Download Unit 2

1/28/2016
Performance Expectations (by the end
of Unit 3, Part 1 you should be able
to…)
DNA, RNA, and Protein Synthesis
Performance Expectations (by the end
of Unit 3, you should be able to…)
• HS-LS3-1: Ask questions to clarify
relationships about the role of DNA and
chromosomes in coding the instructions for
characteristic traits passed from parents to
offspring. (All organisms have DNA. If the
structure of DNA is universal, how come you
don’t look like a fish, or a monkey? What does
inheritance mean (not the kind where you get
money)? )
Where is DNA?
• DNA is located in the nucleus of cells.
• All cells in a person’s body have the same DNA
and the same genes.
• Genes are sequences located in the DNA that code
for specific characteristics.
• HS-LS1-1: Construct an explanation based on
evidence for how the structure of DNA
determines the structure of proteins which carry
out the essential functions of life through
systems of specialized cells. (Proteins carry out
the essential functions of life – remember
enzymes?! How do proteins get made in the
first place? DNA provides the blueprints, or
recipes for proteins, so we’ll look at the
structure of DNA, look at RNA and then study
the process of making proteins.)
What is DNA?
• DNA (deoxyribonucleic acid) is a molecule
that carries most of the genetic
instructions used in the development,
functioning and reproduction of all known
living organisms and many viruses.
• DNA stores biological information – it’s a
blueprint for life processes.
QOD 1/19/2016
• What is the function of DNA? (deoxyribonucleic
acid)
• The “expression” of the genes differs between
cells. For example, a liver cell will make
different proteins than a skin cell.
• No QOD sheets. Write in your notes template.
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1/19/2016 Assignment
• You are reading Chapter 10 in the textbook and
taking notes (outline).
• You’ll complete the Reading Guide worksheet
tomorrow using notes only.
• Write what you need – I won’t be checking for
complete sentences, spelling errors, etc.
• Don’t copy the paragraphs – summarize!
• Once you complete the Reading Guide and I
have checked it, you will have the opportunity to
correct it for your grade – but only if you make a
good faith effort the first time.
QOD 1/20/2016
• What is the shape of DNA?
Include this in your outline….
• What was Rosalind Franklin’s role in
establishing the structure of DNA?
• What’s the monomer of a nucleic acid?
• What are the steps of DNA replication?
What’s a replication fork?
• How does RNA differ from DNA?
• What are the steps of protein synthesis?
QOD 1/21/2016
• What are the base pairing rules in DNA?
No QOD sheets. Write in your notes
template.
History of DNA
History of DNA
An overview of the many
experiments conducted in the 20th
century to further our
understanding of the role and
function of DNA.
• 1928- Fredrick Griffith
▫ He found that when harmless
bacteria are mixed with dead
harmful bacteria, the harmless
bacteria will absorb the genetic
material of the harmful and become
harmful themselves.
▫ The transfer of genetic (hereditary)
material from one cell to another is
called transformation.
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Two strains of Streptococcus pneumoniae bacteria, one virulent and one
not. The heat killed S strain released a hereditary factor that transfers
the disease-causing ability to the harmless cells.
History of DNA
• 1940s- Oswald Avery and colleagues
▫ Avery wanted to know what caused the
transformation in Griffith’s experiment DNA, RNA, or protein.
 Used enzymes to each of the molecules in
heat killed S cells.
 Separately mixed each type with live R cells.
 The cells missing DNA did not transform
the R cells into S cells.
 They concluded DNA was the cause of
transformation.
▫ In other words, they found if harmless
bacteria took in harmful bacteria’s DNA, the
harmless became harmful.
Discovery of DNA
• 1952- Alfred Hershey and Martha
Chase
▫ Wanted to test whether DNA or
protein was the genetic material
that viruses pass on when they
infect an organism.
▫ They used viruses that infect
bacteria (called bacteriophages)
▫ They radioactively labeled the
DNA and the protein (this allowed
them to trace the path of each).
