BIOCHEMISTRY III -PLANTS

Advanced Plant Biochemistry Course

Metabolism encompasses chemical processes that produce specific products within an organism. Metabolism within an animal or plant is complex, involving many different chemical reactions; each having an effect upon others. Despite the complexity of living metabolism, organisms maintain relative stability.

There are two main types of pathways in metabolism:

• Catabolism    Pathways that result in the degradation of biochemical substances.
• Anabolism    Pathways that result in the synthesis or building up of more complex compounds from simpler biochemical substances.

There are four key characteristics common to metabolic pathways:

1. Metabolic pathways are irreversible.
2. Each metabolic pathway has a first committed step.
3. All metabolic pathways are regulated.
4. Metabolic pathways in eukaryotic cells occur in specific cellular locations.

Types of plant reproduction

1. Sexual reproduction is the process where an organism creates offspring with a combination of gametes.  There are two types: allogamy is outbreeding or autogamy is inbreeding.

Allogamy is also known as cross-fertilisation and can occur in flowering and some spore producing plants.  Allogamy guarantees genetic variability.  In plants there are two different forms of allogamy.  Dioecism is where male and female gametes develop on different individuals while monoecious the male and female gametes are developed either on different parts of the same plant or at different times.

Autogamy is usually on one of two or more other propagative mechanisms.  It rarely occurs on its own. Usually there is at least a small degree of allogamy occurring within the species to ensure some gene flow between species.  Some species are considered to have optional autogamy.  This is where both allogamy and autogamy are common.

2. Vegetative, asexual reproduction occurs when a plant creates an identical copy of itself.  This copy is genetically identical to itself.  That is there is no combination of gametes during reproduction.  Asexual reproduction can include budding, pathogenesis, fragmentation and spore formation involving only mitosis.  In plant asexual reproduction nearly all the parts of a plant have been used for reproduction.  This includes the stem, underground stem, leaves and roots.   There are two main types in plants.   Common examples include potatoes, strawberry runners, many plants can be grown from a cutting, and grasses can be grown by division of a crown.

Apomixis is where a seed is produced without a male and female gamete. Essentially a female gamete is formed and then develops into a seed.  Agamospermy is apomixis in flowering plants

Gene Expression

1.  Chromosome structure
2.  Genome organisation.
3.  Cell Differentiation

Transcription
Transcription is the process by which RNA is formed from a DNA template strand in both prokaryotic and eukaryotic cells.  

 An important difference between RNA and DNA is the replacement of T (thymine) with U (Uracil) in RNA, which can also form a H bond with (A) adenine.  Additionally RNA is also a single strand of ribonucleotides instead of DNA’s two strands and RNA polymerase is able to create RNA without an existing strand. 

There are three types of RNA which are used in protein synthesis.  During transcription specific RNA polymerases use a template strand of DNA to create of the three.  They are:

1. Messenger RNA (mRNA) copies the information in the DNA by base pairing and takes the message to where the proteins are assembled;
2. Transfer RNA (tRNA) picks up and transfers the amino acids by means of covalent attachments, to the ribosomes and inserts the correct amino acid into the right place according to the mRNA;
3. Ribosomal RNA (rRNA) this and ribosomal proteins form ribosomal subunits. The rRNA engages with the mRNA to form a catalytic area into which the tRNAs can enter with the attached amino acids.

Prior to initiation of the transcription, the RNA polymerase requires a promoter sequence in the DNA.  The promoter sequence is an area of DNA which is found upstream of where the transcription will start, which in itself is a specific site.

1. Initiation in eukaryotic cells is complex.  RNA polymerase requires transcription factors to help it to bind and start the initiation of transcription. When this occurs the RNA polymerase clears the promoter.  This can fail frequently in which case the promoter is held onto until transcript is formed successfully in which case the promoter is released.

