Chem 32 ch. 13
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What are biomolecules?
Molecules made exclusively by living organisms.
What is an amino acid?
Any compound that has a carboxylic acid and and an amine is an amino acid ( -amine-, carboxylic -acid- ). Though amino acid usually refers to a compound where the carbo acid and amine are separated by a single carbon atom, called the "alpha carbon".
What is an amine?
An amine is a nitrogen N bonded to at least one alkyl group ( CH2-CH... ) and a couple other things ( often two H atoms ) so that 3 of its 5 valence electrons are filled, leaving a lone pair.
A fourth electron can be occupied by another H or something else, giving the N a positive charge.
What is a zwitterion?
A zwitterion is a molecule that has both a positive and negative ionic charge.
In amino acid the carbox acid group reacts with the amino group so that the H at the end of the carbox acid detaches and attaches itself to the N on the amine. This leaves the O on the carbox acid end with a negative charge and the N on the amine side with a positive charge.
The amino acid can exist in the non-zwitterion form but it's normally found in the zwitterion form.
What is the alpha carbon in an amino acid?
It is the carbon that separates the carbox acid and amine.
What is the side chain in an amino acid?
There are 20 amino acids that most proteins are made of.
They each have the same base of amine-C-carbox acid.
The C is the alpha carbon, attached to this is the side chain and it is this part that differentiates the different amino acids.
There are 11 hydrophilic amino acids and 9 hydrophobic amino acids.
The hydrophilic ones have side chains that are attracted to water and the hydrophobic ones have side chains that are not.
The amine and carbox acid parts of amino acids are both attracted to water so even the hydrophobic amino acids can usually dissolve in water.
When hydrophobic amino acids combine to form a protein, the hydrophobic side chains avoid water.
The 11 hydrophilic amino acids can be identified by their side chains...
The side chains will have either OH, NH, or C-O / C=O groups that will be able to bond with water. If it does not have these groups then it is -not- hydrophilic.
Of these 11 hydrophilic amino acids, 6 are -neutral-. They can be identified by their sidechains -not- having any ionized atoms - there are no plus signs or minus signs on any of the side chain atoms and have no charge at physiological pH.
3 of the hydrophilic amino acids are -basic- and are positively charged at physiological pH. They can be identified by the little plus signs on the N atoms. The N atoms also have four things bound to them.
2 of the hydrophilic amino acids are -acidic- and are negatively charged at physiological pH. They can be identified by the minus signs on the O atoms of the side chains.
Amino acids are classified based on their unionized forms, regardless of the pH of the solution they exist in.
Some of the amino acids classified as acidic exist in physiological pH as slightly basic.
Just because it is called "acidic" does not mean it has acidic properties at physiological pH.
Pretty dumb, huh?
Hydrophobic amino acids can be recognized...
By their hydrophobic side chains. They are made up of C and H and do not bond with water.
To recap classifying amino acids...
- Look at the side chain.
- If the side chain is all Cs and Hs then it is hydrophobic and nonpolar.
- If the side chain has OH, OH, or C-O/C=O then it can bond with water and is hydrophilic.
- If the hydrophylic side chain has negatively charged ions ( anions ) then it is acidic.
- If they hydrophilic side chain has positively charged ions ( cations ) then it is basic.
- If they hydrophilic side chain isn't ionized at all then it is polar neutral.
In almost all common amino acids ( except glycine ) the alpha carbon is chiral.
This means that most common amino acids have two possible forms called enantiomers
What is a dipeptide?
When two amino acids bond with each other due to condensation. The OH comes off the carbox acid group of one amino acid and the H comes off the amine group of another amino acid and they bond where the bits came off.
If zwitterion forms of the amino acids are used ( +N amine on one side, -O carbox acid on the other ) then the -O comes off the carbox acid and two Hs come of the amine side and the two broken parts bond together.
What is a peptide group?
The peptide group is where the two zwitterion amino acids bonded together, it kind of looks like O=C-N-H.
The O in this group is strongly positive and the H strongly negative, making this part of the molecule very polar.
What is the peptide bond?
The peptide bond is between the C and the N in the peptide group. It is the bond that is formed between the broken off pieces of the two zwitterion amino acids.
Peptides can be classified by how many amino acids they are made of.
Two amino acids are a dipeptide and share one peptide group.
Three amino acids are a tripeptide and share two peptide groups.
Four amino acids are a tetrapeptide and share three peptide groups.
What is a polypeptide?
A polypeptide is a large number of aminio acids bonded together.
Proteins are actually polypeptides with usually 100 - 500 amino acids, though some are larger and some smaller.
