A protein's amino acid sequence determines its three-dimensional structure ( conformation). In turn, a protein's structure determines the function of that protein. important functions of protein include forming blood cells and making antibodies to protect us from illness and infections. Amino Acids. Proteins are made from. You know that the pH is defined in terms of the proton concentration. pH = -log[ H+] and that this is based on an equilibrium that is reached between an acid (or.
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Protein is one of the nutrients along with carbohydrate, fat, vitamins, minerals, nutrients than others and sometimes we refer to certain foods as “protein foods. amino acids in a protein is dictated by the sequence of the nucleotides in an organisms' genetic code. • These amino acids are called alpha (α)-amino acids. During protein synthesis, the carboxyl group of amino acid at the end of the growing polypeptide chain reacts with the amino group of an incoming amino acid.
Many proteins are made up of multiple polypeptide chains, often referred to as protein subunits. A Complex Protein Assembly. These abbreviations are commonly used to simplify the written sequence of a peptide or protein. Thermodynamic methods such as differential scanning calorimetry DSC can be useful in determining the effect of temperature on protein stability. Clear Turn Off Turn On. The alkyl groups of alanine, valine, leucine and isoleucine often form hydrophobic interactions between one-another, while aromatic groups such as those of phenylalanine and tryosine often stack together.
Thus, proteins are the embodiment of the transition from the one-dimensional world of sequences to the three-dimensional world of molecules capable of diverse activities.
Proteins contain a wide range of functional groups.
These functional groups include alcohols, thiols, thioethers, carboxylic acids, carboxamides, and a variety of basic groups. When combined in various sequences, this array of functional groups accounts for the broad spectrum of protein function.
For instance, the chemical reactivity associated with these groups is essential to the function of enzymes, the proteins that catalyze specific chemical reactions in biological systems see Chapters 8— Proteins can interact with one another and with other biological macromolecules to form complex assemblies.
The proteins within these assemblies can act synergistically to generate capabilities not afforded by the individual component proteins Figure 3. These assemblies include macro-molecular machines that carry out the accurate replication of DNA , the transmission of signals within cells, and many other essential processes.
Some proteins are quite rigid, whereas others display limited flexibility. Rigid units can function as structural elements in the cytoskeleton the internal scaffolding within cells or in connective tissue.
Parts of proteins with limited flexibility may act as hinges, springs, and levers that are crucial to protein function, to the assembly of proteins with one another and with other molecules into complex units, and to the transmission of information within and between cells Figure 3.
Crystals of human insulin. Insulin is a protein hormone, crucial for maintaining blood sugar at appropriate levels. Below Chains of amino acids in a specific sequence the primary structure define a protein like insulin. These chains fold into well-defined more Structure Dictates Function.
The structure of the protein allows large segments of DNA to be copied without the replication machinery dissociating from the more A Complex Protein Assembly.
An electron micrograph of insect flight tissue in cross section shows a hexagonal array of two kinds of protein filaments. Michael Reedy. Flexibility and Function. Upon binding iron, the protein lactoferrin undergoes conformational changes that allow other molecules to distinguish between the iron-free and the iron-bound forms.
By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed. Turn recording back on. National Center for Biotechnology Information , U. This technical brief aims to give the reader a quick overview of protein structure. It will also cover briefly how protein structure can be affected during formulation and some of the analytical methods which can be used both to determine the structure and analyze the stability of the protein.
The term structure when used in relation to proteins, takes on a much more complex meaning than it does for small molecules. Proteins are macromolecules and have four different levels of structure — primary, secondary, tertiary and quaternary.
Amino acids, as their name indicates, contain both a basic amino group and an acidic carboxyl group. This difunctionality allows the individual amino acids to join together in long chains by forming peptide bonds: Sequences with fewer than 50 amino acids are generally referred to as peptides , while the terms protein or polypeptide are used for longer sequences.
