Cell Biology Midterm 1

3 Tenets of Cell Theory

Theodor Schwann (names not asked)

1. All organisms composed of one or more cells

2. Cells are the structural unit of life

Rudolf Virchow

3. Cells come from pre-existing cells.

6 defining features of cells

1. self-containment, very organized

2. Metabolism

3. Growth

4. Genetic info and heredity

5. Reproduction and selection

6. Response to environmental stimuli

Proposed theory of aerobic Eukaryotes

anarobic prokaryotic cell engulfs another aerobic cell and then the membrane of the anarobe pinches in. Produces ER, nuclear membrane, and mitochondria. Also chloroplast in the same way.

Proof of single origin of life?

1. All organisms use the same genetic code with minor variation to translate DNA into proteins.

2. Similarity in Cellular metabolism and processes. ATP (energy), NADH (electron glues). glycolysis, citric acid cycle,

What does a single origin of life imply?

1. Understanding of one organism can be used for other. Cures for human diseases

2. All life forms connected, evolutionary continuity. Proves evolution.

Types of Bonds/Chemical interactions

Covalent (peptide, proteins; phosphodiester, DNA/RNA; Glycosidic, Carbs; Ester, lipids)

Hydrogen (base pairing)

Ionic (enzyme substrate)

Van der Waals (dipoles, happens to most, packing lipids in membrane, also helps protein folding)

Hydrophobic interactions (lipid bilayer, protein folding)

Macromolecules

maco, made of small units (monomers)

Nucleic acids (nucleotides)

Protein (amino acids)

Carbohydrates (monosaccharides)

Lipids (Fatty acids)

RNA and DNA differences

Differences:

DNA is double stranded (single stranded is unstable) while RNA is single stranded

DNA has T while RNA has U

RNA is flexible, more reactive (OH group, more hydrophilic)

Amphipathic

having both a hydrophilic region and a hydrophobic region

triglyceride structure

glycerol + 3 fatty acids. Phosphates can be at the top which can attach polar groups.

Lipids uses

Source of energy and storage

Essential oils (vitamins, omega oils)

Pigments for light storage (carotenoids, tocopherol)

amino acid structure

alpha carbon attached to amino group, carboxylic acid group, hydrogen, r group. R group dictates differences.

categories of amino acids

nonpolar, polar, charged (basic or acidic, Lys+, Arg+, Glu-, Asp-)

How to fold correctly as proteins?

1. hydrogen bonding

2. Hydrophobic interactions

protein secondary structure

alpha helix: hydrogen bonds every 4 AA, stable yet flexible

Beta-pleated sheet: hydrogen bonds between adjacent strands. parallel and antiparallel.

Special cases of secondary structure

coiled coil: two mixed. Amphipathic

Transmembrane: in the membrane, fully hydrophobic

Chaperones

help proteins fold and find tertiary structure correctly by masking hydrophobic areas

tertiary and quaternary

tertiary: 3D shape, Enzyme active sites, ligand binding sites (antibodies)

Quaternary: multiple polypeptides (ex. cooperative binding of oxygen in hemoglobin)

Also disulfide bonds (cystein) and van der waals

What makes budding yeast and green alga good model systems?

They are unicellular, free-living, lab friendly, genetically traceable, and have shared featues with humans and crops.

Budding yeast: cell fundamentals, disease, synthetic biology models.

Green alga: motility, photosynthesis, environmental response

Light microscopy

Uses light, focuses it on specimen.

Cons:

Limited resolution (0.2 micrometer)

needs to be thin as optical diffraction happens

Visualization methods

1. Staining

2. special optics (phase contrast, glow; differential interference-contrast, shadow)1

Fluorescence

light hits, light emitted. Cells not fluorescent but can be tagged. Green fluorescent protein allows this. Fluorescence microscopy.

Fluorescence microscopy

pros:

specific

sensitive

Electron microscopy

Uses electrons. Same problems as LM, except has better resolution (less than 1 nm)

Traditionally: fix (fixatives, preserve) and slice. Uses heavy metal (gold) staining to deflect electrons

Cool way: cryofixation, no chem fixatives

How to tag specific molecules?

fluorescence

antibody (tagged with fluorophore (FM), or hard metals (EM). called immuno staining)

epitope tags (short peptides)

Biotin tagging (humans cant synthesize)

Use of tags to localize

Immuno staining: visualize location of specific protein

Western blotting: Detects and quantifies specific proteins

Flow cytometry: analyzes and sorts cells based on protein expression

Uses of tags to isolate

Immunoprecipitation (IP) isolate specific protein or complex

Affinity chromatography: purify specific protein or protein complex

How many possible codons?

64 (4^3)

degenerate since 20 amino acids

AUG for start

UAA UAG UGA for stop