BIO 3170 Study Guide - Midterm Guide: Phosphodiester Bond, Pyrophosphate, Hydrolysis

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Leture Ojetives DNA Repliation

1. Explain why the reaction of DNA synthesis is favorable on the basis of energy

Reactants: DNA + NTP

• Start of with a DNa strand where a single nucleotide, NTP, will be added at a time.

Products: DNA-NMP + PPi

• The added nucleotide only has one phosphate

• Pyrophosphate is also generated as a product

The first release of energy is from the hydrolysis of the bond between the sugar of the activated

nucleotide and the alpha phosphate

o The hydrolysis of this bond will generate energy

The second release of energy comes from the hydrolysis of PPi into 2 Pi.

Summary: the reaction is favorable mostly because the release of energy that comes from

pyrophosphate hydrolyzing into 2 inorganic phosphates

2. During the reaction of DNA synthesis, why are the nuclotides added in the form of triphosphates

and not in the form of di or mono phosphates?

DNA + NTP → DNA-DMP + PPi

This reaction is favorable because PPi → 2Pi.

• Pyrophosphyate is hydrolyzed into two inorganic phosphates. The reaction is driven to the

right (formation of products).

• Le Chetalie’s piiple alls fo eplaeet of a podut eig degaded 

o Generating my phosphatases

o Formation of the phosphodiester bond to drive the elongation of the DNA chain

Re write reaction

DNA + NDP → DNA-DMP + Pi

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• In the casae where we use a Diphosphate instead of a triphosphate we end up producing

1Pi

• Pi cannot further hydrolyze and drive the reaction to the products thus slows down

elongation of the chain.

Re write reaction

DNA + NMP → DNA-DMP + PPi

• We can generate and elongation of the DNA chain but a very low efficients

DNA + NP →

• Addition of a nucleotide with no phosphates

• No product form

• Phosphodiester bond cannot even be created becayse no phosphate is present

Summary: So the only optimal reaction/ efficite/ generationi of energy for the DNA chain to by

elongated by DNA polymerase is the one in which nucleotids are added in the activated form of

triphosphate

3. During epliatio h is DNA elogated fo 3’ ed ad the dietio is 5’→ 3’

• Coetioall, elogatio ous at the 3’ ed

o 1st reason: enzyme strucuture of DNA polymerase

▪ DNA polymerase is responsible for the catalysis of phosphodiester bonds on

the backbone allows for only positioning and elongation at the 3’OH end

▪ Remember: Reaction where DNA + free activated triphosphate allows for

elogatio at the 3’d

▪ Note: the addition of nucelotides would also occur because there are 3

phosphates i the 5’ ed ad a fee 3’OH goup o the fee atiated

triphosphate

• Difference: pyrophosphate would come from the DNA chain and

not the activated ucleotide whereas in elongation of the 3’OH end

the pyrophosphate comes from th activated nucleotide

o 2nd reason: Proof reading activity of DNA polymerase

▪ 1. A mismatch error occurred in the newly synthesized DNA

▪ 2. DNA polymerase can remove the incorrectly paired nucleotides

• A 3’OH – the monophosphate formed can be removed and the

3’OH ith o phosphate ill e egeeated & aailale fo the

addition for the correct addition of nucleotide and the creation of

the phosphodiester bond.

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• B) 5; END: There will be a removal of the incorrect nucleotide at the

5’ ed ut o it ill eoe the phosphates that ee ogioall

attathced to the incorrectly paried nucleotide. This leaves us with a

5’ ed that is uale to udego pope DNA atalsis eause of

the absence of the triphosphate and the presence of a

monophostphate.

o In trying to add the correct nucleltodie, there is no high

energy bond cleavages and no energy released during the

formation of phosphodiester bonds and therefore not

favorable.

