L8 NUCLEIC ACIDS Flashcards by Summer Moore

What is the function of a nucleic acid?

To store and express genetic information.

Nucleic acids are Biopolymers or macromolecules including DNA and RNA

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What makes up a nucleioside?

Base + 5-carbon sugar

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Define a glycosidic bond.

A covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate

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Name the purine nitrogenous bases.

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Name the pyrimidine nitrogenous bases.

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Name this compound.

Adenosine triphosphate

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Name this structure.

Ribose.

Ribose has an -OH group at the 2’ carbon

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Name this compound

Deoxyribose

It has only an H on the 2’ carbon

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True or false?

Each phosphate compound is added via phosphoannhydride bonds.

True

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What type of bond binds the nucleoside base to phosphates?

phosphodiester bond

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Name this compound

Adenosine diphosphate (ADP)

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Name this compound

Deoxyguanosine

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Name this compound

Adenosine

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Name this compound

Deoxycytidine

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Name this compound

Deoxythymidine

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What is the primary structure of DNA?

A sequence of nucleotides

The phosphate of one deoxyribonucleotide binding to the 3’ carbon of another deoxyribonucleotide forms the sugar-phosphate backbone of the DNA (the side of the “ladder”)

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What type of bond forms between the complimentary nucleiotide bases of DNA that forms the rungs?

Hydrogen bonds

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True or False?

In the primary structure of DNA, the sugar-phosphate backbone is not constant and the bases attach in a selected order.

False.

the sugar-phosphate backbone is constant and the bases are attached randomly

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What type of bond forms the stacked rings of DNA?

Van Der Waals

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Polynucleotide synthesis illustrates the principle of what in thermodynamics?

Coupling, a thermodynamically favorable reaction (nucleoside triphosphate hydrolysis) driving a thermodynamically unfavorable reaction (polymerization)

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True or false?

Hydrolysis of polynucleotides to nucleotides is NOT the thermodynamically favored process.

False

This is why it is coupled to a polymerization reaction

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True or false?

The equilibrium of Polynucleotide synthesis lies far to the hydroloysis side (reactant side) of the phosphodiester bond in the aqueous environment of the cell

True

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What provides the energy to drive incorporation of the nucleotide into a growing polynucleotide chain?

Cleavage of the anhydride bond in the triphosphate

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The polynucleotide has how many residues after polynucleotide synthesis?

n (however many the polynucleotide started with) +1

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List the type of state at each number in the picture

1. The metastable state = of a weaker bond 2. The transitional state 3. The stable state = of a stronger bond

Define a Metastable State

A Particular excited state of an atom, nucleus, or other system. It denotes an intermediate energetic state within a dynamic system **other than the system's state of least energy (the ground state)**.

\_\_\_\_\_\_\_\_ has a longer lifetime than the ordinary excited states and generally a shorter lifetime than the lowest, often stable, energy state, called the ground state.

Metastable state

How are the structures of Thymine and Uracil different?

The have the same structure except that Uracil doesn't have the methyl group on the 6' carbon like thymine does.

Name this compound

Cytosine

Name this compound

Thymine

Name this compound

Guanine

Name this compound

Adenine

Name this compound

Uracil

What is happening in this picture?

Guanine and Cytosine bonding

True or false? Polynucleotides should undergo hydrolysis under conditions existing in living cells, but this hydrolysis is exceedingly slow in the absence of a catalyst.

True

True or False? DNA in cells are not sufficiently stable to serve as a repository of genetic information through successive generations

False. DNA cells are suffieciently stable

True or false? Metastable compounds are thermodynamically favored to break down, do so rapidly, whether a catalyst is used or not.

False. Metastable compounds are thermodynamically favored to break down, **but they do so only slowly unless the reaction is catalyzed**

What is the secondary structure of DNA?

The double helix. 3D arrangements of nucleotide residues with respect to one another.

True or False? The sugar phosphate backbone is ionized and faces outward for favorable interactions with water

True

Nucleic acid bases point _____ and pair up A-T or G-C

Inward

Base pairs are stacked via _______ interactions between heterocyclic rings

Van der waals

How many and what type of bonds are there between adenine and thymine; and guanine and cytosine?

All are hydrogen bonds Adenine - Thymine = 2 H bonds Guanine - Cytosine = 3 H bonds

What is the diameter of a duble helix?

2 nanometers which is kept constant

what is the amount of distance between base pairs in a double helix?

0.34 nanometers

A complete (360˚) turn of the helix takes \_\_\_\_\_; therefore, there are ____ base pairs per turn

3.4 nm; 10 base pairs per turn

\_\_\_\_\_ is when DNA twists around each other to make a more compact shape which can fit into the nucleus

Supercoiling. This is the teriary structure of DNA

What causes the the efficient storage of DNA?

Supercoiling

What allows for genetic stability?

The fidelity of DNA replication and delicate DNA repair systems of cells

What is genetic stability?

a low frequency of genetic changes that occur during each round of replication

The \_\_\_\_\_\_\_separates the two strands by breaking H bonds between bases and results in the formation of a \_\_\_\_\_\_\_.

