DNA double helix structure

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Nucleic acids

DP Biology

Nucleic Acids

DNA and RNA

If I asked you about the information, such as the color of your eyes, your height, your blood type, and even how your body builds proteins. Where is all this information stored? Is it written somewhere inside you? Yes. It is stored in molecules called nucleic acids.

In biology, nothing happens without information. Cells know how to construct, when to divide, and how to respond to the external environment. Nucleic acids are the molecules that keep and carry this information. They are the blueprints of life.

The two principal forms of nucleic acids are:

  • Deoxyribonucleic Acid (DNA)
  • Ribonucleic Acid (RNA)

In unison, they manage to control the structure and function of all the living organisms.

What are Nucleic Acids?

Nucleic acids are large macromolecules composed of smaller, repeating units known as nucleotides. They fall under the four major biopolymers:

  • Carbohydrates
  • Lipids
  • Proteins
  • Nucleic acids

Unlike carbohydrates and lipids, which mainly provide energy, nucleic acids are responsible for the storage of genetic information.

The Basic Unit: Nucleotide

Nucleic acids are formed by a basic unit called a nucleotide. Every nucleotide has three components:

  • A phosphate group
  • A pentose sugar
  • A nitrogen base

For nucleic acids, there are two types of sugar:

  • Ribose Sugar (found in RNA)
  • Deoxyribose sugar (found in DNA)

Nucleotides can have one of two different types of nitrogen bases:

Purines (which have a double ring structure):

  • Adenine (A)
  • Guanine (G)

Pyrimidines (which have a single ring structure):

  • Cytosine (C)
  • Thymine (T) (which is found in DNA)
  • Uracil (U) (which is found in RNA)

Nucleotides are joined together by a specific covalent bond called a phosphodiester bond, making a long structure called polynucleotide.

DNA (Deoxyribonucleic Acid)

DNA is the molecule that contains genetic information for the majority of living organisms. The structure of the DNA molecule was established in 1953 by scientists James Watson and Francis Crick using the information (data) of a scientist called Rosalind Franklin. Watson and Crick called DNA a double helix structure.

Structure of DNA

Consists of two polynucleotide strands. Important features are:

  • The two strands are antiparallel, meaning they run in different directions.
  • The sugar and phosphate make up the backbone of the strand.
  • The nitrogen bases are inward.
  • The bases are paired in a specific way:
    • Adenine (A) pairs with Thymine (T), yielding an A-T pair (this pair has 2 hydrogen bonds)
    • Cytosine (C) pairs with Guanine (G), yielding a G-C pair (this pair has 3 hydrogen bonds)

This specific pairing of bases is called complementary base pairing.

Because of this specific pairing, knowing one strand means you can predict the other strand.

Antiparallel Direction

One strand runs 5' → 3'.

The other runs 3' → 5'.

The numbers represent the carbon atoms in the sugar molecule. This directionality is particularly important in DNA replication and in the synthesis of proteins.

DNA as the Genetic Material

DNA transports genes.

There are sequences of DNA in the genes that code for specific proteins.

Proteins are responsible for the manifestation of the various traits, such as:

  • Enzymes
  • Hormones
  • Structural proteins like collagen

DNA → RNA → Protein

This progression is referred to as the central dogma of molecular biology.

DNA Replication

A cell must duplicate its DNA before it can undergo division. This procedure is termed replication.

The replication takes place during the S-phase of the interphase within the cell cycle.

DNA replication is characterized as semi-conservative.

This suggests that every novel DNA molecule comprises:

  • An authentic strand
  • A strand that is newly synthesized

This was the model validated in 1958 by Matthew Meselson and Franklin Stahl.

Stages of DNA Replication

  • The helicase enzyme undoes the double helix.
  • The chemical bonds of the bases are broken.
  • Every original strand functions as a template.
  • DNA polymerase provides the matching nucleotides.
  • The new strands are formed in accordance with the base-pairing rules.
  • DNA polymerase can only add nucleotides in the 5' → 3' direction.
  • One of the strands (the leading strand) is synthesized without interruption.
  • The other strand (the lagging strand) is synthesized in short sections, known as Okazaki fragments.
  • DNA ligase is the enzyme that joins the Okazaki fragments.

The process of replication is essential, and it ensures the following:

  • Genetic continuity
  • Growth
  • Tissue repair
  • Reproduction

If replication is not accurate, there is the potential for mutations.

