Unit 2 - Lecture 12

Nucleic Acids

__ are the chemical substances that contains genetic information

Nucleic Acids

The genetic information that codes for proteins is contained in __

DNA

__ is the key information storer of the genes that encode proteins. It is what is replicated and passed down from one generation to the next

RNA

__ acts as an intermediate messenger that is transcribed from DNA and provides the templates (called m__s) for the synthesis of proteins in a process called translation

Structure

The __ of nucleic acids is key to their function as genetic information

Inside; Outside

The information contained in the polymer can be accessed from the __ (by separating the strands) as well as the __ (through large grooves in its structure)

Nucelotides

The building blocks of DNA

Polymers

How are nucelotides put together

Nucleic Acid Primary Structure

What is the product of adding nucleotides and polymers together called?

A Base, Sugar, and Phosphate

Nucleotides are composed of what three components?

2.4×10^23

Humans have approximately 40 trillion cells, and each cell has 6 billion base pairs. What number is used to represent this?

Cancer

Just a few few errors in base pairing can cause things such as __

DNA; RNA

Nucleic acids are polymers built for nucleotides for both __ and __

Sugar

The OH group on the __ in nucleotides determine whether it is used for DNA or RNA?

OH

For RNA, the sugar has an __ attached to its 2’ location

H

For DNA, the sugar has an __ attached to its 2’ location

2

How many OH groups are attached to the sugar in an RNA nucleotide?

1

How many OH groups are attached to the sugar in an DNA nucleotide?

Purines and Pyrimidines

The nitrogenous base (aka nucelobase or just base) in a nucleotide has two different different types. What are they?

Purine

A __ nitrogenous base has a bigger structure

Purine

A __ nitrogenous base has 9 carbons and is a double ring

Pyrimidine

A __ nitrogenous base has a smaller structure

Pyrimidine

A __ nitrogenous base has 5 carbons and is a single ring

Adenine - A
Cytosine - C
Guanine - G
Tyrosine - T

DNA uses what bases? What are their abbreviations?

Adenine - A
Cytosine - C
Guanine - G
Uracil - U

RNA uses what bases? What are their abbreviations?

DNA has tyrosine and RNA has uracil

What are the differences between DNA and RNA bases?

Adenine - A
Guanine - G

Which bases are purines?

Cytosine - C
Thymine - T
Uracil - U

Which bases are pyrimidines?

Nucleoside

A base connected to a pentose (5-carbon) sugar is called a __

Ribose

For RNA, the sugar in a nucleoside is __

Deoxyribose

For DNA, the sugar in a nucleoside is __

5; 3

The __’ and __’ positions of the sugar are key positions involved in the building the nucleic acid polymer

2’ OH

The defining chemical difference between RNA and DNA is not which base is attached to it, but rather whether there is the presence or absence of the __

1; Nitrogen

The connection between the base and the sugar in a nucleoside occurs between the __’ position on the sugar and a __ on the base

A Glycosidic Bond (aka an N-Glycosidic Linkage)

The bond between the 1’ of the sugar and nitrogen on the base is called what?

Rotation

The glycosidic bond (aka an N-glycosidic linkage) can have some free __

Nucleotides

__ are nucleosides with phosphoryl group(s) attached via ester linkage

The 5’ on the Sugar

Where does the ester linkage between a sugar (pentose) and phosphoryl group(s) occur in a nucleotide?

Nucleoside Monophosphates

These are what we see in the final nucleic acid polymer

Nucleoside Triphosphates

These serve as high energy building blocks used by the cells to synthesize the nucleic acid polymer

Phosphate
Sugar
Nitrogenous Base

A nucleotide contains what three groups?

Sugar
Nitrogenous Base

A nucleoside contains what two groups?

H

R’ in DNA is what?

OH

R’ in RNA is what?

Ester Linkage

What type of bond is at the 5’?

Nuceloside

If R’’ is an H, the molecule is a what?

Nucelotide

If R’’ is a phosphate, the molecule is a what?

Glycosidic Bond

What type of bond is at the 1’?