What is the primary structure of a protein?
Proteins are made of a long chain of amino acids, the order in which these amino acids are arranged is called the primary structure
What are N-terminal amino acids and C-terminal amino acids?
The N-terminal amino acid is the amino acid at the end of the protein that has the amine group.
The C-terminal amino acid is the amino acid at the other end of the protein that has the carboxylic acid group.
What is an alpha helix protein?
In an alpha helix protein the backbone of the protein forms a tight coil with the side chains pointing outward.
In the alpha helix proteins the positively charged hydrogen and negatively charged oxygen point up and down and attract to each other, helping maintain the helix shape.
This is a secondary structure.
What is a beta sheet protein?
Beta sheet proteins have backbones that lie straight with the side chains pointing up and down. Layers of these proteins lay upon one another to form a sheet.
In beta sheet proteins the positve hydrogen atoms and negative oxygen atoms point towards each other and hold each other together.
This is a secondary structure.
What are beta turns in proteins?
Beta turns occur in beta sheet proteins where a long protein chain bends over on itself, kind of zig-zags.
Proline has a shape that facilitates this because it is almost horseshoe shaped. So, where there is proline in a beta sheet protein there is a beta turn.
What is special about callogen?
It gives tissue of skin, bone, cartilage, etc. its strength.
Callogen is made partially of proline and hydroxyplroline, which is very similar in structure to proline, just has an extra alcohol group on it.
Callogen is also made of glycine which is a very small, compact amino acid. The small size of glycine and the bending-in-on-itself nature of proline and hydroxyproline help build callogen in a tightly wound tripple helix that has a lot of strength.
What are three classes of proteins?
Globular - the polypeptide chain is folded in on itself and it gets all bunched up, like a ball of string. Enzymes and transport proteins are globular proteins. Usually water soluble.
Fibrous - the protein has a long, narrow shape, makes up hair, ligaments, tendonds... long things. Not usually water soluble.
Membrane proteins - anchored in the membranes that surround cells, they come in all kinds of different shapes.
Fibrous proteins usually fold into alpha helix or beta sheet proteins.
Globular and membrane proteins fold into all kinds of different structures.
Fibrous proteins usually fold into alpha helix or beta sheet proteins. These are secondary forms of proteins.
Globular and membrane proteins fold into all kinds of different structures. These are tertiary forms of proteins.
Have the hydrophobic amino acids at the center of the protein.
Have most of the hydrophilic amino acids on the surface of the protein.
Have ionized amino acids with oppositely charged ionized side chains that occur in pairs, positive at pH7 next to negative at pH7.
Have many of their S containing side chains bonded together to form disulphide groups ( S-S ).
When a protein is dissolved in water...
The non-polar hydrophobic side chains turn towards the inside of the protein. This is called the hydrophobic interaction.
The polar hydrophilic side chains turn towards the outside of the protein. This is called the hydrophilic interaction.
Side chains in proteins can interact with each other...
The hydrophilic side chains can bond with each other rather than with the surrounding water.
At pH7 acidic side chains form anions ( negative ) and basic side chains form cations ( positive ) and these attract to each other.
Sulfur containing side chains can form disulfide bonds with each other.
Membrane proteins are in the cell wall or membrane of a cell...
Part of the membrane protein is outside the cell, this part is slightly polar.
Part of the membrane protein is inside the cell, this part is slightly polar.
Part of the membrane protein is within the cell membrane itself and this part is very nonpolar.
What are the primary, secondary, tertiary, and quartenary structure of proteins?
Primary structure is just the specific order of the amino acids that make up the polypeptide chain, there'll be 100 to 500 of them in a row, but sometimes less, sometimes more. They do -not- lie in a perfectly straight line but it makes it easier to think of this structure in that way.
Secondary structure is when the "straight line" of the primary structure curls into an alpha helix or folds into beta sheet shape. The H+ and O- attract to each other and the straight line folds into a coil or zig-zag that is the secondary structure.
Tertiary structure is when the protein / long chain of amino acids / polypeptide has a-helix, b-sheet, and primary structure all along the same polypeptide and the side chains of these different structures interact with each other and pull the different structures together into a kind of globular shape. This is the tertiary structure.
Quartenary structure is when two or more polypeptide chains are attracted to each other due to hydrogen bonding, ionic bonding, disulfide bridges, etc. and stick together due to these bonds.
What is "denatured"?
When the structure of a protein is changed so much that it can no longer carry out its function.
What are some things that can denature proteins?
Heat - atoms move faster and cannot maintain the bonds between amino acids.