A protein can be made up of one or more polypeptide molecules. The end of the peptide or protein sequence with a free carboxyl group is called the carboxy-terminus or C-terminus. The amino acids differ in structure by the substituent on their side chains. These side chains confer different chemical, physical and structural properties to the final peptide or protein.
The structures of the 20 amino acids commonly found in proteins are shown in Figure 1. Each amino acid has both a one-letter and three-letter abbreviation. These abbreviations are commonly used to simplify the written sequence of a peptide or protein.
Depending on the side-chain substituent, an amino acid can be classified as being acidic, basic or neutral. Although 20 amino acids are required for synthesis of various proteins found in humans, we can synthesize only The remaining 10 are called essential amino acids and must be obtained in the diet.
The amino acid sequence of a protein is encoded in DNA. Proteins are synthesized by a series of steps called transcription the use of a DNA strand to make a complimentary messenger RNA strand - mRNA and translation the mRNA sequence is used as a template to guide the synthesis of the chain of amino acids which make up the protein.
Often, post-translational modifications, such as glycosylation or phosphorylation, occur which are necessary for the biological function of the protein.
Stretches or strands of proteins or peptides have distinct characteristic local structural conformations or secondary structure , dependent on hydrogen bonding. The hydrogen bonds make this structure especially stable. The side-chain substituents of the amino acids fit in beside the N-H groups.
The sheet conformation consists of pairs of strands lying side-by-side. The carbonyl oxygens in one strand hydrogen bond with the amino hydrogens of the adjacent strand. The two strands can be either parallel or anti-parallel depending on whether the strand directions N-terminus to C-terminus are the same or opposite. The overall three-dimensional shape of an entire protein molecule is the tertiary structure.
The protein molecule will bend and twist in such a way as to achieve maximum stability or lowest energy state. Although the three-dimensional shape of a protein may seem irregular and random, it is fashioned by many stabilizing forces due to bonding interactions between the side-chain groups of the amino acids.
Under physiologic conditions, the hydrophobic side-chains of neutral, non-polar amino acids such as phenylalanine or isoleucine tend to be buried on the interior of the protein molecule thereby shielding them from the aqueous medium.
The alkyl groups of alanine, valine, leucine and isoleucine often form hydrophobic interactions between one-another, while aromatic groups such as those of phenylalanine and tryosine often stack together.
Acidic or basic amino acid side-chains will generally be exposed on the surface of the protein as they are hydrophilic. The formation of disulfide bridges by oxidation of the sulfhydryl groups on cysteine is an important aspect of the stabilization of protein tertiary structure, allowing different parts of the protein chain to be held together covalently. Additionally, hydrogen bonds may form between different side-chain groups.
As with disulfide bridges , these hydrogen bonds can bring together two parts of a chain that are some distance away in terms of sequence. Salt bridges , ionic interactions between positively and negatively charged sites on amino acid side chains, also help to stabilize the tertiary structure of a protein.
Many proteins are made up of multiple polypeptide chains, often referred to as protein subunits. These subunits may be the same as in a homodimer or different as in a heterodimer.
The quaternary structure refers to how these protein subunits interact with each other and arrange themselves to form a larger aggregate protein complex. The final shape of the protein complex is once again stabilized by various interactions, including hydrogen-bonding, disulfide-bridges and salt bridges.
The four levels of protein structure are shown in Figure 2. Due to the nature of the weak interactions controlling the three-dimensional structure, proteins are very sensitive molecules. The term native state is used to describe the protein in its most stable natural conformation in situ. This native state can be disrupted by a number of external stress factors including temperature, pH, removal of water, presence of hydrophobic surfaces, presence of metal ions and high shear.
The loss of secondary, tertiary or quaternary structure due to exposure to a stress factor is called denaturation. Denaturation results in unfolding of the protein into a random or misfolded shape. A denatured protein can have quite a different activity profile than the protein in its native form, usually losing biological function. In addition to becoming denatured, proteins can also form aggregates under certain stress conditions.