Sunday, 1 May 2011

Biology - Genetic Definitions

Chromosomes

Are paired structures that are made up of strands of chromatin which contains DNA and proteins. In humans, there are 46 chromosomes (23 pairs) in the cell nucleus of regular cells of the body – called somatic cells – as opposed to the gametes (sperm and egg cells), which contain only 23 unpaired chromosomes. A chromosome has a short arm and a long arm, which are held together by a centromere.

DNA – deoxyribonucleic acid

Is the chemical molecule that serves as genetic material. A strand of DNA is a long chain (a polymer) of nucleotides. Each nucleotide of DNA contains a nitrogenous base, a sugar with five carbon molecules called deoxyribose, and a phosphate group. There are four kinds of nitrogenous bases in DNA; adenine (A), thymine (T), cytosine (C) and guanine (G). The nitrogenous bases (nucleotides) can be and are different throughout the long chain of DNA. DNA exists inside the chromosomes.

Genes

Lie along the chain of DNA. They are made up of sections of nucleotides. Some genes can have many nucleotides; others have only a few. Humans have thousands of different genes, which reside on different chromosomes, but on the same chromosomes in all people. For example the gene for cystic fibrosis (CF) is always found in the same location on gene number 7 in all humans. However, not all humans have CF (or any other genetic disorder). Some genes show the effect (they are expressed), whereas other genes do not show an effect (they are repressed).

Alleles

Are the different forms of a trait. They are alternative forms of a gene or base pair sequence that occur on a chromosome. For example, the gene for hair colour resides in a certain location on a certain gene in all humans. However, humans can have many different shades of hair colour; the different shades are represented by different alleles.

Mendel’s Law

Gregor Mendel was a monk in Austria in the mid 19th century. To pass his quiet time, he watched pea plants grow. As he observed subsequent generations of pea plants growing, he noticed subtle changes and wondered how they occurred. He observed the colour of seeds, flowers, and unripe pods; the shape of the seeds and pods, the length of the stem, and the positions of the flowers. Most importantly, he kept accurate records and an accurate account of what plants showed what traits.

During Mendel’s time, the general thought was that the traits of a father blended with the traits of a mother. So a tall father and a short mother were expected to breed average-sized children. Traits in offspring were expected to be averages of the traits in the parents.

One day Mendel crossed a tall pea plant with a short pea plant, expecting to get average-sized pea plants. However, three tall pea plants and one short pea plant grew. He continued to cross tall with short over and over again, the results were similar every time. What he discovered was that offspring carry all the traits of the parents but each offspring is capable of expressing different ones. He figured that these traits were passed from generation to generation by something that he called factors. What Mendel called factors we now call genes.

After studying 28,000 or so pea plants and reviewing his data, Mendel was fairly confident in his research, to be able to state that heredity followed specific patterns. First, he stated that traits are inherited independently of each other – this is Mendel’s Law of Independent Assortment. This law states that each trait or characteristic is found on separate factors (genes), that each factor (or gene) comes in pairs, and that each pair separates on its own.

Mendel also came up with the Law of segregation, which states that during cell division, each allele of a gene pair will randomly move to different gametes. On one of the number 2 chromosomes you have two H alleles; on the other number 2 chromosome you have two h alleles. You have four alleles for hair colour (H, H and h, h) at the locations of the genes for hair colour. When an egg or sperm cell are produced only half of your genetic material goes into each gamete. So, you produce two gametes containing H alleles and two alleles containing h alleles. But each of those alleles separated randomly into the four gametes.

There a multiple genes and alleles for hair colour. Two of the genes may be next to each other, at a particular position on the chromosome, and they will not separate randomly. Their alleles on their paired chromosome will separate randomly though.

Genetic Crosses

When a geneticist writes a genetic equation, the alleles are represented by letters. The dominant traits are usually capitalized and the recessive traits are usually lowercase. Writing the letters that represent the alleles of a gene is called a genotype. A genotype can be written to represent a phenotype, which is the physical result of the expression of a gene.

Phenotypes are created by crosses between different organisms. For example, if you cross a red rose bush with a white rose bush, you would get a rose bush with red or maybe even pink roses. If you were crossing the rose bushes explicitly to see the result of flower colour, you would be performing a monohybrid cross, which cross examines just one trait. Therefore, the phenotype for the first bush is ‘red flowers’ and so the genotype would be RR. The phenotype for the second bush is ‘white flowers’ and so the genotype would be rr.

Copying your DNA

Your DNA does not copy (replicate) itself – only when you create gametes and mate. Every cell in your body needs to be replaced periodically. Cells never stop working and eventually wear out. Cell turnover, as it is called, happens constantly, on any day your body can be replacing some blood cells, skin cells, hair cells and mucous cells (just to name a few types of cell!). Whatever needs to be replaced, the process of DNA replication is the same.

