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Who is the textbook author and what are some research projects he’s working on
Harvey Lodish, Red blood cells and drug delivery
How many human cells are in you, and how many bacteria cells?
~30 trillion each
What is LIPSTIC used for?
Protein-Protein interactions, or cell to cell interactions
Central Dogma was coined by who
Francis Crick
What are three types of cytoskeletal proteins
Microfilaments, intermediate filaments, microtubules. Actin, myosin, and alpha and beta tubulin
Which scientist first proposed C. elegans as a model organism
Sydney Brenner
Which scientist first proposed Drosophilla fruit fly as a model organism
Thomas Hunt Morgan
Which scientist first proposed zebrafish as a model organism
George Streisinger
What are the 8 hydrophobic amino acids
Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Tyrosine.
What are the 4 polar amino acids
Asparagine, Glutamine, Serine, Threonine.
What are the 3 positive and 2 negative amino acids?
Positive: Arg, His, Lys. Negative: Asp, Glu.
Which amino acids are special cases
Cys, Gly, and Pro
Which amino acid acts as a buffer
Histidine
What does Beta mercaptoethanol do?
Breaks disulfide bonds
Which amino acids are most common to be phosphorylated
Serine, Histidine, Tyrosine, and Threonine
Why does DNA have T and RNA have U
T is more resistant to endonuclease activity
Liposome vs micelle
Liposome is a bilayer with hydrophilic inner cavity and micelle is a single layer with hydrophobic core.
The structural unit of the contractile supramolecular complex in striated muscle cell is called
Sarcomere
Motif vs. Domain size
Motif is < 15kDA, Domain is > 15kDA
3 examples of motifs
Helix loop helix (Calcium binding), Zinc finger (DNA binding), and coiled-coil (myosin)
Do most proteins fold spontaneously in vivo
No, they require Hsp70 or chaperonins
What do Hsp70, Hsp40 and GrpE do?
Hsp70 is ATP binding, Hsp40 is substrate binding and GrpE is Nucleotide exchange factor
What is the ubiquitin mediated pathway and which enzyme adds ubiquitin?
Protein degredation, E3 adds ubiquitin.
What molecule binds allosterically to PKA to activate kinase activity?
cAMP
What ion does troponin bind in the actin/myosin muscle contraction complex?
Calcium
What is critical micelle concentration?
When all membrane proteins are encased in a micelle
What detergent is used to isolate membrane proteins
Triton X-100
What is rate zonal centrifugation?
molecules are separated by density via sucrose gradient
What is used to denature proteins for electrophoresis
SDS, this will sort via mass
What is MALDI-TOF
Peptide sequencer using time of flight mass spec from laser ionization. This is done on 2D electrophoresis to analyze chemical composition.
What distinctive structure is found in animal cells and not in plant cells
Gap junction
Rough vs Smooth ER. Lipid synth, Ca2+ storage, secretory proteins.
Lipid synth and drug detox happen in SER. RER is where Ca2+ is stored and secretory proteins are made.
What do the 3 parts of the Golgi Body do?
Cis and Medial modify proteins and the trans face ships them.
Microfilament in prokaryote vs eukaryote, what is the size and function
Prokaryote is Mreb, Eukaryote is actin, used for muscle contraction and it is the smallest fiber
Microtubule monomers, size and function
alpha and beta tubulin, largest fiber, spindle fibers.
Intermediate fiber example and function
Lamin, cytoskeletal connection and cell to cell connection
What metal is used for negative staining in TEM
Uranyl Acetate
What is FACS
Fluorescence Activated Cell Sorter, sorts cells based on fluorescent properties by making flr. cells negatively charged and pushing them into a separate chamber, and counts the number of cells.
About double the red fluorescent cells vs green
Cells are only red or green and not both
What is FRAP
Fluorescent Recovery After Photobleaching. Protein migration dynamics inside cell is measured by creating a small photobleached region and waiting for equilibrium.
What is FRET
Förster Resonance Energy Transfer. Protein protein interaction localization, excited state is transferred between chromophores and different light is emitted.
What is FISH
Fluorescent In-Situ Localization. mRNA localization.
How to separate organelles?
equilibrium density separation (better sep. than rate zonal), endocytic vesicles isolation using bacteria or antibody coated microbeads
Cell lysis techniques
Sonication, tissue homogenizer, Hypotonic solution, specific lysozymes.
What is Abbes equation?
D=0.61λ/NA. This means that the resolution depends on the wavelength of light and the refractive index.
