Section 1 Flashcards
What are non-coding RNAs?
RNA molecules that are not translated into protein
What is the order of biological information flow?
____ —-> ____ —-> ____
DNA –> RNA —> Protein
What is mRNA
- Messenger RNA
- Carries the instructions for building a specific protein to the preexisting ribosomes
When is mRNA synthesized/what happens after this?
- During transcription
- the enzyme RNA polymerase reads a strand of the DNA molecule and pairs RNA bases to the bases in the DNA. This results in a single-stranded RNA molecule, that has a sequence directed by DNA.
- after transcription, mRNA carries the DNA message physically out of the nucleus (in eukaryotic cells) to the ribosomes waiting in the cytosol. Here, the mRNA will be translated into a protein.
Can mRNA be the template for many proteins at once?
Yes
Can one gene encode several mRNAs?
Yes
what is rRNA?
- ribosomal RNA
- a structure within the cytoplasm that is used in protein synthesis
- several strands of rRNA combine with many different ribosomal proteins to form the ribosome complex, creating a factory for protein synthesis. In bacteria and eukaryotes, the ribosomes consist of a large subunit and a small subunit
Which type of RNA is the most abundant in a cell?
a) mRNA
b) rRNA
c) tRNA
rRNA
comprises nearly 85% of all RNA
________ function as an adaptor between nucleic acids and protein.
tRNA
they help translate the mRNA message into protein. One tRNA for each amino acid
what is tRNA?
- transfer RNA
- transfers individual amino acids from the cytoplasm to their appropriate location in the growing polypeptide chain during protein synthesis
Each tRNA contains a sequence of 3 bases, called the ___________.
anticodon
The anticodon is complementary to a small section of the mRNA molecule, called the __________.
codon
What does the codon do in mRNA?
“codes” for a specific amino acid, which is bound to the tRNA molecule
True or false:
All RNAs are transcribed from DNA genes
True
Which ones are purines and which ones are pyrimidines out of the nitrogenous bases? What is the difference?
Purines (have two rings within their structure): A and G
Pyrimidines (have only one ring): T, C and U
What are some differences between DNA and RNA?
- DNA is double stranded, RNA single
- DNA nucleotides contain the five-carbon sugar deoxyribose, RNA nucleotides contain ribose sugar. The difference between these two sugars is a OH group on the 2’carbon
- DNA contains thymine, RNA contains uracil. Uracil lacks a methyl group at carbon atom 5.
What is the similarity in structure between all 20 of the common amino acids?
- A central carbon, known as the alpha carbon atom. This is bonded to four different chemical groups: an amino group, a carboxyl group, an R group, and a lone hydrogen atom
How are polypeptide chains formed?
Peptide bonds between the amino group of one amino acid and the carboxyl group of an adjacent amino acid.
This also makes these chains have directionality at their termini: amino to carboxyl (or N-terminus to C-terminus)
Explain the difference in electronegativity between two atoms affecting what kind of bond it is
- Very small or 0 difference in EN means the bond is purely covalent
- Greater than 0 but less than 1.67 difference in EN is a polar covalent bond (meaning e- are shared between the atoms but biased toward one pole of the two atom bond)
- greater than 1.67 is an ionic bond
Describe the resonance in peptides
The chemical groups that make up the peptide bond must be located in the SAME PLANE.
This is due to the partial double bond of the carbonyl and amino bond, which resists rotation in these positions.
This has consequences for the structure and function of proteins
Describe resonance in nucleic acids
Exists within the bases and in the phosphate group of the phosphodiester bond.
This gives the phosphodiester bond a tetrahedral geometry where the negative charge on the phosphate group can shift between the two oxygen atoms that are not bound to sugars in the backbone.
The bases themselves are conjugated ring systems (they have alternating double and single bonds) giving rise to shared electrons around the ring(s). Additionally, the accuracy of base pairing between two DNA strands, A with T and C with G, results from the dominance of particular resonance structures of the bases.
watch slide 26
How is a salt bridge formed?
When ionic interactions occur between pairs of oppositely charged amino acid side chains.
The amino acids with side chains that most often form salt bridges are: arginine, lysine, aspartic acid and glutamic acid.
What are the three kinds of weak chemical interactions?
Van der waals forces, hydrophobic interactions and hydrogen bonds
What are van der Waals forces?
- non-specific contacts between atoms
- weak interactions, but the additive effect of many of these interactions can be very strong
- when two atoms approach each other, induced fluctuating charges between them cause a weak, non-specific attractive interaction
- however, as the distance between the interacting atoms decreases below a certain point, a more powerful van der Waals repulsive force is caused by overlap of the atoms’ outer electron shells
- for atoms to interact effectively using van der Waals forces, the intermolecular fit must be exact, because the distance between any two interacting atoms must not be much different from the sum of their van der Waals radii
What is the van der Waals radius of an atom?
the distance at which these attractive and repulsive forces are balanced
it is characteristic for each atom
The strongest kind of van der Waals contact arises when a macromolecule contains a surface that precisely fits the shape of the molecule that binds.
Provide two common examples of this.
- Antibody-antigen interactions
- Ligands fitting into a ligand-bonding pocket
What is pi stacking?
Involves attractive, noncovalent interactions between aromatic rings
Can occur between the rings in adjacent DNA bases and involves favourable hydrophobic interactions that contribute to nucleic acid stability
What are pi interactions?
- Pi electron to pi electron
- Called aromatic or pi bonding
- Occurs when two aromatic rings approach each other with their planes overlapping
- contribute to nucleic acid stability
When is hydrogen bonding strong/weak?
- Strongest when the three atoms involved in the bond lie in a straight line
- When the three atoms are structurally constrained (e.g apart of a single protein molecule) the hydrogen bond is weaker
How are the two complementary strands held together in the DNA double helix?
Hydrogen bonding between nucleotide base pairs
A type of weak chemical interaction occurs when two molecules are sufficiently close to induce partial electrical charges of opposite polarity by synchronously altering the distribution of their electrons. These interactions are called:
a) covalent bonds
b) ionic bonds
c) van der Waals
d) hydrogen bonds
e) hydrophobic interactions
van der Waals
___________ between complementary pairs of nucleotide bases links one DNA strand to its partner, forming the double helix
Hydrogen bonding
Which one is the strongest out of the following:
a) van der Waals forces
b) covalent bonds
c) hydrophobic effects
d) Hydrogen bonding
e) pi bonds/stacking
Covalent bonds.