4. Explain the mechanisms of replication of the DNA lagging strand.

• Orientation of the replication fork

o If the fork is moving to the R→

▪ Picture:

o If the fork is moving the the L →

▪ Picture

1st step: addition of the RNA primer(9 bp long) synthesis by DNA primase

2nd: DNA polease il eted ad elogate fo the RNA pie 3’OH Okazaki fagets

3rd: RNase H will digest the RNA primers & DNA polymerase will synthesize new strands

4th: DNA igase sticketes the emtpt spots

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Document Summary

Le(cid:272)ture o(cid:271)je(cid:272)tives dna repli(cid:272)ation: explain why the reaction of dna synthesis is favorable on the basis of energy. Reactants: dna + ntp: start of with a dna strand where a single nucleotide, ntp, will be added at a time. Products: dna-nmp + ppi: the added nucleotide only has one phosphate, pyrophosphate is also generated as a product. The first release of energy is from the hydrolysis of the bond between the sugar of the activated nucleotide and the alpha phosphate: the hydrolysis of this bond will generate energy. The second release of energy comes from the hydrolysis of ppi into 2 pi. This reaction is favorable because ppi 2pi: pyrophosphyate is hydrolyzed into two inorganic phosphates. The reaction is driven to the right (formation of products). Le chetalie(cid:396)"s p(cid:396)i(cid:374)(cid:272)iple (cid:272)alls fo(cid:396) (cid:396)epla(cid:272)e(cid:373)e(cid:374)t of a p(cid:396)odu(cid:272)t (cid:271)ei(cid:374)g deg(cid:396)aded (cid:271)(cid:455: generating my phosphatases, formation of the phosphodiester bond to drive the elongation of the dna chain.

Related Questions

Multiple answers to each question might be possible!

You decide to identify the CFTR mutation by analyzing the genomic DNA of your patients compared to healthy individuals. You specifically are looking to see whether a specific 3' gene truncation has occurred in the patients. You will determine this using hybridization techniques with samples from healthy and CF patients. Which of the following will allow you to accomplish this?

	Using an RNA probe complementary to the region not removed by the truncation.
	Using an RNA probe complementary to the region removed by the truncation.
	Using an DNA probe complementary to the region not removed by the truncation.
	Using an DNA probe complementary to the region removed by the truncation.

To conduct the hybridization experiment, you are trying to decide between using a DNA or RNA probe. Which would be ideal to use and why?

	As both are composed of nucleic acids, using either would result in identical results.
	An RNA probe because RNA has uracil bases.
	An RNA probe because it could also be used in a translation experiment.
	A DNA probe because it is more stable than RNA.
	A DNA probe because RNA cannot bind to DNA.

One step of the Hershey/Chase experiment involved blending the virus/cell mixture before centrifugation and probing the pellet for radioactivity. Why was the blending step necessary?

	To collect the bacteria at the bottom of the tube.
	To break open the bacteria to release the genome.
	To separate the bacteria from the bacteriophages.
	To be able to detect the radioactivity.

Imagine Hershey/Chase had used an RNA virus (genome composed of RNA) instead of a DNA virus in their experiment. Would radioactivity still have been found in the pellet?

	No, because only DNA can be labeled with radioactivity.
	No, because the RNA genome would not enter the bacteria upon infection.
	No, because while DNA and RNA nucleotides are similar, they are not identical.
	Yes, because DNA and RNA nucleotides are similar.
	Yes, because genome in any form (DNA, RNA, protein) would be labeled similarly.

The human genome consists mostly of non-coding DNA. Which of the following are benefits of this?

	Random DNA mutations generally won't affect RNA and protein function.
	It is faster to duplicate the genome when these are present.
	The existence of introns can lead to multiple variations of proteins encoded by a single gene.
	It is unlikely transposons would exist in the genome if there was too much protein coding DNA.

Explain the 5â to 3â directionality of a DNA stand.

	It is due to the fact that the free 5â carbon is on one end and the free 3â carbon is on the other
	It is due to the fact that new nucleotide are added to the 5â carbon of the previous nucleotide
	It is due to the fact that there are 3 phosphate groups attached to the 5â carbon
	It is due to the fact the complementary strand is 3â to 5â
	More than one of the above explain the 5â to 3â directionality

You accidentally add a mutant dNTP (which has an H instead of an OH connected to the 3â carbon) to a reaction where DNA is being replicated. Which of the following is true of this mutant dNTP?

