Chromosomes of eukaryotes are __
long linear DNA molecules plus their associated proteins
Chromosomes of most of __ are circular.
- -prokaryotes, genetic materials of some viruses, DNA of mitochondria, and plasmids
A circular DNA can be generated by __
covalently joining both ends of a DNA molecule (covalently closed circular DNA (cccDNA)
Circular DNA is in topological constrict (cannot very freely rotate)
number of turns of one strand around the other strand
twist number (Tw)
- one twist per ~10 base (positive number)
number of turns of the double strand around itself
- writhe number (Wr)
causes supercoil (writhe)
- opening the 2 strands
If there is no writhe, the cccDNA is called __
relaxed (LK0 = Tw + O)
If LK = Tw - Wr
- LK < LK0
- Supercoil is negative
If LK = Tw + Wr
- LK > LK0
- Supercoil is positive
DNA can be long or short, which changes the LK value, thus to normalize the LK, the __ is calculated
super helical density (σ)
- σ = ΔLK / LK
- ΔLK (Linking difference) = LK - LK°
The supercoil can be resolved by making a temporary break in__ bond(s) of one or both DNA strand(s). This is done usually by __ enzymes.
- After the release of the supercoil (decreasing LK) the phosphodiester bond is restored.
__ introduce a break in one strand’s phosphodiester bond (a nick) and pass the second strand through the generated gap. The two ends of thebroken strand are then re-aligned.
- Type I topoisomerases
__ break both strands of the double helix, creating a “gate” through which a second segment of the double helix is passed. Requires the use of ATP
- Type II topoisomerases
Bacteria also have the enzyme __ which is a type of topoisomerase. Instead of relaxing the DNA, it induces negative supercoil which is favorable for DNA replication and transcription.
circular DNA of the same size but different linking number (LK)
Relaxed circular DNA moves __ in gel electrophoresis than linear DNA. Supercoiled DNA moves __.
slower; faster (as it is more compact)
- The more supercoiled, the faster it moves
Because of 2' OH, RNA double helices are closer to the structure of __
- A-DNA (wide & shallow minor grooves & narrow deep major grooves)
- This structure is not well suited for sequence specific recognition of RNA
The sequence recognition of double helix RNA is achieved by relaying on the structure of __
- hairpin loops, bulges, & distortions of non-canonical base pairs (e.g. tRNA)
__ side chains act as acids or bases which tend to be __ under physiological conditions. Side chains form __ bonds and are often involved in chemical reactions.
- fully charged (+ or -);
This refers to polar charged amino acids
neutral (uncharged) polar amino acids
- Hydrophilic side chains allow them to participate in chemical reactions, form H-bonds, and associate with water.
- post-translational modifications: phosphorylation of OH- groups
Nonpolar amino acids have __ side chains that consist almost entirely of __ atoms.
hydrophobic; C & H
- These amino acids tend to form the inner core of soluble proteins, buried away from the aqueous medium. They play an important role in membranes by associating with the lipid bilayer.
Except __, all amino acids have 4 different groups attached to carbon alpha. This gives them the chirality.
glycine (R group is H)
Amino acids in regular proteins are __ amino acids.
primary structure of proteins
sequence of amino acid residues in the polypeptide chain
secondary structure of proteins
- regular local structures with repeated hydrogen bonds in the backbone
- alpha helix (collagen) & beta sheet (spider silk)
- right handed helix
- hydrogen bonds between the backbone carbonyl (C=O) of one residue & backbone (N) of the amide
- 4 amino acid residues down the chain
- folded structure of an entire polypeptide
- side chain dependent packing of the secondary elements and some other elements between them such as a loop or a turn made of amino acid residues
- can fold into different shapes: fibrous: elongated, often structure roles. globular: compact, often enzymes
In eukaryotes, most protein breakdown involves __
ubiquitin and the proteasome
Ubiquitin is involved in __
- energy-dependent proteolysis reactions
- There are enzymes that attach ubiquitin molecules, single or in chains, to lysine amino acids in other proteins that are targeted for breakdown.
Ubiquitination of a protein depends on the presence or absence of __
amino acid motifs that act as degredation-susceptibility signals and the specific enzymes doing ubiquitination
A protein must be __ before in can enter the proteasome. After entering the proteasome, __
unfolded; the ubiquitinated proteins are degraded in it
- This unfolding probably occurs through an energy-dependent process
Part of the protein penetrates into the major and minor grooves of the DNA in order to __
recognize and achieve direct readout of the sequence (sequence specific binding proteins)
This is usually accompanied by more general interactions with the surface of the DNA molecule, which may simply stabilize the DNA-protein complex.
examples of specific DNA-binding motifs
- helix–turn–helix (HTH) motif
- zinc finger motif
- Leucine zippers
(more detail on Structure of proteins part 2, not sure if more info is needed since they're not on the review slide)