GENETICS, continued...

A bit of review:

We covered, at the end of last lecture, a DIHYBRID CROSS.
  What does this mean?

Another principle to emerge from  this cross:
   INDEPENDENT ASSORTMENT.
The factors, or elements, or genes as we now call them, for different traits act independently of each other
    during formation of gametes.
 E.g., genes for seed shape and flower color assort independently, as if they’re separate entitities that aren’t
    connected to each other, or linked.
 That’s evident in a DIHYBRID CROSS.   (Fig. 13.12).
Notice that the genes for each trait segregate, and recombine, independently of each other.
   INDEPENDENT ASSORTMENT.
Again, this behavior was only made sense when we realized that  chromosomes behave the same way.

Back down to earth.....
 These rules are relatively simplistic.
  Most traits aren’t governed this way. They’re more complex.
   E.g. they’re determined by more than one set of genes.
  Many traits aren’t ‘all or none’, but quantitative.
   Show a range or distribution in phenotype . E.g. fruit size, number of kernels on a corn cob.
    Such traits are determined by QUANTITATIVE TRAIT LOCI, OR QTLs.

  Some traits show incomplete dominance - e.g. flower color in some species.  - Red, white and pink.
 
ALSO, Genes for different traits are often LINKED, on the same chromosome. This changes expected frequencies.

Many traits are not determined by just one gene, but by several or many. They're polygenic.
    E.g., a pigment make require the action of several enzymes in sequence, each encoded by a separate gene.

Also remember, CROSSING OVER, occurs during meiosis.
 So, you do get some reassortment or traits. In other words, predicted percentages of genotypes in offspring
    may be off.
  More crossing over with greater distance between genes.
   If at opposite ends of chromosome, genes on same chromosome can behave as if they aren't; i.e. unlinked.

Finally....
  Transposable elements, or jumping genes. What are they and what do they do?
        Who discovered transposable elements?

THE STRUCTURE OF GENES

Reminder:
We’ve talked about nucleic acids and proteins.
 Proteins, in the form of enzymes, govern nearly all metabolic chemistry inside cells.
    Proteins make us what we are.
 Genes, in the form of DNA, encode the amino acid sequence of polypeptides, which in turn determines how
    they fold, and therefore their enzymatic properties.

 Genes therefore determine the hereditary characteristics of organisms.
  The laws of heredity are based on the behavior of genes.

DNA consists of two very long chains of deoxyribonucleotides.
   (Fig. 13.2).

The two chains wind around each other, helically.
     Like a spiral staircase.

The backbone of each chain consists of linked deoxyribose sugars and phosphates. The phosphate groups link
    adjacent sugars via their 5 and 3 carbons.
 Each strand has a 5’ and a 3’ end.
  At the 5’ end, a phosphate is attached to the terminal sugar.
  At the 3’ end, terminal sugar has a free hydroxyl.
The anti-parallel nature of the two strands means they have opposite polarity.

Each nucleotide contains a nitrogenous base: A,G,T,C.

The double helical nature of DNA is based on the fact that bases facing each other from each strand interact in a
    very specific way determined by the nature of the rings on the bases.
  Remember: A always bonds with T; G with C.  I.e., A=T, G=C, no matter the gene or the organism.
            Whose name is associated with this discovery????

 Without this insight, the structure of DNA would not have been solved.

Thus, the two strands are said to be COMPLEMENTARY as well as ANTIPARALLEL.
  This complementarity is based on HYDROGEN BONDS BETWEEN BASES.
    These are weak bonds between H's and adjacent O's or N's.
   H-bonded bases form the rungs of a ladder.  (Fig. 13.3)

Again, the two strands on a DNA helix are ANTI-PARALLEL.

Implicit in the structure of DNA is a mechanism to make exact copies.

DNA REPLICATION:

If you can unzip the double helix, all you need to do is align new nucleotides with  complementary bases, and
        polymerize them.
You would then have two new identical double helices, each with one old  chain from the parent helix, and one
        new chain formed from nucleotide subunits.
And that’s basically how the cell does it. Of course, the process requires enzymes and controlling proteins.

The process is governed by several enzymes, including DNA POLYMERASE.

During S phase of cell cycle, numerous ‘replication bubbles’ open up along each DNA strand on each
    chromosome. DNA is then replicated in both directions, simultaneously in each bubble, till all the bubbles
        merge. (Fig. 13.4)

GENE EXPRESSION

The process in which the information in genes is converted into the synthesis of proteins.

Now, what about the language of DNA?  What are these ‘elements’ that Mendel discovered?

 Remember, the language of cell metabolism is protein.

The language of proteins is written in a 20 letter alphabet in the form of amino acids.

But DNA is written in how many letters?
So, there is a disjunct. How to translate the DNA alphabet into the alphabet of proteins.
The problem is analogous to a code. What is the genetic code?

It turns out that in the early 1960s, this was perhaps the overriding question in  molecular biology: what sequence
    of DNA bases corresponded to amino acids?

The genetic code is written in triplets of bases, called CODONS.
  64 possible words, but 20 amino acids.
 Turns out that many amino acids are designated by multiple triplets.
  The code is redundant.
  Still, some left over as special signals -- stop codons.
   Mark the end of genes.

So, genes basically consist of a linear order of codons, or triplets, along the DNA .

[Mutations consist of deletions, insertions, substitutions of nucleotides.
 Could be just one nucleotide, or entire gene, or many genes if part of  a chromosome is missing or altered.]

But how is this information in DNA converted into a sequence of amino acids?

Remember, DNA is the master set of genetic instructions.
 It’s housed in the nucleus (but remember, mitochondria and chloroplasts also have genetic information).

Soooooooo, we need to keep certain ideas in mind:
1. We want to use the instructions to make polypeptides (proteins) with a specific sequence of amino acids.
2. The cell makes lots of proteins simultaneously. In other words, lots of genes are being EXPRESSED at the same time.
3. But, not all genes are expressed at the same time and place in an organism. Some yes, but many others no.
4. Proteins are made in the cytoplasm, not the nucleus.
5. It’s advantageous to protect the master set of instructions. Don’t want to chop it up, for example.
6. There’s lots of RNA in the cytoplasm.

The solution is to make a working copy of the instructions, in the form of RNA.  THINK XEROX MACHINE.

     (remember the differences between DNA and RNA?)