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Nucleic Acid and Protein Synthesis: From DNA to Protein

This document outlines the processes of DNA replication, transcription, and translation, which are fundamental to the creation and function of life. It begins by explaining DNA replication, the process by which a cell duplicates its genetic material. This occurs in a semi-conservative manner, meaning each new DNA molecule contains one original strand and one newly synthesized strand. Several enzymes like helicase, DNA polymerase, and DNA ligase play crucial roles in this process. Replication is also bidirectional, occurring in opposite directions along the DNA molecule.

The text further explains the mechanism of semidiscontinuous replication, where the leading strand is synthesized continuously, while the lagging strand is synthesized in short fragments called Okazaki fragments. These fragments are then joined together by DNA ligase.

The document then delves into the concept of mutations, permanent changes in the DNA sequence. These changes can be caused by various factors, including environmental mutagens and errors in DNA replication. Mutations can have diverse effects on an organism's health and can be classified based on their effect on structure, function, and fitness.

Finally, the text explains the process of protein synthesis, which involves two main steps: transcription and translation. Transcription is the process of copying the genetic code from DNA into messenger RNA (mRNA). This occurs in the nucleus and involves the enzyme RNA polymerase. Translation occurs in the cytoplasm and involves the conversion of the mRNA code into a protein sequence using ribosomes and transfer RNA (tRNA).

The document concludes by highlighting the importance of protein synthesis in the production of essential molecules like hormones and enzymes.

Nucleic acid
• Semiconservative Replication
• Bidirectional Replication
• Semidiscontinuous replication
• When a eukaryotic cell divides, the process is called mitosis

• the cell splits into two identical daughter cells


• the DNA must be replicated so that each daughter cell has a copy
  • DNA replication involves several processes:


• first, the DNA must be unwound, separating the two strands


• the single strands then act as templates for synthesis of the new strands,
  which are complimentary in sequence


• bases are added one at a time until two new DNA strands that exactly
  duplicate the original DNA are produced
  DNA Replication
  Parent
  molecule
  Replication
  Daughter
  molecules
  Semiconservative Replication
  • The process is called semi-
  conservative replication
  because one strand of each
  daughter DNA comes from
  the parent DNA and one
  strand is new
  • DNA replication is semi-
  conservative: Each new
  strand of DNA contains one
  parental (old, template)
  strand and one daughter
  (newly synthesized) strand
  • The energy for the synthesis
  comes from hydrolysis of
  phosphate groups as the
  phosphodiester bonds form
  between the bases
  DNA is replicated by the coordinated efforts of a number of proteins
  and enzymes.
  -Topoisomerase: Enzyme uncoils DNA
  -Helicase: Protein that unwinds the DNA double helix.
  -DNA polymerase: Enzyme that replicates DNA using each strand
  as a template for the newly synthesized strand.
  -DNA ligase: enzyme that catalyzes the formation of the
  phosphodiester bond between pieces of DNA.
  Bidirectional Replication
  ◼ Replication forks move in opposite directions.
  ◼ During replication in bacteria (E .coli ) a bubble is initiated the
  origin and circular DNA molecule.
  ◼ Replication is bidirectional both strands of DNA are replicated .
  .
  Semidiscontinuous Replication
  • The enzyme helicase unwinds several sections of parent DNA
  • At each open DNA section, called a replication fork, DNA polymerasecatalyzes the
  formation of 5’
  -3’ester bonds of the leading strand (The strand that is being
  copied in the direction of the advancing replication fork is called the leading
  strand and is synthesized continuously.)
  • The strand that is being copied in the direction away from the replication fork is
  synthesized discontinuously, with small fragments of DNA being copied near the
  replication fork . These short stretches of discontinuous DNA, termed Okazaki
  fragments, are eventually joined (ligated) to become a single, continuous strand. The
  new strand of DNA produced by this mechanism is termed the lagging strand . The
  Okazaki fragments are joined by DNA ligaseto give a single 3’
  -5’ DNA strand.
  New DNA Strands
  Helicase enzyme splits and unwinds the two stranded DNA.
  Forming a New Strand
  A topoisomerase enzyme cuts the DNA strand allowing it to
  twist and relieve pressure.
  An enzyme DNA polymerase is used to add short section of
  DNA to start the process.
  Addition of nucleotides
  An enzyme DNA polymerase III is used to catalyse the addition of DNA
  nucleotides
  When nucleotides are added to a new strand they can only do so in a 5’ (5
  prime) to 3’ direction.
  Nucleotides are added. A joins to T, C joins to G
  5’
  New DNA Strands
  The leading strand (red) is synthesized continuously.
  The lagging strand (pink) is formed in segments called okazaki
  fragments.
  An enzyme DNA polymerase I replaces the RNA primers with
  DNA.
  Filling the Gaps
  The DNA strands continue to form in a 5’ to 3’ direction.
  An enzyme DNA Ligase is used to fill in the gaps in the okazaki
  fragments with nucleotides
  When DNA replication is complete two molecules are formed.
  Because half of each strand is new and half original it is called
  semi conservative replication.
  Mutations
  A mutation is a permanent change of the nucleotide sequence of the genome of an
  organism. Mutations result from unrepaired damage to DNA or to RNA genomes
  (typically caused by radiation or chemical mutagens), errors in the process of
  replication, or from the insertion or deletion of segments of DNA by mobile genetic
  elements.
  Mutations play a part in both normal and abnormal biological processes including:
  evolution, cancer, and the development of the immune system.
  Mutations can be caused by external (exogenous) or endogenous (native) factors, or
  they may be caused by errors in the cellular machinery. Physical or chemical agents
  that induce mutations in DNA are called mutagens and are said to be mutagenic.
  Exogenous factors: environmental factors such as sunlight, radiation, and smoking
  can cause mutations.
  Endogenous factors: errors during DNA replication can lead to genetic changes as
  can toxic by-products of cellular metabolism.
  Classification of mutation types
  The sequence of a gene can be altered in a number of ways. Gene mutations have
  varying effects on health depending on where they occur and whether they alter the
  function of essential proteins. Mutations in the structure of genes can be classified
  as:
  A-By effect on structure
  Small -scale mutations , such as those affecting a small gene in one or a few
  nucleotides, including:
  1-Point mutations, often caused by chemicals or malfunction of DNA replication,
  exchange a single nucleotide for another. These changes are classified as:

