Advanced Environmental Biotechnology II Review of Molecular Biology – DNA and RNA structure and...

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

http://commons.wikimedia.org/wiki/Image:Stylised_Lithium_Atom.svg

http://commons.wikimedia.org/wiki/Image:Rutherford_atom.svg

http://commons.wikimedia.org/wiki/Image:Lewisstructuur_water.PNG

http://commons.wikimedia.org/wiki/Image:Urea3D.png

http://commons.wikimedia.org/wiki/Image:Oxytocin3d.png

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.

Big molecules are often made by adding smaller subunits together

If the subunits are the same then we get a polymer

These are polymers

Many small bits are added

Macromolecules are bigMacro means big

‘poly’ means ‘many’

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

http://en.wikipedia.org/wiki/Amine

http://en.wikipedia.org/wiki/Carboxyl

http://en.wikipedia.org/wiki/Image:AminoAcidball.svg

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


Each protein has a special amino acid sequence

Amino acids can join to form a peptide bond

Proteins have Complex Structures


The amino acid sequence will make the three-dimensional (3D) structure.

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

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


The living cell needs many different chemical reactions


Let’s look at this part

This part also has many reactions and enzymes


This part also has many reactions and enzymes


Let’s look at this small part

There are many enzymes in this small part

Each enzyme has a number like 3.8.1.8

Let’s look at that enzymehttp://www.genome.ad.jp/kegg/pathway/map/map00791.html

Let’s meet atrazine chlorohydrolase

atrazine + H2O 4-(ethylamino)-2-hydroxy-6-(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

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.

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.

NucleotidesThere 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/wehi-tv/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) andtranslating 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

Advanced Environmental Biotechnology II Review of Molecular Biology – DNA and RNA structure and...

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