Molecular Biology

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Molecular Biology

• Molecular biology is the study of DNA
• Its structure
• How it replicates (and assembles to create
  genetically-distinct offspring)
• How it controls the cell by directing RNA and
  protein synthesis
• How does DNA store genetic information, copy it,
  and pass it along from one generation to the
  next?

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DNA and RNA

• DNA and RNA are nucleic acids consisting of long
  chains of nucleotides (collectively called a
  polynucleotide)
• There are 4 types of nucleotides that make up
  DNA, each with a different nitrogenous base
• Adenine (A)
• Cytosine (C)
• Thymine (T)
• Guanine (G)

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Sugar-phosphate backbone
Phosphate group
Nitrogenous base
Sugar
Nitrogenous base (A, G, C, or T)
Phosphate group
DNA nucleotide
Thymine (T)
Sugar (deoxyribose)
DNA nucleotide
DNA polynucleotide
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DNA and RNA

• RNA has the nitrogenous base Uracil (U), instead
  of Thymine (T), and is usually single-stranded
• DNA is double-stranded and forms a double helix
• The 2 sugar-phosphate backbones that form the
  double helix run in opposite directions (5 to 3
  and 3 to 5)

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Each strand of DNA runs in opposite directions
Hydrogen bond
Base pair
Ribbon model
Partial chemical structure
Computer model
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DNA replication depends on specific base pairing

• The specific pairing of bases in DNA is evidence
  for a copying mechanism for the genetic material
• Knowledge of the sequence of bases in 1 strand of
  DNA allows you to determine the sequence in the
  second strand
• When 2 strands of DNA separate, each strand
  serves as a template for the assembly of a
  complimentary strand

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DNA Replication

• The human genome (all genes collectively)
  contains over 6 billion base pairs in 46
  chromosomes (23 homologous pairs)!
• Yet, DNA replication requires only a few hours
  and is astonishingly accurate
• How does this process occur and what controls
  it???

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DNA Replication

• DNA replication requires more than a dozen
  enzymes and other proteins (of course!)
• Replication of DNA begins at specific sites
  called origins of replication
• Origins of replication consist of a specific
  sequence of nucleotides where proteins attach to
  the DNA and separate the strands
• Replication then proceeds in both directions

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Parental strand
Origin of replication
Daughter strand
Bubble
Two daughter DNA molecules
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DNA Replication

• Eukaryotic DNA has many origins of replication
  shortening the overall time needed for the
  replication process
• Replication occurs in bubbles of parental (old)
  and daughter (new) DNA
• Eventually, all the bubbles merge yielding 2
  completed daughter strands of DNA

Daughter strands (grey) Parental strands (blue)
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DNA Replication

• The enzymes that link DNA nucleotides to a
  growing daughter strand are called DNA
  polymerases
• Remember that DNAs sugar-phosphate backbones run
  in opposite directions
• DNA polymerases add nucleotides only to the 3
  end, never to the 5 end
• Thus, a daughter strand grows from 5 to 3 (Say
  what?!!?)

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4?
2?
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DNA polymerase molecule
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3?
5?
Daughter strand synthesized continuously
Parental DNA
5?
3?
Daughter strand synthesized in pieces
3?
5?

• Since the 2 DNA strands run in opposite
  directions, and replication always begins at the
  3 end, the new daughter strand will be laid down
  beginning at its 5 end
• 1 daughter strand is synthesized continuously,
  while the other must work outward from the
  forking point

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Formed 2nd
Formed 1st
Formed last

• The new strand is synthesized in short pieces as
  the DNA strand opens up
• Another enzyme, called DNA ligase then links the
  pieces together to form a single DNA strand

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Thank you, polymerases

• DNA polymerases also carry out a proof-reading
  step to quickly remove any nucleotides that have
  been paired incorrectly during replication
• DNA polymerases and ligases are also involved in
  repairing DNA damaged by harmful radiation or
  toxic chemicals, including those found in
  cigarette smoke!

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DNA Replication

• DNA replication ensures that all cells in a
  multicellular organism carry the same genetic
  information
• DNA replication occurs during interphase!
• The DNA genotype is expressed as proteins, which
  provides the molecular basis for phenotypic
  traits
• DNA dictates the synthesis of proteins which
  determine the traits physically expressed by an
  organism

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DNA is transcribed into RNA and translated into
Protein

• A gene does not build a protein directly
• Instead, a gene dispatches its instructions for
  building proteins in the form of RNA, which in
  turn directs protein synthesis
• The transcription of DNA into RNA and the
  subsequent translation of RNA into proteins is
  considered the central dogma of molecular
  biology

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DNA
Transcription of DNA into RNA
RNA
Nucleus
Cytoplasm
Translation of RNA into Protein
Protein
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DNA is lifethe rest is just translation

• In eukaryotic organisms, DNA is stored in the
  nucleus where it is transcribed into RNA a
  process called transcription
• RNA translates the information from DNA into
  proteins in the cytoplasm (or to be more precise,
  in the ribosomes well come back to this) a
  process called translation

