We are going to talk about two classifications of proteins: fibrous & globular.

Transcription

1 Slide # 13 (fibrous proteins) : We are going to talk about two classifications of proteins: fibrous & globular. *fibrous proteins: (dense fibers) *Their structures are mainly formed of the secondary structure (either a-helices or b-pleated sheets). * They are designed in such a way that fits their functions; they are tough, hard and strong in order to have a structural or supportive role. * They are insoluble in water, because most of amino acids are engaged in bonds making the protein very tight. * Examples: 1- Keratin: it is found in wool, hair, nails, and any place that demands a structural role. Formed of a-helices. 2-collagen : it is the major component of the connective tissue. 3- fibroin : the main component of silk. It is formed of b-sheets. Slide # 14 ( globular proteins) : *they are spherical in shape. *unlike fibrous proteins; they are soluble since they have two regions; hydrophobic one inside, and hydrophilic one outside. *they are found in fluids ( extracellular matrix, intracellular matrix, blood.) *transport proteins are globular ones. *they all have tertiary structure. structure) Slide # 15 : ( 3 *recall that in secondary structure, the bonds are formed between the backbones. On the other hand; in tertiary structure, all the atoms ( from the backbone or the side chain) are involved in forming the bonds. * Tertiary structure gives the final fold of the protein. So, it is a complete protein that is formed of only one polypeptide chain (single protein). If there is more than one polypeptide, it will be a quaternary structure. *single proteins are divided into simple & conjugated. 1- simple proteins : they are made of amino acid units only. They are active after translation and ready to act their roles. 2-conjugated proteins: they are composed of simple proteins combined with a non-proteinous substance. After translation process, they aren't active. There must be another substances ( not amino acids) that added to protein (conjugate it) in order to make it function.

2 *myoglobin is an example of conjugated proteins; that it can't make its function as a storage for oxygen till a chemical substance (heme) is added to it. * insulin is a simple protein. Its sequence of amino acids has 3 disulfide bonds) which formed between cysteins. *some proteins are conjugated with transition metals such as Fe and Cu. Slide# 16 : It is a graph shows different kinds of interactions or forces that stabilize protein structure. Slide # 17 ( 3 and 4 structures): *how could we know the final form of a protein whether it is secondary or tertiary? Actually, it is very hard to distinct between these 2 structures. -almost proteins are secondary structures, but we assume that the final form is tertiary structure. So, as a rule: "all proteins have tertiary structures" *do all proteins have quaternary structures? Of course not. *quaternary structures can be either simple or conjugated. *hemoglobin is a conjugated protein that must have heme groups in order to be active. *quaternary structure is the association of polypeptides. If they are 2 we call it dimer, if 3 we call it trimer and so on. It could have 30 polypeptides! Slides # 18 and #19 ( determination of 3 structure ): There are two ways to determin the tertiary structure of a protein : 1-X-ray crystallography : *the protein must be pure in order to make a crystal. *how to make a crystal? We take one drop of the pure protein which is preserved inside a buffer >> we put this drop on a sheet ( make the drop facing down) >> water will start vaporization >> when it is totally evaporated the protein becomes crystallized>> we get a crystal>> we exposure the crystal to beam of X-rays. * ( the next paragraph explains the exact Technique, it is a copy-paste from google, but it is exactly what the doctor have said, but in a different way ) * "A beam of X-rays strikes the crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their disorder and various other information".

3 2-nuclear magnetic resonance (NMR): *the protein is exposed to a magnetic field >> the electrons vibrate. This table shows the differences between these 2 methods: X-ray crystallography 3-D More accurate since its results show the 3-D structure of proteins. Protein is static since it is in crystal form. This is a disadvantage because the protein in nature is dynamic. Some proteins exist in more than 1 conformation. by this method, we can't know these conformations. Nuclear magnetic resonance 2-D Less accurate Protein samples are dynamic (in aqueous solution). So, it is more valuable. *to get real results, we use the two techniques together. *both X-ray and NMR results processed by computerized Fourier series. Slide # 20 ( complex protein structures) : *posttranslational : means ( after translation). *proteins can bind to lipids/ carbohydrates/ phosphate after translation process (posttranslational). *blood groups : ( A, B, AB, O ) *phosphoproteins : phosphate groups bind to amino acids that have an oxygen in their structures. *** please refer to slides because I didn't write all information which are written in the slides. Slide # 21 ( chemical properties of proteins): 1-protein hydrolysis: *recall that amino acids undergo dehydration reaction to make peptide bonds by removal of water. *hydrolysis is the reverse reaction that involves addition of water in order to break down protein. *it requires special enzymes that can hydrolysis proteins. 2-protein danaturation: *it is the loss of 3D structure of proteins. In other words, it is the loss of the active conformation of protein without any change in the sequence of amino acids.

4 *the protein which is denaturated loses its function. *solubility decreases. For example; eggs become hard by heating. * >50 C the protein loses its final form ( becomes hard material). *mechanical agitation : it is shaking of proteins. For example; we make a cream by shaking egg whites. **any protein we digest, it is not absorbed in the stomach as a protein since the stomach acid can't break proteins. So, it must be broken by enzymes to give a single or dipeptides. *denaturation precedes enzyme work. *detergents : they have a hydrophobic side and hydrophilic side that can attach protein and denature it by changing its 3D structure. *organic compounds ( alcohols) : their OH groups bind to bacterial proteins and denature them. (Alcohols are used in hospitals and put on hands in order to denature bacterial proteins). *most denaturation is irreversible, but there are some which are reversible. Slide # 21 ( protein folding & prediction): *bioinformatics : is the application of computer science and information technology to the field of biology and medicine. *nowadays, we can predict the tertiary structure of a protein. *there are databases about ( the structure, domain etc) on some websites for all known proteins. -you have to enter the protein sequence you need to know and search databases of known structures that are homologous to yours. If they are homologous to each other by 25% or more, you can predict the 3D structure. ( please refer to the slide and look at the chart) Slide # 22 : ( hydrophobic interactions & chaperons) *the red color (inside) indicates the hydrophobic side. *the green color (outside) indicates the hydrophilic side. (you can see these colors if you check the soft copy of slides) **proteins can fold spontaneously by themselves or by the help of other proteins ( chaperons). *hsp 70 : Heat shock proteins. *if a problem happens during folding, it leads to some diseases.

5 Slide #23 : ( structure & diseases) *in the past, they thought that mad-cow disease was due to a virus. But now, it is known that the cause is the prion which is a mis-folded protein, and it causes deterioration in the brain. *it can carry the disease to humans. ( in humans, it is called Creutzfeldt-Jakob desiease) **Alzheimer's disease: causes dementia (loss of memory in adults). I'm really sorry for mistakes