Transcript 6 Review of Molecular Biology

Advanced Environmental
Biotechnology II
Review of Molecular Biology –
DNA and RNA structure and
protein production.
Living things are made up of atoms
Atoms can be joined together to make
molecules
Organic molecules are made by living
things
Organic molecules contain carbon
An example is methane (CH4)
When two methanes are combined, the
resultant molecule is Ethane, which
has a chemical formula C2H6.
Draw ethane
Molecules made up of H and C are
known as hydrocarbons.
When two methanes are combined, the
resultant molecule is Ethane, which
has a chemical formula C2H6.
Draw ethane
Molecules made up of H and C are
known as hydrocarbons.
Big molecules are often made by
adding smaller subunits together
If the subunits are the same then we
get a polymer
Many
small bits
are
added
These
are
polymers
‘poly’
means
‘many’
Macromolecules are big
Macro means big
Cells have organic molecules which are
needed for life.
Many of these are big molecules
(what is the name for big molecules?)
Can you name any types of big
molecules?
Cells have organic molecules which are
needed for life.
Many of these are big molecules
(macromolecules)
Carbohydrates
Lipids
Proteins
Nucleic acids
Can you guess what types of atoms are
in carbohydrates?
Can you guess what types of atoms are
in carbohydrates?
carbon
hydrogen
oxygen – ate is a way of saying a
molecule has lots of oxygen
Proteins
Proteins are polymers of 20 different
amino acids.
Each amino acid has a special side
group of atoms
The side group of atoms makes the
amino acid special
Amino Acid
The amino group on the left and the carboxyl group
on the right
R is the side group of atoms
There are 20 Amino Acids
. Images from Purves et al., Life: The Science of Biology, 4th Edition,
Some Amino Acids
http://en.wikipedia.org/wiki/List_of_standard_amino_acids
Amino Acids have different
Functional Groups
. Images from Purves et al., Life: The Science of Biology, 4th Edition,
Each protein has a special amino acid
sequence
Amino acids can join to form a peptide bond
Proteins have Complex Structures
. Images from Purves et al., Life: The Science of Biology, 4th Edition,
The amino acid sequence will make the
three-dimensional (3D) structure.
. Images from Purves et al., Life: The Science of Biology, 4th Edition,
Functional Groups
Biochemical molecules act certain ways
because of functional groups of atoms
Functional groups are groups of atoms with
their own structure and functions
Example of functional group Polarity
Polar molecules (with +/- charges) like water
molecules and are hydrophilic (water lover)
Nonpolar molecules don’t like water and do not
dissolve in water; are hydrophobic (water fear)
Cells are 70-90% water, so how organic molecules
act together with water affects their function
One of the most common groups is the -OH
(hydroxyl) group which lets a molecule be water
soluble
. Images from Purves et al., Life: The Science of Biology, 4th Edition,
The sequence of amino acids
Because of the different functional
groups different proteins will do
different things
Some proteins are used to build cells
Other proteins have special work to do
These special proteins are enzymes
Enzymes are the tools which cells
use to do things.
We use tools
If we want to hammer a nail
we use a hammer.
We could use a brick
but a hammer would work better.
To open a bottle
we would use a
bottle opener.
If we want to screw in a screw
we could use a knife
but a screwdriver would work
better.
For special screws
we could use special
screwdrivers.
We can use pliers
to hold things.
To hold different things in different
ways we use different pliers.
All of these are tools.
When we have work to do we
use a special tool.
When cells have work to do
they use enzymes
Cells use
enzymes as
tools
Enzymes do
the work in
cells
This enzyme is used to break up
proteins
Different enzymes do different
things
This
enzyme
helps
cells get
energy
from
sugar
Some enzymes need metals to
help them work
Here is an enzyme with
a zinc ion
This enzyme makes
these reactions work
CO2 + H2O => HCO3(in tissues - high CO2
concentration)
HCO3- => CO2 + H2O
(in lungs - low CO2
concentration, in plant
cells)
There are many different types
of enzymes
Some enzymes can work on many
chemical reactions
Toluene dioxygenase from
Pseudomonas putida can take part in
more than one hundred different
reactions.
Some enzymes can do only a few
reactions
Enzymes can
work on the
products of
other
enzymes.
There are
linked
chains of
reactions.
http://www.genome.ad.jp/kegg/pathway/map/map01110.html
The living
cell needs
many
different
chemical
reactions
http://www.genome.ad.jp/kegg/pathway/map/map01100.html
Let’s look
at this part
The living cell
needs many
different
chemical
reactions
http://www.genome.ad.jp/kegg/pathway/map/map01100.html
This part
also has
many
reactions
and
enzymes
http://www.genome.ad.jp/kegg/pathway/map/map01196.html
Let’s look at
this small part
This part
also has
many
reactions
and
enzymes
http://www.genome.ad.jp/kegg/pathway/map/map01196.html
There are many enzymes in this small part
Each enzyme has a number like 3.8.1.8
Let’s look at that enzyme
http://www.genome.ad.jp/kegg/pathway/map/map00791.html
Let’s meet atrazine chlorohydrolase
atrazine + H2O 4-(ethylamino)-2-hydroxy6-(isopropylamino)-1,3,5-triazine + HCl
www.accessexcellence.org/AB/GG/steps_to_Prot.html
Deoxyribonucleic acid (DNA)
DNA contains the genetic instructions which determine
protein structure.