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Genetic information written in codons is
translated into amino acid sequences

• A typical gene consists of hundreds or thousands
  of nucleotides in a specific sequence
• The sequence (and number) of these nucleotides
  determines the protein produced by this gene, and
  hence its resulting phenotype
• DNA must first be re-written (transcribed) as a
  sequence of RNA

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Genetic information written in codons is
translated into amino acid sequences

• Translation then converts the nucleic acid
  language into the polypeptide (protein)
  language
• The sequence of RNA nucleotides dictates the
  sequence of amino acids of the polypeptide being
  produced
• Thus, the RNA molecule acts as a messanger
  carrying genetic information from DNA

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DNA strand
Transcription
RNA
Codon
Translation
Polypeptide
Amino acid
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Genetic information written in codons is
translated into amino acid sequences

• In order for translation to proceed, the sequence
  of the 4 nucleotides in RNA (A,U, C,G) must
  somehow specify the 20 amino acids used to make
  up proteins
• The flow of information from gene to protein is
  based on a triplet code genetic instructions for
  the amino acid sequences of a polypeptide chain
  are written in DNA and RNA as a series of 3-base
  words, called codons

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The Genetic Code

• The genetic code is a set of instructions
  indicating which codons are translated into which
  amino acid
• The genetic code does not only specify which
  codons code for which amino acids, but also
  specify start and stop signals, which begin
  and end protein synthesis, respectively
• For each of the 20 amino acids, there are 2-4
  codons which code exclusively for them

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Second base
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First base
Third base
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The Genetic Code

• The genetic code is nearly universal humans
  cells can translate bacterial RNA and vice versa

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Transcription

• An enzyme called RNA polymerase attaches to an
  area of one of the DNA molecules in the double
  helix and moves along the DNA strand reading
  the nucleotides
• It then selects complimentary nucleotides and
  links them one by one via hydrogen bonds
• A nucleotide sequence called a promoter serves as
  a start signal, while a terminator sequence
  marks the end of transcription

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RNA polymerase
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DNA of gene
Promoter DNA
Terminator DNA
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Initiation
Area shown in Figure 10.9A
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Elongation
Growing RNA
3
Termination
Completed RNA
RNA polymerase
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RNA nucleotides
RNA polymerase
Direction of transcription
Template strand of DNA
Newly made RNA
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Messenger RNA

• The type of RNA that encodes amino acid sequences
  is called messenger RNA (mRNA)
• In eukaryotic cells, mRNA leaves the nucleus
  where it had been transcribed and enters the
  cytoplasm
• Before mRNA can leave the nucleus, it is modified
• A tail and cap are added
• Introns are removed

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Introns are intervening sequences of DNA which do
not code for amino acids must be removed Exons
are the coding regions, parts of the gene which
remain and are translated into amino acids
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A cap and tail are added to protect the mRNA
strand, facilitate its transport out of the
nucleus and to help ribosomes bind to it
Exon
Exon
Exon
Intron
Intron
DNA
Transcription Addition of cap and tail
Cap
RNA transcript with cap and tail
Introns removed
Tail
Exons spliced together
mRNA
Coding sequence
Nucleus
Cytoplasm
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Transfer RNA

• In order to convert the 3-letter codons of
  nucleic acids into a single amino acid, a cell
  must employ a molecular interpreter, transfer RNA
  (tRNA)
• tRNA recognizes the codons in the mRNA molecule
  and picks out the appropriate amino acids for
  incorporation into the growing polypeptide

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Transfer RNA

• tRNA recognizes codons from mRNA via a special
  triplet of bases called an anticodon, which is
  complimentary to the codon on the mRNA
• When the codon of mRNA complements the anticodon
  of tRNA, the appropriate amino acid is laid down
  at the other end of the tRNA molecule

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Amino acid attachment site
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Hydrogen bond
RNA polynucleotide chain
Anticodon
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Transfer RNA

• For each amino acid, there is a specific type of
  tRNA that it will bind to
• And for each tRNA, there is a specific enzyme
  which binds the amino acid to its specific tRNA
  molecule
• How many enzymes (or tRNA molecules for that
  matter) are there?

