B.1.2 Flashcards
(12 cards)
Structure of an amino acid
The structure of an amino acid consists of an alpha carbon bonded to a carboxyl group and an amine group either one opposite the other, as well as bonding with a singular hydrogen and an R-group; these other two being opposite each other as well.
All amino acids have the same basic structure said above but the part that sets them apart is the R-group. The R-group is not an actual group, it is a place holder, the R-group changes depending on the amino acids.
The way that amino acids bond to make polypeptide chains is with peptide bonds using condensation reactions between the amine group and the carboxyl group. Depending on what the R-group is, a peptide reaction could occur there as well.,
Essential amino acids in diet (vegan stuff)
There are 20 essential amino acid types that organism need, plants for instance can make all of them by themselves through photosynthesis, but animals like humans cannot and must get the amino acids through consumption. Humans can produce 11 out of the 20 amino acids on their own but they need to get the 9 missing from their food. Vegans, since they do not eat foods that come from animas that have similar contents of amino acids that humans need they must take supplements to maintain a healthy diet since plants lack in some areas.
pH and temp on protein structure
Messing with pH or temperature on proteins will cause them to denature because it breaks the structure of the protein and breaking the structure causes the protein to not be able to do its function anymore.
For temperature, increasing the one of a protein will cause it to start moving faster therefore working faster but at one point if the temperature continues to increase the protein will denature since it will move so fast it will break down. This is seen in eggs in the egg white, when non cooked the egg white is transparent because all the proteins are aligned, but once it is cooked it turns white because all the proteins are no longer aligned and all over the place.
For pH, it is because the charges are changed, both negatively and positively in acidic or alkaline solutions. What happens is that the changes in charge break the ionic bonds in the proteins or causes new unhelpful ones to appear.
What happens is that the bonds between R-groups in 3 dimensional proteins are broken down since they’re weaker and therefore the protein denatures and becomes unstable, this is often irreversible.
Proteome
All the expressed proteins found in the body
Polypeptide reaction
For a dipeptide to form, two amino acids need to create a peptide bond through a condensation reaction. This happens with the -OH of the carboxyl group reacts with the -H of the amine group, joining together removes these molecules to create H2O and joins the C and N forming the peptide bond. This process takes place in the ribosome. When forming larger chains (more than 2 is an oligopeptide, more than 20 is a polypeptide, a combination of polypeptides is a protein) the new amino acids is always added to the carboxyl group of the growing polypeptide.
Secondary protein structure
Inside the polypeptide chain that forms the primary structure, the peptide bonds between amino acids generates polar groups that attract each other and create folding in the chain, The oxygen in the carboxyl group (C=O) is slightly negatively charged and the hydrogen of the amine group (N-H) is slightly positively charged, this causes hydrogen bonds between the newly formed polar groups. These hydrogen bonds happen on non-adjacent polar groups and cause regular and unvarying structures.
The alpha-helix is an example of the secondary structure. This type is when the polypeptide is folded in a helix-like shape. Due to the hydrogen bonds between every 4 amino acids the chain coils spirally.
Another example is the Beta-pleated shape where the polypeptide chain becomes pleated because of the hydrogen bonds between parallel parts of the chain. Each of these parallel parts runs in te opposite direction, forming a pleated shape.
Conjugated proteins
Conjugated proteins are proteins that have non-polypeptide components involved in the protein structure and its functions, these non-polypeptide components are called the prosthetic group.
EXAMPLE OF CONJUGATED PROTEIN
Haemoglobin is a conjugated protein that is made of four polypeptides, each one bonding to a haem group (this being the prosthetic group part).
The 4 polypeptides are divided into 2 alpha globin plus 2 beta globin polypeptides each of theme bounded to a haem group.
The haem group contains an iron that binds to oxygen reversibly in the lungs and transports it to the body tissues where it is released. The haem group can also bind reversibly to carbon dioxide.
EXAMPLE OF A NON-CONJUGATED PROTEIN
Insulin is a globular protein that is synthesized in the liver. In translation it is in the primary protein structure as a single polypeptide chain but during protein processing it is spit into 2 polypeptides joined by 3 covalent disulfide bonds.
When insulin binds to the target cell it stimulates glucose uptake into the cell to be stored as glycogen that way it reduces glucose blood levels.
Another example is collagen, it is a fibrous protein that is made up of 2 polypeptides that are wound around each other that form a helix shape with a high tensile strength. The polypeptide chains are joined together by hydrogen bonds. These proteins are found in skin, blood vessel walls, ligaments, and tendons having a structural function.
