Biology 100

1
Chapter 8DNA and RNA

• Biology 100

2
Structure of DNA

• Deoxyribonucleic Acid (DNA) serves as the
  memory/blueprint for proteins in the cell.
• The building block of DNA (and RNA) is the
  nucleotide
• What composes the nucleotide?
• Phosphate Group
• 5C deoxyribose sugar (ribose sugar for RNA)
• Nitrogenous base
• Two important functions of DNA
• Pass genetic info
• Control synthesis of a protein

3
Structure of DNA

• There are 4 different bases in DNA
• Adenine (A) and guanine (G) have double rings.
  These are known as Purines.
• Thymine (T) and cytosine (C) have single rings.
  These are Pyrimidines.
• On a single strand, the
• phosphate group of one
• nucleotide forms a covalent
• bond with the sugar of the next.

4
Structure of DNA

• The base pairs of DNA are
• Thymine pairs with Adenine
• Guanine pairs with Cytosine
• Give the complementary strand
• A T C G G T C A C T G G
• T A G C C A G T G A C C

5
Structure of DNA

• Rosalind Franklin suggested that the structure of
  DNA was a helix.
• In1953, James Watson and Francis Crick took some
  of Rosalinds x-ray diffraction images of DNA and
  correctly determined that it was a double helix.
• Using Tinker toys, they made their model of DNA.
• The final structure of DNA
• Sugar-phosphate bond on
• the outside, and the nitrogen
• bases on the inside,
• connected by hydrogen
• bonds.

6
Structure of DNA

• DNA has bases pair up in groups of two. Guanine
  will pair with Cytosine, and Adenine will pair
  with Thymine.
• This is known as base complementarity.
• DNA resembles a ladder with the sides of the
  ladder formed by the sugar-phosphate backbones.
  The rungs are the complementary bases held
  together by hydrogen bonds.
• The ladder is twisted like a spiral helix, known
  as the double helix.

7
DNA Replication

• Cells constantly grow and divide, so DNA needs to
  be copied for each new cell.
• First, DNA helicase unwinds the DNA double helix
  for about 1,000 nucleotides and forms a
  replication bubble.

8
DNA Replication

• Then, DNA polymerase assembles a complementary
  new strand on each old one, using free DNA
  nucleotides, building two strands in opposite
  directions.

9
DNA Replication

• DNA ligase attaches one new strand to the
  previously replicated segment, and helicase
  unwinds another section.

10
DNA Replication

• After replication, there are two molecules of
  identical DNA.
• Each DNA will have one strand from the original
  DNA molecules (the parent strand), and one from
  the replicated DNA (daughter strand).
• This makes the strand semiconservative.
• DNA Replication

11
DNA Replication

• Once every 10,000 bases, DNA polymerase adds the
  wrong nucleotide.
• Before proceeding to the next nucleotide, it
  proofreads the copy against the parental strand
  and corrects the error most of the time.
• The actual error rate is about 1 or 2 errors per
  billion nucleotides.
• If each human diploid cell contains 6.2 billion
  nucleotides, are any two cells actually
  identical?

12
Why is the DNA code important?

• The order of the nitrogenous bases in DNA is the
  genetic information that codes for proteins.
• Proteins help provide the cell with structure.
  Enzymes are also made of proteins, which help
  carry out chemical reactions.
• A gene is a section of the DNA double helix with
  information for synthesizing a specific protein.

13
RNA

• Ribonucleic Acid (RNA)is the other type of
  nucleic acid used in protein production.
• RNA is single-stranded, and has ribose as its 5C
  sugar.
• In RNA, the base pairs are
• Uracil with Adenine
• Guanine with Cytosine
• Find the complementary strand
• A C U G G U A C
• U G A C C A U G

14
Cell Differentiation

• All cells will use the information in their DNA
  to produce the same house-keeping proteins.
• But differentiated cells will express (turn on)
  genes that have the information for proteins
  which support their specific activities.
• In the end, only a small fraction of genes are
  expressed in any particular cell type.

15
Cell Differentiation

• Different differentiated cells also like to vary
  in the level of expression, how much of a protein
  is synthesized.
• Individual cells vary their level of expression
  of a gene over time as demand for their protein
  product increases and decreases.

