Download Section 6 - DNA history. (most of this will serve only as conversation

Section 6
- DNA history.
(most of this will serve only as conversation for your next cocktail-party, but you should know at
least about Watson and Crick!)
• 1869, Miescher determined that a substance inside the nucleus of a cell didn’t behave like
regular proteins. he named it nuclein (later renamed DNA).
• 1930s, Hammerling determined that the DNA in the nucleus was responsible for the
transmission of traits.
• 1952, Hersey and Chase determined that DNA from a bacteriophage and not the protein
coat resulted in the new viral DNA.
• 1953, Watson and Crick determined the structure of DNA. they were Canadian.
• 2000s, the Human Genome Project
- DNA Structure.
DNA is short for DeoxyriboNucleic Acid.
there are three basic units which link together to form a ladderlike molecule:
1. phosphate groups
2. sugars (deoxyribose)
3. nitrogenous bases, of which there are four types:
i. adenine (usually shortened to A)
ii. cytosine (usually shortened to C)
iii. guanine (usually shortened to G)
iv. thymine (usually shortened to T)
a “nucleotide” is formed by one sugar, one phosphate group and one nitrogenous base.
of the four nitrogenous bases, two are purines (adenine and guanine), which have double-ring
structures, and two are pyrimidines (thymine and cytosine), which have single-ring structures.
one way to remember: “pure silver taxi”; “pur AG TC”
(A and G are purines, while T and C aren’t)
each of the two strands are antiparallel to the other strand, which means one strand runs from 5¢
to 3¢ , while the other strand runs from 3¢ to 5¢ . only the 5¢ to 3¢ strand is usually written.
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5¢ means the end with the phosphate group, while 3¢ means the end with the hydroxyl group.
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bases of one strand are paired with bases from the other strand such that complementary base
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pairs are joined (ie, A is paired with T, G is paired with C).
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when C bonds to G, three hydrogen bonds are formed, but when A bonds to T, only two
hydrogen bonds are formed.
- separating DNA strands.
• DNA strands cannot be simply pulled apart as they are held together by hydrogen bonds
and twisted around each other to form a double-helix.
• DNA helicase, an enzyme, unwinds the strands by breaking the bonds
• the separated strands are kept apart by special proteins (single-stranded bonding proteins
“SSB”s). these proteins inhibit the formation of hydrogen bonds.
• after the strands of DNA are split apart, they can be replicated
- steps to building complementary DNA strands.
replication begins in two directions from the origin. the junction of the two strands is called the
replication fork. replication occurs toward the replication fork on one strand and away from it on
the other.
1. DNA polymerase III (an enzyme) is required to synthesize DNA in the 5¢ to 3¢ direction.
2. RNA primer is required at the 3¢ end to initiate elongation. this is removed later.
3. DNA polymerase III now starts to add bases to the growing complementary strand.
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4. the strand that used the 3¢ to 5¢ template is called the leading strand and is built toward
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the replication fork.
5. the other strand that used the 5¢ to 3¢ strand is called the lagging strand. it is built away
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from the replication fork. it is built in short fragments
6. RNA primers are being continuously added as DNA polymerase III builds short segments
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known as Okazaki fragments.
7. RNA primers are removed and appropriate bases are inserted.
8. DNA ligase, another enzyme joins the Okazaki fragments into one strand.
9. as the two strands of DNA are synthesized, two double-stranded molecules are produced
and twist into a helix.
DNA
replicates semi-conservatively: each daughter molecule receives one strand from the
parent molecule and one newly synthesized strand.
- some DNA replication terms.
• anneal. the pairing of complementary strands of DNA through hydrogen bonding
• DNA helicase. an enzyme for unwinding DNA
• 5¢ to 3¢ direction. from the phosphate group to the hydroxide group
• 3¢ to 5¢ direction. from the hydroxide group to the phosphate group
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• primer. initiates the starting point for the attachment of nucleotides
- RNA (RiboNucleic Acid).
RNA is a molecule similar to DNA, with four major differences:
property
DNA
RNA
sugar
deoxyribose
ribose
pairing of bases
A-T, C-G
A-U, C-G
structure
double-stranded
single-stranded
location
nucleus
nucleus and cytoplasm
there are three major classes of RNA molecules:
1. messenger RNA (mRNA), which acts as an intermediate between DNA and the ribosomes.
mRNA is translated into protein by the ribosomes.
2. transfer RNA (tRNA), which acts to transfer the appropriate amino acid to the ribosome to
build a protein as directed by the mRNA.
3. ribosomal RNA (rRNA), which forms the ribosome which assembles polypeptides
- the genetic code.
• DNA and RNA use the order of nitrogenous bases within their structures to code for
specific proteins.