1. Transition: this occurs when a purine is substituted with another purine or when
   a pyrimidine is substituted with another pyrimidine.


2. Transversion: when a purine is substituted for a pyrimidine or a pyrimidine
   replaces a purine.
   Point mutations that occur within the protein coding region of a gene may be
   classified into three kinds, depending upon what the erroneous codon codes for:

• Silent mutations, which code for the same (or a sufficiently similar) amino acid.


• Mis-sense mutations, which code for a different amino acid.


• Nonsense mutations, which code for a stop and can truncate the protein.
  2-Insertions: add one or more extra nucleotides into the DNA. They are usually
  caused by transposable elements, or errors during replication of repeating
  elements
  3-Deletions remove one or more nucleotides from the DNA.
  2 -Large-scale mutations in chromosomal structure
  Changes that affect entire chromosomes or segments of chromosomes can cause
  problems with growth, development, and function of the body's systems. These
  changes can affect many genes along the chromosome and alter the proteins
  made by those genes. Conditions caused by a change in the number or structure
  of chromosomes are known as chromosomal disorders. These changes can occur
  during the formation of reproductive cells or in early fetal development. Many
  cancer cells also have changes in their chromosome number or structure. These
  changes most often occur in somatic cells during a person’s lifetime.
  B- By effect on function
  1-Loss-of-function mutations result in the gene product having less or no
  function.
  2-Gain-of-function mutations change the gene product such that it gains a new
  and abnormal function.
  3-Dominant negative mutations (also called anti-morphic mutations) have an
  altered gene product that acts antagonistically.
  4-Lethal mutations are mutations that lead to the death of the organisms that carry
  the mutations.
  5-A back mutation or reversion is a point mutation that restores the original
  sequence and hence the original phenotype.
  C-By effect on fitness
  In applied genetics, it is usual to speak of mutations as either harmful or beneficial.
  1-A harmful, or deleterious, mutation decreases the fitness of the organism.
  2-A beneficial, or advantageous mutation increases the fitness of the organism. .
  3-A neutral mutation has no harmful or beneficial effect on the organism.
  4-A nearly neutral mutation is a mutation that may be slightly deleterious or
  advantageous, although most nearly neutral mutations are slightly deleterious.
  EXAMPLE:
  Sickle-cell disease. The replacement of A by T at the 17th nucleotide of the gene
  for the beta chain of hemoglobin changes the codon GAG (for glutamic acid) to GTG
  (which encodes valine). Thus the 6th amino acid in the chain becomes valine instead
  of glutamic acid.
  -Sickle-shaped cells don’t move easily through blood. They’re stiff and sticky and
  tend to form clumps and get stuck in blood vessels.
  The clumps of sickle cell block blood flow in the blood vessels that lead to the limbs
  and organs. Blocked blood vessel can cause pain, serious infection, and organ
  damage.
  Patient with cystic fibrosis
  also known as mucoviscidosis, is an autosomal recessive genetic disorder that affects
  mostly the lungs but also the pancreas, liver, and intestine. Difficulty breathing is the
  most serious symptom and results from frequent lung infections.
  Other symptoms including
  sinus infections, poor growth, and infertility—affect other parts of the body.
  CF is caused by one of many different mutations in the gene
  The main signs and symptoms of cystic fibrosis are salty-tasting skin.
  Protein Synthesis
  The two main processes involved in protein synthesis are