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Translation

• mRNA leaving the nucleus enters the cytoplasm
  where it binds to a ribosome (Remember, all cells
  contain ribosomes)
• Translation begins when the mRNA molecule arrives
  at the ribosome
• While mRNA was being synthesized, tRNA molecules
  were already uniting with their specific amino
  acids

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Translation

• The tRNA molecules then begin transporting their
  amino acids to the ribosomes to meet the mRNA
  molecule
• Ribosomes are made up of proteins and a type of
  RNA called ribosomal RNA (rRNA)
• The ribosomes contain binding sites for both mRNA
  and tRNA

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tRNA-binding sites
Large subunit
mRNA binding site
Small subunit
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Next amino acid to be added to polypeptide
Growing polypeptide
tRNA
mRNA
Anticodon of tRNA
Codons of mRNA
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New peptide bond forming
Growing polypeptide
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Elongation
A succession of tRNAs add their amino acids to
the polypeptide chain as the mRNA is
moved through the ribosome, one codon at a time.
Codons
mRNA
Polypeptide
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Termination
The ribosome recognizes a stop codon. The
polypeptide is terminated and released.
Stop codon
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Translation

• Translation begins with a start codon, and ends
  with a stop codon
• The amino acid methionine (Met) is always
  translated by the start codon (AUG)
• What would the anticodon look like?
• Stop codons (UAA, UAG, and UGA) do not code for
  amino acids but instead act only as signals to
  end translation

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Review

• Describe the differences between mRNA, tRNA and
  rRNA
• What bases are found in DNA? In RNA?
• Which molecule has codons? Anticodons?
• What is transcription? Translation? Which happens
  first and where does each occur in the cell?

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Mutations

• A single change in the amino acid coded for by a
  gene can lead to mutation
• and a single change to a single nucleotide can
  lead to a change in amino acid!
• Mutations can be caused
  by a nucleotide addition,
  deletion or substitution
• Insertions or deletions are
  the most disastrous

www.milehive.com/.../x-men-origins-wolverine.jpg
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Mutations

• The production of mutations can occur
  spontaneously during DNA replication or by a
  mutagen, a physical or chemical agent such as
  X-rays and ultraviolet light (physical)
• What would happen if a mutation occurred in an
  intron? An exon?

http//www.ninjaturtles.com/
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Viruses

• A virus is a fragment of nucleic acid surrounded
  by a protein coat
• Viruses are infectious they are parasites that
  can reproduce only inside living cells
• The host cell provides most of the components
  necessary for replicating, transcribing and
  translating the viral DNA!

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You can run, but you cant hide

• Viruses infect bacteria, archaea, protists,
  plants and animals, and are found in nearly every
  ecosystem on Earth!
• Viruses contain genes made of DNA or RNA
• The protein coat (or membrane in some cases)
  allows the virus to penetrate the host cell

Viral DNA
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Viruses

• Viruses cause illness because they attach to a
  cell, and inject their DNA into it
• The host cell is then instructed by the viral
  DNA to produce more copies of itself and to
  translate proteins, which together serve to
  assemble more viruses!
• Eventually the cell lyses and releases an army of
  viruses

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Lytic cycle of viruses
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Phage attaches to bacterial cell.
Phage injects DNA.
Phage DNA directs host cell to make more
phage DNA and protein parts. New phages assemble.
Cell lyses and releases new phages.
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Viruses

• The common cold is caused by viruses containing
  RNA, as are measles, mumps, AIDS and polio
• DNA viruses cause hepatitis, chicken pox and
  herpes
• Glycoproteins on the viruss outer coat enable it
  to attach to receptor proteins on the host cells
  plasma membrane (very specific!)

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Got NyQuil?

• The amount of harm caused by viruses depends
  largely on how quickly an organisms immune
  system responds to fight the infection, and also
  on the ability of the infected tissue to repair
  itself
• Our respiratory tract can efficiently replace
  damaged cells by mitosis and we usually recover
  quickly from colds, but damage done to nerve
  cells by the Poliovirus is permenant

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How do viruses spread?

• Ever wonder why we sneeze and cough when were
  sick???
• Cold sores, herpes, chicken pox..

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Viral DNA may become part of the host chromosome

• Viruses reproduce via the host cell as previously
  described in the lytic cycle
• But viruses can also reproduce via an alternative
  route called the lysogenic cycle
• During a lysogenic cycle, viral DNA is replicated
  without destruction of the host cell
• In this case, viral DNA is incorporated into the
  host cells DNA and is replicated every time the
  host cell prepares to divide

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Lytic and Lysogenic viral cycles
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Phage
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Attaches to cell
Bacterial chromosome
Phage DNA
Cell lyses, releasing phages
Phage injects DNA
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2
Many cell divisions
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Lytic cycle
Lysogenic cycle
Phages assemble
Lysogenic bacterium reproduces normally,
replicating the prophage at each cell division
Phage DNA circularizes
Prophage
3
5
6
OR
New phage DNA and proteins are synthesized
Phage DNA inserts into the bacterial chromosome
by recombination
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Viruses

• The bacteria that cause diphtheria, botulism and
  scarlet fever would be harmless were it not for
  the viral DNA encoded into their DNA!
• Mutations of existing viruses are a constant
  source of new, emerging viruses
• RNA viruses are usually the culprit errors in
  replication are not subject to the types of
  proofreading mechanisms that help reduce
  mutations in DNA replication

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Question of the day (or century, millennium, etc
.)

• Are viruses alive????
• Do they reproduce?
• Do they grow and develop?
• Do they take in energy and process it to perform
  their activities?
• Do they respond to their environment?
• Do they adapt?

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Want to learn more?