Biomolecular structure - Wikipedia
Nucleic Acids Research, Volume 27, Issue 1, 1 January , Pages –, and phenetic descriptors for protein domain relationships. . with the ultimate goal of being able to predict the function of a new protein from its. Introduction and Goals. There are four major families of macromolecules ( proteins, nucleic acids, The flow of information is from DNA to mRNA to protein. .. The complementary relationships between the nucleotides are as. Different types of proteins. The structure and properties of amino acids. Formation of peptide bonds.
Most lipids spontaneously aggregate when placed in water. This can be clearly seen when oil is mixed with water; the oil is not soluble in the water, therefore, it beads up to form droplets of oil.
Finally, there are some lipids that function as lipid-soluble hormones, used as signals for intercellular communication. Five Types of Important Lipids Figure 7. Saturated and unsaturated fatty acids.
The chemical composition and structure of two fatty acids, one saturated palmitate and one unsaturated oleateare shown. Note that the double bond in oleate causes a kink in the molecule.
Carbon atoms are shown in black, hydrogen atoms are shown in blue, and oxygen atoms are shown in green. There are five major types of lipids: A fatty acidis a long, unbranched chain of hydrocarbons with a carboxyl COOH group at one end. The number of carbons varies amongst different fatty acids, and can range from 12 to 20 carbons. In addition, fatty acids vary in the number and position of double bonds between their carbons. Fatty acids without double bonds are referred to as saturated fatty acids.
Fatty acids with only a few double bonds are referred to as unsaturated fatty acids. Fatty acids with many double bonds are referred to as polyunsaturated fatty acids.
As illustrated in Figure 7, saturated fatty acids are linear molecules, whereas unsaturated molecules have a kink due to their double bonds. A triacyglycerol also called a triglyceride is composed of three fatty acids linked to a glycerol molecule see Figure 8.
Triacylglycerols are commonly referred to as fats or oils, and are predominantly energy-storage molecules. This is the fat we try to "burn off" by exercise and restricting our diets.
A triacylglycerol can contain three different fatty acids that vary in length and level of saturation. Triacylglycerol derived from plants, which we commonly refer to as oils e. The level of saturation of the fatty acids affects their state. Saturated fatty acids can be packed together closely in a tight and orderly fashion.
The kinked nature of unsaturated fatty acids prevents tight packing and results in a lower melting temperature for plant oils, therefore, they are liquid at room temperature. Partially hydrogenated fats e.
Phospholipids, Terpenes and Sterols Figure 8. Four types of lipids. The chemical structures of four different lipids are shown.
Difference between Proteins and Nucleic Acids
A triacylglycerol, a phospholipid phoshphotidylcholinea sterol cholesterol and a terpene geraniol. Phospholipids are used predominantly in the formation of biological membranes. A phospholipid is similar to a triacylglycerol. It is composed of glycerol, two fatty acid chains, and a phosphate group that is also linked to a small polar group see Figure 8 for an example. A phospholipid is amphipathic, having both polar and nonpolar regions. The highly polar "head" is comprised of the phosphate and polar group, and the long hydrophobic "tail" is comprised of the two fatty acid chains.
When mixed with water, phospholipids spontaneously form a lipid bilayer. The lipid bilayer is two layers of phospholipids arranged in a tail-to-tail configuration, with their polar heads on the outside of the bilayer, in contact with water, and their hydrophobic tails pointing toward each other, shielded from the water.
This feature makes them important to membrane structure. The properties of the lipid bilayer will be discussed in greater detail in Tutorial 4 entitled Membrane Structure and Function.
Phospholipids are a major component of biological membranes, where they comprise the bulk of the lipid bilayer. Terpenes are comprised of long-chain hydrocarbons derived from a common, five-carbon subunit see Figure 8for an example. Terpenes have diverse functions and include molecules such as carotenoid pigments and the visual pigment retinal derived from vitamin A.
Sterols are structurally distinct from other lipids. Instead of long-chain hydrocarbons, sterols are composed of multiple, four-carbon, ring structures. Cholesterol see Figure 8which is a component of the plasma membrane of animal cells, is a sterol.
Other sterol molecules include the hormones testosterone and estrogen. Summary This tutorial described the structures and properties of three families of macromolecules: Nucleic acids are macromolecules that store, transmit and express the genetic information of a cell.
DNA is the stored genetic material. Nucleotides are composed of three functional groups: Nucleotides in RNA contain the bases adenine and guanine both purinesand cytosine and uracil both pyrimidines. Nucleotides in DNA contain the bases adenine, guanine, cytosine and thymine also a pyrimidine. DNA is double-stranded, and the two strands of DNA are held together by hydrogen bonds between the nitrogenous bases of complementary nucleotides.
The complementary relationships between the nucleotides are as follows: The A-T base pair has two hydrogen bonds, and the G-C base pair has three. The structure of most double-stranded DNA is a right-handed double helix.
Polysaccharides are polymers of monosaccharides simple sugars linked via a glycosidic bond. They function in the cell as storage and structural molecules. Disaccharides are composed of two monosacchrides linked by a glycosidic bond. These processes may involve multi-protein complexes e.
Structure is determined by several factors Covalent and non-covalent bonding govern the three dimensional structures of proteins and nucleic acids which impacts function. The amino acid sequences observed in nature are highly selected for biological function but do not necessarily adopt a unique folded structure. The structure and hence function of macromolecules is governed by foundational principles of chemistry such as: The sequence and hence structure and function of proteins and nucleic acids can be altered by alternative splicing, mutation or chemical modification.
Sequences and hence structure and function of macromolecules can evolve to create altered or new biological activities. Structure and function are related Macromolecules interact with other molecules using a variety of non-covalent interactions. The specificity and affinity of these interactions are critical to biological function. Although there are plans to assign the more regular architectures automatically, all architecture groupings are currently assigned manually. A homologous family Dictionary is now available within CATH, which contains functional data, where available, for each protein within a homologous family.
Multiple structure based alignments are also available, coloured according to secondary structure assignments or residue properties and there are schematic plots showing domain representations annotated by protein-ligand interactions DOMPLOTS A. Thornton, submitted to Protein Engng. The topology of each domain is illustrated by schematic TOPS diagrams http: Figure 3 View large Download slide CATH wheel plot showing the population of homologous families in different fold groups, architectures and classes.
The size of the outer wheel represents the number of homologous families in CATH whilst each band in the outer wheel corresponds to a single fold family. It can be seen that most fold families contain a single homologous family. The superfold families are shown as paler bands, containing many homologous families.
The inner wheel shows the population of homologous families in the different architectures. We have also recently set up a Web Server 11which enables the user to scan the CATH database with a newly determined protein structure and identify possible fold similarities or evolutionary relationships. The latest release of CATH version 1. Currently 32 different architectures are recognised. Grouping proteins on the basis of sequence, structure and functional similarity gives evolutionary homologous families H-level.
Whilst recognising more distant structural similarity with no accompanying sequence or function similarity gives rise to different fold groups T-level. Implications for Structural Genomics As the sequence databases grow rapidly, the need to interpret these sequences and assign functions to specific genes becomes increasingly important. Many techniques exist for matching protein sequences and thereby inheriting functional information.
However, for very distant homologues there is often no detectable sequence similarity, despite conservation of 3D structure and function.
For these cases, evolutionary relationships and thereby functions can only be assigned by comparing the structures. Therefore, a number of structural genomics initiatives are being proposed 14 which aim to identify all the folds in nature with the ultimate goal of being able to predict the function of a new protein from its known or probable structure.
The important questions to ask are how many more folds do we need to determine before we have the complete set?