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3.3 & 7.1 DNA Structure
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| A DNA is composed a deoxyribose, a phosphate group and a

nitrogen base (Adenine, Cytosine, Thymine, and Guanine).
| The phosphate group is covalently bonded to the carbon of
the deoxyribose and then nitrogenous base is attached to the
deoxyribose.|
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y| Adenine, Cytosine, Guanine, and Thymine.
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| Two DNA nucleotides can be linked together by a covalent

bond between the sugar of one nucleotide and the phosphate
of another. More nucleotides can be added to form a single
strand.|
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y| DNA molecules consist of two strands of nucleotides which are then wound together
to form a double helix. These are formed between the bases of two strands.
y| Œowever, it is formed by complementary base pairing because Adenine only forms
hydrogen bonds with Thymine and Cytosine only forms hydrogen bonds with
Guanine.
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y| The sides of the ladder of DNA consist of alternating phosphate groups and
deoxyribose (a sugar). The two sides are antiparallel, meaning that the sugar and
phosphates are running in opposite directions (one looks "upside down"). Each side
has a 5' end and a 3' end. If a strand is structured from 3' to 5', that means that the
sugar-phosphate backbone runs from sugar to phosphate. Since the sides are
antiparallel, one side goes in the 3' to 5' direction, and the other goes in the 5' to 3'
direction. There are two types of nucleotides, pyrimidines and purines. Pyrimidines
hydrogen bond to purines to create the rungs of the DNA ladder.
y| Thymine and cytosine are pyrimidines, adenine and guanine are purines.
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y| A nucleosome is a section of DNA wrapped up by eight smaller protein molecules
called histones. Another histone seals the octamer of histones to the DNA double
strand molecule.
y| A nucleosome is a basic unit of DNA packaging. it consists of 8 histones (histone is a
kind of protein) with the DNA double helix wrapped around it. This "bead' is
fastened onto the "string" of DNA by another histone.
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y| Nucleosomes enable the DNA molecule to be super coiled to make chromosomes about
8000 times smaller in length and help regulate transcription.

 
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y| Not all of the base sequences in DNA are translated. Œighly repetitive base sequences are
not translated. They consist of sequences of between 5 and 300 bases that may be repeated
up to 10 000 times. They constitute 5-45% of eukaryotic DNA. Single-copy genes or unique
genes are translated and constitute a surprisingly small proportion of eukaryotic DNA.|
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y| Eukaryotic genes can contain exons and introns.

3.4 & 7.2 DNA Replication
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y| ºecause the nitrogenous bases that compose DNA can only pair with
complementary bases, any two linked strands of DNA are complementary. This
ensures that the old base sequence is conserved.
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y| DNA replication occurs in a 5' to 3' direction.
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y| The process of replication begins at specific nucleotide sequences called the origins
of replication on the DNA strand. It is at these points that a

splits the DNA into
its two antiparallel strands.
y| {n the strand running in the 5'è3' direction, DNA polymerase III latches on at one
end of the opening, called the replication bubble, and begins to continuously lay a
new DNA strand from free nucleotides in the nucleus. As always, an exact copy of
the now-detached strand is formed from this template due to base-pairing rules.
y| At the same time that DNA polymerase III is laying new DNA, helicase is continuing
to split the strands, thus allowing replication to continue uninterrupted.
y| {n the opposite strand running 3ǯè5', replication is not so simple. ºecause new
strands have to be laid in the 5'è3' direction, DNA polymerase III cannot lay
continuously as it can on the other strand. Instead, RNA primase lays short
segments of RNA primer nucleotides at many points along the strand.
y| Polymerase III fills in between the RNA primers with DNA nucleotides, until it
comes into contact with another RNA primer. DNA polymerase I replaces the RNA
primer with DNA.
y| Although the lagging strand is completely made up of DNA nucleotides, between the
RNA primer points that are now replaced by DNA nucleotides there are small gaps;
these segments of DNA are called {  
 . {nce these fragments have
been laid, they are joined by yet another enzyme known as  
, which
attaches DNA into the gaps between fragments and completes the new strand.
y| The 3'è5' strand with {kazaki fragments is called the lagging strand, while the
leading strand is the continuously replicating one.
y| The two daughter DNA molecules are identical in base sequence to each other and
to the parent molecule, because of complementary base pairing (Adenine pairs with
Thymine and Cytosine with Guanine). Each of the new strands is  


to
the template on which it was made and 
 to the other template.

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y| DNA replication is initiated at many points in eukaryotic chromosomes.

