acid
Definition
the pH at which exactly half of the carboxylic acid or amine residues are charged.
Term
Nucleotides
Definition
Are composed of a nitrogen-containing base (A, C, G, T and U), a five-carbon sugar (ribose or deoxyribose) and one or more phosphate groups
Term
phosphodiester bonds
Definition
Polymers of nucleotides form through the formation of phosphodiester bonds. They form between the phosphate group of one nucleotide and the hydroxyl group on the sugar of another.


The bond is between the phosphate of one nucleotide and a hydroxyl (OH) group on the sugar of another nucleotide
Term
phospholipid structure of bacteria and eukaryotes
Definition
Bacterial and eukaryotic lipids have fatty acids attached to glycerol via ester bonds
Term
phospholipid structure for archaeabacteria
Definition
Archaeal lipids have fatty acids attached to glycerol via ether bonds
Term
Catabolism
Definition
involves the breakdown of organic molecules (food stuff) and the release of energy.
Term
Anabolism
Definition
involves the formation of organic molecules and the use of energy.
Term
Oxidation and Reduction
Definition
Oxidation refers to the removal of electrons and reduction means addition of electrons. Reduced molecules contain more energy than oxidized molecules


Reduction requires energy/oxidation releases energy
Term
Robert Hooke
Definition
observations of "little boxes" led to Cell Theory
Term
Cell Theory
Definition
states that all living things are composed of cells
Term
Antoni Van Leeuwenhoek
Definition
Used microscopes to identify "animalcules" in rainwater and other specimens. First documented observation of microorganisms.
Term
Universal Features of Cells (4)
Definition
The structure and function of nucleic acids (DNA and RNA)
The production and composition of proteins
A requirement for free energy
Being enclosed by a selectively-permeable membrane
Term
Structure and Function of Proteins
Definition
Proteins have a 3D structure based on their amino acid sequence.
Proteins are enzymes that act as catalysts for specific chemical reactions
Some proteins act as regulatory proteins and can promote production of other proteins
Term
Phototrophs
Chemoorganotrophs
Chemolithotrophs
Definition
Phototrophs get free energy from sunlight
Chemoorganotrophs get free energy from oxidation of organic molecules
Chemolithotrophs get free energy from oxidation of inorganic molecules
Term
Semipermeable membranes do what?
Definition
allow for the uptake of nutrients and the export of waste
Term
3 Domains of life
Definition
Prokaryotes, Archaea, Eukaryotes
Pro- and Archaea are pre-nucleus
Eukaryotes have a true nucleus and include all multicellular organisms, but are also single cell organisms
Eukaryotes do not have a cell wall.
Term
Why use model systems?
Definition
All cells are descended from a common ancestor
Use simple systems to study a biological question and extrapolate the results to higher organisms.
Term
What makes a good model organism?
Definition
represent the simplest possible system to study a biological question.

Amenable to genetic manipulation
Reproduce rapidly
Easy to grow in a laboratory
Term
Model Organisms
Definition
E. coli - a model prokaryote
Yeast - lowest eukaryote, few genes, haploid, cheap, and fast growing
Drosophila (Fruit fly) - Diploid, easy and cheap to grow, oldest organism for genetics, multicellular organism
Nematode - unusual life cycle make it suitable for genetics, easy and cheap to grow, precise timing of development from single cell to adult with 959 cells
Mouse - foremost model for vertebrate studies, development, immunology, mammalian genetics
Arabidopsis thaliana - plant model, easy to grow indoors, produces thousands of offspring in 8-10 weeks, genome is completely sequenced
Term
Techniques
Cell Biology
Definition
Use microscopy to reveal size, shape, and location of cell components
- Immunofluorescence = using antibodies to visualize specific protein
- Green fluorescent protein (GFP) = adding GFP tag to a protein allows visualization of the hybrid protein in living cells
Term
Techniques
Biochemistry
Definition
Use fractionation and x-ray crystallography to reveal molecular structure and chemistry of purified cell constituents
Term
Techniques
Genetics
Definition
Identify mutant phenotypes and determine genotypes to reveal roles of healthy genes and consequences of damaged genes
Term
Techniques
Developmental Biology
Definition
reveals changes in cells as they specialize
Term
Techniques
Molecular Biology
Definition
Use DNA cloning, Polymerase chain reactions, and Western blotting to reveal the molecular basis of biological activity
Term
Techniques
Genomics
Definition
Use DNA microarrays to reveal differences in structure and expression of entire genomes
- monitor global patterns of gene expression
- detect all the mRNAs present in a cell (identify which genes are active)