• the four different bases (A, T, C, G) are used to code for the 20 different amino acids used
to make proteins.
• three bases arranged in a specific sequence are called a codon (ex. AUG)
• because there are 64 possible combinations for four bases arranged into codons of three
bases apiece, some amino acids are coded for by different codons.
• there is one START codon - AUG, which also codes for the amino acid methionine
• there are three STOP codons - UAA, UAG, UGA.
- protein synthesis.
the nucleotide sequences within a molecule of DNA must be transcribed to a molecule of
mRNA, which can leave the nucleus and move to a ribosome, where it is translated into a
polypeptide, which folds to become a protein, which can be used for cellular functions.
- transcription (three easy steps!).
1. initiation. RNA polymerase binds to the DNA at a specific site known as the promoter
region, near the beginning of the gene. the promoter region is a characteristic base pair
pattern rich in A and T bases (because A-T bonds are easier to break). this serves as the
recognition site for RNA polymerase to bind, because it takes less energy
2. elongation. using the DNA as a template, RNA polymerase pulls together the appropriate
ribonucleotides and builds an mRNA transcript. this occurs in the 5¢ to 3¢ direction. RNA
polymerase chooses one strand to act as a template for RNA synthesis (called the template
strand). the strand not used is called the coding strand.
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3. termination. RNA recognises a signal to stop transcribing. this is called a terminator
sequence. the mRNA is release from the DNA and will eventually leave the nucleus.
- topping and tailing.
before mRNA leaves the nucleus,
• a cap is added to the 5¢ end which protects the mRNA from digestion enzymes as it moves
to the cytoplasm. it also helps in initializing translation
• a tail is added to the 3¢ end (lots of adenine nucleotides!)
- introns and exons.
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• the primary transcript is made up of coding regions, called exons and non-coding regions
called introns
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• because the primary transcript contains sections that do not code for the protein, if they
are translated to amino acids, it will not fold to form the proper protein
• in order to combat this problem, before the primary transcript leaves the nucleus, the
introns are removed by splicesosomes, which cut out the introns and join together the
exons to form the mRNA transcript.
• introns may take up half of a given gene, and exist in order that a gene may code for more
than one polypeptide by using different combinations of exons and introns
• the frequency of introns is related to the complexity of the gene and the organism. a
bacterium has an average of 0 introns per gene, while a mouse has an average 7 introns
per gene
- translation.
a process by which a ribosome assembles amino acids in a specific sequence.
mRNA acts as a set of instructs for assembling amino acids into a specific order, while tRNA
brings the required amino acids to form the protein. tRNA folds up on itself and forms three
loops whose free ends come together.
leu
¸
˝ amino acid
˛
A¸
C ˝codon to which all amino
C ˛ acids attach to tRNA
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GAU } anticodon
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- translation (3 easy steps!).
1. initiation. this occurs when a ribosome recognizes a specific sequence on the mRNA and
binds to that site. the ribosome moves along the mRNA, three nucleotides at a time, where
each set of three nucleotides codes for a specific amino acid
2. elongation. a tRNA delivers the appropriate amino acid and the polypeptide chain is
elongated.
3. termination. elongation occurs until a STOP codon is reached (ie UAA, UAG, UGA). the
ribosome falls away from the mRNA and the polypeptide chain is released.
after translation, the polypeptide chain is moved to the smooth endoplasmic reticulum, where it
is altered by adding phosphates, adding sugars or by enzymes.
- properties of proteins.
• proteins determine phenotypical characteristics
• serve as antibodies and hormones
• drive cellular processes (enzymes)
• manifest genetic disorders by their absence (or presence in an altered form ex. sickle-cell
anemia)
- mutations.
errors made in the DNA sequence that are inherited, which may cause detrimental side-effects,
no side-effects or positive side effects.
there are two types of mutations:
1. chromosomal mutations, which affect many genes or even the entire organism (ex. trisomy
21)
2. point mutations (or gene mutations), which affect a single gene (examined in detail in this
course)
- point mutations.
“silent mutations” occur and do not have an effect on the function of the cell. these usually occur
in the non-coding introns of DNA, as they are cut out of the primary mRNA during transcription
“missense mutations” are a change in the base sequence of DNA. this alters a codon, leading to a
different amino acid. missense mutations can be broken into frameshift mutations and nonsense
mutations.
• frameshift mutations occur when the reading frame is changed. these are caused by
i. substitution mutations, where one base pair is substituted for another
ii. deletion mutations, where one or more nucleotides are removed from the sequence
iii. insertion mutations, where a nucleotide is inserted into the nucleotide sequence.
• nonsense mutations occur when a change in the DNA sequence causes a stop codon to
replace a codon specifying an amino acid. these are usually lethal to the cell.