▫ They found DNA was injected into
the bacteria to infect it, not
protein. So DNA was the genetic
material in viruses.
Hershey and Chase
Discovery of DNA
• 1953- James Watson, Francis Crick,
Rosalind Franklin, and Maurice
Wilkins and the structure of DNA.
▫ Franklin and Wilkins discover DNA
is helical by use of X-ray diffraction.
▫ Watson and Crick obtain Franklin’s
photograph without permission.
▫ Using the photograph and other
information, Watson and Crick build
a model of DNA and determine it is a
double helix.
▫ Watson, Crick and Wilkins went on
to win the Nobel Prize in 1962.
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DNA Structure
• DNA is a double helix.
Structure of DNA
• Remember that there are four macromolecules
(the molecules of life): carbohydrates, lipids,
proteins and nucleic acids
• Nucleic acids are polymers. (DNA is a polymer.)
• The monomer of a nucleic acid is a nucleotide.
▫ Monomers: small units that make up larger units
called polymers.
One strand of
DNA is a long
polymer of
nucleotides.
One strand of
DNA has
many millions
of
nucleotides!
phosphate
deoxyribose
bases
DNA Structure
• Nucleotides (the
monomers of DNA)
have 3 parts:
1.Nitrogenous
base (there are 4
kinds)
2.Phosphate Group
3.5 carbon sugar
called deoxyribose
DNA Structure – Parts of Nucleotides
• Nitrogenous bases:
▫ Contain nitrogen and is a
base
▫ Purines- (double ringed)
 Adenine (A)
 Guanine (G)
▫ Pyrimadines- (single
ringed)
 Cytosine (C)
 Thymine (T)
nucleotide
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Hydrogen Bonding
• A purine (A or G) will easily form a hydrogen
bond with a pyrimidine (T or C). This is because
of their structure and the availability of bonding
sites.
• Hydrogen bonds are weak but there are
millions and millions of them in a single
molecule of DNA.
DNA Structure
• If DNA was a spiral
staircase…
▫ The alternating sugar
and phosphates would
be the hand rails.
▫ The bases would be the
steps.
▫ But, they would be weak
steps as they are only
held together by
hydrogen bonds.
DNA Structure
• Base pairing rules in DNA:
▫
▫
▫
▫
Hydrogen bonds form between specific pairs.
Adenine ALWAYS pairs with Thymine.
Cytosine ALWAYS pairs with Guanine.
These pairs (A-T and C-G) are called
complementary base pairs.
▫ Each complimentary pair contains one single and
one double ringed base
DNA Structure
• DNA is made up of 2
straight chains of
nucleotides
• The bases on each of those
chains are attracted to each
other and form hydrogen
bonds.
• The force of thousands or
millions of hydrogen bonds
keeps the two strands of
DNA held tightly together.
DNA Structure
• Since the sugar-phosphate
“hand rails” of DNA never
change, we often simplify
DNA into the letters of the
nitrogenous bases.
• For example, this DNA
strand can be simplified
to…
TGAC
ACTG
DNA Structure
• Because of the base pairing rules, one strand of
DNA is complementary to the other strand
(otherwise they would not stick together!)
▫ The order of the nitrogenous bases on DNA is
called its base sequence
▫ So if one strand has a base sequence of TGCC, the
other strand will have ACGG.
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Let’s Practice
• Write the complimentary strand for…
“The Double Helix” Video
• http://www.hhmi.org/biointeractive/doublehelix
TGACCGAT
ACTGGCTA
TGGCCAATATA
ACCGGTTATAT
“The Double Helix” Video Questions
1.
2.
What are the chemical components of a DNA molecule? (There are three.)
How are the instructions for the traits of an organism determined?
a. The proportions of A, T, C and G in DNA molecules.
b. The order of nucleotides in DNA molecules.
c. The length of DNA molecules.
