Nucleic Acids and Protein Synthesis

Nucleic Acids and Protein Synthesis

Overview

  • Nucleic acids store and transmit genetic information and are essential for protein synthesis.
  • The central dogma of molecular biology outlines the flow of genetic information: Replication, Transcription, and Translation.

What are Nucleic Acids?

  • Nucleic acids are unbranched polymers composed of repeating monomers called nucleotides.
  • Two types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
  • DNA stores genetic information and transmits it from one generation to another.
  • RNA translates the genetic information in DNA into proteins for cellular function.

DNA and Chromosomes

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

Nucleotide Structure

  • Nucleotides are the building blocks of nucleic acids.
  • Three components:
    • Sugar (Monosaccharide)
    • Nitrogen-containing base
    • Phosphate Group
  • A nucleotide consists of a phosphate group, a monosaccharide, and a nitrogen-containing base.

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 FORMATION

Nucleosides

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

Naming Nucleosides

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

Example: Cytidine

  • D-ribose + cytosine → cytidine
  • Cytidine is a ribonucleoside.
  • N-glycoside bond is formed.
  • Chemical structure of cytidine shown.

Example: Deoxyadenosine

  • D-2-deoxyribose + adenine → deoxyadenosine
  • Deoxyadenosine is a deoxyribonucleoside.
  • N-glycoside bond is formed.
  • Chemical structure of deoxyadenosine shown.

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".

Example: Cytidine 5'-monophosphate (CMP)

  • Cytidine + phosphate → cytidine 5'-monophosphate
  • CMP is a ribonucleotide.
  • Phosphate group attached to the 5' carbon of cytidine.

Example: Deoxyadenosine 5'-monophosphate (dAMP)

  • Deoxyadenosine + phosphate → deoxyadenosine 5'-monophosphate
  • dAMP is a deoxyribonucleotide.
  • Phosphate group attached to the 5' carbon of deoxyadenosine.

Summary of Nucleic Acid Components

  • Nucleoside: A monosaccharide + a base
    • A ribonucleoside contains the monosaccharide ribose.
    • A deoxyribonucleoside contains the monosaccharide 2-deoxyribose.
  • Nucleotide: A nucleoside + phosphate = a monosaccharide + a base + phosphate
    • A ribonucleotide contains the monosaccharide ribose.
    • 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

  • Table summarizing the names and abbreviations of bases, nucleosides, and nucleotides for both DNA and RNA.
    • 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)

ADP and ATP

  • ADP is an example of diphosphate.
  • ATP is an example of triphosphate.

Nucleic Acid Formation

  • A dinucleotide is formed by joining two nucleotides.
  • Nucleic acids are polymers of nucleotides joined by phosphodiester linkages.
  • Phosphodiester linkage connects the 5'-phosphate group of one nucleotide to the 3'-OH group of another.

Polynucleotides

  • 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.

Nucleic Acid Structure

  • The variable portion is the sequence of bases.
  • The backbone is an alternating sugar-phosphate chain.
  • Nucleotide, Base, Phosphate-Sugar repeating units.

Discovery of DNA Structure

  • 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.

Role of X-ray Crystallography

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

Characteristics of DNA Double Helix

  • The two strands run in opposite directions; one runs from the 5’ end to the 3’ end and the other runs from the 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
  • Hydrogen Bonding

Chromosome Structure

  • HISTONES: DNA helices wind around a core of protein molecules called histones.
  • 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 makes a copy of itself.
  • Transcription: DNA is transcribed into RNA.
  • Translation: RNA is translated into protein.
  • Reverse transcription can occur from RNA to DNA.

    DNA \xrightarrow{Replication} DNA \xrightarrow{Transcription} RNA \xrightarrow{Translation} Protein

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 molecules, each containing a strand from the parent DNA and one new strand.

Steps in Replication

  • 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 Process

  • 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.

End Result of Replication

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

RNA vs DNA

FeatureRNADNA
LOCATIONIn all parts of the cellWithin the nucleus
STRUCTURESingle-strandedDouble-stranded
SUGARRiboseDeoxyribose
Base PairingA=U; G=CA=T; G=C
FUNCTIONSynthesis of proteinsStorage and transfer of genetic information

Transcription

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

Types of RNA

  • Ribosomal RNA (rRNA): Provides the site where polypeptides are assembled during 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 Structure

  • 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

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

Direction of Transcription

  • 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.

Sample Problems (Transcription)

  • Problems demonstrating how to derive the mRNA and informational strand from a template DNA strand.
  • Given the template strand 3’ – C T A G G A T A C – 5’, the mRNA strand is 5’ – G A U C C U A U G – 3’ and the informational strand is 5’ – G A T C C T A T G – 3’.
  • Given the template strand 3’ – G C T T C G T G G C – 5’, the mRNA strand is 5’ – C G A A G C A C C G – 3’ and the informational strand is 5’ – C G A A G C A C C G – 3’.

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 and tRNA Anticodon

  • The mRNA codon is matched by the tRNA anticodon to bring the correct amino acid.
  • Examples: ACA, GCG, AGA, UCC (mRNA codons).

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 acids.
  • 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 Examples

  • Examples showing the relationship between DNA template strand, mRNA, tRNA anticodons, and the resulting polypeptide.
  • DNA template strand: TAC AAC CCT CGG CCT AGT
  • DNA template strand: TAC GGC CGC AAG CAT TGT

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 Mutations

  • A point mutation is the substitution of one nucleotide for another.
  • Example showing a normal DNA sequence and a sequence with a substitution.
  • Original DNA: AAA ATG GAA GAG
  • Mutated DNA: AAA ATC GAA GAG

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.

Classes of Mutations

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

Missense Mutations

  • 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 Mutations

  • 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

  • Table summarizing characteristics of various genetic diseases:
    • Tay-Sachs disease: Mental retardation; caused by a defective hexosaminidase A enzyme
    • Sickle cell anemia: Anemia; occlusion and inflammation of blood capillaries, caused by defective hemoglobin
    • Phenylketonuria: Mental retardation; caused by a deficiency of the enzyme phenylalanine hydroxylase
    • Galactosemia: Mental retardation; caused by a deficiency of an enzyme needed for galactose metabolism
    • Huntington's disease: Progressive physical disability; caused by a defect in the gene that codes for the Htt protein

Viruses and Vaccines

  • 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.
  • 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.