Molecular Genetics

Topic Notes

Additional Support Materials

i.e. animations, quizzes, pictures,  worksheets

 Structure and Function of Nucleic Acids

Nucleic Acids problem set 
(The Biology Project, University of Arizona)

DNA - Detailed picture 
(provided by: Access Excellence)  

 

Replication - DNA Synthesis

 

Animation of DNA replication 
(provided by: New Century College)

Interactive animation of DNA replication and Protein synthesis 
(provided by: pbs) 

DNA replicating itself (picture) 
(provided by: Access Excellence)  

Central dogma of molecular biology 
(provided by: Access Excellence)  

The Genetic Code

Codons and the genetic code
(provided by: Access Excellence)  

The Genetic Code
Sample pages from Biozone workboo

 

DNA and Protein Synthesis

 

 

 

 

 

 

 

 

 

RNA synthesis & processing
(provided by: Access Excellence)
  

mRNA - Exons and Introns 
(provided by: University of Alberta)

Exons and Introns
(provided by: Access Excellence)  

Role of mRNA in protein synthesis 
(provided by: Access Excellence) 

Overview of Protein Synthesis 
(provided by: Access Excellence) 

Protein Synthesis-Animations&Qu's 
(provided by: curriculum revision with educational technology)

Overview of Transcription&Translation 
(provided by: University of Virginia)

Transcription animation
(provided by: ThinkQuest) 

Animation of Transcription 
(provided by: New Century College)

Animation of Translation 
(provided by: New Century College) 

Transcribe a DNA sequence and translate it into a protein 
(provided by: genetics sci. learning center)

Nucleic acids & protein synthesis Multiple choice Qu's 
(provided by: nelsonthornes.com)


Useful Genetics Websites:

DNA structure, replication, transcription, translation and protein synthesis 
(provided by: New Century College) 

Genetic Science Learning Center

National Human Genome Research Institute

DNA Interactive

NEW Your Genes, Your Health - Very good and informative website about genetic diseases and how they are inherited

 

 


 

Molecular Genetics
[back to top]

 

Genetics is the study of heredity (from the Latin genesis = birth). The big question to be answered is: why do organisms look almost, but not exactly, like their parents? There are three branches of modern genetics:

 

Structure and Function of Nucleic Acids [back to top]

DNA and its close relative RNA are perhaps the most important molecules in biology. They contain the instructions that make every single living organism on the planet, and yet it is only in the past 50 years that we have begun to understand them. DNA stands for deoxyribonucleic acid and RNA for ribonucleic acid, and they are called nucleic acids because they are weak acids, first found in the nuclei of cells. They are polymers, composed of monomers called nucleotides.

Nucleotides   [back to top]

 Nucleotides have three parts to them:                             

Base:

Adenine (A)

Cytosine (C)

Guanine (G)

Thymine (T)

Uracil (U)

 

 

Nucleotide Polymerisation   [back to top]

Nucleotides can join together by a condensation reaction (results in the removal of water) between the phosphate group of one nucleotide and the hydroxyl group on carbon 3 of the sugar of the other nucleotide.  The bonds linking the nucleotides together are strong, covalent phosphodiester bonds. 

The bases do not take part in the polymerisation, so there is a sugar-phosphate backbone with the bases extending off it. This means that the nucleotides can join together in any order along the chain. Many nucleotides form a polynucleotide.

Each polynucleotide chain has two distinct ends

 

Structure of DNA   [back to top]

The three-dimensional structure of DNA was discovered in the 1950's by Watson and Crick. The main features of the structure are:

    

 

  

 

 

Function of DNA   [back to top]

DNA is the genetic material, and genes are made of DNA. DNA therefore has two essential functions: replication and expression.

·         Replication means that the DNA, with all its genes, must be copied every time a cell divides.

·       Expression means that the genes on DNA must control characteristics. A gene was traditionally defined as a factor that controls a particular characteristic (such as flower colour), but a much more precise definition is that a gene is a section of DNA that codes for a particular protein. Characteristics are controlled by genes through the proteins they code for, like this:

Expression can be split into two parts: transcription (making RNA) and translation (making proteins).   These two functions are summarised in this diagram (called the central dogma of genetics).

