1.

Studying cells
• Light microscope: can magnify cells up to 1000x and resolve details of 0.2µm.
Can be done on live cells.
• TEM: magnify up to 1x10
6
times, resolve details of 2-6 nm. Electrons shot from
electron gun passes through condenser lens and hits specimen, bounces through
objective and projector lens onto a viewing screen. Cannot be done on live cells.
• Tomography: 3D reconstruction of object from series of projections
• Fluorescence Microscopy: dyes used to stain cells detected with fluorescence
microscope. These dyed objects show up in bright color on a dark background.
• Confocal microscopy: pinhole aperture in detector that only allows fluorescence
emitted from plane of focus to be included in the image. Then a laser beam
scans across the specimen to give a clear 2-D image.
• X-ray crystallography: x-rays right wavelength to resolve atoms. Crystals im-
mobilize proteins and enhance weak signals. A protein crystal is a large solvent
channel with active enzymes and have the same density as cytoplasm.
• Bragg’s Law: sin θ =

2
×
1
d
A low angle means large interplanar spacings so
diffraction patterns will have small spacings.
2. Parts of the cell
• Lipid bilayer encloses the cell and its organelles
• Cytoskeleton
– Intermediate filaments: enable cells to withstand mechanical stress
– Microtubules: create series of tracks on which vesicles and organelles can
move
– Actin filaments: essential for movement
• Nucleus: enclosed within double membrane that forms the nuclear envelope and
contains DNA. Usually individual chromosomes are not visible because DNA is
dispersed – only visible during replication because they coil up
• Mitochondria: contain an inner and outer membrane as well as their own DNA.
They generate chemical energy through oxidation of sugar molecules, producing
ATP. In cellular respiration, they consume oxygen and release CO
2
1
• ER: synthesizes membrane-bound and secreted proteins. Carbohydrates added
to newly synthesized proteins while in ER. Rough ER coated with ribosomes.
ER contiguous with membrane of nuclear envelope.
• Golgi Apparatus: consists of stacks of flattened membrane-enclosed sacs. Re-
ceives/modifies molecules made in ER. Cargo travels between ER and Golgi in
vesicles that pinch off from one and fuse with another.
• Lysosomes: degradative compartments with proteases (enzymes that cleave
other proteins). Membranous sacs of hydrolytic enzymes that are active at
acidic pH.
• Peroxisomes: contains reactions involving H
2
O
2
• Endosomes: low pH compartments that transport endocytosed cargo
3. Macromolecular structure
• Macromolecules created by covalently linking monomers into long polymers
– Sugars are energy sources for cells
– Proteins catalyze reactions and have many other functions
– Nucleic acids store and transmit hereditary information
• Structure of DNA
– Composed of 4 nucleotides: A, T, C, G. Sugar-phosphate backbone attached
to base forms one strand–connected to other strand via hydrogen bonding
– Each strand complementary to partner, so can act as template for synthesis
of new complementary strand
• RNA
– Can fold into complicated 3D shapes due to intramolecular basepairing.
Hairpin structures result from regions of sequence that are complementary
to each other.
• Proteins
– What they do:
∗ Catalysis: enhances reaction rates (polymerase makes polymers from
monomers)
∗ Transport and storage (hemoglobin)
∗ Immune protection (antibodies)
2
∗ Control of gene expression (repressors)
∗ Mechanical support (collagen)
– Enzymes are proteins that catalyze chemical reactions. Substrates are at
beginning of reaction, products are at end of reaction.
– Held together by:
∗ Electrostatic forces: attraction between opposite charges
∗ Hydrogen bonds: Hydrogen shared between electronegative atoms
∗ Van der Waals forces: fluctuations in electron clouds around molecules
oppositely polarize neighboring atoms
∗ Hydrophobic forces: hydrophobic groups interact unfavorably with wa-
ter and pack together to exclude water molecules. Involves above forces
– Structure:
∗ Primary structure: sequence
∗ Secondary structure: α-helix, β-sheet
∗ Tertiary structure: how secondary structural elements are arranged to
form compact structure
∗ Quaternary structure: relative arrangement of two or more individ-
ual polypeptide chains. Proteins can contain one or multiple types of
polypeptides.
· Leucine zippers: leucine region arranged as parallel coil. Basic re-
gion interacts with DNA and formation of different leucine zipper
homo/hertodimers allows combinatorial action of gene regulatory
proteins. By binding as a dimer, it doubles DNA contact area and
the tightly associated dimers can bind at more dilute concentrations
than monomers.
· Zinc finger/DNA complex: each finger contacts 3 basepairs in major
groove. Binds as modules to adjacent sites on DNA.
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