DNA is a long polymer of nucleotides (a polynucleotide).
DNA encodes the sequence of the amino acid residues in
proteins using the genetic code, a triplet code of
nucleotides.
In prokaryotes, including the eubacteria and archaea, DNA
is not separated from the cytoplasm by a nuclear
envelope.
Chloroplasts and mitochondria also carry DNA.
During cell division, DNA is replicated.
Overview
DNA consists of a pair of molecules, organized as strands running
start-to-end and joined by hydrogen bonds along their lengths.[
Each strand is a chain of chemical "building blocks", called nucleotides,
of which there are four types: adenine (abbreviated A), cytosine (C),
guanine (G) and thymine (T)
These bases of nucleic acids can be arranged in the polymer in any
order, giving the molecules a high degree of uniqueness.
A strand of DNA contains genes, areas that regulate genes, and areas
that either have no function, or a function yet unknown. Genes can
be loosely viewed as the organism's "cookbook" or "blueprint".
Each base on one strand forms a bond with just one kind of base on
another strand, called a "complementary" base: A bonds with T and
C bonds with G.
http://en.wikipedia.org/wiki/DNA
http://en.wikipedia.org/wiki/DNA
Molecular structure
Each molecule is a strand of DNA: a
chemically linked chain of nucleotides,
each of which consists of a sugar
(deoxyribose), a phosphate and one of
five kinds of nucleobases ("bases").
Because DNA strands are composed of
these nucleotide subunits, they are
polymers.
http://en.wikipedia.org/wiki/DNA
Because pairing causes the nucleotide
bases to face the helical axis, the sugar
and phosphate groups of the nucleotides
run along the outside; the two chains they
form are sometimes called the
"backbones" of the helix.
Bonds between the phosphates and the
sugars link one nucleotide to the next.
http://en.wikipedia.org/wiki/DNA
Nucleotides
There are five kinds of nucleotides, which can be named by the names
of their bases. These are adenine (A), thymine (T), uracil (U),
cytosine (C), and guanine (G). U is rarely found in DNA.
RNA usually contains U in place of T, but in certain RNAs such as
transfer RNA, T is always found in some positions.
The difference between DNA and RNA is the sugar, 2-deoxyribose in
DNA and ribose in RNA.
A to T pairing forms two hydrogen bonds and C to G forms three
hydrogen bonds.
The GC content and length of each DNA molecule makes the pairing
stronger.
The temperature required to break the hydrogen bond, is the DNA’s
Melting temperature (also called Tm value).
Nucleotide sequence
The sequence of nucleotides along a DNA strand defines a
messenger RNA sequence which then defines a protein.
The genetic code consists of three-letter 'words' (termed a
codon) formed from a sequence of three nucleotides (e.g.
ACT, CAG, TTT).
These codons can then be transcribed into messenger
RNA.
The code is then translated for each amino acid to make a
protein.
Most amino acid, have more than one possible codon.
There are also three 'stop' or 'nonsense' codons.
Genetic Code
http://www.bioss.sari.ac.uk/~dirk/genomeOdyssey/go_1966.html
Transcription
A DNA sequence is enzymatically
copied by an RNA polymerase to
produce a complementary RNA.
Transcription goes in the 5' → 3'
direction.
Transcription is divided into 3 stages:
initiation, elongation and termination.
RNA polymerase
RNA polymerase is an enzyme responsible for
making RNA from a DNA template.
It does this by constructing RNA chains through a
process termed transcription.
RNA polymerase is a nucleotidyl transferase that
polymerizes ribonucleotides at the 3' end of an
RNA transcript. RNA polymerase enzymes are
essential and are found in all organisms, cells,
and many viruses.
Look at movie “Transcription”
http://www.wehi.edu.au/education/wehitv/dna/index.html
Ribonucleic acid (RNA)
RNA is a nucleic acid polymer consisting of
nucleotide monomers.
RNA nucleotides contain ribose rings and uracil.
RNA acts as
the template for translation of genes into proteins,
(messenger RNA)
transferring amino acids to the ribosome to form
proteins, (transfer RNA) and
translating the transcript into proteins. (ribosomal
RNA)
Ribosomal RNA (rRNA)
Ribosomal RNA (rRNA) is the main component of the ribosome.
The ribosome makes proteins.
The rRNA and about 70 – 80 ribosomal proteins fold up into two
complex folded structures.
rRNA decodes mRNA into amino acids (at center of small ribosomal
subunit) and interacts with the tRNAs during translation by providing
petidyltransferase activity (large subunit).
rRNA is the most conserved (least variable) gene in all cells. Genes
that encode the rRNA (rDNA) can be used to identify an organism's
taxonomic group, and calculate related groups.
In Bacteria, Archaea, Mitochondria, and Chloroplasts the small
ribosomal subunit contains 16S rRNA.
S means Svedberg units which is a measure of how quickly the
particles sediment.
The large ribosomal subunit contains two rRNA species (the 5S and
23S rRNAs).
rna.ucsc.edu/rnacenter/ribosome_images.html
http://tigger.uic.edu/classes/phys/phys461/phys450/ANJUM04/ribosome.jpg
rna.ucsc.edu/rnacenter/ribosome_images.html