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y| DNA replication copies DNA to produce new molecules with the same base sequence. It
is semi-conservative because each new molecule formed by replication uses one new
strand and one old strand which is conserved from the parent DNA molecule.
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3.5 & 7.3 Transcription
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y| Transcription is carried out in a 5' to 3' direction (from phosphate to sugar). The 5'
end (phosphate) of the RNA nucleotide is added to the 3' end (sugar) of the part of
the RNA molecule which has already been synthesized.
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y| The sense strand is the coding strand and has the same base sequence as the mRNA (with
uracil instead of thymine). The antisense strand is transcribed and has the same base
sequence as tRNA.
y| The sense strand is also called the non-template strand, and the antisense strand is also
called the template strand.

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y| RNA polymerase separates the two strands of the DNA and bonds the RNA
nucleotides when they base-pair to the DNA template.
y| RNA polymerase binds to parts of the DNA called promoters in order for separation
of DNA strands to occur.
y| Transcription proceeds as nucleoside triphosphates (type of nucleotide) bind to the
DNA template and are joined by RNA polymerase in the 5' to 3' direction.
y| Transcription ends when RNA polymerase reaches a termination site on the DNA.
When it reaches the terminator, the RNA polymerase releases the RNA strand.
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y| Eukaryotic RNA needs the removal of introns to form mature mRNA. This is because
the introns are Œighly Repetitive Sequences, or non-coding sequences.
y| Introns contain nucleotides that do not code for amino acids.
y| After introns are removed after transcription and before translation, the exons are
joined. This process is called
.
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1. The number of strands.
y| DNA has two strands forming a double helix.
y| RNA has one strand.
2. The type of sugar.
y| DNA has a deoxyribose.
y| RNA has a Ribose.
3. The nucleotides.
y| DNA has A,C,G,T
y| RNA has A,C,G,U, (Uracil replaces Thymine)
3.5 & 7.4 Translation
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y| Each amino acid has a specific tRNA-activating enzyme that help to tRNA to combine
with its complimentary mRNA codon. The enzyme has a 3-part active site that
recognizes three things: a specific amino acid, ATP, and a specific tRNA. The enzyme
attaches the amino acid to the 3' end of the tRNA. The amino acid attachment site is
always the base triple CCA.
y| It is important to note that each tRNA molecule can attach to one specific amino
acid, but an amino acid can have a few tRNA molecules with which is can combine.
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y| A ribosome consists of two subunits: small and large. These two subunits separate
when they are not in use for protein synthesis.
y| In eukaryotes, the large subunit consists of three different molecules of rRNA
(ribosomal RNA) and about 45 different protein molecules. A small subunit consists
of one rRNA molecule and 33 different protein molecules.
y| A ribosome can produce all kinds of proteins. It has a mRNA binding site, and two
tRNA binding sites where the tRNA are in contact with the mRNA.
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y| Translation consists of initiation, elongation, and termination.
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y| Translation occurs in a 5' to 3' direction, the ribosome moves along the mRNA
toward the 3' end.
y| The start codon is nearer to the 5' end than the stop codon.
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1.| Initiation:
y| {nce the RNA reaches the cytoplasm, it attaches its 5' end to the small subunit of the
ribosome. AUG is called the start codon (remember: codon is a base triple on the mRNA)
because it initiates the translation process.
y| The anticodon on one end of a tRNA molecule is complimentary to a specific codon on
the mRNA, meaning that the anitcodon and the codon bond by hydrogen bonds. The
codon AUG hydrogen bonds with a tRNA molecule holding the amino acid methionine
(the initiator tRNA).
y| The large ribosomal subunit has two tRNA binding sites: the P site and the A site. tRNA
molecules in these sites attach to the mRNA "conveyor belt". tRNA molecules move from
the A site to the P site (because the mRNA moves that way), so when initiation is done
the initiator tRNA is in the P site.
2.| Elongation:
y| Another tRNA (let's call it tRNA "X") carrying a specific amino acid attaches itself to the
next codon at the A site of the larger subunit. These two amino acids (methionine and
the amino acid on X) now make a peptide bond with each other.
y| The initiator tRNA breaks off and tRNA X moves from the A site to the P site. Then
another tRNA molecule (tRNA "Y") attaches to the codon in the A site. The amino acid
that is attached to tRNA Y makes a peptide bond with the amino acid from tRNA X.
y| The codon keeps moving through the ribosome in a 5' to 3' direction (from A to P). (In
actuality, it is the ribosome that is moving across the mRNA chain.) This makes the A
site vacant for another tRNA to attach a new amino acid etc. etc.
3.| Termination:
y| The stop codon is one that does not code for an amino acid and that terminates the
translation process. The polypeptide is released and the mRNA fragments return to the
nucleus.
y| These nucleotides are recycled and used for RNA and DNA synthesis. tRNA also is
returned to its free state and attaches to its specific amino acid so as to be ready for the
translation process when needed.


