DRM Biology Y11 - proteins 1 PROTEINS The essence of life

2DRM Biology Y11 - proteins What is a protein? Proteins are very long chains of thousands repeated monomers called amino acids. These chains of amino acids are also known as polypeptides. Proteins are : very big structurally complex have their shapes adapted to several different functions functionally sophisticated most abundant molecule in cells (15% of cell’s dry mass)

3DRM Biology Y11 - proteins The building blocks: amino acids There are 20 aminoacids. Each amino acid consists of an amino group (NH 2 ), a carboxyl or acid group (COOH), one atom of H and one residue or radical (R) group which varies in each amino acid. The R group ranges from a single H atom to a set of several different atoms forming a side chain. The R group gives the amino acid its properties and hence the protein characteristics. It is the one involved in molecule-molecule interactions in the folding of the protein.

4DRM Biology Y11 - proteins The structure of an amino acid In solution, amino acids tend to ionise (the COOH loses its H becoming COO-) and the NH 2 turns to H 3 N + ; that is why they are represented like this: polar chargedpolar charged ACIDIC... negatively charged ASP & GLU R group with 2nd COOH that ionizes above pH 7.0 ACIDIC... negatively charged ASP & GLU R group with 2nd COOH that ionizes above pH 7.0 BASIC... positively charged LYS, ARG, HIS mcb 2.14* R group with 2nd amide that protonates below pH 7.0 BASIC... positively charged LYS, ARG, HIS mcb 2.14* R group with 2nd amide that protonates below pH 7.0 POLAR UNCHARGED... SER, THR, ASN, GLN, TYR, are soluble in water, i.e., hydrophilic mcb 2.14* POLAR UNCHARGED... SER, THR, ASN, GLN, TYR, are soluble in water, i.e., hydrophilic mcb 2.14* NON-POLAR... (aliphatic) ALA, VAL, ILE, LEU, PHE, TRP contain only hydrocarbons R groups = hydrophobicity mcb 2.14* NON-POLAR... (aliphatic) ALA, VAL, ILE, LEU, PHE, TRP contain only hydrocarbons R groups = hydrophobicity mcb 2.14* AROMATIC & SPECIAL PHE,TRP,TYR,GLY,PRO,CYS contain R groups with ring structures & others mcb 2.14* AROMATIC & SPECIAL PHE,TRP,TYR,GLY,PRO,CYS contain R groups with ring structures & others mcb 2.14*

5DRM Biology Y11 - proteins According to their R groups, the amino acids can be: polar neutral polar acidic polar basic (all hydrophylic) or non polar (hydrophobic)

6DRM Biology Y11 - proteins Some examples of amino acids

DRM Biology Y11 - proteins7 The peptide bond

DRM Biology Y11 - proteins8 The peptide bond showing the condensation reaction

DRM Biology Y11 - proteins9 Forming the polypeptide chain: now 4 aa together

10DRM Biology Y11 - proteins Protein structure levels: an overview Proteins are not just a long chain of amino acids. In the cell, the sequence of aminoacids folds to adquire a spherical shape. This happens thanks to the interactions between the R groups of the different amino acids that form the chain. As the R groups tend to group together, the protein folds in a seconday structure and then a further folding will lead to a tertiary structure.

11DRM Biology Y11 - proteins Protein structure: level I During protein synthesis, amino acids are joined in a long sequence or chain called the primary structure.

12DRM Biology Y11 - proteins Protein structure: level II The primary structure can later fold in 3 ways: the alfa helix, the beta sheet or irregularly. This further folding is the secondary structure.

13DRM Biology Y11 - proteins Further folding of the secondary structure leads to a rounder shape called the tertiary structure. This tertiary structure is held by different types of interactions between the R groups of the amino acids: the H bonds, the S-S bonds, the ionic “bonds” and the non polar or hydrophobic interactions. Protein structure: level III Notice these are NOT covalent bonds because they do not involve atoms of the same amino acid but of different amino acids that may be very far away in the primary structure.

