Quizzes 1-3 Flashcards
Which contain polar bonds:
NH2, CH3, O=O, OH, COOH
NH2, OH, and COOH
True or false: within cells, sodium ions are usually surrounded by a shell of oriented water molecules
True
True or false: as individual monosaccharides join to form a polysaccharide, water is released as part of the chemical reaction
True
In this type of bond/interaction, the electrons are physically shared between the interacting atoms
Covalent bonds
If a particular carbon atom is present in a stable, geometrically planar structure, it must have at least one of these bonds
Double bonds
An acidic amino acid like aspartate interacts with a basic amino acid like lysine in this manner
Ionic bond
How do enzymes act
By decreasing the activation energy
Tyrosine
Can be phosphorylated
A low dissociation constant (Kd) suggests…
…a strong binding interaction
Which has the most energy: a H bond, an ionic bond, a carbon-carbon bond, or the bond between the 2nd and 3rd phosphates of ATP?
A carbon-carbon bond
Eukaryotic cells are typically __% water by weight
70%
True or false: when salt dissolves in water, it breaks down into individual ions, each of which is surrounded by a shell of water molecules
True
True or false: in an aqueous solution, the aggregation of smaller lipid droplets into a single large lipid droplet is energetically unfavorable
False. It is favorable
True or false: when you dissolve freeze-dried protein powder in water, the proteins break down into individual amino acids
False
True or false: Hsp60 chaperonins exist only in higher vertebrates
False
True or false: humans have ~100x more protein coding genes than nematode worms or fruit flies
False
Which of the following can be observed in a standard light microscope without super-resolution?
A virus, a bacterium, a red blood cell, ATP synthase, a single protein, a carbon atom
A bacterium and a red blood cell
In a pair of western blots from 2D gels, you find that “your favorite protein” resolves as a single “dot” in the sample of untreated cells but as a pair of side-by-side “dots” (along the X axis) in the sample of cells that were treated with drug X overnight. What is the MOST likely explanation for this result?
In the untreated sample, your protein is phosphorylated. In the treated sample, your protein exists in both a phosphorylated and unphosphorylated form.
Functions of IDRs
Protein binding region with the capacity to bind to many different diverse partners
A flexible tether
In combination with others to form a diffusion barrier
Signaling via covalent modifications
What techniques are most commonly used to determine whether two proteins function in the same molecular complex?
Co-immunolocalization and co-immunoprecipitation
True or false: a mutation in the first 3’ splice site such that the first splice is made to the second 3’ splice site might lead to a smaller than normal mRNA being produced
True
True or false: a mutation in the first 5’ splice site such that the first splicing reaction starts with the second 5’ splice site might lead to a smaller than normal mRNA being produced
False
What changes could repress transcription?
Methylation of histone tails
Replacement of histones near the promoter with specialized histones that are normally restricted to centromeric regions
What would increase the fraction of AB dimers?
Increase the concentration of B, esp if B is “rate limiting”
Introduction of a scaffolding protein that can bind to both A and B
True or false: In some cases, an exon might be spliced out as if it was an intron
True
Carboxyl Terminal Domain (CTD) of RNAP 2
Functions as a scaffold to recruit different RNA processing factors
Consists of ~50 copies of a repeating sequence of 7 AAs
Can be phosphorylated in distinct patterns that determines both its 3D structure and potential binding partners
True or false: RNAP 2’s CTD bind to the TATA box
False
True or false: RNAP 2’s CTP is proteolytically cleaved off by TFIIH so that the RNAP complex can leave the pre-initiation complex and transcribe the gene
False
True or false: RNAP 2’s CTD functions as a loading station for NTPs
False
This modification adds a negative charge
Phosphorylation
Kinases carry out this modification
Phosphorylation
When histones in a region of DNA have this modification, it is likely that the genes in that region are being expressed
Acetylation
This modification can cause a protein to be tethered to the cytosolic side of the plasma membrane
Palmitylation, addition of a fatty acid
True or false: snRNAs lack the ability to actually cut the RNA or ligate it back together
False
What does snRNA stand for
small nuclear RNAs
True or false: some snRNAs base pair with each other to help hold everything together
True. This ensures that the RNA fragments are not lost
True or false: some snRNAs base pair with the splice sites and branch points of the pre-mRNA
True. This is key to the recognition process
What are the functions of TFIIH?
Kinase, helicase
True or false: TFIIH does transcript termination
False. It has kinase and helicase activity tho
Under what circumstances might a protein be subjected to poly-ubiquitination?
The protein has exposed hydrophobic residues
The protein has an exposed DEAD box
True or false: the C terminal domains of the core histones are intrinsically disordered
False
True or false: over evolutionary time, you would predict that a particular calcium-binding protein will evolve to become every stronger in its calcium-binding affinity
False
Promoter
Region of DNA where RNA polymerase II and “friends” (rest of the complex) assemble
Branch point
A sequence in the middle of an intron that is critical for splicing
Exon
A transcribed region that is retained in the fully processed mRNA
Intron
A transcribed region that is ultimately excised from the fully processed mRNA
Poly-A tail
A non-transcribed region that is part of the fully processed mRNA
Where is the first cut made during splicing?
5’ exon-intron junction
