Nucleic Acids and Protein Synthesis

Nucleic Acids and Protein Synthesis

Lesson Outline

• Identify and classify nucleic acids based on their structural composition and types.
• Outline the central dogma of molecular biology (Replication, Transcription, and Translation).

Nucleic Acids

• Nucleic acids are unbranched polymers composed of repeating monomers called nucleotides.
• Two types:
  • DNA (deoxyribonucleic acid): Stores the genetic information of an organism and transmits that information from one generation to another.
  • RNA (ribonucleic acid): Translates the genetic information contained in DNA into proteins needed for all cellular function.

DNA Molecule & Chromosomes

• Chromosome: A threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.
• Humans have 46 chromosomes (23 pairs).

Nucleotide

• Building blocks of Nucleic Acids
• Three Components:
  • Sugar (Monosaccharide)
  • Nitrogen-containing base
  • Phosphate Group
• A nucleotide structure showing phosphate, nitrogen-containing base, and monosaccharide components is shown.

Nucleoside Formation

• Both RNA and DNA have an Aldopentose sugar.
• The N-containing base is one of 5 types.
  • Sugar Component
  • Nitrogen-containing base
    • Pyrimidine
    • Purine
• Two-types of Base RNA & DNA

Nucleoside

• A nucleoside is formed by joining a carbon of the monosaccharide with the N-atom of the base.
• NUCLEOSIDE = MONOSACCHARIDE + NITROGEN-BASE

Naming a Nucleoside

• Pyrimidine base = use the suffix "-idine".
• Purine base = use the suffix "-osine".
• For deoxyribonucleosides, add the prefix "deoxy-".
• NUCLEOSIDE = MONOSACCHARIDE + NITROGEN-BASE

Cytidine Example

• D-ribose + cytosine = cytidine
• Cytidine is a ribonucleoside.
• N-glycoside bond is formed.

Deoxyadenosine Example

• D-2-deoxyribose + adenine = deoxyadenosine
• Deoxyadenosine is a deoxyribonucleoside.
• N-glycoside bond is formed.

Nucleotide Formation

• Nucleotides are formed by adding a phosphate group to the 5'-OH of a nucleoside.
• Nucleotides are named by adding the term: "5'-monophosphate".

Cytidine 5'-monophosphate Example

• Cytidine + phosphate = cytidine 5'-monophosphate
• Cytidine 5'-monophosphate is also known as CMP

Deoxyadenosine 5'-monophosphate Example

• Deoxyadenosine + phosphate = deoxyadenosine 5'-monophosphate
• Deoxyadenosine 5'-monophosphate Also known as dAMP

Summary of Nucleic Acid Components

• Nucleoside
  • Components: A monosaccharide + a base
  • RNA: A ribonucleoside contains the monosaccharide ribose.
  • DNA: A deoxyribonucleoside contains the monosaccharide 2-deoxyribose.
• Nucleotide
  • Components: A nucleoside + phosphate = a monosaccharide + a base + phosphate
  • RNA: A ribonucleotide contains the monosaccharide ribose.
  • DNA: A deoxyribonucleotide contains the monosaccharide 2-deoxyribose.
• DNA
  • A polymer of deoxyribonucleotides
  • The monosaccharide is 2-deoxyribose.
  • The bases are A, G, C, and T.
• RNA
  • A polymer of ribonucleotides
  • The monosaccharide is ribose.
  • The bases are A, G, C, and U.

