# Structural Biochemistry/Genetic Bases

Genetics is a subdivision of biology which focuses its study on heredity as well as the mutations and variations that exist in living organisms. Genetics attempts to describe these variations through study of the molecules involved in the processes of transcription, translation, gene expression, and hereditary patterns. The most prominent molecular structures studied are DNA, RNA, and the numerous helper proteins involved in nearly every process including genetics.
Biochemical structure and function is necessary for understanding the workings of genetic molecules.

## Structure of DNA

There are a total of four different deoxyribonucleotdies: deoxyguanylate (G), deoxyadenylate (A), deoxycytidylate (C), and deoxythymidylate (T). The three groups that compose a nucleotide are a nitrogenous base (2 carbon-ringed purines for A & G or 1 carbon-ringed pyrimidines for C & T), a pentose (5-carbon sugar), and a phosphate group. In double stranded DNA, deoxyadenylate (A) and deoxythymidylate (T) are found complementary to each other, forming two hydrogen bonds, and deoxyguanylate (G) is paired with deoxycytidylate (C) forming three hydrogen bonds.
DNA molecules are made up of two complementary strands, which are linear polymers of the four different nucleotide bases mentioned above. The two strands are held together by hydrogen bonding between the base pairs, forming a double helix with the sugar-phosphate group on the outside and the bases on the inside. This 3D structural arrangement of the DNA molecule, proposed by James Watson and Francis Crick in 1953, is crucial to its role as the storage of hereditary information in two ways. Since the base pairs take about the same shape, they are able to fit very well into the double helix structure regardless of their sequence. This lack of constraint allows the sequence of bases within a DNA strand to be an efficient method of information storage. Furthermore, the base-pairing enables each DNA strand to act as a template for its counterpart strand, allowing the stored information to be passed on an duplicated.
It's important to note that the hydrogen bonds between the base pairs are weaker than the covalent bonds found within the bases themselves. This feature of DNA enables the bonds between the base pairs to be reversibly broken, which is necessary for biochemical processes, such as transcription of DNA to mRNA in protein synthesis. Nevertheless, the hydrogen bonds are strong enough to allow for the stable formation of the double helix structure.

## DNA, RNA, and their differences

Deoxyribonucleic acids combine to form a double-stranded macromolecule of deoxyribonucleotides that stores genetic information encoded through the specific patterning of nitrogenous base pairings. The double-stranded structure of DNA is well preserved unlike RNA which may take many forms. This is because DNA nucleotides possess a negatively charged phosphate group which creates electrostatic repulsion between other negatively-charged phosphate groups in the structure.
RNA also contains the same negatively charged phosphate groups, yet the single-stranded nature of RNA allows it to hydrogen bond with itself via base pair bonding, with the repelling phosphate groups pointed away from each other. This allows for diverse structures of RNA that achieve different functions based on the specific structure, similar to proteins.
The information contained in DNA is used in the production of proteins. The genetic code in DNA can be transcribed into RNA which can then be translated into proteins. The main difference between DNA and RNA is that RNA has the nitrogenous base Uracil (U) and the sugar ribose whereas DNA has the nitrogenous base thymine (T) and the sugar deoxyribose. However, it is important to note that while DNA is usually double stranded, there are exceptions to this rule. Likewise, RNA can at times be double stranded. Another interesting contrast between DNA and RNA is that while DNA is normally coiled linearly into neatly arranged chromosomes that are contained within the nucleus, RNA is drifts freely through the cytoplasm in an unorganized manner.