3. The two strands of a DNA molecule are held together by hydrogen bonds between the ___________.
4. In the 1950s when Watson and Crick were working on their model of DNA, many scientists did not think that DNA carried the
genetic code.
a.
What was the other type of molecule that some scientists thought might carry genetic information?
b.
Why did this other type of molecule seem a likely candidate?
5. The following table is a sample of the data Erwin Chargaff published in 1952. Which of the following observations can be
supported by the data in the table?
a. All organisms contain about the same amounts of adenine and thymine in their DNA.
b. The proportions of adenine + thymine and guanine + cytosine are the same in all organisms.
c. Larger organisms have greater amounts of each nitrogenous base than smaller organisms have.
d. The total length of DNA molecules in all organisms in about the same.
6. In one or two sentences, explain how these observations helped Watson and Crick build their mode of DNA.
7. Why do you think the proportions of nitrogenous bases in the DNA of two different human tissues (thymus and sperm) are
about the same?
8. The image shows the famous photo B51 taken in May 1952 by Rosalind Franklin and her student Raymond Gosling. This x -ray
diffraction pattern provided information about the positions of atoms in a DNA molecule.
Proportions of Nitrogenous Bases in
the DNA of Different Organisms
Organism Tissue
%Adenine %Guanine
%Cytosine
%Thymine
Yeast
31.3
18.7
17.1
32.9
Sea urchin
Sperm
32.8
17.7
18.4
32.1
Rat
Bone
marrow
28.6
21.4
21.5
28.4
Human
Thymus
30.9
19.9
19.8
29.4
Human
Sperm
30.3
19.5
19.9
30.3
a. What is the clue in this photo that revealed DNA is a helix?
b. Measurements revealed that the distance between the two strands was always equal. Explain how this
information helped Watson and Crick build a successful model of DNA.
c. Was this information consistent with the data obtained by Chargaff? Why or why not?
QOD 1/25/16
• What are the three parts of a nucleotide?
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Why would DNA need to replicate?
• Approximately 2 trillion cells are produced by an
adult human body every day.
• All cells come from the division of preexisting
cells.
• Remember, all cells in a person’s body have the
same DNA.
DNA Replication
• DNA Replication is the process by which DNA is
copied in a cell before the cell divides.
DNA Replication
DNA Replication
• First, enzymes called
helicases separate the two
strands of DNA.
▫ Helicases break hydrogen
bonds.
▫ The Y-shaped region
formed as bonds are
broken is called the
replication fork.
DNA Replication
• Next, enzymes called DNA
polymerases add
complimentary nucleotides to
the separated strands of DNA.
▫ Nucleotides are found
floating freely in the
nucleus.
▫ The addition of new
nucleotides occurs in
opposite directions on each
strand (one toward the
replication fork and one
away from it).
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DNA Replication
• Replication of DNA proceeds in opposite
directions on each strand.
• On one strand, DNA replicates in the direction of
the replication fork.
• On the other strand, short fragments are
replicated in the reverse direction.
DNA Replication
• On the strand that is moving away from the
replication fork, DNA polymerase synthesizes a
short fragment at a time and connects them into
a strand at the ends.
• These fragments are called Okazaki Fragments,
after the scientist who discovered them.
DNA Replication – Why do strands go in
opposite directions?
• When two strands of DNA bind together, they
line up in opposite directions (remember, each
nucleotide is paired with its partner).
• One end is called the 5’ (five prime) end and one
end is called the 3’ (three prime) end.
• This refers to the five carbon sugars in DNA.
Each carbon is assigned a number. Carbons
assigned the number five and carbons assigned
the number three are at different ends.
• DNA polymerase can replicate DNA only in the
direction of 5’ to 3’.
DNA Replication
• Several replication forks form on
the DNA strand and the process
continues until all of the DNA has
been replicated.
▫ If only one was formed it would
take too long to replicate DNA
(53 days for humans!!)
• When replication is finished,
there are two DNA molecules.
Each has one old strand and one
new strand.
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DNA Replication
• Replication is usually very accurate.
