The relationship between genes and proteins

All living things carry out countless chemical reactions and that these reactions are catalysed (accelerated) by proteins called enzymes. Many of these reactions take place in sequence, so that one chemical product becomes the substrate (starting material) for the next reaction. These sequences of reactions are called pathways, and the substrates within a pathway are called intermediates.
Mutagens are used to introduce mutations into genes and then observe the effects of these mutations on biochemical pathways.
Most genes contain the information for making one polypeptide. Genes do more than one thing:

  • first, they are replicated faithfully;
  • second, they direct the production of RNAs and proteins;
  • third; they accumulate mutations and so allow evaluations.
Experiments that establish relationships between genes, proteins, cells and functions.

Experiments that establish relationships between genes, proteins, cells and functions.

http://www.bx.psu.edu/~ross/workmg/TxnRNAPolCh10_files/image002.png

Pathway for Gene Expression

From DNA to Protein

From DNA to Protein

Genetic Recombination and Mapping

Genes on separate chromosomes behave independently in genetic experiments whereas genes on the same chromosomes behave as though they are linked. However, genes on the same chromosome usually do not show perfect genetic linkage. The offspring that have a new combination of alleles that are not seen in the parents are called recombinants.

Recombinants are produced due to crossover between homologous chromosomes (i.e. carrying some alleles of the same genes) during meiosis (gamete formation). Recombination is the process that brings together a new combination of alleles. Genetic mapping (or genetic linkage) is the tendency of alleles that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction.

Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be genetically linked (the nearer two genes are to one chromosome, the lower is the chance of a swap occurring between them and the more likely they are to be inherited together). If two loci recombine with a frequency of 1%, they are said to be one centimorgan apart. These rules apply both to eukaryotes (organisms whose genetic material is confined to a nuclear compartment) and to prokaryotes (organisms whose genetic material is not confined to a nuclear compartment).

The cell nucleus has a mixture of compounds called nucleins. The major component of nuclein is deoxyribonucleic acid (DNA), with a related compound called ribonucleic acid (RNA). Both DNA and RNA are long polymers – chains of small compounds called nucleotides. Each nucleotide is composed of a sugar, a phosphate group and a base. The chain is formed by linking the sugars to one another through their phosphate groups.

Protein is made of chain composed of links called amino acids. The amino acids in proteins are joined by peptide bonds, so a single protein chain is called a polypeptide.

Example of Genetic Linkage

Genetic Linkage

Cellular Structure

schematic of plant and animal cell structures

Schematic of plant and animal cell structures

  1. The nucleus is a discrete structure within the cell that contains genetic material, DNA.
  2. DNA is usually present in a cell as a network of fibers, called chromatin.
  3. During mitosis, DNA molecules form the condensed chromosome structure by coiling and supercoiling around specialized proteins.
  4. The centrosome is a structure composed largely of microtubles. Paired centrosomes organise the formation of spindle fibers during mitosis.
  5. The endoplasmic reticulum (ER) is a network of membranes throughout the cell; cells have both smooth and rough ER.
    1. The rough ER is studded with ribosomes, giving it a rough appearance.
    2. The bound ribosomes of the ER synthesize proteins destined for secretion from the cell or that are to be incorporated into the membrane or into specific vacuoles.
    3. The smooth ER synthesizes lipids, phospholipids and steroids. It also carries out the metabolism of carbohydrates, detoxification of natural metabolism products and of alcohol and drugs, steroid metabolism and attachment of receptors on cell membrane proteins.
  6. The Golgi apparatus is a continuation of the membrane network of the ER. The Golgi apparatus is part of the endomembrane system. It packages proteins into membrane-bound vesicles inside the cell before the vesicles are sent to their destination. It is of importance in the processing of proteins for secretion, containing a set of glycosylation enzymes that attach various sugar monomers to proteins or they transfer through the apparatus.
  7. Ribosomes that are free in the cytosal synthesize proteins that remain in the cell and are not transported through the endoplasmic reticulum and Golgi apparatus.
  8. The mitochondrion is the site of energy production in the cell. It consists of a double membrane system. The outer membrane is smooth and the inner membrane has convoluted folds. It can divide independently of the cell and contains its own double standard DNA.

 

Chromosome Theory of Inheritance

The notion that chromosomes carry genes is the Chromosome Theory of Inheritance. Genes are observable objects in the cell nucleus.

 

The Phenotype is an observable characteristic of an organism. Most chromosomes, called autosomes, occur in pairs in a given individual. The X chromosome is an example of a sex chromosome.

 

Each gene has its place on a chromosome, called the locus.

 

Diploid organisms (such as human beings) have two copies of all chromosomes (with the exception of sex chromosomes). Thus they have two copies of most genes. The two copies can either be the same alleles, in which case the organism is homozygous, or different alleles, in which case the organism is heterozygous.

 

The genotype is the allelic constitution of the organism.

 

The wild-type genotype is the most common (generally accepted standard) phenotype of an organism. This is sometimes called the standard type. Mutant alleles are generally recessive, though not always.

 

Diagram of Chromosome Theory of Inheritance

Chromosome Theory of Inheritance

DNA Structure

DNA is a complex, double-stranded polysaccharide composed of a backbone containing phosphate groups bonded to deoxyribose sugar.

Two phosphate groups are covalently bonded to each ring-shaped sugar. One is linked to the third carbon (3′) and the other to the fifth carbon (5′), forming what is called a 3′-5′ glycosidic bond. This confers directionality to each nucleoside. The physical torsion on the molecule due to this structure causes DNA to twist and form a double helix.

DNA Structure

DNA Structure

Solving Modified Fibonacci Challenge

The challenge involves solving a modified version of the Fibonacci series, as explained on the project page: https://www.hackerrank.com/challenges/fibonacci-modified

My submission was as follows:

Use BigIntegers, number can grow really quickly!

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