Resolution of brightfield vs TEM and SEM
0.2 um for brightfield, 0.2nm for TEM and 2nm for SEM
What is Immunohistochemistry?
Primary antigen is dispensed, incubated, and then excess is washed off. Secondary antigen with chromophore is dispensed and glows where primary antigen is bound. This allows for in vitro staining.
Who first used GFP
Roger Tsien
What is STORM Microscopy?
Stochastic Optical Reconstruction Microscopy. Small amount of excitation allows for 20-30nm resolution after pinpointing where the light came from and reconstructing the image.
What is the difference between GMP, G, dGMP, and dG?
GMP contains a ribose sugar, guanine base, and a phosphate. G contains a guanine base and a ribose sugar. dGMP contains a deoxyribose sugar, a guanine and a phosphate. dG contains a deoxyribose sugar and a guanine base.
What’s the difference between adenine and adenosine?
Adenine is just the base, but Adenosine contains a ribose sugar.
What does DAPI do?
It’s a fluorescent dye that binds to the minor groove of DNA
Why is DNA more stable than RNA?
The two hydroxyl groups on RNA make it easy for strand separation via nucleophilic attack of hydroxide.
What is Tm and how is it affected by GC% content?
Melting temperature and it increases with high GC content.
In transcription what enzyme unwinds the DNA?
RNA polymerase II. (technically in eukaryotes it is a transcription factor but it is commonly referred to as part of RNA polymerase)
What are the three chambers of a ribosome?
Exit, Peptide, Amino Acid.
What enzyme adds the amino acid to tRNA?
Aminoacyl-tRNA Synthetase
How many proteins make up a Eukaryotic Ribosome and how many rRNA fragments?
About 80 proteins and 4 rRNA molecules. (Prokaryotes have ~60 proteins and 3 rRNA)
What % of a ribosome is rRNA by weight?
50% for humans and 60% for bacteria
Where are rRNA, and ribosomal proteins made?
rRNA is made in nucleolus, Proteins made in RER and transported back to nucleolus. Over 150 proteins help in ribosome assembly.
What causes Major and Minor groove?
The strands are not diametrically opposed due to the glycosidic bonds.
In DNA replication which polymerase synthesizes the leading and the lagging strand?
DNA polymerase ε synthesizes leading strand and DNA polymerase δ synthesizes lagging strand.
After proofreading from DNA polymerase how many base mismatches are present?
1 per 100 million.
What enzymes detect a base pair mismatch and activate mismatch excision repair? What is it meant to fix?
MSH2 and MSH6. (MLH1 and PMS2 come in after to recruit helicase and endonuclease and fix the area). It is meant to fix errors from DNA polymerase during replication.
What enzymes are involved in Base Excision repair, and what does it do?
DNA glycosylase, APEI Endonuclease, AP lyase, DNA polymerase β, and Ligase. It is meant to fix T-G mismatch due to deamination.
What are the functions of DNA glycosylase, APEI Endonuclease, AP lyase, DNA polymerase β, and Ligase?
All are part of Base Excision Repair. Glycosylase removes T, APEI nicks DNA, AP lyase fully removes the sugar, and then DNA polymerase β and ligase repair the DNA.
What is Nucleotide excision repair and what enzymes are involved?
It detects distorted DNA structures like TT dimers and cuts out that section. XP-C finds distortion and binds, TFIIH, RPA, and XP-G open the strand. Then XP-G and XP-F cut out section, and DNA polymerase β and ligase repair the area.
Is Huntington’s disease dominant, recessive, or x-linked recessive?
Autosomal dominant
Name 2 examples of X-linked recessive diseases.
Hemophilia A, Muscular Dystrophy
Cystic Fibrosis is an example of what kind of inheritance pattern?
Autosomal Recessive
What are the 3 steps to PCR and what temperature are they performed?
Denaturation at 90-95C. Annealing at 60C. Extension at 60C
What is the purpose of adding CaCl2 for bacterial transformation?
It creates a bridge between negative bacteria and negative DNA and increases transformation efficiency.
What is Western Blotting and what reagents are used?
SDS Protein electrophoresis followed by transfer to a plate and addition of fluorescent antibody.
What is Northern Blotting and what reagents are used?
mRNA electrophoresis followed by transfer to a plate and addition of nucleotide probe w/ fluorescent dye.
What is Southern blotting and what reagents are used?
DNA electrophoresis followed by transfer to a plate and addition of nucleotide probe w/ fluorescent dye.
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