Download Intro, show Jurassic Park, relate to all other units, Discuss history

Intro, show Jurassic Park, relate to all other units, Discuss history DNA in each
cell weighs 6 millionth of a gram. All the people’s DNA (5.8 billion) total weight
would be 1/30th of a gram
The total length of DNA is thousands of times larger than the nucleus. (2.2 m) It has to
be condensed so that its length is reduced by a factor of 8000. Small proteins are
responsible for packing DNA into units called nucleosomes. The proteins are called
histones. (remember, prokaryotes have naked DNA). The organization needed so that it
can be wound up and unwound every time it needs to replicate (mitosis & meiosis) and
not make mistakes is amazing.
Nucleosome – basic unit of DNA packing. DNA wound around a core of proteins,
histones. Each nucleosome contains 8 histones. A chromosome is one DNA molecule
and histones.
Epigenetic – methyl groups on histones, regulate the opening and closing of DNA
coil, therefore controls the turning on and off of genes, can be effected by the
environment. Nova vodcast.
Structure of Nucleotide
A nucleotide consists of a nitrogen containing base, a 5-carbon sugar and one or more
phosphate groups (PO4). Their functions are varied  ATP, combine to form coenzymes and building blocks for nucleic acids. There are two types of sugars possible –
ribose for RNA C5H10O5 and deoxyribose C5H10O4.
Symbols – the sugar is represented as
the phosphate as
and the nitrogen
base as
The nitrogen bases are also called organic bases and are there are 5 types;
adenine, cytosine, guanine, thymine and uracil. A,T, C, G for DNA and A, U, C, G for
RNA. **Always write the names out in full at least in an answer.
HL - G bonds to C by a triple hydrogen bond and T to A by a double hydrogen bond. C
and T are called pyrimidines and A and G are called purines.
One base + one sugar + one phosphate = nucleotide - the monomer for the polymer
nucleic acid. Nucleic acids are long chain molecules (larger than proteins). DNA
(deoxyribonucleic acid) is a nucleic acid and so is RNA (ribonucleic acid).
When chromosomes are stained for karyotypes, the A-T band stains differently than
the C-G band
Structure of a Nucleic Acid
Using the sugar – deoxyribose, a covalent bond(a phosphodiester linkage bond) between
the phosphate of one nucleotide and the sugar of the next, and a hydrogen bond between
the nitrogen bases.
*Drawing – labelled phosphate linked to labelled sugar by single bond, labelled base,
linked base, sugar and phosphate labelled as nucleotide, covalent bonds labelled,
hydrogen bonds labelled, at least two nucleotides properly linked, A-T, G-C pairing
question asked for 2 different complimentary paired nucleotides. For HL
Textbook p.62 #3,4,6,7
Chromosomes are made up of DNA. The huge molecule is in the shape of a double helix.
The sides of the ladder are made up of sugars and phosphates. The rungs are nitrogen
bases. The bases exhibit complementary base pairing. 10 base pairs per turn of the helix.
The sugar and phosphates never change but the nitrogen bases are unique for each gene.
Gene –sequence of nucleotides that controls a trait, can be inherited, the order of the
nucleotide nitrogen bases determines the information.
*one gene contains the information to produce one polypeptide. 3.5.5 use to be thought
but now many exceptions (most genes need 10 000 to 150000 code letters to made up the
gene.)
Many genes do not code for a polypeptide but regulate how other genes are expressed.
Only identical twins have the same base pairs on their DNA.
HL stuff
Less than 10% of the DNA is know to code for polypeptides – called unique sequences.
Apart from the regulator genes, the function of the rest is unknown. But this unknown
part consists of a lot of repetitive sequences which technology has found a use for - so
most of our DNA is “useless” repetitive sequences.
Distinguish between unique and highly repetitive sequences in nuclear DNA [5]
Unique sequences
Highly repetitive sequences
Occur once in genome
Occur many times
Long base sequences
Short sequences/5-300 bases
Genes
Not genes
Translated/coding sequences
Never translated
Small differences between individuals
Can vary greatly
Exons are unique sequences
Introns include repetitive
Smaller proportion of genome
Higher proportion of genome
Satellite DNA is repetitive; Repetitive sequences are used for profiling; Prokaryotes do
not usually contain repetitive sequences
Mainly HL but SL needs the forensics part
“There is a remarkable variability in genome size among eukaryotes that has little to do
with complexity or coding genes. For eg. a newt has six times the genome size of a
human. Much of the variation is due to non-coding, tandemly (one behind the
other)repeating DNA. A substantial portion of human DNA is composed of repetitive
DNA in which short sequences are tandemly repeated in arrays.
Tandemly repetitive sequences, commonly called satellite DNA, can be several thousand
base pairs. They tend to cluster around the centrosomes and telomeres
In general, satellite DNAs show exceptional variability among individuals particularly
with regard to the number of repeat at a given locus – used in forensics.”
All somatic cells have the same number of nucleotides and therefore the same base pairs.
So how do cells differentiate? They do so by having some genes inactivated.
Lots of terms – think of using yarn to knit a sweater. The yarn is made of wool but
you can’t call it a sweater until you actually weave it into something. Wool is the
nucleotides, the yarn is nucleic acid, because the nucleotide is wool, not cotton, it is a
DNA nucleic acid. Weave it into a sweater – chromatin to chromosomes.
Wool