▫ There is only about one error for every BILLION
nucleotides added!
▫ The reason is that DNA polymerases also
“proofread” the DNA and fix any errors during
replication.
DNA Replication
• If an error does occur, it results in a different
nucleotide sequence in the new DNA strands.
▫ This is called a mutation.
▫ A change in even one nucleotide can be very
harmful to an organism (for reasons we will see
later).
▫ Some mutations can affect the growth of cells,
causing growth to accelerate, which results in
cancer.
▫ Changes can be good- mutations sometimes lead
to adaptations and therefore evolution.
QOD
DNA Replication Animation
• http://www.hhmi.org/biointeractive/dnareplication-basic-detail
• What’s wrong with this statement?
Given the DNA strand
5’ AAT CGC AGC 3’
the complementary strand is
5’ TTA GCG TCG 3’
Genetic Code
Genetic Code
• DNA is the “code” for hereditary
characteristics.
• The genetic code is how organisms store
hereditary information and translate it into
amino acids (the monomers, or building
blocks, of proteins).
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Genetic Code
• DNA codes for all of the body’s proteins (such as
enzymes).
▫ Genes are sequences located in the DNA that code
for specific characteristics.
▫ For example, the code (or gene) for the production
of the protein melanin is in your DNA and creates
your hair and skin color.
▫ The code or recipe for all of the enzymes that help
you digest your food is located in your DNA.
The Human
Genome
• A genome is the complete
genetic content of an
organism.
• We now know the human
genome.
▫ Biologists have deciphered 3.2 billion base pairs in the
46 human chromosomes. The human genome is so
large it would take 10 years to read the base sequences.
▫ These sequences code for about 30-40,000 genes.
▫ We are still researching which sequences code for
which genes.
Genetic Code
• The “code” or “recipe” within DNA cannot be
read directly.
▫ DNA cannot leave the nucleus and proteins
are made in the cytoplasm of cells.
▫ So the code is transcribed (copied) and
translated (turned into something useful)
by ribonucleic acid (RNA).
Genetic Code
• Remember, proteins make us who we are.
▫ They are responsible for chemical reactions
occurring in us (enzymes) and for the hereditary
characteristics that we have (such as eye color).
▫ The building blocks (or monomers) of proteins are
amino acids.
▫ DNA holds the recipe for the amino acid sequence
of all the proteins we need to make.
Protein
Synthesis
• RNA directs
protein
synthesis,
which is the
making of
proteins from
DNA.
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DNA vs RNA
• Both are made of nucleotides.
• Both are involved in protein synthesis.
• DNA has the sugar deoxyribose, while RNA has
the sugar ribose.
• RNA uses the nitrogenous base uracil instead of
thymine (used in DNA).
• RNA is single stranded, while DNA is double
stranded.
• RNA is usually MUCH shorter than DNA.
Protein Synthesis Video
• http://vegas.pbslearningmedia.org/resource/nv
ra.sci.prosynth/protein-synthesis/
RNA
• There are several types of
RNA involved in protein
synthesis.
RNA
▫ Messenger RNA (mRNA)
– carries the genetic
instructions from the DNA to
the ribosomes.
 DNA is in the nucleus.
Ribosomes are in the
cytoplasm.
RNA
▫ Ribosomal RNA (rRNA) – part of the ribosome
 The function of ribosomes in the cell is to
make proteins.
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RNA
▫ Transfer RNA
(tRNA) –
transfers the
amino acids to the
ribosomes to make
proteins
Protein Synthesis
We’ve got the blueprints and the
tools – now what?
• DNA is the blueprint used for constructing
proteins, and RNA is the guide.
• The process of developing the guide from the
blueprint is called transcription.
Protein Synthesis:
Transcription (RNA synthesis)
• Step 1: Transcription (to re-write)
• DNA is too large to go from the nucleus to the
cytoplasm, so only pieces of DNA are copied into
RNA. This RNA then travels from the nucleus to
the cytoplasm.