A microarray tells us changes gene expression during disease progression, in response to drugs, and during development
Term
Techniques
Proteomics
Definition
Monitors the presence and interactions of numerous proteins simultaneously
Term
Definition:
Cell
Definition
smallest living unit in an organism
Term
Definition:
Eukaryotic cells
Definition
compartmentalized, resulting in membrane-bound, functionally distinct organelles
Term
Structural Commonalities of prokaryotic and eukaryotic cells
Definition
All cells:
Are composed primarily of water and carbon compounds
Are enclosed in a lipid membrane (separates life from the environment)
Contain ribosomes (translate mRNAs into proteins)
Contain DNA as the genetic material (instruction for making the cell)
Term
Cell walls
Definition
cell walls are external to the cell membrance and are usually composed of carbohydrates.
Prokaryotes have a cell wall composed of peptidoglycan.
Arcahea cell walls are composed of pseudomrein (or S-Layers, surface layers of protein)
Algae and Plants have cell walls of cellulose
Animal cells don't have cell walls, but have a glycocalyx - a think outer layer of carbohydrates.
Term
Glycocalyx
Definition
made up of oligosaccharide side chains of glycolipid, integral membrance glycoproteins and proteoglycans.
Term
Size of lipid bilayer?
Definition
5 nM
Term
Prokaryotic cells (11)
Definition
-Lack membrane enclosed organelles
-DNA in the form of a closed circle
-DNA not enclosed in a membrane but may be attached to the inner membrane of the cell.
-May have extra-chrosomal plasmids that can endow the cell with useful traits.
-Inclusion bodies are often found in the cytoplasm that are used to store energy or carbon reserves.
-Possess a cytoskeleton that helps to localize structures within the cell and plays an essential role in cell division and polarity determination.
-Posses extracellular appendages - flagella are used for propulsion
-Pili are used for attachment.
-Structurally, little divergence (sperical, rod-shaped, spiral)
-Metabolically diverse (phototrophs, chemoorganotrophs, chemolithotrophs)
-Though both eukaryotes and prokaryotes can fix CO2 and generate oxygen, only prokaryotes can fix nitrogen and make it available for other organisms.
Term
Eukaryotic cells (12)
Definition
-May have evolved from a collection of prokaryotes living symbiotically (the endosymbiotic theory)
-Ribosomes are larger than prokaryotic ribosomes (80s vs. 70s)
-Possess an extensive network of membrane enclosed compartments
-Cytosol is the site for protein synthesis and degradation as well as metabolism
-Posses a true nucleus enclosed by a double membrane perforated with nuclear pores to connect with the cytosol.
-The space between the nuclear double membranes is continuous with the endoplasmic reticulum, which is a network of branching tubules and sacs that run throughout the cell. The Rough ER is studded with ribosomes and is involved with protein synthesis. The smooth ER is involved with lipid synthesis, detoxication of harmful molecules, and Ca2+ sequestration.
-The Golgi apparatus was first identified by Camillo Golgi and serves as a site for the synthesis and/or modification of molecules destined for transport out of the cell as well as the modification of imported molecules. It consists of a cis face (closest to the nucleus) and a trans face (closest to the cell membrane).
-Mitochondria serve as the site of oxidative phosphorylation in the cell and contain an outer membrane and an inner membrane that are separated by an intermembrane space.
-Chloroplasts belong to the plastid family and are only found in plant cells. They can function in either photosynthesis or the storage of various molecules (starch or pigments). Chloroplasts have 2 membranes and form thylakoids, which are the sites of photosynthesis (in the inner membrane).
-Peroxisomes have a single membrane and carry out oxidative reactions and are involved in the breakdown of toxins (ethanol) and fatty acids.
-Lysosomes are membrane bound compartments containing hydrolytic enzymes (acid hydrolases) and are responsible for digesting macromolecules into monomers
-Cytoskeletons are made up of 3 major types of proteins - actin filaments (stain red and form a contractile ring that pinches the cell into two), microtubules (stain green and rearrange to form the bipolar mitotic spindle), and intermediate fibers. They serve to organize the internal and external structure of the cell.
Term
hydrogen is the exception to the equal neutrons and protons why?
Definition
has no neutron
Term
Largest amount of chemical elements in the body by percentage
Definition
Hydrogen (65%), Oxygen(25%), Carbon(10%), Nitrogen (2%)
Term
All elements found in living organisms have a common chemical property
Definition
they have unfilled outermost electron shells which can participate in reactions
Term
Covalent bonds
Definition
are formed by atoms sharing electrons - strongest and unaffected by presence of water
Term
Ionic bonds
Definition