	It can be incorporated into DNA strand but cannot form a phosphodiester bond with an incoming wild type dNTP
	It can be incorporated into a DNA strand but cannot base pair with a complementary nucleotide
	It can be incorporated into a DNA strand and can form a phosphodiester bond with an incoming dNTP, but only if it is another mutant dNTP
	It cannot be incorporated into a DNA strand.

Why does DNA polymerase utilize an RNA primer?

	DNA polymerase is unable to initiate strand synthesis but RNA polymerase can
	DNA polymerase can only add a dNTP to an rNTP
	DNA synthesis proceeds in the 3â to 5â when initiating strand synthesis
	Chromosomal DNA contains interspersed RNA fragments
	The RNA primer increases stability of the newly synthesized strand

rosehippopotamus950

Question 401 pts

Kinetic energy is the stored energy that can be used for motion.

True

False

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Question 411 pts

When an electron is transferred from one atom to another, and the two atoms are then electrically attracted to one another, a(n) ________________ bond is formed.

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Question 421 pts

Changing the number of ____________ of an atom would change the chemical properties of the atom.

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Question 431 pts

Forming molecules and breaking down molecules in biological organisms usually requires the use of _________ to help the reaction proceed faster.

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Question 441 pts

Organic molecules have a core composed of .

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Question 451 pts

The building blocks of carbohydrates are

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Question 461 pts

Water molecules crossing a membrane from high to low concentration is .

active transport

cell fate

facilitated diffusion

osmosis

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Question 471 pts

Choose the membrane molecule responsible for the passage of polar molecules and ions into and out of the cell.

phospholipids

transmembrane channel proteins

cell surface proteins

carbohydrate chains

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Question 481 pts

The simplest cells are .

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Question 491 pts

Which of the following membrane bound organelles are found inside bacterial cells:

nucleus

organelles are not found in prokaryotic cells

mitochondria

chloroplasts

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Question 501 pts

Which of the following is a specialized components of the cell, is associated with the rough endoplasmic reticulum, and is responsible for making proteins.

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Question 511 pts

Proteins are sorted, modified, and packaged by the _____________ and later transported to the outside of the cell.

ribosomes

golgi bodies (golgi apparatus)

nucleus

mitochondria

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Question 521 pts

Dehydration synthesis is a process of linking two smaller subunits together to form a polymer. Which of the following statements below is true of dehydration synthesis?

Oxygen is consumed.

A water molecule is removed from the molecules.

A water molecule is added to the molecules

Carbon dioxide is given off.

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Question 531 pts

Proteins are made up of _________ held together by peptide bonds.

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Question 541 pts

Which of the following gives an amino acid its properties?

NH2

R Group or functional group

COOH

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Question 551 pts

The final three-dimensional shape of a protein that includes the bonding of two or more polypeptide chains is call its _____ structure.

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Question 561 pts

How do DNA and RNA differ?

all statements are differences between DNA and RNA.

DNA is double stranded while RNA is single stranded.

They have different sugars.

Thymine is present in DNA but not in RNA.

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Question 571 pts

Which of the following is a component of a DNA nucleotide?

phosphate

a nitrogen containing base

All are components of a nucleotide.

5-carbon sugar

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Question 581 pts

Cell membranes are made up of several different types of molecules. Select the membrane molecule below that is made up of a polar region and two non-polar fatty acid tails.

transmembrane proteins

carbohydrate chains

phospholipids

cell surface proteins

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Question 591 pts

Two organelles which are believed to have once been free-living bacterial cells are ____________ and ______________.

chloroplasts and mitochondria

golgi apparatus and endoplasmic reticulum

ribosomes and nucleolus

peroxisomes and lysosomes

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Question 601 pts

The is an extensive system of internal membranes responsible for producing carbohydrates and lipids.

smooth endoplasmic reticulum

rough endoplasmic reticulum

nucleolus

mitochondria

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BIO 3170 Study Guide - Midterm Guide: Phosphodiester Bond, Pyrophosphate, Hydrolysis

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