Protein Synthesis Transcription
▫ An enzyme called RNA
polymerase binds to a
gene’s promoter region.
 A promoter is just a
specific nucleotide
sequence where the RNA
polymerase can attach.
▫ The RNA attaches to the
RNA polymerase and the
DNA begins to uncoil.
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Protein Synthesis Transcription
• The RNA polymerase adds
complimentary nucleotides
resulting in a straight chain
RNA molecule.
▫ The DNA code
determines which bases
will be added (A with U, T
with A, and G with C).
▫ For example: if the DNA
code for a gene is
ATCCGTT, then the RNA
will be UAGGCAA.
▫ Remember, RNA does not
have thymine, it has
uracil!!
Protein Synthesis Transcription
• The copying of DNA
continues until the RNA
polymerase reaches a
termination signal.
▫ That is a specific sequence
of nucleotides that tells the
RNA polymerase to “STOP”
and release the RNA and
DNA.
▫ The RNA is mRNA, because
it is the messenger of the
“code” from the DNA to the
ribosomes.
Transcription – Trimming the
transcribed mRNA.
• Once the mRNA is completed, it gets “trimmed”,
or spliced.
• Introns are parts of genes that are noncoding –
they do not code for proteins.
• Exons are parts of genes that code for proteins.
• Genes have introns and exons, side by side.
• During the process of RNA splicing, introns are
removed and exons joined to form a contiguous
coding sequence. This "mature" mRNA is ready
for translation.
Protein Synthesis Protein synthesis:
Translation
• Step 2: Translation (to make useful)
• The RNA is then made into something useful,
like assembling amino acids into proteins in the
ribosome.
Translation
• Once the newly made
mRNA leaves the nucleus it
attaches to a ribosome at
the promoter region.
• Ribosomes will “read” 3
nucleotides in the RNA
code at a time.
▫ These 3 nucleotides are
called codons.
▫ Each codon codes for an
amino acid, a START
signal, or a STOP signal.
messenger RNA
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Protein Synthesis -
Translation
Protein Synthesis -
Translation
• For example, the
sequence AUG codes for
the amino acid
methionine and means
START (it is the only one
that means start).
▫ ALL mRNA molecules
start with AUG,
otherwise, they would
not have a start region
for protein synthesis.
• The RNA is
translated into amino
acids, which are put
together to form
proteins (or
polypeptides).
• The translation occurs
with the help of tRNA,
which carries the
amino acids.
Protein Synthesis -
Protein Synthesis -
Translation
• When the ribosome reads the
start sequence (AUG), a tRNA
molecule comes along with the
anticodon.
▫ The anticodon is the
complementary sequence,
UAC.
▫ The complementary bases
bond with each other and the
amino acid methionine begins
the protein synthesis within
the ribosome.
▫ tRNA transfers amino acids
to the ribosome.
Codon Chart
Translation
• There are only 20 amino
acids.
• Most amino acids have
more than one codon.
▫ For example, Leucine’s
codons are UUA, UUG,
CUU, CUC, CUA, and
CUG.
• But each codon codes for
ONLY 1 amino acid.
▫ For example, CUU only
codes for Leucine and
nothing else.
Protein Synthesis -
Translation
• After the start sequence,
the ribosome moves to the
next codon.
▫ Let’s say the next codon
is GUC.
▫ Now a tRNA that has the
anticodon CAG would
attach to the ribosome
and it would carry the
amino acid valine.
▫ The amino acid valine
would attach to the
methionine from before
(now we have a
dipeptide)!
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Protein Synthesis -
Translation
• This process continues
and the polypeptide
grows until the STOP
codon is reached.
▫ UAA, UAG, and UGA
are the only stop
codons.
▫ The protein, ribosome
and all RNA is released
to perform other
needed functions.
• How do I keep the steps of protein synthesis
straight?
• Alphabetical order (transcription, then
translation)
Protein Synthesis - Overview
• Amino acids are listed by their CODON!!!