DNA looks like a twisted ladder, with the nucleotide bases forming the ‘rungs’ of the ladder. During replication the DNA strand must ‘unzip’ so that the rungs are split apart with one nucleotide one each side of the strand. Each side of the original DNA strand becomes a template strand upon which the new complementary strand forms. The ‘unzipping’ of the DNA helix is initiated by the enzyme known as helicase.

The entire DNA strand does not unzip all at one time. Only part of the original DNA strand opens up at one time. When the top of the helix is opened, the original DNA strand looks like a Y. This partly open/partly closed area where replication is going on is called the replication fork.

The nitrogen bases that make up each nucleotide along the strand of DNA include adenine (A), guanine (G), cytosine (C) and thymine (T). In a molecule of DNA, A always pairs with T and C always pairs with G: A – T, C – G.

As the enzyme DNA polymerase moves along the template strand, of a base says A then a T is added to the growing complementary strand. If a base on the template strand says G then a C is added to the growing complementary strand.

The order of the bases is important because the order of bases delineate the genes, and the genes dictate what amino acids are produced, and the amino acids determine which proteins are produced, and proteins are needed in every cell of your body. Proteins make up cell structures themselves, as well as enzymes that initiate cellular processes that keep you alive.

The DNA polymer works continuously on the side known as the leading strand. The other side looks messy because the process does not occur smoothly. On the lagging strand, the DNA polymerase reads the template strand and assembles the new bases in fragments. These fragments are called Okazaki fragments, and they are then joined together by the enzyme DNA ligase to form the new complementary strand.

The replicating DNA strand needs energy to go through the steps of reading the template, producing the complementary base, and joining the base to the growing strand. The molecules of the sugar deoxyribose provide that energy. The phosphate bonds that are broken apart when the original strand of DNA ‘unzips’ provides the chemical energy needed to get the whole process started.

DNA Mistakes

Believe it or not, the newly created DNA strand in cells are proofread before cell division is finalized. If a mistake is detected, it’s back to the template strand. The nucleotide that as inserted in error is removed, and the correct one is put in place. If the proofreading function goes awry, mismatch repair enzymes are available to shore things up. Error recognition and repair mechanisms exist in organisms with eukaryotic cells, the details of how they function are not as well understood.

If a mistake in a new strand of DNA goes undetected or unpaired, the mistake becomes a mutation. A mutation is a deviation from the original DNA strand. The nucleotides are not in the same sequence. Although mutations can and do cause serious defects, not all mutations are bad.

The following list explains how mutations, which are usually caused by certain chemicals or radiation affect humans:

Substitutions

These types of mutations occur when the wrong nucleotide is put in for another nucleotide, for example, if the code for a particular gene read 5’ –A-T-C-G-T-C-A-G-3’, the correct complementary sequence for the code on the new strand of DNA would be 3’ –T-A-G-C-A-G-T-C- 5’.

Genetic code is written in a specific direction, because DNA is a double helix in which two strands intertwine, confusion can easily be created when trying to keep track of the ends of the strands. To avoid confusion, one strand of DNA is labelled 3’ (3 prime) and the other 5’ (5 prime), the strand should be read in the 5’ to 3’ direction.

In the example above, the third base over should be guanine (G) instead of cytosine (C). That base could have been passed over during the ‘reading’ of the strand of DNA, or a new cytosine base could have been put in instead of the guanine base. In either case it is wrong, so it is classed as a mutation. Because the mistake involves only one base it is known as a point mutation. There is a chance that the protein that the gene creates would not be affected by this mutation and is, therefore, called a silent mutation.

Deletions

If during the creation of a new strand of complementary DNA, a nucleotide is read but the complementary base is not inserted, the complementary strand is missing a nucleotide, this type of mutation is called a deletion. These mutations can cause serious diseases.

Insertions

If an extra nucleotide is slipped into a newly developing complementary strand, the rest of the strand is read wrong. This type of mutation is called a frameshift mutation because the reading of the frames of genetic code is shifted.

Producing Proteins

Ribonucleic acid (RNA) is very similar to DNA, except for these differences:

RNA is single stranded

It contains the sugar ribose instead of deoxyribose

It uses uracil (U) as a nitrogenous base instead of thymine (T)

The nucleotides in RNA pair up as: A – U and C – G. RNA bases can pair up, even though the RNA molecule is single-stranded, this is because RNA has a secondary structure and can fold up and base pair with itself where complementary. RNA molecules are important for the production of proteins, and, just after DNA has been replicated, the complementary strands produce proteins.

DNA harbours the genes that code for what proteins will be produced in your body. But the code buried in segments of DNA is not what initiates protein production. Firstly, the DNA must be ‘rewritten’ into a strand of RNA, and the mRNA carries the information out of the cell’s nucleus to the ribosomes. At a ribosome, the original message is translated, and then the appropriate protein can be produced. Protein synthesis is initiated on the ribosomes that exist free in the cytoplasm. The ribosomes that are attached to the ER to make proteins to be secreted or transported to other organelles.