PCAT Exam: Chemical Processes - Basic Biochemistry Processes

Basic units of organic compounds are often called monomers. Repeating units of linked monomers are called polymers. The most important polymers found in all living things can be divided into just four categories: carbohydrates, lipids, proteins, and nucleic acids. This may be surprising since there is so much diversity in the outward appearances and functions of living things present on Earth.

Carbon (C), hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P) are the major elements of most biological molecules.

Carbon is a common backbone of large molecules because of its ability to form four covalent bonds.

DNA and RNA
Nucleic acids have two important duties in the body. As monomers, they are crucial for energy transfer. As polymers, they are a fundamental component of genetic material. Nucleotides are the monomer units that assemble to form nucleic acids.

Nucleotides have three components: a nitrogenous base and a phosphate functional group, both of which are attached to a five-carbon (pentose) sugar. There are two classes of nitrogenous bases, purines and pyrimidines. The two types of purines are guanine (G) and adenine (A), while the three types of pyrimidines are thymine (T), cytosine (C), and uracil (U). The two types of pentose sugars are deoxyribose and ribose. Nucleotides containing deoxyribose are termed deoxyribonucleic acid (DNA).

DNA utilizes guanine, adenine, cytosine, and thymine as its nitrogenous bases. Nucleotides containing ribose are termed ribonucleic acid (RNA). RNA utilizes guanine, adenine, cytosine, and uracil as its nitrogenous bases.



Chromosomes, Genes, Proteins, RNA, and DNA
Chromosomes are composed of hundreds to thousands of genes. Human cells contain 23 pairs of chromosomes for a total of 46 chromosomes. Genes are inherited in pairs, one from each parent.
Proteins are made of long chains of amino acids. In total, there are 20 amino acids, 11 of which humans can synthesize on their own and the remaining 9 of which are procured through diet. DNA contains the information for the synthesis of proteins, but that information on DNA has to undergo transcription and translation by RNA in order to produce proteins.

Codons
A codon represents a sequence of three nucleotides, which codes for either one specific amino acid or a stop signal during protein synthesis. Codons are found on messenger RNA (mRNA).
Twenty essential amino acids are utilized in the process of protein synthesis. The full set of codons encompasses 64 possible combinations and is termed the genetic code. In the genetic code, 61 codons represent amino acids and three codons are stop signals. The genetic code is redundant due to the fact that a single amino acid may be produced by multiple codons. For example, the codons AAA and AAG produce the amino acid lysine. The codons UAA, UAG, and UGA are stop signals. The codon AUG codes for both the amino acid methionine and the start signal. As a result, AUG when found in mRNA, marks the initiation point of protein translation.

RNA
Ribonucleic acid (RNA) plays crucial roles in protein synthesis and gene regulation. RNA is made of nucleotides consisting of ribose (a sugar), a phosphate group, and one of four possible nitrogen bases—adenine (A), cytosine (C), guanine (G), and uracil (U). RNA utilizes the nitrogenous base uracil in place of the base thymine found in DNA. Another difference between RNA and DNA is that RNA is typically found as a single-stranded structure, while DNA typically exists in a double-stranded structure.
RNA can be categorized into three major groups—messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).

Messenger RNA (mRNA) transports instructions from DNA in the nucleus of a cell to the areas responsible for protein synthesis in the cytoplasm of a cell. This process is known as transcription. Transfer RNA (tRNA) deciphers the amino acid sequence for the construction of proteins found in mRNA. Both tRNA and ribosomal RNA (rRNA) are found in the ribosomes of cells. Ribosomes are responsible for protein synthesis. The process is known as translation, and both tRNA and rRNA play crucial roles. Both translation and transcription are further described below.

DNA
Deoxyribonucleic acid, or DNA, contains the genetic material that is passed from parent to offspring. It contains specific instructions for the development and function of a unique eukaryotic organism. The great majority of cells in a eukaryotic organism contains the same DNA.
The majority of DNA can be found in the cell’s nucleus and is referred to as nuclear DNA. A small amount of DNA can be located in the mitochondria and is referred to as mitochondrial DNA. Mitochondria provide the energy for a properly functioning cell. All offspring inherit mitochondrial DNA from their mother. James Watson, an American geneticist, and Frances Crick, a British molecular biologist, first outlined the structure of DNA in 1953.
The structure of DNA visually approximates a twisting ladder and is described as a double helix. DNA is made of nucleotides consisting of deoxyribose (a sugar), a phosphate group, and one of four possible nitrogen bases—thymine (T), adenine (A), cytosine (C), and guanine (G). It is estimated that human DNA contains three billion bases. The sequence of these bases dictates the instructions contained in the DNA making each species singular. The bases in DNA pair in a particular manner—thymine (T) with adenine (A) and guanine (G) with cytosine (C). Weak hydrogen bonds between the nitrogenous bases ensure easy uncoiling of DNA’s double helical structure in preparation for replication.