16
Adult Stem Cells

• In most cases, once a cell have become
  differentiated, it is locked into that path and
  cannot be transformed into another cell type.
• In contrast, stem cells are unspecialized cells
  that renew themselves in this undifferentiated
  form.
• Under appropriate conditions, some cells
  differentiate to fulfill specific needs that an
  organism has.
• Stem cells in bone marrow (adult stem cells)
  specialize into any role that blood cells
  undertake in the body.
• These stem cells are multipotent - capable of
  many roles, but not all.

17
Adult Stem Cells

• Recent research has indicated that some adult
  stem cells may be even more flexible than
  previously thought, perhaps close to pluripotent.
• They may not only be able to differentiate into
  the specialized cells characteristic of their
  tissues, but they may also be able to specialize
  into other cell types.

18
Fetal Stem Cells

• Embryonic (fetal) stem cells are pluripotent.
• Cultured cells can be induced to specialize into
  all types of adult cells.
• They are typically obtained from an early
  developmental stage, the blastocyst.
• Embryonic stem cells are also available in
  umbilical cord blood.

19
Stem Cells

• After extracting undifferentiated cells from a
  blastocyst, cells are cultured on feeder plates.
• If the embryonic stem cells are allowed to clump
  together, they can spontaneously differentiate.
• By including specific molecules into the cultures
  or otherwise changing conditions, the clumps can
  be directed to differentiate into specific cell
  types.

20
Bone Marrow

• Individuals may suffer deficiencies in red or
  white blood cells caused by cancer, anemia,
  inherited genetic diseases, or immune-system
  disorders.
• Typically, healthy bone marrow, containing
  blood-forming stem cells, is extracted from a
  donor.
• The bone marrow is introduced into the
  recipients blood.
• The new stem cells repopulate the bone marrow and
  restore the population of blood cells.

21
Potential Application of Stem Cells

• Type-1 Diabetes
• In type 1 (juvenile) diabetes, the immune system
  attacks insulin-producing cells in the pancreas,
  leading to diabetes elevated glucose levels.
• New stem cells may be able to replace to the lost
  cells.
• Heart Disease
• If cardiac muscle cells are deprived of oxygen
  because of blocked arteries, they die and are
  replaced by scar tissue.
• Stem cells may allow regeneration of cardiac
  tissue if they can differentiate into muscles
  cells and integrate into the heart.

22
Potential Application of Stem Cells

• In individuals with Parkinsons disease, neurons
  which produce the neurotransmitter dopamine die,
  leading to uncoordinated movements.
• Preliminary studies indicate that neural stem
  cells can be injected into the brains of
  Parkinsons patients, reducing disease symptoms

23
Potential Application of Stem Cells

• A patients DNA is extracted and injected into an
  enucleated egg.
• A similar technique was used to produce the first
  cloned mammal, the sheep Dolly, in 1996.
• The embryonic stem cells would then induced to
  develop into a specific tissue needed by the
  patient.

24
Protein Synthesis

• Also known as the central dogma of gene
  expression.
• Protein synthesis occurs in two steps,
  transcription and translation.
• In transcription, a gene, a region of information
  contained in the order of nucleotides in DNA, is
  copied as RNA.
• In translation, information on mRNA is used to
  direct the order with which amino acids are
  linked together to form polypeptides at the
  ribosomes.

25
How information is stored in DNA

• The genetic code is a language in which all
  words are three letters long (triplets) and
  combinations of the nitrogen bases.
• The letters A,T,C,G in DNA or A,U,C,G in RNA,
  are the alphabet.
• As triplets, 43 combinations 64 words
• There are 20 amino acids commonly used in
  proteins. Each word is a code for an amino
  acid.
• 64 words are more than enough to specify 20 amino
  acids
• Each word, a unique combination of three
  nucleotides, is called a codon.

26
Genetic Code

• Each codon indicates only one amino acid.
• There is more than one codon for most amino
  acids. Except for tryptophan or methionine, each
  amino acids has 2-6 possible codons.
• The 3rd position, the wobble position is less
  critical in dictating specific amino acids.

27
Genetic Code

• AUG is the start codon (Methionine), which tells
  the mRNA to begin translation. If AUG is not
  found, translation will not begin.
• There are three stop codons (UAA, UAG, UGA) the
  protein will be released.

28
Genetic Code

• During translation, codons are read without pause
  or skipping from the start codon to the stop
  codon.
• The start codon establishes the reading frame,
  the blocks of 3 nucleotides that will translated.
• Any nucleotide is part of only one triplet, they
  do not overlap.