Names of Bases, Nucleosides, and Nucleotides

• DNA
  • Adenine (A) -> Deoxyadenosine -> Deoxyadenosine 5'-monophosphate (dAMP)
  • Guanine (G) -> Deoxyguanosine -> Deoxyguanosine 5'-monophosphate (dGMP)
  • Cytosine (C) -> Deoxycytidine -> Deoxycytidine 5'-monophosphate (dCMP)
  • Thymine (T) -> Deoxythymidine -> Deoxythymidine 5'-monophosphate (dTMP)
• RNA
  • Adenine (A) -> Adenosine -> Adenosine 5'-monophosphate (AMP)
  • Guanine (G) -> Guanosine -> Guanosine 5'-monophosphate (GMP)
  • Cytosine (C) -> Cytidine -> Cytidine 5'-monophosphate (CMP)
  • Uracil (U) -> Uridine -> Uridine 5'-monophosphate (UMP)

Nucleotide Phosphorylation

• ADP is an example of DIPHOSPHATE
• ATP is an example of TRIPHOSPHATE

Nucleic Acid Formation

• Nucleic acids are polymers of nucleotides joined by phosphodiester linkages.
• A dinucleotide example is shown with a phosphodiester linkage.

Polynucleotide

• A polynucleotide contains a backbone consisting of alternating sugar and phosphate groups.
• A polynucleotide has one free phosphate group at the 5’ end and one free OH group at the 3’ end.
• In DNA, the sequence of the bases carries the genetic information of the organism.

Polynucleotide Composition

• Variable Portion: Sequence of bases
• Backbone: Alternating sugar-phosphate chain

DNA Discovery by Watson and Crick

• In 1953, James Watson and Francis Crick concluded that the DNA molecule appears as a three-dimensional double helix.
• DNA consists of two polynucleotide strands that wind into a right-handed double helix.

DNA Discovery by Franklin and Wilkins

• Rosalind Franklin and Maurice Wilkins used X-ray crystallography to study DNA's structure, which helped Watson and Crick with their discovery.

DNA Double Helix Characteristics

• The two strands run in opposite directions; one runs from 5’ end to the 3’ end and the other runs from 3’ end to the 5’ end.
• The sugar-phosphate groups lie on the outside of the helix and the bases lie on the inside.

Complementary Base Pairs

• There are complementary base pairs that always hydrogen bond together in a particular manner:
  • Purine = Pyrimidine
  • A = T; C = G

Chromosome Structure

• Histones: DNA helices that wind around a core of protein molecules.
• Nucleosomes: Group of histones in chains.
• Chromatin: Chain of nucleosomes.
• Gene: A sequence of nucleotides in DNA or RNA that encodes the synthesis of specific proteins.

Central Dogma of Molecular Biology

• DNA -> RNA -> Protein
• Replication: DNA -> DNA
• Transcription: DNA -> RNA
• Translation: RNA -> Protein
• Reverse transcription: RNA -> DNA

Replication

• REPLICATION is the process by which DNA makes a copy of itself when a cell divides.
• SEMICONSERVATIVE REPLICATION: The original DNA molecule forms two new DNA molecule, each of which contains a strand from the parent DNA and one new strand.

Replication Process

• First step in Replication is the unwinding of the DNA Helix.
• The enzyme that causes the DNA Helix to unwind is called DNA Helicase.
• The point at which the unwinding occurs is called Replication Fork.

Replication Details

• Catalyzing the replication process is with the help of DNA Polymerase enzyme.
• Leading Strand
  • Grows continuously
  • Sequence is 5’ to 3’ direction
• Lagging Strand
  • Aka “Okazaki Fragments”
  • Synthesized in small fragments
  • Sequence is 3’ to 5’ direction
• DNA Ligase – enzyme that joins the lagging strand together.

Replication End Result

• The end result of the Replication Process is the formation of two new strands of DNA (Daughter DNA).

RNA vs DNA

Transcription

• Is the ordered synthesis of RNA from DNA; the genetic information stored in DNA is passed onto RNA
• Three types of RNA molecules are:
  • Ribosomal RNA (rRNA)
  • Messenger RNA (mRNA)
  • Transfer RNA (tRNA)

Types of RNA

• Ribosomal RNA (rRNA)
  • Provides the site where polypeptides are assembled during the protein synthesis.
• Messenger RNA (mRNA)
  • Carries information from DNA to the ribosomes.
• Transfer RNA (tRNA)
  • Brings the amino acids to the ribosomes for protein synthesis.

tRNA details

• tRNA is drawn as a cloverleaf shape, with an acceptor stem at the 3’ end, which carries the needed amino acids, and an anticodon, which identifies the needed amino acids.