Changing the pH of the surrounding solvent - if the solvent is made very acidic then it can disrupt the ion-ion bonds by adding extra Hs to ions.
Agitation - will simply mechanically break the bonds.
Adding ionic substances like soap - again, messes with the ion-ion bonding.
Putting the proteins in a different solvent - proteins may do fine in water where the hydrophobic interactions and hydrophilic interactions keep the protein held together but when there aren't so many H+ and O- for things to attract to or repel from the attractions can fail and the protein changes shape.
What is an enzyme?
An enzyme is a catalyst that can speed up a reaction yet not be consumed by the reaction. It can also determine very specifically the result of the reaction.
Enzymes are proteins, or, protein catalysts.
What are substrates?
Substrates are the reactants that an enzyme uses to produce a specific product.
What are three steps an enzyme goes through to catalyze substrates?
The enzymie binds to the substrate(s).
It breaks bonds and helps create new ones.
It releases the product.
What is the active site of an enzyme?
It is a cavity in the enzyme into which the substrates will fit. The fit into the active site by simply fitting in by accident, bumping into it, or could be attracted to it due to ionic charges at the active site attracting oppositely charged substrates.
The active site will also change shape to hold the substrate(s) firmly in place.
What is the enzyme-substrate complex?
It is the point in enzyme catalysis of a substrate where the substrates actually become attached to the enzyme.
The amino acid side chains at the active site hold the substrate in place in a specific orientation.
What is the enzyme-product complex?
It is the combination of the active site and the product that is created post-reaction.
What is the "activity" of any enzyme?
The activity of an enzyme is the number of times it can carry out a reaction in one second. Typically between 10 to 1000 times a second but can be as slow as more than a second per reaction or as fast as 1 million reactions per second.
What things can affect enzyme activity?
Temperature - different enzymes work best at certain temperatures.
pH of solvent - different enzymes work best at certain pH levels.
What is a competetive inhibitor?
A competitive inhibitor is a substrate that will fit into the active site of an enzyme but cannot be catalyzed by the enzyme so it just kind of awkwardly sits there until it detaches unchanged and leaves the active site.
What is an effector in regards to enzymes?
An effector is a molecule that can bind to cavities in the enzyme ( which are not the active site ) that change the shape of the active site.
Positive effectors change the shape of the active site so that catalysis is possible.
Negative effectors change the shape of the active site so that catalysis is slowed down but not completely stopped.
What is a cofactor?
A cofactor is an ion or molecule ( but not an amino acid ) that is required by an enzyme to be able to catalyse substrates.
What are the two categories of cofactors?
1. Certain metal ions, ones found in human nutrition. These ions are mostly covalently bonded to the enzyme. We get these metals from the food we eat.
2. Coenzymes. FAD, NAD+, etc.. FAD will permanently bond with the enzyme, NAD+ will just kind of bump into the enzyme and hang around long enough to fascilitate catalyzation. It actually performs as a substrate.
What are coenzymes?
Complex organic molecules that our bodie build froms maller pieces. Our bodies can manufactures some of these smaller pieces but others must come from the food we eat.
B vitamins cannot be manufactured by our bodies and must be consumed so our bodies can use them to make the coenzymes.
The proteins that make up our bodies eventually break down into the amino acids that made them up.
The proteins that make up our bodies eventually break down into the amino acids that made them up.
What are essential amino acids?
They are amino acids that our bodies need but are not able to manufacture. They are...
What are complete and incomplete proteins?
Complete proteins are proteins that contain all the essential amino acids that our bodies cannot make. They are complete because they have all the amino acids we need. Complete proteins come from animals.
Incomplete proteins are proteins that do not have all of these essential amino acids, incomplete proteins come from plants.
What are nonessential amino acids?
They are amino acids that our bodies are able to make on their own.
Our bodies need nitrogen from amino acids to make other amino acids.
We may be able to manufacture some of our own amino acids but we need nitrogen from -other- amino acids to do this.
Dietary requirement for protein has two parts...
1. Essential amino acids - the amino acids we cannot manufacture ourselves and need to consume from food.
2. Total protein - We need to eat enough protein to get the nitrogen from the amino acids they are made of to build other amino acids.
What is nitrogen fixation?
The process in which bacteria take N2 from the environment ( N2 being unusable by most organisms ) and process it into N4 ( ammonium ).
N4 is then able to be absorbed by plants but most of it is actually broken down by the bacteria responsible for the nitrogen fixation into NO2- or NO3-.
Plants can absorb these ions and turn them -back- into ammonium ions.
Bacteria can also take the nitrate and nitrite ions and turn them -back- into N2. This completes the nitrogen cycle.
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