29
Codons

• Which codon is it?
• UUU
• Phenylalanine
• UGA
• Stop
• AUG
• Methionine (Start)
• GAA
• Glutamic Acid

30
Types of RNA

• Messenger RNA (mRNA) has the specific information
  necessary to place amino acids in the correct
  order to build the right polypeptide.
• Simply put, it is the template to guide the
  synthesis of a chain of amino acids that form a
  protein.

31
Types of RNA

• Transfer RNA (tRNA) molecules carry specific
  amino acids from the cytoplasm to the ribosome.
• Each tRNA has an amino acid binding site to which
  a specific amino acid is attached.
• Each tRNA has an anti-codon region, an area
  complementary to the codon on mRNA.

32
Types of RNA

• Ribosomal RNA (rRNA) combines with proteins to
  form ribosomes.
• The rRNA and protein molecules combine to form
  large ribosomal subunits and small ribosomal
  subunits in the nucleolus.

33
Transcription

• Transcription occurs in three parts
• Initiation, the key enzyme, RNA polymerase, finds
  the correct region of DNA to begin the process.
• Elongation, the DNA double helix unwinds a bit
  and RNA polymerase makes a RNA copy of the DNA
  template.
• Termination, the RNA polymerase reaches the end
  of the gene and releases the RNA molecule.

34
Synthesis of RNA

• A gene consists of several sections.
• The promotor sequence is the site where
  transcription factor proteins and RNA polymerase
  bind initially.
• The core of the gene consists of the protein
  code, the information required for synthesizing a
  protein.
• The termination sequence indicates the end of the
  gene, the end for transcription.

35
Transcription - Initiation

• In eukaryotes, proteins called transcription
  factors bind to the promotor region.
• They assist the binding of RNA polymerase to the
  correct spot.

36
Translation - Elongation

• Once RNA polymerase binds, the DNA double helix
  begins to unwind.
• One strand has the information for the gene, the
  coding strand.
• RNA polymerase copies the coding strand as an RNA
  strand.

37
Transcription - Termination

• Elongation continues until RNA polymerase reaches
  a specific DNA sequence called a terminator.
• At this point the new RNA strand is either
  released or cut free.

38
Translation of Proteins

• Translation also has three stages
• In initiation, mRNA, tRNA, and the small and
  large ribosomal subunits are brought together.
• In elongation, the information on the mRNA is
  used to order tRNA carrying the correct amino
  acids.
• At termination, the components, including the new
  polypeptide, separate.

39
Translation - Initiation

• Initiation starts when mRNA binds to the small
  ribosomal subunit.
• The initiator tRNA, carrying the amino acid
  methionine, binds because of its complementary
  anticodon to the start codon.
• Next, the large ribosomal subunit connects to
  this complex.

40
Translation - Elongation

• The next tRNA with the correct amino acid slip
  into place.
• The ribosome catalyzes a peptide bond between
  amino acids.
• The old tRNA is released.
• The whole complex mRNA and tRNA with growing
  polypeptide, slides down the ribosome by 3
  nucleotides (translocation).

41
Translation - Elongation

• The next tRNA with an anticodon matching the next
  codon slips into place.
• This cycle of tRNA positioning, peptide bond
  formation, old tRNA release, moving of the mRNA
  tRNA polypeptide continues.

42
Translation - Termination

• When the process reaches the stop codon, a
  release factor protein enters the ribosome.
• The release factor breaks the bond between the
  last tRNA and the polypeptide.
• The polypeptide floats away
• The mRNA is released.
• Protein Synthesis

43
Control of Protein Synthesis

• As part of differentiation, cells turn some genes
  off and others on.
• Plus, they can control how quickly/often a gene
  is transcribed and how often a mRNA from that
  gene is translated.
• If a section of chromosome is tightly coiled
  (like during mitosis), transcription factors and
  RNA polymerase cannot access the promotor
  sequence.
• Any genes in these regions are turned off.

44
Control of Protein Synthesis

• If acetyl groups (-COCH3) are attached to histone
  proteins at a section of DNA, transcription
  occurs more easily.
• If methyl groups (-CH3) are attached to the DNA
  itself, the methylated genes are turned off.
• Enzymes actively control which sections of a
  chromosome have methylation and acetylation

45
Control of Protein Synthesis

• Without activated transcription factors, a gene
  will be transcribed, but at a low level.
• If activated transcription factors are present,
  RNA polymerase can bind more easily to the
  promotor.
• Transcription occurs faster.
• Often activated transcription factors will
  enhance transcription of several genes whose
  proteins will work together in the cell.