No one knows exactly how many genes we humans have to control all our characteristics, the latest estimates are 60-80,000. The sum total of all the genes in an organism is called the genome.

The table shows the estimated number of genes in different organisms:

Species

Common name

length of DNA (kbp)*

no of genes

phage

virus

                    48

              60

Escherichia coli

Bacterium

                4 639

         7 000

Saccharomyces cerevisiae

Yeast

              13 500

         6 000

Drosophila melanogaster

fruit fly

            165 000

     ~10 000

Homo sapiens

Human

         3 150 000

     ~70 000

*kbp = kilo base pairs, i.e. thousands of nucleotide monomers.

 Amazingly, genes only seem to comprise about 2% of the DNA in a cell. The majority of the DNA does not form genes and doesn’t seem to do anything. The purpose of this junk DNA remains a mystery!

 

RNA    [back to top]

RNA is a nucleic acid like DNA, but with 4 differences:

Messenger RNA (mRNA)

mRNA carries the "message" that codes for a particular protein from the nucleus (where the DNA master copy is) to the cytoplasm (where proteins are synthesised). It is single stranded and just long enough to contain one gene only. It has a short lifetime and is degraded soon after it is used.

Ribosomal RNA (rRNA)

rRNA, together with proteins, form ribosomes, which are the site of mRNA translation and protein synthesis. Ribosomes have two subunits, small and large, and are assembled in the nucleolus of the nucleus and exported into the cytoplasm.

 

Transfer RNA (tRNA)

tRNA is an “adapter” that matches amino acids to their codon. tRNA is only about 80 nucleotides long, and it folds up by complementary base pairing to form a looped clover-leaf structure. At one end of the molecule there is always the base sequence ACC, where the amino acid binds. On the middle loop there is a triplet nucleotide sequence called the anticodon. There are 64 different tRNA molecules, each with a different anticodon sequence complementary to the 64 different codons. The amino acids are attached to their tRNA molecule by specific enzymes. These are highly specific, so that each amino acid is attached to a tRNA adapter with the appropriate anticodon.

Replication - DNA Synthesis   [back to top]

DNA is copied, or replicated, before every cell division, so that one identical copy can go to each daughter cell. The method of DNA replication is obvious from its structure: the double helix unzips and two new strands are built up by complementary base-pairing onto the two old strands.

  1. Replication starts at a specific sequence on the DNA molecule called the replication origin.

  2. An enzyme unwinds and unzips DNA, breaking the hydrogen bonds that join the base pairs, and forming two separate strands.

  3.  The new DNA is built up from the four nucleotides (A, C, G and T) that are abundant in the nucleoplasm.

  4.  These nucleotides attach themselves to the bases on the old strands by complementary base pairing. Where there is a T base, only an A nucleotide will bind, and so on.

  5.  The enzyme DNA polymerase joins the new nucleotides to each other by strong covalent bonds, forming the sugar-phosphate backbone.

  6.  A winding enzyme winds the new strands up to form double helices.

  7.  The two new molecules are identical to the old molecule.

DNA replication can take a few hours, and in fact this limits the speed of cell division. One reason bacteria can reproduce so fast is that they have a relatively small amount of DNA.

The Meselson-Stahl Experiment    [back to top]

This replication mechanism is sometimes called semi-conservative replication, because each new DNA molecule contains one new strand and one old strand. This need not be the case, and alternative theories suggested that a "photocopy" of the original DNA could be made, leaving the original DNA conserved (conservative replication). The evidence for the semi-conservative method came from an elegant experiment performed in 1958 by Meselson and Stahl. They used the bacterium E. coli together with the technique of density gradient centrifugation, which separates molecules on the basis of their density.

1.       Grow bacteria on medium with normal 14NH4

 

 These first two steps are a calibration.  They show that the method can distinguish between DNA containing 14N and that containing 15N.

