Transcription and Translation:  Processing and Translation

Compartmentalization allows for RNA processing before translation.

In RNA processing both ends of mRNA are altered through cutting and splicing (sometimes).

Alterations:

The 5' end is capped off with a modified guanine nucleotide.  This 5' cap protects the mRNA from hydrolytic enzymes and is an "attach here" sign for small ribosomal subunits.  To the 3' end a poly-A tail is added; this helps inhibit degradation and facilitates the export of mRNA from the nucleus to cytoplasm.

Splicing (cut and paste)

Intervening sequences are called introns.  Pre-mRNA is called heterogeneous nuclear RNA (hnRNA).  Small nuclear ribonuclear proteins are snRNPs (its RNA = snRNA).  A spliceosome is several snRNPs that cut out introns and join the exons together to form a consistent mRNA chain.

A Ribozyme is an RNA molecule that functions as a catalyst (self-splicing).

Different cells in same organism make different proteins from a common gene.  Introns facilitate recombination of exons between alleles because of the extra spacing...the probability of crossing-over increases.

Domains

These are the structural and functional components that make protein architecture.  An example might be the active site of an enzyme.  Exon segments in a gene containing introns and exons might code for different domains of a protein.

Translation

It is interpreted by transfer RNA (tRNA).  tRNA transfers amino acids from cytoplasm to ribosome.

An Anticodon is the tRNA complement of the codons on mRNA.  It binds to mRNA codons.

The tRNA structure is 80 nucleotides long.  When expressed 2-dimensionally it looks like a clover.  When expressed 3-dimensionally it has a L-shape to it.  Its function is to attach the amino acid at the 3' end.  A uracil tRNA anticodon can pair with either adenine or guanine in the 3rd position.  This is called a wobble; however, the most versatile component of tRNA is inosine - an adenine altered after tRNA synthesis.  Inosine can bond with uracil, cytosine, or adenine; thus CCI can bond to GGU, GGC, and GGA (all three code for the amino acid glycine).

Aminoacyl-tRNA synthesis (tRNA with the amino acid attached)

There is one synthetase for each amino acid.

1. active site bonds to ATP and amino acid

2. ATP loses 2 phosphates and binds to amino acid forming AMP (adenine monophosphate)

3. corresponding tRNA covalently bonds to amino acid

4. AMP displaced from active site

5. enzyme releases aminoacyl-tRNA (activated tRNA)

Ribosomes

These are subunits (large and small) join only when they attach to mRNA.  Ribosomes are aggregates of proteins and rRNA (60% of a ribosome's weight is this most abundant type of RNA).  Prokaryotes have smaller ribosomes than eukaryotes with different compositions that allow antibiotics like tetracycline and streptomycin to paralyze them without harming eukaryotic RNA.  The P site is the peptidyl binding site; the A site is the aminoacyl binding site.

Key stages in translation (NOTE:  energy comes from GTP)
          1.  initiation
          2.  elongation
          3.  termination

Steps to Peptide Formation

1. Methionine-tRNA + initiation codon (AUG) then large ribosome unit attaches

2. a) initiation codon (AUG) + initiation tRNA (Methionine or Met) uses hydolysis of GTP to power
   b) large ribosome catalyzes peptide bond between polypeptide extending from P site and the new one just arriving in A site
   c) tRNA at P site is released; A site tRNA goes to P site; another tRNA fills in the A site in the 5' - 3' direction
   d) this translocation takes 60 milliseconds using GTP

3. UAA, UAG, UGA are the stopping codons
   a protein called a release factor binds to the termination codon in the A site causing the ribosome to bond HOH instead of amino acid to the polypeptide chain, causing the hydrolysis of the polypeptide from the tRNA in the P site

Polyribosomes are series of ribosomes.  When one moves from initiation codon and another ribosome binds to the initiation codon....

Polypeptide to Protein

Post-translational modifications:
     polypeptides are attached to sugars, lipids, phosphate groups or others.
     enzymes remove one or more amino acids from the leading (amino) end.
     enzymes may cleave polypeptide into 2 or more parts.

Polypeptidyl singal sequences (function: dispatch proteins to their target)

The growing polypeptide chain cues the ribosome to be bound or free.  Secretory proteins are marked by signal sequence of about 20 amino acids that is recognized by signal-recognition particles.  Signal-recognition particles are adapters, binding ribosome to receptor protein on endoplasmic reticulum membrane.  Here synthesis continues and peptide chain moves into cisternal space.

Question:  if mRNA molecule lacks a segment that programs synthesis of ER signal sequence what would happen?

Next:  "Mutations and other problems."