formed by the transfer of electrons from one atom to another - lose most of its strength in presence of water
Term
Hydrogen Bonds
Definition
formed when two electronegative atoms share and electropositive hydrogen atom (water molecules) - loses some strength in presence of water
Term
van der Waals forces
Definition
are weak, but not affected by water. created at minimum energy states at which attractive and repulsive forces precisely balance. Zero energy is the energy when the two nuclei are at infinite separation.
Term
Hydrophobic forces
Definition
caused by hydrophobic molecules avoiding water by interacting with other hydrophobic molecules. Important for the proper folding of protein molecules.
Term
What is the most abundant molecule in cells
Definition
water, then proteins, RNA, miscellaneous small metabolites
Term
What are the names of larger units of these building blocks:
Sugars
Fatty Acids
Amino Acids
Nucleotides
Definition
Polysaccharides
Fats, lipids, membranes
proteins
nucleic acids
Term
Sugar chemical formula
energy source - glucose
Definition
(CH2O)n using a condensation reaction forming a glycosidic bond
disaccharide has 11 different linkages
Term
Polysaccharides include:
Definition
Starch and glycogen (used to store energy)
Cellulose and Chitin (used for structure)
Glycoproteins (oligosaccharide bound to proteins) and glycolipids (oligosaccharide bound to lipids)
Term
monomers assemble via what bonds?
Definition
covalent bonds to form macromolecules. Energy is required for the formation of the bonds.
Term
In Photosynthesis
Definition
energy carriers drive a carbon fixation process in which sugars are manufactured from CO2 and water.
Term
glycogen and triglycerides - food reserves
Definition
animals store glucose reserves in this form. They have many branch points. plants store it as starch, which has fewer branch points.
Triglycerides/fats only differ in plants and animals by the types of fatty acids they are composed of
Term
granules in animal cytoplasm
adipocytes
where stored in plants?
Definition
cytoplasm storage of glycogen
adipocytes are the animal storage place for triglycerides
both starch and triglycerides are stored in the chloroplasts where they are manufactured
Term
obtaining energy from sugars
Definition
series of 10 oxidation reactions which breaks down sugar into energy, CO2 and H2O. The energy is stored in carrier molecules such as ATP, GTP, NADH, and NADPH.
Term
Adenosine Triphosphate
Definition
ATP - Energy carrier, nucleotide. Adenine + ribose + tri phosphoanhydride bonds
Term
NADP+
Definition
Nicotinamide adenine dinucleotide phosphate carries high energy electrons and hydrogen atoms
Term
Activated carrier molecules widely used in metabolism
Definition
ATP - phosphate group
NADH, NADPH, FADH3 - carries electrons and hydrogens
Acetyl CoA - acetyl group
Carboxylated biotin - carboxyl
S-Adenosylmethionine - methyl group
Uridine diphosphate glucose - glucose
Term
Glycolysis
Definition
A series of enzymatic reactions that results in the oxidation of glucose (C6) to 2 molecules of pyruvate (C3).
Results in the net syntheis of 2 molecules of ATP and 2 NADH.
It occurs in the cell cytosol and does not require O2.
Term
Fermentation
Definition
Glycolysis inthe absence of O2, NADH reduces pyruvate to regenerate oxidized NAD+.
Different cells produce different end products - lactic acid in muscles, ethanol and CO2 in anaerobic organisms.
Term
Pyruvate can be oxidized to what by pyruvate dehydrogenase
Definition
Acetyl CoA and CO2
Term
Where are pyruvate and fatty acids oxidized?
Definition
In mitochondria
Term
Krebs Cycle, TCA, Citric Acid Cycle
Definition
an 8-step process for the oxidation of acetyl CoA by combining with citrate and is eventually oxidized to two molecules of CO2. Generates 1 GTP, 3 NADH, and 1 FADH2. Also creates lots of important intermediates along the way.
Term
Oxidative Phosphylation
Definition
In the presence of O2, NADH donates 2 electrons to an electron carrier chain. The electrons are eventually combined with O2 to generate H2O and lots of ATP.
Term
Pyruvate kinase deficiency
Definition
creates hemolytic anemia. lack of enzyme production
Term
Warburg effect
Definition
Otto Warburg found that the rate of glycolysis in tumor cells goes up 200x
Term
Why do we need to study proteins
Definition
Proteins constitute most of the cell's dry mass and execute nearly all of the cell's functions.
Term
Amino Acid side chains determine what?
Definition
If the amino acid will be charged or uncharged, polar or non-polar
Term
Proteins are folded using what noncovalent forces
Definition
electrostatic attractions, hydrogen bonds, ven der Waals attractions, hydrophobic interacions (nonpolar side chains move to inside and folds it into compact conformation)
Term
What are the 3 protein folding conformations
Definition
alpha helix - result from hydrogen bonding between N-H and C=O groups. Twists around itself to form a rigid cylider, turns after every 3.6 amino acids. found in cell membrane proteins like transport proteins and receptors.

