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Nucleic Acids: DNA and RNA
Function of DNA and RNA
DNA stores genetic information. RNA converts genetic information into proteins.
Building Blocks: Nucleotides
Just like amino acids are the building blocks of proteins, nucleotides are the building blocks of both RNA and DNA.
Components of a Nucleotide
Every nucleotide consists of three components:
A phosphate group A five-carbon sugar A nitrogenous base (amine)
The Sugar Component: Ribose vs. Deoxyribose
The five-carbon sugar, also called a carbohydrate, is where the fundamental difference between DNA and RNA lies.
One type of nucleotide contains ribose. The other contains deoxyribose.
Numbering
In nucleotides, the sugar carbons are numbered with primed numbers (1', 2', 3', 4', 5') to differentiate them from the nitrogenous base numbering.
Key Difference
The key difference between ribose and deoxyribose is at the 2' carbon position.
Ribose has an oxygen (OH) at the 2' position. Deoxyribose has only a hydrogen (H) at the 2' position. The "D" in DNA stands for "deoxy," indicating the removal of an oxygen.
Importance of the 3' Position
The 3' carbon position is identical in both sugars and always has an OH group.
Anti-Parallel Alignment
The numbering of the sugars is essential when discussing how nucleotides align in an anti-parallel manner to form a helix, known as the 5' end and 3' end.
Identifying DNA vs RNA
To determine if a molecule is RNA or DNA, look at the 2' carbon:
If there is an oxygen, it's RNA (ribose). If there is only a hydrogen, it's DNA (deoxyribose).
Other Terms for the Sugar Component
Pinto Sugar Carbohydrate Sugar
Nitrogenous Bases
The nitrogenous bases are amine bases. There are two categories of nitrogenous bases:
Pyrimidines Purines
To determine if a sugar is deoxyribose or ribose, look at the 2' position. If there is nothing on the 2' position, it is deoxyribose.
Linking Nucleotides and Phosphodiester Bonds
Nucleotides link together through phosphodiester bonds. Instead of a carbon, there is a phosphorus in the bond. The bond occurs on the carbon.
Backbone Structure of DNA
The backbone of a DNA molecule consists of alternating sugar and phosphate groups. The amine bases are bonded off away from the backbone. The pattern, like the primary sequence for amino acids, also exists for nucleic acids.
Colorful Picture of Phosphodiester Bond
The 3' position of the sugar (ribose or deoxyribose) bonds to the phosphate group. This results in a 3' end at the bottom and a 5' end at the top of the molecule.
Carbon Numbering
The numbers with primes (e.g., 3', 5') come from the numbering of carbons in carbohydrates (C1, C2, C3, C4, C5). The prime numbers are used because the base atoms get the non-prime numbers.
Visual Representation of DNA Structure
Sugar, phosphate, sugar, phosphate pattern with amine bases sticking out. Recognition of the 5' end is important. It is a 5' end because the phosphate ends with the 5' carbon bond (C5').
Complementary Base Pairing in DNA
The double helix shape in DNA is due to a single ring bonded to a double ring. Purines (double rings) take up more space than pyrimidines (single rings). To maintain the fit, a pyrimidine always bonds to a purine. In DNA: Adenine (A) always bonds to Thymine (T). Guanine (G) always bonds to Cytosine (C). Examples of mnemonic devices for remembering base pairing: Apples on a Tree (A and T) and Cars in the Garage (C and G) Appalachian Trail (AT) and Gas Chromatography (GC)
Base Pairings and Hydrogen Bonds
It is important to be able to connect base pairs because we will be looking at DNA- based pairs.
Connecting Base Pairs
Come up with a way to remember how to connect base pairs.
GC: General Contractor, Gas Chromatography AT: Art Teacher
The order of the base pairs does not matter, only that they are always paired to each other.
Hydrogen Bonds
Adenine (A) and Thymine (T) have two hydrogen bonds. Guanine (G) and Cytosine (C) have three hydrogen bonds.