Fibrous and globular proteins
Fibrous proteins
These type of proteins have a structural role and are themselves structured in either strands or sheets (seen in collagen or spider silk), these are formed usually by repeated amino acid sequences and is usually the primary structure of proteins (little times can be secondary but never tertiary or quaternary structures). They appear as filaments or narrow fibers. They are not soluble in water and have more stability in more varied conditions. (See collagen and spider silk for examples).
Globular proteins
These types are used to catalysis, transport, or a specialized role. They have a more rounded shape and are structured by folding up polypeptides, many bonds between the R-group of amino acids in the tertiary structure and some in the quaternary structure. Globular proteins are soluble in water and are more sensitive to changes in temperature or pH. (For examples of this see insulin, immunoglobulin etc.)
Primary Protein structure
The primary structure in proteins is the most basic structure and is seen in fibrous proteins. It is defined as a polypeptide chain where the carboxyl group bonds to the amine group between amino acids with peptide bonds. They all have the same backbone of (N-C-C-N-C-C-N…) with differing R-groups.
The bonds in this chain are angled and there can be rotations between the alpha carbon and the carboxyl and amine group bonds but not between the peptide bonds.
Proteins have a precise, predictable and repeatable structure determined by the primary structure.
Tertiary protein structure structure
The tertiary structure depends on the secondary and primary structures before it. What happens is that basically the polypeptide chain folds and coils further to form a complex 3D structure that is determined by the interactions between the R-groups of the amino acids.
The different kinds of intramolecular interactions are:
- Ionic bonds: Bonds between a positively charged and a negatively charged R-group
- Hydrogen bonds: Bonds that are between slightly negatively charged and slightly positively charged atoms of the R-groups.
- Disulfide covalent bonds: Bonds between the sulfur atoms of cysteine (meaning has a sulfur in the R-group) R-groups, this is the strongest bond of all.
- Hydrophobic interactions: Bonds between non-polar R-groups. It’s usually in the interior of the molecule to avoid contacting with water, and its a weak bond.
Examples of proteins
RUBISCO (globular protein)
This polypeptide is an enzyme that catalyses the reaction that takes carbon dioxide from the atmosphere. It’s the most abundant protein found on Earth, found in photosynthetic organisms such as plants, and algae, especially high concentrations in algal cells and leaves. It provides a source of carbon from which all carbon compounds needed for living organisms are produced.
INSULIN (globular protein)
Insulin is a hormone that signals many cells to absorb glucose and helps reduce the glucose concentration in the blood (important because too much glucose in blood can cause osmotic issues). Affected cells have receptor proteins on their plasma membrane which insulin can bind to. The cells that secrete insulin are called pancreatic beta cells, this secreted insulin then is transported by the blood.
Since type I diabetics cannot produce enough insulin they need to periodically inject synthetically produced insulin to correct their blood sugar concentration.
IMMUNOGLOBULINS (globular protein)
Immunoglobulins are better known as antibodies used in the immune system. These antibodies have 2 antigen binding sites on each “arm”, this is to provoke an immune response incase there is a pathogen (who would be releasing the antigens). These binding sites change drastically between immunoglobulins to be able to respond to a wide variety of pathogens. The binding sites are not the only parts of immunoglobulin that cause a response, for example they act as a marker to phagocytes which can engulf the pathogen.
RHODOPSIN (globular protein)
This protein is a pigment that absorbs light, it is found in the rod cells in the retina (the light sensitive area in the back of the eye). Rhodopsin allows for vision in very dim light since very low light intensities can be detected. They way it works is, retinal molecules absorbe a single photon of light which changes shape causing a change to the opsin/rhodopsin then the rod cell sends a nerve impulse to the brain.
COLLAGEN (fibrous protein)
Collagen is a rope-like protein made of 2 polypeptides wound together, it forms a mesh of fibres in skin and in blood vessel walls that helps resist tearing. This protein gives strength to tendons, ligaments, skin, and blood vessel walls, it also forms part of teeth and bones, and helps prevent cracks and fractures to bones and teeth. About a quarter of all protein in the human body is collage.
SPIDER SILK (fibrous protein)
This type of collagen is incredibly strong, it is stronger than steel and tougher than Kevlar. When it is first made its bottom region contains polypeptides that form parallel arrays, in the middle region it seems like a disordered tangle. When it is stretched the polypeptide gradually extends which makes the silk extendible and very resistant to breaking.
Quaternary structure
The quaternary structure is when 2 or more polypeptides that have the tertiary structure join together, they can be conjugated or not conjugated.