Coiled coil structures where two alpha helices wrap around each other. Hydrophobic side chains face inward. Form framework for many elogated proteins like alpha keratin.

Beta pleated sheets - core of many proteins contain these. Caused by hydrogen bonding between neighboring polypeptide strands creating very rigid structure. These can run in parallel orientation or anti-parallel orientation.
Term
Alpha Helix structure
Definition
result from hydrogen bonding between N-H and C=O groups. Twists around itself to form a rigid cylider, turns after every 3.6 amino acids. found in cell membrane proteins like transport proteins and receptors.
Term
Coiled Coil structure
Definition
where two alpha helices wrap around each other. Hydrophobic side chains face inward. Form framework for many elogated proteins like alpha keratin.
Term
Beta pleated sheets
Definition
core of many proteins contain these. Caused by hydrogen bonding between neighboring polypeptide strands creating very rigid structure. These can run in parallel orientation or anti-parallel orientation.
Term
Levels of protein organization
Definition
Primary - amino acid sequence
Secondary - stretches of the polypeptide chain that form alpha helices and beta pleated sheets
Tertiary - three dimensional organization
Quaternary - a protein molecule formed of more than one polypeptide
Term
The Cell Doctrine
Definition
1838 by Schleiden and Schwann and stated that all plant and animal tissues are made up of cells. This doctrine marked the birth of cell biology.
Term
Stains used for microscopy
Definition
dyes - eosin, hematoxylin, Gram Stain
Radioisotopes
Fluorophores
Fluorescent antibodies
Fluorescent Tags (GFP, CFP, RFP)
IR dyes and tagged proteins
Photophores-photoactivation, photobleaching
Luminescent proteins-Aequorin
Term
Size of cells
Light Microscope resolution size and size of objects that can be viewed
Definition
10-20 micrometers
.2 micrometer apart, .5 micrometer wide
Term
Microscope lenses
Definition
condenser lens, objective lens, ocular lens
Term
apoenzyme
Definition
inactive enzyme without the cofactor
Term
holoenzyme
Definition
activated enzyme with cofactor - complete
Term
cofactor
Definition
inorganic molecule required for holoenzyme
Term
coenzyme
Definition
organic molecule needed for holoenzyme
Term
negative feedback (feedback inhibition)
Definition
the product inhibits the previous step thereby inhibiting its own production. Most common step of regulation. Reversible.
Term
allosteric enzymes
Definition
in feedback inhibition the inhibitor binds in such a way that it brings conformational change and that makes the active site non-functional.
Term
Protein phosphorylation
dephosphrylation
Definition
Common regulatory modification in higher eukaryotes.