Phosphodiester

Nucleotides are joined together through __ bonds. They are the backbone of nucleic acid structure

3;5

One side of the phosphate in a phosphodiester bond is linked to the __’ of a sugar and the other side is linked to the __’ of another sugar

Phosphodiester

__ bonds form by 3’OH nucleophilic attack on activated 5’P

1. Base activation of 3’OH

2. Nucleophilic attack of 3’ OH on an “activated” 5’ phosphate

What are the two steps in a phosphodiester bond formation?

Leaving Group

activated in phosphodiester bond formation means there is a __ attached to the 5’ phosphate to drive the reaction forward

5’;3’

Nucleic acid strands are always synthesized and polymerized in the __ to __ direction

Cleavage

Nucleic acids can also be broken down by the __ of phosphodiester bonds

Base activation of a water molecule allows for a nucleophilic attack on the phosphodiester bond

How are phosphodiester bonds cleaves?

Phosphodiester Bond Formation

What is being shown?

Phosphodiester Bond Cleavage

What is being shown?

Triphosphate

The incoming nucleotide in phosphodiester bond formation always has to be a __ so that there is a leaving group present

Yes

Can phosphor bond formation be repeated?

Nuclease

What is the protein that breaks down nucleic acids in phosphodiester bond cleavage?

Watson-Crick-Franklin

Nucleotides interact through hydrogen bonding to form __ base pairs

3

Cytidine, Guanosine and Thymidine all have __ H-bond donor or acceptor regions

2

Adenosine has __ H-bond donor or acceptor regions

Donors

1

Acceptors

2

Donor’ Acceptor

__ and __ pairs have to line up between two bases or H-bonding will not be good

Antiparallel

__ strands are required for proper hydrogen bonding to form Watson-Crick-Franklin base pairs in nucleotides

Unfavorable

If the wrong bass pairing occurs it is energetically __

Watson-Crick-Franklin (WCF)

__ H-bonding occurs between bases on strands oriented anti-parallel to one another

2

Adenine and thymine forms __ H-bonds

3

Guanine and cytosine forms __ H-bonds

3

All base pairs have an A^o length around __

Watson-Crick-Franklin Base Pairing

What is being shown?

B

The _-form of a double stranded helix is more stable

10.4

There are __ base pairs per turn in a double stranded helix

Outside

In a B-form double stranded DNA double helix, the sugar phosphate backbone is on the __

Inside

In a B-form double stranded DNA double helix, the nucleobases are on the __

Inside

A/T and C/G base pairs are on the __ of the helix

Van der Waals Interactions
Pi-Stacking

What are the two base-stacking interactions?

Bulge

Base pairs that are paired correctly stack perfectly and are smooth and __ free

Planar

Nucleobases have a __ geometry

Hydrophobic

Van der Waals interactions occur between __ nucleobase faces

Steric

Van der Waals interactions in base stacking causes __ effects

Electronic

Pi-stakcing in base stacking causes __ effects

Stabilization

Base-stacking interactions have the effect of re-enforcing the individual A/T and C/G hydrogen-bonding interactions to drive massive __ in the larger context of the dsDNA helix. They work together to strengthen the double helix

Asymmetrical

B-form DNA double-helix structure is __

Major

Which groove is wide and deep?

Minor

Which groove is shallow and narrow?

Grooves

Even when the two strands of DNA are joined together, the B-form double helix presents two __ which provide access to the nucleobases from the outside

Groove

Each base will have a major and minor __

Acceptors; Donors

Each major and minor grooves have hydrogen __ and __

Major

Proteins can bind to double stranded DNA through the __ groove in a sequence specific manner

Major

Which type of groove bonding is more common?

B-form

The __ DNA double helix forms when two separate strands of DNA interact through Watson-Crick-Franklin (WCF) base pairing

T

A pairs with __

G

C pairs with __

Shorter

The A-form double helix is __ than the B-form

Riboswitch

Structured RNA that binds two small molecules and tailors gene expression to produce more or less of the small molecule or export it from the cell. Is dependent on the ligand

Transfer RNA

tRNA is short for what?