• the formation of mRNA from DNA (transcription)


• the conversion by tRNA to protein at the ribosome (translation)
  Transcription takes place in the nucleus, while translation takes place in the
  cytoplasm
  Transcription: process by which the DNA genetic code is read and transferred
  to messenger RNA (mRNA). This is an intermediate step in protein expression.
  Translation: The process by which the genetic code is converted to a protein,
  the end product of gene expression.
  Genetic information is transcribed to form mRNA much the same way it is
  replicated during cell division
  TRANSCRIPTION (Nucleus)


• DNA mRNA
  TRANSLATION (Cytoplasm)
  -mRNA protein
  Importance of Protein Synthesis
  -Production of hormones
  -Production of enzymes
  Transcription :
  only one of the DNA strands is copied (coding or antisense strand). An RNA polymerase
  replicates the DNA sequence into a complementary sequence of mRNA (template or sense
  strand).
  mRNAs are transported from the nucleus to the cytoplasm,
  where they acts as the template for protein biosynthesis (translation).


• The mRNA is positioned in the ribosome through complementary pairing of the 5’

untranslated region of mRNA.

• Transfer RNA (tRNA): t-RNAs carries an amino acid and catalyzes amide bond formation.
  Transcription: The conversion of a DNA sequence to mRNA.
  There are three distinct phases to transcription:
  ① Initiation: RNA polymerase recognizes a promoter site (specific sequence) of DNA
  upstream to the gene and locally unwinds the DNA to create a template.
  ② Elongation: The polymerase moves along the gene synthesizing a complementary copy
  of the DNA template, but using nucleoside triphosphates as precursors ATP (serve as a
  source of energy for cellular reactions).
  ③ Termination: When the polymerase encounters a termination sequence it releases the
  RNA and dissociates from the DNA to end transcription.
  The Genetic Code: a set of rules that determines how an mRNA is translated into an
  amino acid sequence, where the sequence is read as triplets called codons.
  The genetic code is common for most organisms.
  Each codon specifies an amino acid, except UAG, UGA and UAA (stop codons – where do
  I end?)
  .
  AUG, that codes for Methionine, also serves as an initiation codon (where do I start?)
  Translation:
  the formation of proteins from the mRNA code (read in the 5’ to 3’direction) by ribosomes:
  ① Activation of Amino Acids:
  The amino acid is covalently bound to its corresponding tRNA.
  ② Initiation: The mRNA-ribosome complex is formed and the first aminoacyl-tRNA
  (initiator tRNA) binds to the first codon.
  ③ Elongation: The other codons are read sequentially by the ribosome that associates with
  the appropriate aminoacyl tRNA (amino acids covalently bound to tRNA) and the
  polypeptide sequence grows from N- to C-terminus.
  ④ Termination: When the ribosome encounters the stop codon, it releases the polypeptide
  and ceases protein synthesis
  ⑤ Folding and Posttranslational Processing:
  The protein must fold properly to be active and may
  or may not be modified by enzymes (portions cleaved off or substituents added).