## Evolution of mitochondria and chloroplasts

Eukaryotes evolved from prokaryotes. This occurred when an aerobic bacteria infected the cell of an anaerobic eukaryote to become what we now know as the mitochondrion. Mitochondria have a double cell membrane and contain its own DNA. This suggests that the evolution of mitochondria stems from the idea that the combination or ingestion of two bacterial sources created the mitochondria. A similar evolutionary path has been theorized for the creation of chloroplasts. Chloroplasts are similar to mitochondria in that it also has a double membrane and its own DNA. However it originated from cyanobacteria. The chloroplast has its own DNA which codes for redox proteins involved in electron transport in photosynthesis.
Mitochondrial genomes have been sequenced and confirm that mitochondria originated from a eubacterial source, specifically known as the α-proteobacterial ancestor and not from an archaebacterial source. The closest known relative to mitochondria are α-proteobacteria. This was determined by phylogenetic analysis of protein-coding genes, ribosomal RNA (rRNA) and mitochondrial DNA (mtDNA). mtDNA in proteins and fungi have been thoroughly studied. These studies indicate that ATP production, coupled with electron transport and translation of mitochondrial proteins are common to all mitochondrial genomes and can be directly traced back to the α-proteobacterial ancestor.
A multidisciplinary approach has been used to analyze the mechanism and specific timeline of chloroplast evolution. Several sources of evidence demonstrate that all chloroplasts are derived from a single endosymbiotic cyanobacterium. Consequently, they differentiated into various eukaryotic taxa by the means of several secondary endosymbioses. A Comparative genomics approach has been used to study the evolution of chloroplasts. The genome of chloroplasts is significantly reduced when comparing to the genome of free cyanobacteria. However, the high similarities between the existing parts support the theory of evolution from cyanobacterial sources.
References Gray, Micheal; Burger, Gertraud; Lang, Franz B. The origin and early evolution of mitochondria. Genome Biology 2001, 2(6):reviews1018.1–1018.5 http://genomebiology.com/2001/2/6/reviews/1018
Tomitani, Akiko. Origin and early evolution of chloroplasts.Institute for Research on Earth Evolution, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho 2-15, Yokosuka 237-0061, Japan