Transcription
Transcription refers to a portion of DNA being copied into RNA, specifically mRNA. It represents the first crucial step in gene expression. The process begins with the enzyme RNA polymerase binding to the promoter region of DNA, which initiates transcription of a specific gene. RNA polymerase then untwists the double helix of DNA by breaking weak hydrogen bonds between its nucleotides. Once DNA is untwisted, RNA polymerase travels down the strand reading the DNA sequence and adding complementary nitrogenous bases. With the assistance of RNA polymerase, the pentose sugar and phosphate functional group are added to the nitrogenous base to form a nucleotide. Lastly, the weak hydrogen bonds uniting the DNA-RNA complex are broken to free the newly formed mRNA. The mRNA travels from the nucleus of the cell out to the cytoplasm of the cell where translation occurs.

Translation
Translation refers to the process of ribosomes synthesizing proteins. It represents the second crucial step in gene expression. The instructions encoding specific proteins to be made are contained in codons on mRNA, which have previously been transcribed from DNA. Each codon represents a specific amino acid or stop signal in the genetic code.
Amino acids are the building blocks of proteins. Ribosomes contain transfer RNA (tRNA) and ribosomal RNA (rRNA).

Translation occurs in ribosomes located in the cytoplasm of cells and consists of the following three phases:
 1. Initiation: The ribosome gathers at a target point on the mRNA, and tRNA attaches at the start codon (AUG), which is also the codon for the amino acid methionine.
2. Elongation: A new tRNA reads the next codon on the mRNA and links the two amino acids together with a peptide bond. The process is repeated until a polypeptide, or long chain of amino acids, is formed.
3. Termination: The ribosome disengages from the mRNA when it encounters a stop codon (UAA, UAG, or UGA). The event releases the polypeptide molecule. Proteins are made of one or more polypeptide molecules.

Lipids
Lipids are a class of biological molecules that are hydrophobic, meaning they don’t mix well with water. They are mostly made up of large chains of carbon and hydrogen atoms, termed hydrocarbon chains. When lipids mix with water, the water molecules bond to each other and exclude the lipids because they are unable to form bonds with the long hydrocarbon chains. The three most important types of lipids are fats, phospholipids, and steroids.
Fats are made up of two types of smaller molecules: glycerol and fatty acids. Glycerol is a chain of three carbon atoms, with a hydroxyl group attached to each carbon atom. A hydroxyl group is made up of an oxygen and hydrogen atom bonded together. Fatty acids are long hydrocarbon chains that have a backbone of sixteen or eighteen carbon atoms. The carbon atom on one end of the fatty acid is part of a carboxyl group. A carboxyl group is a carbon atom that uses two of its four bonds to bond to one oxygen atom (double bond) and uses another one of its bonds to link to a hydroxyl group. Fats are made by joining three fatty acid molecules and one glycerol molecule.


Phospholipids are made of two fatty acid molecules linked to one glycerol molecule. A phosphate group is attached to a third hydroxyl group of the glycerol molecule. A phosphate group has an overall negative charge and consists of a phosphate atom connected to four oxygen atoms.
Phospholipids have an interesting structure because their fatty acid tails are hydrophobic, but their phosphate group heads are hydrophilic. When phospholipids mix with water, they create double-layered structures, called bilayers, that shield their hydrophobic regions from water molecules. Cell membranes are made of phospholipid bilayers, which allow the cells to mix with aqueous solutions outside and inside, while forming a protective barrier and a semi-permeable membrane around the cell.
Steroids are lipids that consist of four fused carbon rings. The different chemical groups that attach to these rings are what make up the many types of steroids. Cholesterol is a common type of steroid found in animal cell membranes. Steroids are mixed in between the phospholipid bilayer and help maintain the structure of the membrane and aids in cell signaling.

Proteins
Proteins are essential for most all functions in living beings. The name protein is derived from the Greek word proteios, meaning first or primary. All proteins are made from a set of twenty amino acids that are linked in unbranched polymers. The combinations are numerous, which accounts for the diversity of proteins. Amino acids are linked by peptide bonds, while polymers of amino acids are called polypeptides. These polypeptides, either individually or in linked combination with each other, fold up to form coils of biologically functional molecules, called proteins.
There are four levels of protein structure: primary, secondary, tertiary, and quaternary. The primary structure is the sequence of amino acids, similar to the letters in a long word. The secondary structure is beta sheets, or alpha helices, formed by hydrogen bonding between the polar regions of the polypeptide backbone. Tertiary structure is the overall shape of the molecule that results from the interactions between the side chains linked to the polypeptide backbone. Quaternary structure is the overall protein structure that occurs when a protein is made up of two or more polypeptide chains.



Carbohydrates
Carbohydrates consist of sugars and polymers of sugars. The simplest sugar type of sugar is a monosaccharide, which has the empirical formula of CH2O. The formula for the monosaccharide glucose, for example, is C6H12O6. Glucose is an important molecule for cellular respiration, the process of cells extracting energy by breaking bonds through a series of reactions. The individual atoms are then used to rebuild new small molecules.

Polysaccharides are made up of a few hundred to a few thousand monosaccharides linked together. These larger molecules have two major functions. The first is that they can be stored as starches, such as glycogen, and then broken down later for energy. Secondly, they may be used to form strong materials, such as cellulose, which is the firm wall that encloses plant cells, and chitin, the carbohydrate insects use to build exoskeletons.