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Protein structure group 100241353
- 1. Proteins
- 2. What is protein? Protein structure Secondary Structure: • Stretches or strands of proteins have distinct structural conformations dependent on hydrogen bonding. • The two main types of secondary structure are the α-helix and the ß-sheet. α-helix ß-sheet Primary Structure : • Proteins are produced when DNA is transcribed and translated, producing a chain of amino acids. • The primary structure of the protein is the order of amino acids in this chain. • Proteins are polymers made up of hundreds or thousands of monomer units called amino acids, which are attached to one another by peptide bonds. • Proteins are one of the end products of the decoding process in cellular DNA. • Proteins like collagen and myosin compose structural or motor elements in cells. • Proteins also serve as the catalysts for virtually every biochemical reaction that occurs in living things.
- 3. Hemoglobin Tertiary Structure: • The overall three-dimensional shape of a protein molecule is the tertiary structure. • Certain species in protein molecules will interact causing it to bend and twist in such a way as to achieve maximum stability or lowest energy state. Quaternary Structure: • The quaternary structure refers to how proteins subunits interact combine with one another and prosthetic groups to form larger complexes. • The quaternary structure of the protein is its final form.
- 4. Amino Acids and Their Sidechains -There are twenty different amino acids used by humans to form proteins. -They all share the NH2CHCOOH backbone but have different side chains containing varying functional groups. -Amino acids from proteins by making polymer chains via the peptide bond (OC-NH) through a condensation reaction. -Amino acids like serine and histidine contain oxygen and nitrogen respectively, this allows them to form hydrogen bonds with nearby amino acids, pulling them in closer, changing the shape of the protein. -Some amino acids like leucine have large alkyl chains, making them non-polar providing a hydrophobic effect for that section of the protein. -Conversely amino acids like glutamine is highly polar due to its CONH2 functional group, providing a hydrophilic effect. Leucine Glutamine -Some amino acids have acidic (glutamic acid) or basic (lysine), when near one another, they interact electrostatially, bringing the two amino acids closer together causing the protein to fold. -Cysteine is a sulfur containing amino acid which bonds with other cysteines to form disulfide bonds which are very stable links that fold the protein lowering its entropy. -Creighton, T.E., 1990. Protein folding. Biochemical journal, 270(1), p.1.
- 5. History/ How it was discovered? • The 1950s was the age of understanding the structure and function of polypeptides through the introduction of spectroscopic techniques, although it was 1819 when the first amino acid Leucine was discovered. • Linus Pauling was credited with introducing the first substantial development through his discovery of the spiral structure. • This formed the basis upon which Watson and Crick were able to identify the structure of DNA as a double helix. • Additionally, Pauling pioneered the concept of the hydrogen bond. [1] • In 1955 British biochemist Frederick Sanger first investigated the primary structure of a protein through this experiment identifying the amino acid sequence in Insulin resulting in him winning a Nobel Prize. • Christian Anfinsen was also incredibly influential in this field, with his main achievement of protein folding theory; “the native conformation is determined by the totality of interatomic interactions and hence, by the amino acid sequence, in a given environment ” as he so characterized in his 1972 Nobel acceptance speech. [2] • The abilities of computational protein structure prediction in recent years has played an instrumental role in the aiding the discovery of the 40,000 known proteins (figure accurate as of 2006) • [1] chemproject (upenn.edu) (accessed March [2] Figure 1: shows a proteins spiral structure including hydrogen bonds present in both α-helix and β-sheet proteins
- 6. Protein synthesis • How are proteins in our bodies produced? • 1. DNA unwinding so it can be copied. • 2. mRNA is extracted to cytoplasm • 3. Ribosomes read the mRNA • 4. tRNA brings amino acids to the ribosomes • 5. Ribosomes create a long polymer chain – primary protein. 1.https://www.ck12.org/chemistry/protein-synthesis-in-chemistry/lesson/Protein- Synthesis-CHEM/ (accesed March 2021).