2. Elongation proceeds with RNA polymerase traversing the DNA template strand.  The RNA copy is produced using base pairing (the ability of nucleotide bases to pair with other nucleotide bases, in DNA A-T, C-G, in RNA, A-U, C-G).

3. Two types of termination have been observed. Termination of RNA transcription can stop when the new transcript reaches a G-C rich hairpin followed by several U’s.  Alternatively other terminations seem to require a protein known as Rho factor.

Translation
Translation the process by which mRNA is decoded to form polypeptides.  This is an extremely complicated process in which 20 different amino-acid residues are linked in accurate order specified by mRNA.  The mRNA is used as a template to produce an amino acid chains used to form proteins.

Basically the mRNA’s genetic information is coded as a sequence of ribonucleotides.  Translational machinery ‘reads’ the sequence of nucleotide triplets called codons.  Each of these codes for a specific amino acid.  

The translation is done by the ribosome and tRNA.  The ribosome is a multi-subunit (large and small subunit) that contains proteins and rRNA, essentially it is the factory.   The process starts off with the small subunit binds to the RNA and moves until it encounters the start codon (AUG).  There a large subunit and an initiator tRNA.  The initiator tRNA binds to the P site on the ribosome. 

 tRNA transports amino acids to the ribosome.  tRNA has a site called an anticodon.  This is a complementary triplet to the mRNA triplet.  An enzyme catalyses the bond between tRNA and the amino acid that fits the tRNA’s anticodon.  This reaction produces a molecule of aminoacyl-tRNA.  This molecule travels into the ribosome and binds to the A site. In the ribosome it is able to base pair with the next codon on the mRNA.  The amino acid is linked to the preceding amino acid with a peptide bond. The initiator tRNA is then released from the P site allowing the ribosome to more one codon down and shifting the new tRNA to the P site and opening up the A site for new aminoacyl-tRNA.  The process stops when the ribosome reaches the STOP codons (UAA, UAG, UGA).

Eukaryotic DNA Replication
A double strand of DNA replicates by unwinding and separation of its parental strands (this is referred to as a replication fork), while production of a complementary strand produces two identical DNA strands. This process is recognised as a semi-conservative model.    This means that each copy contains one of the original strands and one new strand.  DNA has one replication origin point where DNA replication starts. It is believed that the complexity involved in DNA replication is necessary to maintain the strict accuracy required for maintenance of the genomic integrity.
  
During the S phase, DNA is synthesised.  As mentioned above the DNA double helix is separated by DNA helicases.  This unwinds the DNA forming a replication fork. Bound to each of them are helix destabilising proteins to prevent rejoining of the parent strands. As these parent strands are unwound complementary strands are produced by hydrogen bonding of free DNA nucleotides. DNA polymerase joins up the nucleotides using phosphodiester bonds.  Each parent strand then serves as a template for a copy of itself resulting in two identical DNA molecules.  The DNA may attach to the cytoplasmic membrane and are physically separated as the cell elongates before mitosis.

DNA Polymerases
DNA polymerase is an enzyme whose function is to carry out all forms of DNA replication.  It does not begin the replication, this must be done by a primer, but it does extend the existing DNA strand.  The primer adds several RNA nucleotides opposite the DNA nucleotides on the parent strand.  This creates an RNA primer.  DNA polymerase III (one of 5) then replaces the primer and eventually replaces the RNA nucleotides with proper DNA nucleotides

Leading and Lagging Strands
The leading strand is the newly made strand that is forming towards the replication fork.  It is forming in the direction of 5’ to 3’ as the fork advances.  The other strand is known as the lagging strand.  It to is synthesised in a 5’ to 3’ direction, but is done so in segments known as Okazaki fragments.  These are joined covalently sometime after their production in a reaction catalysed by DNA ligase.  This is referred to as semi-discontinuous replication. 

Because DNA is very long, the replication process can occur at several different places simultaneously, eventually joined together to make a complete chain.  It is also worth noting how extremely accurate the process is. Generally DNA is copied with less than one mistake per billion nucleotides.