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y| The genetic code is a triplet code- three bases code for one amino acid. A group of three
bases is called a codon.
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y| Polypeptides are long chains of amino acids.
y| Amino acids must be linked up in a precise sequence to make a polypeptide.
y| Genes store the information needed to make a polypeptide in a coded form.
y| The sequence of bases in a gene codes for the sequence of amino acids in a
polypeptide.
y| The information in the gene is decoded during the making of the polypeptide.
7.5 Proteins
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1.| Primary structure:
y| A linear sequence of amino acids joined by peptide linkages. There are about 20
different amino acids.
y| ºasic order of amino acids in the polypeptide protein chain, before any folding or
bonding between amino acids has occurred.
y| Proteins are usually not functional on the primary level, and all proteins have a
primary structure.
2.| Secondary structure:
y| The repeated, regular structure protein chains take due to hydrogen bonding
between amino acids.
y| The secondary structure is usually in the form of an alpha helix (similar to a DNA
chromosome) or a beta- pleated sheet (similar in form to the corrugations of
cardboard).
y|   -Œelix is maintained by hydrogen bonds. The helix makes up keratin (skin, nails,
hair).
y| · -Pleated Sheet flat zig-zag amino acid chain. The sheets make up fibroin (silk).

Î| Alpha helix is due to hydrogen bonding within one polypeptide chain, while the beta pleated
sheet is due to hydrogen bonding between separate polypeptide chains. ºoth structures are
fibrous and form structural proteins.

3.| Tertiary structure:

y| The complex, three-dimensional protein shape resulting from the folding of the
polypeptide due to different types of bonds between the amino acids.
y| These bonds include hydrogen bonds, disulphide linkages and electrovalent bonds.
y| A disulphide linkage is where one of the amino acids, cysteine, contains sulfur.
y| Two of these can have a bond between their sulfur atoms which results in a
disulphide linkage which leads to a folding in the chain.
y| An electrovalent bond is between the negative and positive molecules or amino acid
groups along the chain.
y| Globular.
4.| Quaternary structure:
y| The most complicated form of a protein.
y| It encompasses the primary, secondary and tertiary, and then adds another level:
the quaternary is one or more peptide chains bonded together.
y| This is the functional form of many proteins, but again, just as not all proteins have
secondary or tertiary structure, not all proteins have a quaternary structure.
y| Œaemoglobin is a common example.
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y| üibrous proteins are in their secondary structure, which could be in the alpha helix
or beta pleated forms. They are made of a repeated sequence of amino acids that can
be coiled tightly around in a pattern that makes it a very strong structure. Two
examples are keratin (in hair and skin) and collagen (in tendons, cartilage, and
bones).
Î| Chain extended
Î| Insoluble
Î| Resistance to pŒ temperature changes
Î| Structural material

y| Globular proteins are in their tertiary or quaternary structure, which is folded,

