Section 1

Question 1

What are non-coding RNAs?

Answer 1

RNA molecules that are not translated into protein

Question 2

What is the order of biological information flow?

____ —-> ____ —-> ____

Answer 2

DNA –> RNA —> Protein

Question 3

What is mRNA

Answer 3

• Messenger RNA
• Carries the instructions for building a specific protein to the preexisting ribosomes

Question 4

When is mRNA synthesized/what happens after this?

Answer 4

• 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.

Question 5

Can mRNA be the template for many proteins at once?

Answer 5

Yes

Question 6

Can one gene encode several mRNAs?

Answer 6

Yes

Question 7

what is rRNA?

Answer 7

• 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

Question 8

Which type of RNA is the most abundant in a cell?

a) mRNA
b) rRNA
c) tRNA

Answer 8

rRNA

comprises nearly 85% of all RNA

Question 9

________ function as an adaptor between nucleic acids and protein.

Answer 9

tRNA

they help translate the mRNA message into protein. One tRNA for each amino acid

Question 10

what is tRNA?

Answer 10

• transfer RNA
• transfers individual amino acids from the cytoplasm to their appropriate location in the growing polypeptide chain during protein synthesis

Question 11

Each tRNA contains a sequence of 3 bases, called the ___________.

Answer 11

anticodon

Question 12

The anticodon is complementary to a small section of the mRNA molecule, called the __________.

Answer 12

codon

Question 13

What does the codon do in mRNA?

Answer 13

“codes” for a specific amino acid, which is bound to the tRNA molecule

Question 14

True or false:

All RNAs are transcribed from DNA genes

Answer 14

True

Question 15

Which ones are purines and which ones are pyrimidines out of the nitrogenous bases? What is the difference?

Answer 15

Purines (have two rings within their structure): A and G

Pyrimidines (have only one ring): T, C and U

Question 16

What are some differences between DNA and RNA?

Answer 16

• 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.

Question 17

What is the similarity in structure between all 20 of the common amino acids?

Answer 17

• 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

Question 18

How are polypeptide chains formed?

Answer 18

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)

Question 19

Explain the difference in electronegativity between two atoms affecting what kind of bond it is

Answer 19

• 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

Question 20

Describe the resonance in peptides

Answer 20

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

Question 21

Describe resonance in nucleic acids

Answer 21

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.

Question 22

watch slide 26

Question 23

How is a salt bridge formed?

Answer 23

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.

Question 24

What are the three kinds of weak chemical interactions?

Answer 24

Van der waals forces, hydrophobic interactions and hydrogen bonds

Question 25

What are van der Waals forces?

Answer 25

- 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

Question 26

What is the van der Waals radius of an atom?

Answer 26

the distance at which these attractive and repulsive forces are balanced it is characteristic for each atom

Question 27

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.

Answer 27

1. Antibody-antigen interactions 2. Ligands fitting into a ligand-bonding pocket

Question 28

What is pi stacking?

Answer 28

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

Question 29

What are pi interactions?

Answer 29

- 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

Question 30

When is hydrogen bonding strong/weak?

Answer 30

- 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

Question 31

How are the two complementary strands held together in the DNA double helix?

Answer 31

Hydrogen bonding between nucleotide base pairs

Question 32

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

Answer 32

van der Waals

Question 33

___________ between complementary pairs of nucleotide bases links one DNA strand to its partner, forming the double helix

Answer 33

Hydrogen bonding

Question 34

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

Answer 34

Covalent bonds.