Transcription Process Description

• Transcription is the synthesis of mRNA from the DNA.
• Template strand
  • Used to synthesize RNA.
• Informational strand
  • Not used; “non-template strand”

Transcription Direction

• Transcription proceeds from the 3’ end to the 5’ end of the template.
• The difference between mRNA and the information DNA strand is that the base U replaces T on mRNA.

RNA Polymerase

• RNA Polymerase is the enzyme that synthesizes RNA from a DNA template in the transcription process.

Example Problem 1

• From the template strand of DNA below, write out the mRNA and informational strand of DNA sequences:
  • TEMPLATE STRAND: 3’ – C T A G G A T A C – 5’
  • mRNA STRAND:
  • INFORMATIONAL STRAND:

Example Problem 2

• From the template strand of DNA below, write out the mRNA and informational strand of DNA sequences:
  • TEMPLATE STRAND: 3’ – G C T T C G T G G C – 5’
  • mRNA STRAND:
  • INFORMATIONAL STRAND:

The Genetic Code

• A sequence of three nucleotides (a triplet) codes for a specific amino acid.
• Each triplet is called a codon.
• For example: UCA is a codon for the amino acid Serine; UGC is a codon for the amino acid Cysteine.

Translation and Protein Synthesis

• Process of transferring genetic information from RNA to a sequence of amino acids in a protein.
• Occurs in ribosomes.

mRNA Codon & tRNA Anticodon

• mRNA Codon tRNA Anticodon Amino Acid
  • ACA
  • GCG
  • AGA
  • UCC

Three Stages of Translation

• 1. INITIATION
  • Initiation begins with mRNA binding to ribosome.
  • A tRNA brings the first amino acid, always at codon AUG.
  • AUG = START CODON
  • AUG = Methionine
• 2. ELONGATION
  • Elongation proceeds as the next tRNA molecule delivers the next amino acid, and a peptide bond forms between the two amino acid.
• 3. TERMINATION
  • Translation continues until a stop codon is reached, which is called termination; the completed protein is then released.
  • STOP CODONS
    • UAG
    • UGA
    • UAA

Translation Example 1

• DNA template strand: TAC AAC CCT CGG CCT AGT 3'end
• mRNA:
• tRNA anticodons:
• Polypeptide: 5'end

Translation Example 2

• DNA template strand: TAC GGC CGC AAG CAT TGT 3'end
• mRNA:
• tRNA anticodons:
• Polypeptide: 5'end

Mutations and Genetic Diseases

• A mutation is a change in the nucleotide sequence in a molecule of DNA.
• Some mutations are random, others are caused by mutagens – chemicals that alter the structure of DNA.

Point Mutation

• A point mutation is the substitution of one nucleotide for another.
• Example shown.

Deletion Mutation

• A deletion mutation occurs when one or more nucleotides is/are lost from a DNA molecule.

Insertion Mutation

• An insertion mutation occurs when one or more nucleotides is/are added to a DNA molecule.

Silent Mutation

• A silent mutation has a negligible effect to the organism, because the resulting amino acid is identical.

Missense Mutation

• A mutation that produces a protein with one different amino acid usually has a small to moderate effect on the protein overall.
• For some proteins, such as hemoglobin, substitution of just one amino acid can result in the fatal disease sickle cell anemia.

Nonsense Mutation

• If a mutation causes a big change, like producing a stop codon, the remainder of the protein will not be synthesized, which can have catastrophic results.

Genetic Diseases

Viruses

• A virus is an infectious agent consisting of a DNA or RNA molecule that is contained within a protein coating.
• It is incapable of replicating alone, so it invades a host organism and makes the host replicate the virus.

Vaccine

• A vaccine is an inactive form of a virus that causes a person’s immune system to produce antibodies to the virus to ward off infection.