2.       Grow bacteria for many generations on medium with 15NH4

 

3.       Return to 14NH4 medium for 20 minutes (one generation)

 This is the crucial step.  The DNA has replicated just once in 14N medium.  The resulting DNA is not heavy or light, but exactly half way between the two.  Thus rules out conservative replication.

4.       Grow on 14NH4 medium for 40 mins (two generations)

 After two generations the DNA is either light or half-and-half. This rules out dispersive replication.  The results are all explained by semi-conservative replication.

 

The Genetic Code   [back to top]

The sequence of bases on DNA codes for the sequence of amino acids in proteins. But there are 20 different amino acids and only 4 different bases, so the bases are read in groups of 3. This gives 43 or 64 combinations, more than enough to code for 20 amino acids. A group of three bases coding for an amino acid is called a codon, and the meaning of each of the 64 codons is called the genetic code.

 

SECOND BASE

 

U

C

A

G

F

I

R

S

T

 

B

A

S

E

(5'end)

U

UUU

Phe

UCU

Ser

UAU

Tyr

UGU

Cys

U

T

H

I

R

D

 

 

B

A

S

E

 

(3'end)

UUC

UCC

UAC

UGC

C

UUA

Leu

UCA

Ser

UAA

Stop

UGA

Stop

A

UUG

UCG

UAG

UGG

Trp

G

C

CUU

Leu

CCU

Pro

CAU

His

CGU

Arg

U

CUC

CCC

CAC

CGC

C

CUA

Leu

CCA

Pro

CAA

Gln

CGA

Arg

A

CUG

CCG

CAG

CGG

G

A

AUU

Ile

ACU

Thr

AAU

Asn

AGU

Ser

U

AUC

ACC

AAC

AGC

C

AUA

Ile

ACA

Thr

AAA

Lys

AGA

Arg

A

AUG

Met

ACG

AAG

AGG

G

G

GUU

Val

GCU

Ala

GAU

Asp

GGU

Gly

U

GUC

GCC

GAC

GGC

C

GUA

Val

GCA

Ala

GAA

Glu

GGA

Gly

A

GUG

GCG

GAG

GGG

G

*** Note that this table represents bases in mRNA.  There are some tables that may only show the DNA code

There are several interesting points from this triplet code:

 

DNA and Protein Synthesis  [back to top]

Transcription - RNA Synthesis

DNA never leaves the nucleus, but proteins are synthesised in the cytoplasm, so a copy of each gene is made to carry the “message” from the nucleus to the cytoplasm. This copy is mRNA, and the process of copying is called transcription.

Translation - Protein Synthesis [back to top]

 1.  A ribosome attaches to the mRNA at an initiation codon (AUG). The ribosome encloses two codons.

 

2.  met-tRNA diffuses to the ribosome and attaches to the mRNA initiation codon by complementary base pairing.

 

3.  The next amino acid-tRNA attaches to the adjacent mRNA codon (leu in this case).

 

4.  The bond between the amino acid and the tRNA is cut and a peptide bond is formed between the two amino acids.

 

5.  The ribosome moves along one codon so that a new amino acid-tRNA can attach. The free tRNA molecule leaves to collect another amino acid. The cycle repeats from step 3.

6.  The polypeptide chain elongates one amino acid at a time, and peels away from the ribosome, folding up into a protein as it goes. This continues for hundreds of amino acids until a stop codon is reached, when the ribosome falls apart, releasing the finished protein.

 A single piece of mRNA can be translated by many ribosomes simultaneously, so many protein molecules can be made from one mRNA molecule. A group of ribosomes all attached to one piece of mRNA is called a polysome.

 Post-Translational Modification   [back to top]

In eukaryotes, proteins often need to be altered before they become fully functional. Modifications are carried out by other enzymes and include: chain cutting, adding methyl or phosphate groups to amino acids, or adding sugars (to make glycoproteins) or lipids (to make lipoporteins).  

 


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Last updated 20/06/2004