Proteins - Biology

A peptide bond is formed between the carboxyl group and amino group of adjoining amino acids. The energy in proteins is released when peptide bonds are broken. Peptide bonds also determine the primary structure of proteins.

An ionic bond is formed when one element loses an electron and another element gains an electron. Ionic bonds most frequently form between metals and non-metals, and are not commonly seen in proteins.

A glycosidic bond is formed between a carbohydrate and another molecule. Glycosidic bonds can help form carbohydrate polymers, like glycogen, or link sugars to other groups, like in the DNA backbone.

An ester bond can be found in fatty acids, and contains a carbonyl group next to an ether linkage.

Collagen is the most abundant protein in the human body. It adds great strength and flexibility to skin, tendons, and ligaments. These qualities are characteristic of structural proteins.

Globular proteins are generally rounded, protecting a nonpolar center from the aqueous environment around the protein. Most cytoplasmic proteins and enzymes are globular proteins. In contrast, fibrous proteins are generally elongated and designed for structural support; collagen is a fibrous protein, in addition to a structural protein. Integral proteins span the plasma membrane, often creating channels.

Proteins are classified into several categories based on where they perform their function. Peripheral membrane proteins span only one side of the lipid bilayer and thus have mobility. Unlike integral membrane proteins, which span the entire lipid bilayer, peripheral membrane proteins have the liberty of traveling from layer to layer as well as flip flop between the two bilayers.

Isomers are molecules that have the same molecular formula, but have different chemical structures. Isomerases are enzymes that are able to rearrange the structure of a molecule while keeping its chemical formula the same.

A protein consists of amino acids. Essential amino acids cannot be synthesized by the body, and must be included in the diet. A protein containing all of the essential amino acids is called a complete protein. An incomplete protein lacks one or more of the essential amino acids.

Neurotransmitters are chemicals that relay messages from one cell to the next. Enzymes are protein catalysts that speed up biological reactions. Minerals are inorganic compounds and are not present in the body in large amounts, with the exception of hydroxyapatite crystal found in bones. Electrolytes are ionic salts in the blood, tissue fluids, and cells, such as sodium, potassium, and chlorine.

Protein quaternary structure involves interactions between different subunits. Each subunit will be created by folding an independent polypeptide chain into a 3-dimensional tertiary structure. The joining of these independent subunits results in quaternary structure. In order for a protein to have quaterary structure, it must have multiple subunits; this means it must consists of at least two polypeptide chains.

During initiation, the first tRNA molecule will bring the first amino acid to the ribosome. Although the following amino acids will enter at the A site, the first amino acid is positioned in the middle P site. The large ribosomal subunit will then attach, and translation can begin.

During the subsequent elongation phase of translation, tRNA/amino acid complexes will enter the ribosome at the A site, transfer to the P site, and then exit through the E site. Only the first complex will begin in the P site, during initiation.

tRNA is responsible for bringing individual amino acids to the ribosome in order to be incorporated into the protein. It has an anticodon that attaches to a specific codon found on the mRNA. Once the tRNA and mRNA are bound, a peptide bond if formed between the amino acid residue from the tRNA and the amino acid chain on the ribosome. This is how amino acids are added to the growing protein.

The genetic code is considered both degenerative and unambiguous. A codon will only code for one amino acid, making the code unambiguous. In contrast, multiple codons can code for the same amino acid, making it degenerative. For example, UGU will always code for cysteine, but UGC also codes for cysteine.

Nearly every living organism uses the same genetic code. tRNA anticodons are complementary to mRNA codons; they are not the same code.

As amino acids are added to a polypeptide during translation, tRNA molecules will enter the A site of the ribosome. The tRNA is then transferred to the P site, where a peptide bond is formed between the amino acid residue and the amino acid chain. Finally, the tRNA moves to the E site to release its tRNA and exit the ribosome.

The small subunit of eukaryotic ribosomes is 40S and the large subunit is 60S. These combine to form the ribosome, which is 80S in sedimentary size.

For prokaryotes, the ribosome subunits are 30S and 50S to form a total of 70S total unit.

The ribosome contains three sites: the A, P, and E sites.

The A site is where activation occurs, starting translation. This is where a tRNA molecule enters the ribosome and matches its anticodon to the mRNA codon.

The tRNA then shifts over to the P site to attach the amino acid. The ribosome facilitates the formation of a peptide bond, adding the amino acid to the chain.

At the E site, the empty tRNA exits the ribosome and dissociates from mRNA.

DNA contains genetic information that is transcribed into mRNA. This process is known as transcription, and occurs in the nucleus. After modification in the nucleus, mRNA exits the nucleus and enters the cell cytoplasm. In a process called translation, mRNA (in conjuction with tRNA and a ribosome) is used as a template to join amino acids to form specific polypeptides.

In summary, DNA is transcribed into RNA, which is translated into protein.

At the beginning of translation, mature mRNA will travel into the cytosol and attach to the small ribosomal subunit first. This signals the larger subunit to come and attach in order to begin elongation of the polypeptide.

Note that ribosomes do not have an "active site." Active sites are the region of a protein that will bind a substrate and initiate a catalytic change. Ribosomes are not proteins; they are composed of ribosomal RNA (rRNA), and thus do not have active sites.

During translation, the ribosome binds to mRNA and to the appropriate tRNAs. On the ribosome, the mRNA condons are translated into the amino acid sequence of a protein with the help of the tRNA anticodons.

Transcription refers to the synthesis of an RNA molecule from a DNA template. Transformation occurs when a bacterium is able to absorb and incorporate genetic material from the extracellular environment. Transfusion is the transfer of blood from a donor to a recipient. Transfection is the infection of bacteria by phage DNA.

The tRNA carries the amino acid specified by its anticodon. The anticodon base pairs with the codon on the mRNA to ensure the correct amino acid is added to the new protein that is being made. Thus there is a specific tRNA for each codon.

Ribosomes are made up of rRNA and proteins. rRNA synthesis, and ribosome assembly takes place in the nucleolus.

While one might quickly calculate that 90 nucleotides/3 would yield a 30 amino acid sequence, it is important to remember that while the first 3 nucleotides will encode for an amino acid to start translation (methionine), the last 3 nucleotides do not. They simply stop translation and signal for the growing polypeptide chain to be released from the ribosome-tRNA translation complex without actually adding another amino acid to the end of the chain.

The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes, and a modified methionine (f-Met) in prokaryotes. The most common start codon is 5' AUG 3'. The start codon is preceded by a untranslated region which includes the ribosome binding site in prokaryotes.

5' UAA 3', 5' UGA 3', 5' UAG 3' are all stop codons.