14DRM Biology Y11 - proteins The quaternary structure refers to the spatial relationships between individual polypeptide chains in a multi chain protein. The quaternary structure can be shown by the proteins consisting of two or more polypeptide chains, which may be same or different. One of the best known examples of a multi subunit protein is haemoglobin, the oxygen-carrying protein of RBCs and collagen, a protein found in the connective tissue acting as support. Protein structure: level IV

DRM Biology Y11 - proteins15 Let’s check: protein structure

16DRM Biology Y11 - proteins When folding goes wrong Cells have a mechanism of checking and disposing of misfolded proteins. When this mechanism fails, cells accumulate misfolded proteins causing brain degeneration (as in Alzheimer’s disease). When this mechanism fails, cells accumulate misfolded proteins causing brain degeneration (as in Alzheimer’s disease). Sometimes, certain “naughty” proteins called prions act as infectious agents causing severe brain damage, as in spongy encephalopathies such as Creutzeld-Jacob disease in humans, scrapie in sheep, or BSE (mad cow disease). So knowing how a protein folds is crucial to understand its functions and discover drugs to cure or prevent diseases. So knowing how a protein folds is crucial to understand its functions and discover drugs to cure or prevent diseases.

DRM Biology Y11 - proteins17 Prions: normal and abnormal normal abnormal

18DRM Biology Y11 - proteins Scientists have already determined the functions of many proteins using a variety of methods. For example, they can determine: How big a protein is How big a protein is Where it's located in an organism or even inside a cell Where it's located in an organism or even inside a cell Whether it interacts with DNA, RNA, nucleotides, membranes, or other proteins Whether it interacts with DNA, RNA, nucleotides, membranes, or other proteins Whether it's changed by the cell after being made Whether it's changed by the cell after being made Whether it can change other proteins by modifying them or breaking them into pieces Whether it can change other proteins by modifying them or breaking them into pieces

19DRM Biology Y11 - proteins What disrupts normal structure? Proteins are sensitive to several environmental factors that may destroy the interactions between the R groups of aminoacids, causing a change in shape as the tertiary structure is now broken. This process is called DENATURATION. The most important factors are: pH pH Temperature Temperature Presence of heavy metals or high concentrations of salts Presence of heavy metals or high concentrations of salts

DRM Biology Y11 - proteins20 Structure is adapted to function Different parts of our cells and our body require different types of proteins, so the protein’s shape will determine its function. Basically, proteins can be either GLOBULAR or FIBROUS. Examples are keratin, collagen and silk. FIBROUS proteins are very strong and flexible, with polypeptide chains arranged in parallel helices, they form part of structures like cartilage, hair and nails, they are reactive with acids, they are insoluble in water, they are made by a few repeated amino acids, they show predominance of secondary structure, and they are not easily affected by temperature or pH. Examples are keratin, collagen and silk. Examples are enzymes, haemoglobin, blood plasma proteins, etc. GLOBULAR proteins are spherical in shape, are easily affected by pH or temperature, are made by several different kinds of amino acids, they are soluble in water, and show predominance of tertiary structure. Examples are enzymes, haemoglobin, blood plasma proteins, etc.

DRM Biology Y11 - proteins21 So what are proteins for? Proteins are essential macromolecules that have several functions in a cell and in a body. It’s not just “for growth and repair”! Some are: Antibodies (defense) Contractile (muscle, cytoskeleton) Enzymes Hormones Storage Transport Structural (hair, nails, silk, membrane proteins) Cell signalling (cell-cell communication) Cell self-recognition (cell’s ID) Osmotic and pH balance Receptors Pathogen-host interaction (viruses infect cells through proteins on cell membranes)

DRM Biology Y11 - proteins22

23DRM Biology Y11 - proteins Protein deficiency There are two types of this illness, each with separate signs of protein deficiency to watch for. In both, the signs of protein deficiency are clear and recognizable. The first kind is called Marasmus. This kind is a form of near starvation and is less common in the western world. It occurs most frequently in the third world in infants who are given diluted baby formula. The indicators of this kind of malnutrition are: Weight loss, fatigue and exhaustion, loss of natural fat stores (like the flesh around the bottom), muscle wastage, and susceptibility to illness and infection due to a poorly functioning immune system. The other kind of this type of malnutrition is called Kwashiorkor. It is common in cases where the affected person has a diet that is very low in protein, but high in carbohydrates. The indicators include: muscle wastage, fluid retention, and the liver becoming enlarged and fatty. In the western world, people most at risk for this dangerous condition are strict vegans and people suffering from anorexia or athletic anorexia.