## Genetics in Biochemistry

The DNA sequence determines the protein composition through codons, which are a set of three nucleotide bases. The linear sequence of deoxyribonlueotides has a complementary strand held together by hydrogen bond, forming a double helix. Before the cell divides, the strands separate to form another complementary strand, thus creating two identical DNA strands.
Although this process is very efficient, occasionally a mutation will occur. A mutation is a mistake in the replication process and may lead to changes in the function, expression, or structure of the protein it encodes for. The mutation may result in a change of an amino acid residue, which affects the folding of the protein and therefore its function. Somatic mutation occurs in non-reproductive cells and only occurs in that certain organism. This type of mutation does not get passed down to their offspring by their genes. Mutations that occur in the reproductive cells will be replicated and passed down on to progeny.
Mutations occur at random and can either be harmful or beneficial to an organism. The factor of it being beneficial or harmful depends on their environment and how it affects their survival. Most mutations are harmful and may cause malfunctioning of important biological processes and decrease the overall fitness of the organism. Such a mutation is generally selected against and will disappear as quickly as it had appeared. A beneficial mutation, on the other hand, increases the fitness of the organism. If passed on to the progeny, these mutations will most likely be selected for and gradually grow within the population.
Occasionally, a DNA stand is duplicated twice, resulting in double the amount of chromosomes in a particular cell. This duplication can be passed on to the next generation and is generally not harmful. As different mutations appear in the two sets of chromosomes, new functions distinct functions are taken up by each pair.
Mutations can be classified as point mutations, in which a single amino acid is changed, or frameshift mutations, which affect the sequence of all amino acids following the mutation. The range of effect varies as well. There may be no change, small change, or a huge change in their phenotype depending on the mutation.
Point mutations, also known as single base substitution, can be categorized by the type of substitution that occurs. Transitions involve either the substitution of a purine base to another purine base or the substitution of a pyrimidine base to another pyrimidine base. Transversion involves the substitution of a purine with a pyrimidine or a pyrimidine with a purine. Point mutation may be harmless but it could also be harmful. It may reduce or lessen the function of a gene resulting in lethality. A life example of result of point mutation is sickle-cell anemia. The glutamic acid in amino acid chain is swapped with valine in beta globin chain of haemoglobin. Valine is less polar than glutamic acid and causes problems in the proper function of the cell.
Frameshift mutations include insertions, deletions, and duplication of nucleotides by a number that is not divisible by three. Essentially, any mutation that results in completely different sequence of amino acid after the point of mutation is considered to be a frameshift mutation because it shifts the triplet framework and thereby disrupts all subsequent amino acid sequence. The resulting protein may be nonfunctional. Insertion is the addition of one or more nucleotide base-pairs into the sequence, and deletion is the disappearance of one or more nucleotide base-pairs from the sequence. Duplication occurs when one or more nucleotide base-pairs is repeated in the sequence. Not all insertion, deletion, and duplication result in a frameshift mutation.
Additionally, mutations can be classified by their functional effects. There are four such categories: nonsense, missense, silent, and neutral mutations. A nonsense mutation results in the formation of a stop codon, which may truncate the protein. A missense mutation is one that results in a codon that codes for a different amino acid. A silent mutation does not produce a change in amino acid sequence. A neutral mutation is one that results in a codon that codes for an amino acid that is different, but similar to the original amino acid such that the original function is preserved.
Another type of mutation is back mutation, or reversion. It involves a nucleotide change back to its original sequence where a point mutation had occurred. Consequently, the original function is restored.
One of the major themes in biology and chemistry is that the form fits function and vice versa. DNA is a prime example of that ideology. The structure of DNA not only allows for its near-perfect replication and repair, but its specific sequence determines the specific protein that will be made.
Information in DNA is encoded by its linear sequence. The process in which the information stored in this 1-dimensional form turns into a 3-dimensional protein form is completed via an intermediary RNA. First, the linear sequence of DNA is transcribed into its complementary RNA strand called the messenger RNA (mRNA). The mRNA is then translated on a ribosome into a polypeptide chain. This polypeptide chain folds via noncovalent interactions and with the help of “molecular chaperones”. Ultimately, the structure of the protein is determined by the amino acid sequence of the polypeptide chain. The structure of the protein is crucial to its function.
In somewhat recent years, DNA sequencing has become quite popular. DNA sequencing refers to any biochemical method to determine order of the nucleotide bases, guanine, thymine, adenine, and thymine. DNA sequencing has allowed for scientific advancements and through it, many scientists have been able to recreate genomes of various plants and animals including humans (The Human Genome Project).
One important purpose in sequencing DNA is to compare the different DNA sequences of different animals. In a project led by David H. Haussler, scientists compared the DNA sequences of 19 different mammals to reconstruct a significant portion of a genome of what could possibly be a common ancestor. This ability to reconstruct ancestral genome is more reliable than trying to extract DNA from a fossil. By reconstructing the ancestral genome, the researchers were able to see how DNA changed in each evolutionary lineage. They could see all the different mutations that occurred in each genome to lead to the current mammal form. They were also able to see which DNA sequences were necessary and which were not as well as which are necessary now and which are not.
Sequence comparisons do not only pertain to DNA sequences; there are also RNA sequence comparisons and protein sequence comparisons. Sequence comparisons are usually carried out by sequence alignments. In sequence alignments, the two rows of residue are aligned so that similar nucleotide sequences are in successive columns. There are two main types of sequence alignment – global and local alignments. Global alignment is good for sets that are very similar and are of roughly equal size. The global alignment attempts to align the whole strands. Local alignments, on the other hand, are better for dissimilar sets. Local alignments attempt to align certain segments within the whole strands. There is also a hybrid method called the semi-global method or "glocal" methods. These methods try to find the best possible alignment. As mentioned above, comparing DNA sequences and finding similarities reveals evolutionary relationships. However, more importantly finding similarities also reveals functional and structural relationships. It is through sequence comparisons that mutations are revealed as well.
To read more about Haussler’s research click here: http://www.sciencedaily.com/releases/2004/11/041130205441.htm