▫ The three nucleotide sequence on the mRNA.
DNA
mRNA
tRNA
A
U
A
T
A
U
G
C
G
C
G
C
Protein Synthesis - Overview
Protein Synthesis - Overview
•This is an mRNA
strand- figure out the
original DNA code.
A→T
U→A
C↔G
mRNA Strand:
AUG/ACG/GAG/CUU/CGG/AGC/
UAG
Protein Synthesis - Overview
•Now figure out the
anticodons (found on the
tRNA).
DNA Strand:
TAC/TGC/CTC/GAA/GCC/TCG/A
TC
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Protein Synthesis - Overview
A→U
U→A
C↔G
mRNA Strand:
AUG/ACG/GAG/CUU/CGG/AGC/
UAG
tRNA Strand:
UAC/UGC/CUC/GAA/GCC/UCG/A
UC
Protein Synthesis - Overview
• Now use the CODON
chart to figure out the
amino acid sequence.
• Remember to use the
codons from the
mRNA to determine
amino acid sequence.
Protein Synthesis - Overview
•1 - UAC
•2 - UGC
•3 - CUC
•4 - GAA
•5 - GCC
•6 - UCG
•7 - AUC
Protein Synthesis - Overview
•1 – Methionine
(start)
•2 - Threonine
•3 – Glutamic Acid
•4 - Leucine
•5 - Arginine
•6 - Serine
•7 - STOP
Let’s Break the Genetic Code
1. Start with DNA:
TACTAGCTAACC
2. Write the complimentary strand for mRNA
AUGAUCGAUUGG
3. Identify the codons on the mRNA
AUG-AUC-GAU-UGG
4. Identify the anticodons on the tRNA
UAC-UAG-CUA-ACC
5. Identify the amino acid sequence from the mRNA
Met - Iso - Asp - stop
Mutations
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Genetic Mutations
Genetic Mutations
• Any change in the DNA sequence is called
a mutation.
▫ Mutations can effect body cells.
• Not all mutations are bad.
 Example = CANCER
▫ Mutations can effect reproductive cells.
 These are called germline mutations and can
be passed from parent to child.
 If a child inherits a germline mutation from
his or her parents, every cell in their body
will have this error in their DNA.
 Germline mutations are responsible for
inherited genetic disorders.
Genetic Mutations
• Types of DNA
mutations:
▫ Point
▫ Frameshift
▫ Inversion
• Some mutations result in characteristics
that give the organism a greater chance of
survival.
• Example: Sickle cell anemia (deflated look of
red blood cells) is caused by a mutation,
however it is beneficial to people in Africa who
often contract malaria – the parasite can no
longer attach to their red blood cells, therefore
they aren't affected
Point mutations
• Occurs when a single base
changes. Types:
▫ Silent mutation- no
amino acid change
▫ Missense- changes
amino acid that is coded
▫ Nonsense- changes
sequence to a stop codon
Frameshift Mutation
• A single base pair in DNA is
deleted or added.
• It changes everything
“downstream” – after the
base pair.
• This type of mutation can
make the DNA
meaningless and often
results in a shortened
protein.
Inversion
• In an inversion mutation, an entire section of
DNA is reversed.
• A small inversion may involve only a few bases
within a gene, while longer inversions involve
large regions of a chromosome containing
several genes.
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Causes of Mutations
Examples
▫ THE DOG BIT THE CAT.
▫ THE DOB ITT HEC AT.
▫ THE DOG BIT THE CAT.
▫ THE DOG BIT THE CAR.
▫ The fat cat ate the wee rat.
▫ The fat tar eew eht eta tac.
• Frameshift
• Point
• Inversion
• Spontaneous:
▫ Mistake in base pairing during DNA
replication
• Mutagen – agent that causes DNA change
▫ High energy radiation
 X rays
▫ Chemicals
 Dioxins, asbestos, benzene, cyanide,
formaldehyde
▫ High temperatures
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