- 7. Human genome project • The hundred thousand genome project was set up in 1990 in order to map out 3 billion base pairs in a human genome! • The inovation of chemists turned this possible. • Process was driven by the power of chemical research and computing. • The mapping of human genome offers a chance to treat life threatening sicknesses. 1. A. Andrew Burrows B. John Holman C. Andrew Parsons D. Gwen Pilling E. Gareth Price; Chemistry3, Oxford University press, Great Clarendon Street, Oxford, OX2 6DP, United Kingdom, Third edition, 2017, Chemistry: the central science, 4-6.
- 8. Lab-instigated protein synthesis • Cultured meat is an upcoming scheme in which meat will be grown/printed in a lab rather than taken from an animal or with the use of excessive antibiotics. [1] Not only is it better for the animal, but it is also better for the environment. • Scientists have been able to grow skin in a lab too. They were then able to implant these tissues into living mice, and the tissues formed connections with other organ systems such as nerves and muscle fibres. This work opens a path to creating functional skin transplants for burn and other patients who require new skin.[2] [1] HK Handral et al., Critical Reviews in Food Science and Nutrition, 2020 early access [2] https://www.sciencedaily.com/releases/2016/04/160401144507.htm accessed March 2021
Editor's Notes
- What is a protein? – back to some basic biology, Proteins are polymers made up of thousands of amino acids joined by peptide bonds. They are formed by translation and transcription of DNA by ribosomes. There are 3 types, fibrous (keratin and collagen in hair/nails), globular (haemaglobin and insulin), and membrane (such as intrinsic proteins embedded in the phospholipid bilayer of all cells) Primary Structure – The primary structure of a protein is simply the order of amino acids in the chain and is read from the amino terminal end to the carboxyl terminal end. 500 AA in nature Secondary Structure – Tthe order of amino acids in the protein influences which amino acids can interact through hydrogen bonds and form dipole moments. These intermolecular interactions cause the protein to twist and fold, mainly forming alpha helices and beta pleated sheets
- Tertiary Structure – TS is simply the 3D shape; This can come from further bending or folding or it can be due to Different amino acids can containing species that can then form bonds with other amino acids. Cysteine is an amino acid contains sulfur so is able to form disulfide bonds. These species also interact with surrounding water molecules and can even repel other species in the protein. Quaternary Structure – The quaternary structure is formed when multiple proteins can come together forming larger protein complexes to carry out certain functions. Non-protein species, known as 'prosthetic groups', can also bind with proteins to augment their function. One example of this is hemoglobin, it is comprised of 2 lots of 2 different 'globulin' proteins that are centered around the iron containing prosthetic group 'heme', which allows the protein to bind to oxygen molecules and transport it through the blood stream.
- Amino Acids – amino acids are the monomer units that form the polymers we call proteins. They form peptide bonds with adjacent amino acids in a condensation reaction. All amino acids have the same the alpha amino acid backbone but each type of amino acid has a different side chain. These side chains contain various functional groups with differing properties which ultimately determine the shape and therefore the function of the protein. Hydrogen Bonding – hydrogen bonds can form between lone pairs belonging to Fluorine, Nitrogen or Oxygen atoms and exposed hydrogen atoms. Some amino acids like serine and histidine contain Oxygen and Nitrogen atoms respectively, this allows them to form hydrogen bonds with nearby amino acids altering the shape of the protein. Polar/Non-polar – Amino acids like leucine and isoleucine have large alkyl groups for side chains, making them less polar and therefore less hydrophilic. Other side chains are rich in polar bonds, making the amino acid more hydrophilic, causing repulsion between these types of amino acids. More hydrophilic amino acids also tend to face the outside of the protein since proteins mostly subside in aqueous conditions, further effecting the shape of the protein. Acid/Base - Electrostatic attractions form between acidic and basic side chains, these attractions cause the protein to fold. Though having two like charged amino acids together causes electrostatic repulsion to occur, opening up the protein structure. Disulfide bridges – some amino acids like Cysteine contain sulfur atoms that can bind to other sulfur atoms on other Cysteine side chains, forming disulfide bridges. This binds the two amino acids together forming a strong link between the two sections of the amino acid chain. -Each of these functional groups work together in sequence to form and maintain the most thermodynamically stable protein strcture tailored to its specific function.