Phosphorylation is addition of phosphate group as modification of amino acid side chain (covalently linked).

Phosphorylation and dephosphorylation regulate conformational properties of protein complexes.
Term
Protein kinases
Definition
add phosphate groups
Term
protein phosphatase
Definition
removes phosphate group
Term
Fluorescence Microscope
Definition
A fluorescent molecule absorbs light at a given wavelength and then emits light at a longer wavelength
Use GFP, DAPI, rodamine B
Term
Indirect immunocytochemistry
Definition
Use primary and secondary antibodies and fluorescein to visualize specific antigens
Term
Enzyme linked immunocytochemistry
Definition
attach color producing enzyme to primary or secondary antibody. example - alkaline phosphotase.
Term
Confocal Microscope
Definition
uses lasers - Z stacking, reduced background noise, use fluorophore probes
Term
GFP from Aequoria victoria
Definition
Green Fluorescent Protein, gene can be introduced into other species
Term
Fluorescence Resonance Energy Transfer (FRET)
Definition
method to establish protein-protein interaction and proteins in macromolecular complexes using combinations of fluorescent proteins
Term
Photoactivation
Definition
method to establish signal transduction and movement of cytoskeletal proteins.
-inactive photosensitive fluorophore probe (caged molecules)
-activated with laser light-photoactivation
Term
Fluorescence recovery after photobleaching (FRAP)
Definition
method to establish diffusion experiments, active transport, binding and dissociation rates.

A strong focused pulse of laser light will extinguish, or bleach, the fluorescence of GFP.

Based on time to recover after bleaching with strong laser light.
Term
Atomic force microscopy
Definition
Has a tip made up of silicon that can measure the mechanical force.
Can visualize single molecules
unfolds individual protein
measures the energetics of domain folding
gives mechanical properties of protein molecules
Term
Electron Microscopy
Definition
The light microscope can resolve structures that are 0.2 μm apart or greater.

The electron microscope can resolve structures that are 0.1 nm apart or greater.
Term
Light microscopy vs. Transmission electron microscopy (TEM)
Definition
Differences:
•An electron beam as a source of illumination.
•Lenses in the light microscope are made of glass, but in EM are magnetic coils, which focus the electron beam.
•Specimen is placed in a vacuum.
•The specimen is stained with electron-dense material (metals such as osmium tetroxide) that absorbs electrons.

Advantage:
•Resolution 200 times better than light microscope.

Disadvantages:
•Sample preparation is very laborious.
•EM cannot be used to view living cells (a sample is chemically frozen).
Term
Scanning Electron microscopy
Definition
Cheaper than TEM
directly gives 3D structure
has z stacking capacity
Uses electrons that are scattered to make image
provides great depth of field
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