yarn

sweater



Nucleotide
nucleic acid
chromatin
DNA REPLICATION
**Note, this is replication, making a new copy of the DNA. IT is NOT synthesis or
Translation or Transcription. Occurs for mitosis or meiosis just at the end of
interphase. When would I need to make a complete, new copy of all of my DNA???
Briefly – the DNA will untwist and unzip along its total length. – this is the ONLY time it
will unzip totally. This means that the nucleosomes have to untwist from their nice small
package. And this is the time we can actually see the DNA in distinct form – called
chromosomes.
Once unzipped, new nucleotides will come in and complementary base pairing will
occur. (the new nucleotides are made from the food you eat) The process is called
semi-conservative. ****
Conservation of base sequences means saving the base sequences in the right order →
done by complementary base pairing
Once completed, the DNA will zip back up, twist up into its nucleosome with its histones
and get back to work.
Sounds tooo easy?? You’re right. Remember, all that is YOU is in the base pairs and
they must get it right. They must bond to the right base and there are a lot of
combinations and there’s not a lot of room to work in there. ONE base pair mistake – a
substitution where T becomes A – leads to sickle-cell anaemia.!!
First you have to unwind the DNA and keep it unwound until you’re done. (like a slinky,
it wants to twist back up) This is done by a compound called helicase. Helicase also
breaks the hydrogen bonds between the nitrogen bases to separate the two sides.
Then another compound comes in, called DNA polymerase. This compound will aid in
the process of adding the COMPLEMENTARY nucleotides to the unwound DNA.
DID YOU NOTICE that both if these compounds end in ‘ase’???? That’s because they
are enzymes catalyzing the reactions. DNA polymerase can add 50 nucleotides/second.
But bacteria can add 500/second??
But you can’t just start this replication anywhere. It is far too important. It starts with
certain sites on the DNA called origin of replication. Eukaryotic cells have lots of these
sites but Prokaryotes only have one. (maybe too simple?)
Once all the DNA has been replicated – IN A SEMI-CONSERVATIVE MANNER – the
two DNA will zip back up and rewind around their histones to form the nucleosomes.
Notice how you have conserved the base sequences by using complementary base pairing
and semi-conservative processes.***** There are enzymes, which will cruise up and
down the two ‘new’ DNA to check for mistakes. Any mistakes will be cut out and the
correct nucleotides put in.
WHAT AN AMAZING SYSTEM!! The process is very rapid and very
accurate – only one in a billion are incorrectly paired. Requires the cooperation of over a
dozen different enzymes.
HL
Page 289 figure 16.16 in Campbell good
The process stays the same, just MORE terms. As usual.
Lets go back to the nucleotide. You can number the carbons in the sugar (pentose). By
doing so, the phosphate attaches to C5 and the nitrogen base to C1. When one nucleotide
joins to another, the phosphate of one will attach to the C3 of the other.
CHECK DIAGRAMS.
* know where phosphate bonds to DNA sugar *
A DNA strand then ends up with one side having a phosphate on the 5’ end and the 3’ on
the other end. To make it so that the complementary bases can actually, physically bond
together, and maintaining the 3’  5’ linkage, the two strands of DNA are anti-parallel.
(just like holding hands, one hand has to be one way and the other the opposite way to fit
properly)
The sequence of nucleotides is given in the 5’ to 3’ direction. (someone had to decide and
this is what they picked)
Now, what about DNA replication? The process is the same but…….
DNA must replicate in a 5’  3’ manner. And it is semi-conservative. So, here goes.
1. Helicase untwists and breaks hydrogen bonds
2. single-strand binding protein (which is an enzyme) keeps the two strands open
3. there is one strand 5’ 3’, called the leading strand and its anti-parallel strand, called
the lagging strand.
4. taking the leading strand, DNA polymerase III can ONLY add to existing nucleotides
(must be a union job) so someone has to start the first nucleotide or prime it. RNA
primer, with a few RNA nucleotides, will bind to the old DNA. Of course, RNA primase
will catalyze this reaction.
5. now DNA polymerase III can start attaching the new DNA nucleotides. BUT
6. we need some energy to do this. The new nucleotides come with their own built in
energy. They are in the form of (wait for the name..) deoxyribonucleosides triphosphates.
(really, just a nucleotide with two extra phosphate groups, giving you a total of three. Is
this starting to sound familiar??) There are 4 types; dATP, dCTP, dGTP, and dTTP.
7. two of the phosphate groups will detach, supplying the energy to attach the nucleotide
to the old DNA strand and it will grow in a 5’  3’ direction.
8. now, once we are finished the leading strand, complementary bases and semiconservative, we have to get rid of the RNA nucleotides as the sugar is different. So, in
comes DNA polymerase I. It will remove the primer nucleotides and replace it with
DNA nucleotides. (why he can’t do the whole strand, I don’t know. Again probably a
union rule)
But what about the lagging strand? I know you were worried about him so……
9. remember, DNA polymerase III can only add new nucleotides in a 5’  3’ direction
but this strand is in a 3’  5’ direction. What it does is; makes little pieces, in 5  3 and
attaches them to the lagging strand. The little pieces are called Okazaki fragments and
DNA ligase is the ‘glue’ that sticks the small pieces together. (It’s like backstitching, or
re-threading the string through elasticized pants or – taking 2 steps forward to one step
back) The pieces or fragments are still growing in a 5’  3’ manner and attached in a
3  5 strand
The two new DNA will zip-up, coil back up and the nucleotide codes will be preserved
by complementary base pairing and semi-conservative duplication.
Like a zipper – handle is DNA polymerase III.
* genetic code – determines how the base sequence of mRNA is expressed as amino acid
sequences* , is a triplet code, a series of bases on mRNA, three bases code for one amino
acid
** note need to know for prokaryotes – the difference is prokaryotes only have one
replication point.