46
Control of Protein Synthesis

• Some genes are transcribed more often because of
  the presence of enhancer DNA regions.
• Activators that bind to the enhancer region make
  it easier to transcription factors and RNA
  polymerase to bind to the promotor.
• Other DNA regions, called silencers, decrease the
  rate of transcription.

47
Control of Protein Synthesis

• Once a mRNA has finished transcription of one
  polypeptide, it is available to produce another.
• Eventually, the mRNA will be degraded, but the
  rate of degradation is under active control.
• The mRNA that is translated into a protein which
  assists iron absorption is degraded much faster
  when the cell has abundant supplies of iron.

48
Protein Synthesis

• In bacteria, one gene is transcribed into one
  mRNA which is translated into one protein.
• In eukaryotes, one gene can produce several
  different proteins.
• Eukaryotic gene include exons which have
  information for proteins and introns which do
  not.
• The introns are removed during post-transcriptiona
  l processing.
• The exons are joined together.

49
Protein Synthesis

• In alternative splicing, some sections of the
  original mRNA are removed in some versions, but
  other sections are removed in other versions.
• The result is that the same gene can produce two
  different proteins.
• Alternative splicing is behind the observation
  that the 20,000 genes in the human genome lead to
  80,000 to 100,000 different proteins.

50

• In fruit flies, the gene for sex determination
  contains two possible stop signs.
• In some individuals, the first stop codon is
  removed.
• The protein that is translated from this splicing
  leads to the development of a female fruit fly.
• If the first stop codon is not spliced, no
  functional protein is transcribed.
• The fruit fly develops as a male

51
Point Mutation

• Mutations are changes in the DNA sequence of an
  organism.
• The changes may be as minor as altering a single
  nucleotide to deletion/addition of whole
  chromosomes or even sets of chromosomes.
• In a point mutation, a single nucleotide is
  changed to one of the other three.
• If the change occurs outside a gene or if it does
  not impact the amino acid put in place, then it
  is a silent mutation.
• Both GGG and GGA are codons for glycine.

52
Mutation

• A nonsense mutation occurs when the change
  switches a codon from indicating an amino acid to
  a stop codon.
• Translation of the mRNA that results will lead to
  a non-functional protein.
• A missense mutation results in the substitution
  of one amino acid for another during translation.
• While GGA is the codon for glycine, the mutated
  GCA is the codon for alanine.
• Consequences of changes in the primary structure
  of a polypeptide range from minor to
  catastrophic.

53
Mutations Sickle Cell Anemia

• Sickle cell anemia is the result of a missense
  mutation.
• The mutated protein leads to sickle-shaped red
  blood cells and sickle cell anemia.

54
Sickle Cell Anemia

• Without modern medical treatment, most
  individuals with sickle cell anemia die in the
  late teens.
• Yet, the sickle cell mutation is common in parts
  of India and central Africa.
• These are areas with high frequencies of the
  malaria parasite.
• Before drug treatments, individuals with two
  normal hemoglobin genes would die from malaria.
• Individuals with one normal hemoglobin gene and
  one sickle cell gene are resistant to malaria.

55
Insertion/Deletion

• An insertion mutation adds one or more
  nucleotides to a DNA sequence.
• A deletion mutation removes one or more
  nucleotides from a DNA sequence.
• Both mutations cause frameshifts and changes in
  primary structure of polypeptides because
  ribosomes will read the wrong sets of three
  nucleotides during translation.

56
Chromosomal Mutations

• Some mutagens or genetic accidents can cause
  breaks on chromosomes which may result in
  separate chromosomes.
• Movements of segments from one chromosome to
  another - translocations and insertions
• Loss of whole segments - deletions.
• The pieces may become inserted into similar
  chromosomes (duplication) or oriented in the
  opposite direction (inversion).

57
Chromosome Mutations

• Errors during meiosis and fertilization (rarely
  mitosis) can result in cells which have too many
  or too few chromosomes.
• This usually upsets the balance of genes which
  lead to normal development.
• In humans, this usually results in spontaneous
  abortion of the embryo long before birth.

58
Chromosomal Mutation

• In the most common form of Down syndrome,
  individuals have three copies of chromosomes 21,
  the smallest chromosomes with the fewest genes.
• These individuals have characteristic physical
  appearance, and physiological and mental
  challenges.
• The risk of Down syndrome increases dramatically
  as the age of the mother increases.
• 0.04 of births for mothers lt 30
• gt1.25 of births for mothers gt 30