DNA helicase; replication fork

\_\_\_\_\_\_\_\_\_\_\_bind tightly separated strands of DNA apart in order to prevent the single-stranded regions from reannealing.

Single-stranded DNA-binding proteins

DNA polymerases cannot initiate new DNA synthesis without what?

a preceeding -OH group on the 3' carbon

DNA synthesis is started by what?

**Primase**. It starts the process by making a small piece of RNA called a **primer**

What is required for DNA polymerase to catalyze chain elongation?

A short ribonucleic acid (RNA) sequence (up to 12 bases long, oligonucleotide), **Primer.** ## Footnote **The primer also marks the starting point for the construction of the new strand of DNA**

When an incoming nucleotide is joined to a primer, it supplies \_\_\_\_\_\_\_, so that the growing strand itself serves as primer for the next polymerization reaction

another free 3′-OH end

\_\_\_\_\_\_\_\_\_\_binds to the primer and will make the new strand of DNA

DNA polymerase

The leading strand, is made \_\_\_\_\_\_\_, adding bases one by one in the 5’ to 3’ direction

Continuously

the lagging strand, cannot be made continuously because of what?

it runs in the opposite direction, 3' to 5'

DNA polymerase can extend the strand to only how many nucleotides at a time in the direction of 5′ to 3′ from the replication forks?

1000 nucleotides at one time

True or false? Each Okazaki fragment is NOT started with an RNA primer

False.

DNA polymerase can only make the lagging strand in a series of small chunks called Okazaki fragments because of what?

Because DNA polymerase can only extend the strand in 1000 nucleotides at one time in the 5' to 3' direction

\_\_\_\_\_\_\_\_ synthesize new DNA only by adding nucleotides to a 3′-OH group and therefore extend a DNA strand in the 5′ to 3′ direction

DNA polymerases

What are the substrates for DNA polymerases?

The four deoxyribonucleotides: Deoxyadenosine Triophosphate (**dATP**) Deoxyguanine Triophosphate (**dGTP**) Deoxycytidine Triophosphate (**dCTP**) Deoxythymine Triophosphate (**dTTP**) and a single-stranded template DNA

True or False? DNA polymerase can catalyze the reaction between two free nucleotides.

False. ## Footnote No DNA polymerase can catalyze the reaction between two free nucleotides, even if one has a 3′-OH group and the other a 5′-phosphate. **Polymerization can occur only if the nucleotide with the 3′-OH group is hydrogen bonded to the template strand.**

Once the new DNA has been made, the enzyme _______ removes all the RNA ______ from both strands of DNA.

exonuclease; primers

What happens after exonuclease removes all the RNA primers from both DNA strands?

Another DNA polymerase then fills in the gaps that are left behind with DNA

How is the continuous double strand formed?

the enzyme DNA ligase seals up the fragments of DNA in both strands to form a continuous double strand.

How is DNA replication semiconservative?

DNA replication is semi-conservative because each DNA molecule is made up of one old, conserved strand of DNA and one new one

True or False? When copying is complete, there will be two double-stranded daughter DNA molecules, each identical in sequence to the parent molecule.

True

True or False? The unraveling of DNA double helix form the super coil does not cause strain.

False. It does cause strain. This strain is relieved by enzyme-catalysed cutting and repair of DNA chain

Define Topoisomerases

Topoisomerases are enzymes that modify state of DNA supercoiling

True or False? For replication and transcription to occur, two parental DNA strands must be separated, and **this cannot be accomplished in a supercoiled molecule**

True

Which amino acid residues are involved in the chain breaking process?

Tyrosine

How does Topoisomerase II help relieve the strain of DNA unraveling?

Relieves the strain in the DNA helix by temporarily cleaving the DNA chain and crossing an intact strand through the broken strand

How do the Tyrosine residues on Topoisomerase II aid the chain breaking process?

The residues form temporary covalent bonds to DNA that allows the enzyme to break the strand apart to form the gap in which a new strand will be inserted.

What is the mechanism that Topoisomerase II uses?

The enzyme **pulls the chains apart** to create a gap. The **intact strand of DNA is passed through the gap** and the **break** is **resealed**

True or false? The rate at which a molecule migrates through a gel matrix in an electric field depends on its dimensions

True

True or False? The smaller or more compact superhelical forms will move faster than the relaxed forms on in gel electrophoresis.

True

Which of the following statements is **not true** about DNA secondary structure? a. There is a minor groove and a major groove. b. A purine base pairs up with a pyrimidine base. c. The phosphate groups are positioned to the inside of the structure. d. The base pairs are stacked.

c. The phosphate groups are positioned to the inside of the structure.

What is the significance of base pairing to the function of DNA? a. It neutralises basic groups and controls the cell pH. b. It means that the chains of DNA are complementary allowing replication. c. It stabilises the molecule such that cell lifetime is increased. d. It prevents water interacting with the nucleic acid bases.

b. It means that the chains of DNA are complementary allowing replication.

True or False? The subsequent deamination of methylated cytosine at 5' position results ina an uracil base which is detected by DNA repair system.

False. It results in a thymine base. Uracil only results if deanimated from regular cytosine.