Exam 1 ( Ppt 5) Flashcards
Differences between DNA and RNA
1) backbone of RNA contains ribose instead of 2’-deoxyribose
2) RNA contains Uracil in place of Thymine in the DNA
Pairing Comparison of T:A and U:A
Both bind A at its 1,6 position via their 3,4 position
RNA is usually found as a…?
single polynucleotide chain
RNA Chains Fold Back to Form “Looped Out” Forms (i.e bulge, internal loop, hairpin, pseudoknot)
Some Viruses Can Control Protein Synthesis through…?
Pseudoknot
RNA Can Form ___-____-____ Base Pairing
“Non-Watson-Crick base pairs can be found in all combinations in RNA, in which GA and GU are the most abundant in ribosomal RNA.” Prof Ye
RNA can fold up into complex tertiary structures frequently involving these unconventional base pairing
How to identify the highly varied and complex RNA structures
1) Mutate and Map Method
Mutate and Map Method
Each nucleotide is replaced with its complement;
Each mutant is chemically modified by SHAPE
Treated with a chemical reagent (N-methylisatoic anhydride) selectively acylates 2’-OH of nucleotoides that are unpaired;
The position of unpaired nucleotides is then determined by reverse transcriptase using a DNA primer. It will be ceased when encountering 2’-acylated nucleotide.
Directed Evolution Selects RNAs that…?
Bind Small Molecules (ligands)
then gets selected for and recovered and amplified by PCR or mutagenesis
Ribozymes
Ribosomal enzymes
RNase P
1st ribozyme discovered
cleaves a segment of RNA from the end of a precursor tRNA and transforms it into a mature tRNA molecule.
Why is DNA not similarly susceptible to alkaline hydrolysis?
??? it is often in its condensed form unless a specific region is being acted on.
Stability via nucleosome structure and histone tail associations
Where does the protein synthesis take place?
Ribosome, CYTOPLASM (RER)
Building Block of protein
Amino acids =>
contains Amino group, Carboxyl group, Side chain
Importance of Amino acids
1) divalent cation
2) Salt bridge (Ionic lock)
Peptide bond:
the covalent link between amino acid in a protein, which is formed by a condensation reaction with a water molecule elimination.
Torsion angles
The Ψ (phi) torsion angle corresponds to the rotation about the Cα—C bond;
The φ (psi) torsion angle corresponds to the rotation about the N—Cα bond.
3 Important Amino Acids
Glycine: R group = proton, not chiral, most
conformational freedom than any other amino
acid.
Proline: side chain has a covalent bond already, making
it the least conformational freedom
Cysteine: disulfide bond and it can dimerize
Protein structures can be described at __ levels. What are they?
Primary: Peptide bond, vanderwaal forces
Secondary: H bonding, dimers, Pi stacking forces, covalent bonds?
Tertiary: 1 polypeptide chain, 3D config,
Quaternary: more than 1 polypeptide chain, 3D config
Which one can form the bigger pleated beta-pleated sheet?
“The parallel arrangement is less stable because the geometry of the individual amino acid molecules forces the hydrogen bonds to occur at an angle, making them longer and thus weaker. Contrarily, in the anti-parallel arrangement the hydrogen bonds are aligned directly opposite each other, making for stronger and more stable bonds.” -https://chem.libretexts.org/
Most common Post-Translation Modification (PTM)
phosphorylation
Anfinsen Refolding Experiment
showed that Gene not only encode amino acid sequence but also 3D structure