- Recognised as a class of biological macromoleules in 1789 by Antoine Fourcroy. By 1837 Gerhardus Johannes Mulder was able to analyse some common animal and plant proteins where he found that the majority of proteins shared the same empirical formula (C400H620N100O120) The biggest structural discovery before the 1950's was the peptide bond by Emil Fisher and Franz Hofmeister. Discovering the spiral structure of proteins consequently enabled DNA coding to be understood by geneticists, helping them to understand the prevalence of inherited genetic disorders and generate techniques in which to treat them. Frederick Sanger used the partition chromatography technique to identify free amino acids located at the N terminals of the insulin polypeptide chains. To summarise his findings Christian Anfinsen used his thermodynamic hypothesis to state that it was the intrinsic structure of proteins which is the most stable version of that polypeptide in its respective environment.
- Proteins are used in variety of ways in the human body. It is the most abundant substance in the body apart from water. But how all these proteins in our bodies are produced? The key here is DNA, simply DNA is a chain of millions of nitrogenous bases, Adenine, Guanine, Cytosine and Thymine. Sections of these bases are called genes and each gene is responsible for producing a different protein. In the gene there are bases which are grouped into triplets known as codons that have a corresponding amino acid and the sequence of these bases determines the primary structure of proteins. In order for this sequence to be translated into a protein, it first must undergo transcription into mRNA. DNA is locked into a double strand in order to keep the base sequence safe so enzymes are used to separate the strand. More enzymes are then used to pair up complementary bases in RNA rather than DNA, this new strand is called mRNA. The mRNA is then transported out into the cytoplasm where it is then transported to structures called ribosomes. Ribosomes are combinations of protein and RNA that pair up the mRNA base triplets to their corresponding amino acids with the use of tRNA molecules. Once in the ribosome, peptide bonds are formed between the adjacent amino acids, forming a long chain of amino acids that make up the primary structure of a protein. This is how DNA is used to consistently produce proteins with a specific structure. The abundance of genes determines how much of a protein is expressed which then determines all characteristics expressed by an organism
- The HGP aka the hundred thousand genome project is by far one of the most ambitious projects in the history of humanity. It's an international project set up in 1990 in order to map out 3 billion base pairs in a human genome. To identify the sequence of DNA chemists have designed a system that pairs different coloured fluorescent molecules to corresponding bases, the sequence of these colours tells you the sequence of bases. This technique was developed by the Sanger institute in Cambridge. When it was first developed it took years to process the DNA of one person and cost millions, now it takes a matter of hours and is commercially available to everybody. Genome sequencing opens up a whole new approach to medicine since it reveals what each patients DNA is producing allowing treatments to be personalized to each patient. It also allows genetic disorders to be tackled far more effectively since the specific nature of the genetic disorder can be identified. Gene editing is another promising future field of medicine that will rely heavily on genome sequencing.
- Cultured meat - the concept of producing meat sustainably in laboratory conditions without the sacrifice of animal life and the excessive use of antibiotics. 3D printing could offer unique solutions for the vital issues of cultured meat production; particularly on regulating the protein, fat, and other nutritional content, along with providing realistic texture.Consumer attitudes towards meat are shaped by sensory aspects of meat (e.g., appearance, texture, flavour; the type of meat (e.g., red meat, white meat, fish; marketing factors (e.g., price, label, brand; s well as health and ethical concerns. Skin grafting – involves stem cells and excess amino acids to help grow new skin in a lab. initially struggled to grow sebaceous glands. With moreand more people going vegan/vegetarian, meat substitutes are needed now more than ever. Cultured meat the concept of producing meat sustainably in laboratory conditions without the sacrifice of animal life and the excessive use of antibiotics. 3D printing could offer unique solutions for the vital issues of cultured meat production; particularly on regulating the protein, fat, and other nutritional content, to help fight against rising numbers of obesity along with providing realistic texture. Consumer attitudes towards meat are shaped by sensory aspects of meat (e.g., appearance, texture, flavour; or the type (red. White, fish); s well as ethical concerns so this is being researched contantly.