Hydrogen bonding is anytime a hydrogen is bonded to either a nitrogen, an oxygen, or a fluorine.
DNA vs. RNA
Up until now, we've pretty much been talking about DNA, a nucleotide where we have deoxyribose.
Hydrogen Bonds
Hydrogen bonds hold complementary base pairs together.
When in doubt in chemistry or biochemistry, guessing hydrogen or cholesterol, respectively, often leads to the correct answer.
Phosphodiester Bonds
Phosphodiester bonds hold nucleotides together in a strand.
DNA's Double Helix Structure
Pyrimidines and Purines
The double helix structure of DNA is due to:
A pyrimidine always bonding to a purine, ensuring consistent sizing. The specific sizes of these bases and the hydrogen bonding between them result in efficient packing and the characteristic double helix shape.
Anti-Parallel Strands
DNA consists of two strands described as anti-parallel. This means they are parallel but oriented in opposite directions.
One strand runs 5' to 3', having a free 5' carbon at one end and a free 3' carbon at the other. The other strand runs 3' to 5', with the order inverted.
In a 5' to 3' strand, the backbone consists of sugar, phosphate, sugar, phosphate, and so on.
Writing Complementary Base Sequences
Given a DNA sequence, you can write its complementary base sequence:
- If the given sequence starts with 5', the complementary sequence starts with 3', and vice versa.
- Pair the bases: T pairs with A C pairs with G
Example:
If the primary sequence (5' to 3') is T C G A, then the complementary base sequence (3' to 5') is A G C T.
Building Blocks and Base Pairing
Nucleotide Structure
The backbone consists of repeating units of sugar and phosphate, with each sugar attached to a base.
You don't need to memorize the structures of the bases. You should be able to identify whether a base is a pyrimidine or a purine.
Writing Complementary Sequences: An Example
Given a sequence with the 5' end identified, and the bases labeled (e.g., G, T, A, C), you can write the complementary base pair sequence.
For example, if you have a sequence 5'-G T A C-3', the complementary sequence would be 3'-C A T G-5'.
Additional Notes
It is conventional to write DNA sequences from 5' to 3'. Even if a sequence is presented "backwards" (starting with 3'), you can still determine the complementary sequence by starting with 5' and following the base pairing rules.
Practice
Transcription
Information from DNA is copied into a new molecule of RNA, specifically messenger RNA (mRNA). Uracil (U) replaces thymine (T) in RNA.
Translation
mRNA is translated into proteins using codons. Codons are groups of three bases on the mRNA.
A codon is three nucleotide or base sequences in mRNA. Each codon corresponds to a specific amino acid.
The sequence of codons determines the sequence of amino acids, forming the primary structure of a protein.
Codon Charts
Codon charts are used to determine which amino acid is encoded by a specific codon.
Using a Codon Chart
- Find the first base of the codon in the chart (read from the center out).
- Find the second base.
- Find the third base.
- The amino acid encoded by that codon will be indicated at the intersection of these three bases.
Example
The codon CCA codes for proline.
- Start with C (center).
- Go to C.
- Go to A.
The codon AUG codes for methionine.
- Start with A.
- Go to U.
- Go to G.
Central Dogma: Codons and Protein Synthesis
Codon Charts and RNA Translation
Codons are used to translate RNA into proteins. A codon chart helps decipher the relationship between mRNA sequences and the corresponding amino acids. The primary sequence, or the order of codons, determines the specific protein. Exam will have a codon chart available, either as a header or footer.
Reading Codon Charts
Always read the chart in the 5' to 3' direction. Use the chart to translate mRNA into amino acids. Multiple codons can code for the same amino acid, meaning the code is degenerate.
Nucleosides vs. Nucleotides
A nucleoside is essentially a nucleotide without the phosphate group.
A nucleoside is a nucleotide without the phosphate group. It's a precursor to a nucleotide.