creating a globular, three-dimensional shape. Two examples are all enzymes and
microtubules (form centrioles, cilia, flagella, and cytoskeleton).
Î| Chain folded
Î| Soluble colloidal
Î| Susceptible to pŒ temperature changes
Î| Compact, rounded molecules
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y|  
  have non-polar (neutrally charged) R groups.
y|    have R chains with polar groups (charged either positive or
negative).
y| Proteins with a lot of
amino acids make the proteins hydrophyllic and
therefore able to dissolve in water.
y| Proteins with many  
 amino acids are more hydrophobic and are less
soluble in water. With these abilities, proteins fold themselves so that the
hydrophilic ones are on the inner side and allow hydrophilic molecules and ions to
pass in and out of the cells through the channels they form. These channels are vital
passages for many substances in and out of the cell.
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y| Transport: hemoglobin transports oxygen around the body within a blood cell.
y| Contraction of muscles: actin and myosin responsible for the contraction of muscles.
y| Defense: antibodies that fight against disease are made of proteins.
y| Structure: nails (keratin) or tendons (collagen).
3.6 & 7.6 Enzymes
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1.| Enzyme: globular proteins used to catalyze chemical reactions.
2.| Active site: the binding site on the surface of an enzyme where catalysis occurs.
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y| Metabolic pathways consist of chains and cycles of enzyme catalysed reactions.
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y| The active site for an enzyme is very specific in shape, with very precise chemical
properties. Active sites match the shape of their substrates. {ther molecules do not
fit or do not have the same chemical properties. The enzyme is therefore substrate
specific. This enzyme is a Dzlockdz, and the substrate is the Dzkeydz which can open it.
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y| This is an extension of the lock-and-key model. It accounts for the broad specificity
of some enzymes. The induced fit model of enzymes states that the active site of an
enzyme does not fit perfectly with the substrate, as would a lock and key. Instead,
the fit is not quite perfect; thus when a substrate collides with an enzyme and enters
the active site, the substrate is stressed in a way that allows its bonds to break
easier. When another collision occurs with the substrate in the active site, the bonds
are then broken and the substrate released. Enzymes can process reactions such as
this very rapidly.
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y| All reactions, either with or without enzymes, need collisions between molecules in
order to occur. Many molecules have strong bonds holding them together, and as
such require powerful collisions at high speed in order to break these bonds.
Œowever, increasing the rate of collision to a rate at which these reactions would
occur would require prohibitive amounts of energy, usually in the form of heat.
Enzymes, by stressing substrate bonds in such a way that a weaker collision is
required to break them, reduce the amount of energy needed to cause these
reactions to occur, or the activation energy.
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y| Substrate concentration: At low substrate concentration, the enzyme activity is
proportional to the substrate concentration, because of random collision between
substrate and enzyme. Thus the more substrate the higher the rate. Œowever at a high
substrate concentration, at some point all active sites are occupied so raising the
substrate concentration has no effect.
 y| Temperature: Enzyme activity increases as temperature increases, often doubling with
each 10°C. This is because collision between substrate and active site happen more
frequently at higher temperatures, due to fast molecular movement. Œowever at high
temperatures enzymes are denatured and stop working. This is because heat causes
vibrations inside the enzyme, which break bonds needed to maintain the structure.
y| pΠlevels: There is an optimum at which enzyme activity is fastest (mostly pΠ7), and as
pΠincreases or decreases from its optimum, enzyme activity is reduced (acids and
alkali denature enzymes).
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y| Denaturation: a structural change in a protein that results in a loss of its biological
properties. This can be caused by pΠor by temperature.
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y| †actose: The sugar present in milk. †actose is obtained from Kluveromyces and lactis.
†actose can be converted to glucose and galactose using the enzyme lactase (di-
saccarharide). ºiotechnology companies culture the yeast and extract the enzyme in order
to produce lactose free milk.
y| Pectinase makes juice more fluid and easy to separate from pulp.
y| üructose is widely used in food manufacturing because it is much sweeter than
glucose. It is made from starch, usually found in maize. Amylase is needed to break
down the starch into glucose.
y| Amylase is obtained from fungi.
y| Used to break Starch into glucose, which is then converted into fructose using the
enzyme glucose isomerase.
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y| Competitive inhibition occurs when an inhibiting molecule structurally similar to
the substrate molecule binds to the active site, preventing substrate binding.
Examples are the inhibition of butanedioic acid (succinate) dehydrogenase by
propanedioic acid (malonate) in the Krebs cycle, and inhibition of folic acid
synthesis in bacteria by the sulfonamide prontosil (an antibiotic).
y| Non-competitive is an inhibitor molecule binding to an enzyme (not to its active
site) that causes a conformational change in its active site, resulting in a decrease in
activity. Examples include Œg, Ag, Cu and CN inhibition of many enzymes (eg
cytochrome oxidase) by binding to SΠgroups, thereby breaking -S-S- linkages; and
nerve gases like Sarin and DüP (diisopropyl fluorophosphate) inhibiting ethanyl
(acetyl) cholinesterase.

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y| Allostery is a form of non-competitive inhibition. The shape of allosteric enzymes
can be altered by the binding of end products of an enzyme to an allosteric site (an
area of the enzyme seperate from the active site), thereby decreasing its activity.
y| Metabolites, a type of allosteric inhibitor, can act as allosteric inhibitors of enzymes
earlier in a metabolic pathway and regulate metabolism according to the
requirements of organisms; they are a form of negative feedback.
y| Examples include ATP inhibition of phosphofructokinase in glycolysis and inhibition
of aspartate carbamoyltransferase (ATCase) which catalyses the first step in
pyrimidine synthesis.