RNA (Ribonucleic Acid)

RNA is different from DNA in 3 main ways:

  1. RNA is typically single-stranded
  2. RNA has ribose sugar
  3. RNA has uracil (U) in place of thymine (T)

RNA is essential in the process of protein synthesis, which occurs in three types of RNA:

  • mRNA (Messenger RNA), which carries the genetic code from DNA to ribosomes
  • tRNA (Transfer RNA), which transports the amino acids to the ribosomes during the process of protein synthesis
  • rRNA (Ribosomal RNA), which is part of the ribosome itself, is also the site of protein synthesis

Transcription

Transcription is the process by which information is transferred from DNA to mRNA, and it occurs in the nucleus in eukaryotes.

Steps of transcription include:

  1. Binding of RNA polymerase to the promoter region
  2. Separation of DNA strands
  3. One strand of DNA serves as the template.
  4. The template strand of DNA is paired with complementary RNA nucleotides:
    • A pairs with U
    • T pairs with A
    • G pairs with C
    • C pairs with G

As a result of these pairs, an mRNA strand is created.

Modified mRNA exits the eukaryotic nucleus, leaving the chromosomal DNA behind, and moves into the cytoplasm.

RNA Processing (Eukaryotes)

In eukaryotes, mRNA requires the following modifications:

  • Removal of introns (non-coding regions).
  • Joining of exons (coding regions).
  • Addition of a 5' cap and Poly-A tail.

Translated mRNA is now ready.

Translation

Translation means to build a protein. This occurs in the cytoplasm on the structures called ribosomes.

In translation, the following occurs:

  1. mRNA is attached to a ribosome.
  2. A tRNA with a complementary anticodon binds to the ribosome.
  3. Amino acids are joined by peptide bonds.
  4. This means the polypeptide chain will continue to grow.
  5. A stop codon will end translation.
  6. The end product will be a specific protein.

The final product is a functional protein.

The Genetic Code

The genetic code consists of 3 bases.

The bases in mRNA code for amino acids.

Every 3 bases equals 1 codon.

For example, AUG is a start codon that means to include Methionine in the protein.

The number and types of codons:

  • There are 64 codons
  • There are 20 amino acids for the ribosomes to use in building the protein

The genetic code is:

  • Universal (the same in almost all organisms)
  • Degenerate (multiple codons can code for the same amino acid)
  • Non-overlapping (each nucleotide is part of only one codon)

Mutations

Mutations are an alteration of the DNA sequence.

Types of mutations:

  • substitution
  • insertion
  • deletion

Types of mutations include:

  • Silent (no change in protein)
  • Missense (amino acid difference)
  • Nonsense (stop codon created)

Mutations can be:

  • harmful
  • neutral
  • beneficial

In the context of evolution, mutations are very important because they provide the genetic diversity needed for evolution to occur.

DNA Packaging

DNA must be compacted to fit inside the nucleus because it is very long.

In eukaryotes: DNA is wrapped around protein (histones) to form nucleosomes. These nucleosomes coil to form chromatin (which is further coiled to form a chromosome during cell division). Each chromosome is made of 1 very long DNA molecule.

Prokaryotes:

  • DNA is circular and in the cytoplasm
  • no histones (except some archaea)

Eukaryotes: DNA is linear, found in the nucleus, and has histones associated with it.

In addition, prokaryotes may have plasmids (small circular DNA).

Chargaff's Rules

Erwin Chargaff determined:

  • amount of A = amount of T
  • amount of G = amount of C

This is Chargaff's rule, which supports base pairing.

Importance of Nucleic Acids

Nucleic acids are important because they:

  • store hereditary information
  • control the synthesis of protein
  • provide a means for reproduction
  • provide the means for variation and evolution
  • are considered the main molecules of life

As a result of this, life cannot exist without DNA and RNA.

Conclusion

Molecules of inheritance are nucleic acids. DNA keeps the instructions. RNA helps translate the instructions into proteins. Cells maintain life and information through successive generations by replication, transcription, and translation.

Understanding nucleic acids enables understanding of genetics, biotechnology, medicine, evolutionary biology, and even forensics.

The entire complexity of an organism, from one fertilized cell to the whole organism, begins with the order of the nucleotides in the DNA.