ch. 3: Replication, Catalysis and Ribozomes

Question 1

In template-directed polymerization, which of the following (can be more than 1) involve hydrogen bonding, and which involve covalent bonding?
a. Breaking of two phosphates off of the 5’ C of an incoming nucleotide.
b. Attraction of A to U, and G to C.
c. Addition of new monomer to the 3’ C of the end of a growing polymer of RNA.
d. The process that determines the complementary base pairs.

Answer 1

hydrogen bonding: b. Attraction of A to U, and G to C & d. The process that determines the complementary base pairs
covalent bonding: a. Breaking of two phosphates off of the 5’ C of an incoming nucleotide & c. Addition of new monomer to the 3’ C of the end of a growing polymer of RNA

Question 2

What ingredients did Spiegelman include in the test tube at the very start of his experiment?

Answer 2

single “species” of RNA that was about 3000 nucleotides long, protein enzyme that catalyzes replication of RNA, and all 4 of RNA monomers

Question 3

Describe in words what a catalyst does.

Answer 3

it speeds up a particular chemical reaction by lowering energy needed to activate a reaction, allowing it to proceed with a lower input of energy

Question 4

What is so important about three-dimensional shape of RNA or protein?

Answer 4

its 3D shape gives it proof that RNA is able form this shape to catalyze itself to polymerize

Question 5

What gives any single-stranded RNA molecule its three-dimensional shape?

Answer 5

its long RNA strand makes antiparallel/internal hydrogen bonds

Question 6

What is a “ribozyme”?

Answer 6

RNA enzymes that are capable of catalyzing reactions

Question 7

Explain what we mean when we say that the newly forming RNA strand in template-directed RNA synthesis is “antiparallel”

Answer 7

it’s the “antiparallel” because it’s the compliment of the original strand. This means that it’s nucleotide bases are matching up to one another based on what is there (A to U, G to C), in which they form internal hydrogen bonds to connect to one another, forming its 3D shape

Question 7

Explain what we mean when we say that the newly forming RNA strand in template-directed RNA synthesis is “antiparallel”

Answer 7

it’s the “antiparallel” because it’s the compliment of the original strand. This means that it’s nucleotide bases are matching up to one another based on what is there (A to U, G to C), in which they form internal hydrogen bonds to connect to one another, forming its 3D shape

Question 8

undirected polymerization

Answer 8

making of RNA polymer by nucleotides adding at random (no template to follow)

Question 9

template-directed polymerization

Answer 9

making of new RNA polymer by adding nucleotides based on original RNA polymer (complement)

Question 10

In the previous chapter, you read about how, in an environment of continuous polymerization and depolymerization, the only way a specific molecular form can persist is if it can replicate itself. Explain how RNA replicates itself. Use the terms: nucleotide, hydrogen bond, A-U, G-C, complement, complement of the complement, replica

Answer 10

RNA replicates itself by using the original strand created as a template. It uses the attraction of A to U and G to C to attract the nucleotides and form an H bond between the complementary base pairs. This eventually forms a complement of the original RNA polymer and the process keeps repeating, making a complement of the complement (replica), which is the original RNA strand made

Question 11

substitution mutation

Answer 11

receives a different base pair that’s not complementary and causes a mutation because the complement of the complement no longer matches the original strand, creating a new mutation

Question 12

deletion mutation

Answer 12

deletes a nucleotide from the polymer, which causes polymer to become shorter than original as complements are made

Question 13

addition mutation

Answer 13

adds an extra nucleotide to polymer, which creates a polymer longer than the original as more and more complements are made

Question 14

duplication mutation

Answer 14

complete strand is duplicated and added to one another which doubles length of strand, creating a much longer polymer as more complements are made

Question 15

The persistence delivered by replication is not sufficient for evolution of chemical form. What else is needed? Why?

Answer 15

For the evolution of the chemical form, there needs to be more variety and mutations. They’re needed to create new substances that can be adaptable in an environment (survival of the fittest) and create all different types of other forms and life. Variation is the key concept to natural selection

Question 16

natural selection

Answer 16

idea that genetic variants can survive better in certain environments if they’re able to replicate in that environment

Question 17

Answer the following questions about the experiments Sol Spiegelman performed in the 1970’s on RNA.
a. He started with a test tube with salt water. What additional ingredients did he add?

Answer 17

single species of RNA that was 3,300 nucleotides long, a protein enzyme that catalyzed the replication of RNA, and RNA monomers

Question 18

After several minutes, Spiegelman put a sample from the first test tube into a second one. List the ingredients present in the second test tube before he transferred the contents of the first test tube.

Answer 18

replicase enzymes, “building blocks”/RNA monomers (nucleotides)

Question 19

What three hypotheses were supported by Spiegelman’s experiment?

Answer 19

RNA can replicate out of cells
RNA replication exhibits natural selection
small RNA’s replicate faster than larger RNA’s

Question 20

What part of this experimental set-up was least like what we think happened in the primordial soup leading to RNA replication?

Answer 20

the use/existence of a protein catalyst

Question 21

How did the contents of the final test tube differ from the contents of the first?

Answer 21

RNA was shorter in Gen 74, the most common nucleotide was not 3,300 nucleotides long, and there were many species of varying RNA

Question 22

exergonic reaction

Answer 22

reaction is spontaneous
energy is released
delta G is less than 0

Question 23

endergonic reaction

Answer 23

reaction isn’t spontaneous
energy is absorbed
delta G is greater than 0

Question 24

Be able to describe how an enzyme works: Include active site, induced fit, reactants,
products, what hydrogen and covalent bonds are made and broken.

Answer 24

Enzymes are catalysts made of proteins, so it’s a protein molecule that helps a reaction lower the energy needed to start the reaction. First, substrates bind to the enzyme at its active site with an induced fit (when active site changes shape when it binds to a substrate). Enzymes are also very specific and have very specific jobs. Hydrogen bonds hold substrates in the enzyme until it makes/breaks covalent bonds between the substrates and then hydrogen bond breaks once covalent bond is made and releases substrates

Question 25

Name and describe the function of the type of ribozyme that is thought to have accelerated replication of RNA polymers in the primordial soup. Explain how this ribozyme was able to speed up RNA replication

Answer 25

Ribozyme is a catalyst made of RNA. In this case, an RNA strand folded up against itself because it had complementary bases, which allowed it to cleave other RNA’s. It then binds to a straight chain of RNA and begins the process of adding a nucleotide, holding it there and moving down and adding another nucleotide. As a result of it’s position, it allows it to bind multiple nucleotides at the same time making it quicker and more efficient. It then continues by breaking off the phosphates and making covalent bonds and repeating the whole process.