Unit 1.5 Flashcards
- protein monomer
amino acids (20 different ones)
protein chemistry
- recognize them by carbon, hydrogen, oxygen and nitrogen and sulfur
- only biological molecule that has sulfur, this is a defining feature
- amino acid starts with a carbon, a carboxyl, an amino and they are acidic
protein naming
- _________ amino acid
o beginning is based on R group and has 4 possible names
• carbon and hydrogen R only: nonpolar
• R is polar: polar
• if there is a NH3+ or any plus: basic
• if there is a o- or anything negative: acidic
• Exception: cysteine has a sulfhydryl which would be non polar but it is actually polar. it will form a covalent bond called a disulfide bridge. This acts polar like so is classified as so
R groups differ in
- size
- shape
- polarity (interactions with water)
- ionization
o acidity, basicity - special additions
o functional groups
o sulfur - We can classify them as polar, non-polar, charged acidic or charged basic.
polymer formation
- condensation synthesis
- forms a peptide bond: c (with double bonded oxygen) with nitrogen (with a hydrogen attached)
- forms dipeptides then polypeptides
- protein name is used when a polypeptide has a job or a function to perform!
4 levels of structure of a protein
primary all to quaternary (only large proteins have this)
- primary
just order of amino acids in a polypeptide determined by the DNA
- secondary
a. 2 types of folding that occur due to R groups and some chemistry of carboxyl and amino functional groups which creates some attraction or repulsion based on the order of amino acids
i. alpha helix
ii. beta pleated sheet
* Kind of randomly mixed versions of both. Determined by the DNA but seems random to us (see ribbon model picture).
- tertiary
a. sometimes, there are positive and negatively charged functional groups in amino acids. This creates a bending and shifting in the molecule to create a 3d shape
b. a series of interactions between R groups (not functional groups!). Folds the polypeptide into a globular shape
tertiary interactions
hydrogen bonds, disulphide bridges, ionic bonds, van der waals, hydrophobic exclusion
hydrogen bonds (tertiary interactions)
(in water)
- found often in proteins
- weak intermolecular force\
disulfide bridge (tertiary interactions)
(in water)
- only in two copies of the same amino acids
- creates a strong covalent bond between sulfur and itself. sulfur can make two bonds
- only happens to cysteine
- intramolecular
ionic bond (tertiary interactions)
(in water)
- any basic functional groups and acidic functional group
- this will form an ionic bond due to their opposite charges
wan der waals force (tertiary interactions)
(in water)
- weak forces (London Dispersion)
- represented by a dotted line
hydrophobic exclusion (tertiary interactions)
- all nonpolar things kind of don’t have any charges for water to attach to
- this causes the things to be excluded
chaperone protein
- can help a polypeptide chain to come together in such a way that these above bonds form
- quaternary
o only some go through this stage
o chemical interactions (most common is hydrogen bond) hold together multiple polypeptide chains
• hemoglobin consists of 4 polypeptide chains that carry oxygen (2 alpha, 2 beta). you can carry more stuff per molecule
protein designation
only 3,4 has a protein designation. You can call a polypeptide chain in tertiary and quaternary a “protein” since it has a function.
proteins and R Groups
- Because the 3rd and 4th structures depend on interactions between R-groups, any change in the environment or any alteration of the R-group characteristics (e.g. by binding to another molecule) can result in a change in the shape of the protein.
- It is these changes in shape that allow proteins to do work = contracting muscles, facilitating chemical reactions, pumping nutrients, receiving chemical signals, etc.
why is A variety of functional groups in the R portion of amino acids important
Different chemical properties along the length that can contribute to the three dimensional folding of the protein
why is 20 different monomers that can polymerize important
A large variety of polymers can be formed, which accounts for the many functions of proteins
why is formation of large polymer chains that have four levels of structure important
One advantage of quaternary structure is that individual peptides can be used as modules in several different functional proteins, allowing more total proteins to be produced by a limited genome.
Another advantage is that a single protein may have multiple active sites, allowing it to catalyze several reactions at once, or to transport several cargo molecules.
active site
binding site for substrate
substrate
the thing that the enzyme breaks down
enzyme substrate complex
the substrate bound to the enzyme together
Describe the effects that enzymes can have on substrates.
Enzymes will lower the activation energy, which is the energy to start a reaction. They will do this by stressing or distorting the bonds of the substrate (reactants) in order to speed up the formation of a product. They are biological catalysts, which means they can be used more than once and are unchanged in the reaction.
denature
prevent it from binding and acting on its substrate. unfolding enzyme. can be refolded but only when the structure is shifted slightly.
pH, temperature, salt can denature an envy,e
rate of reaction remains high
as long as tertiary structure remains
amino acids are replenished in body
through diet.
salty solutions`
- disrupt osmotic gradient
- mess up tertiary folding
- looks like the same graph as an ion
temperature vs rate of reaction
- graph looks a little sideways bell curve. top is “optimal temperature”
- only right side ends due to denatured enzyme
- at the cooler temperatures, the molecules move less so the enzyme would have very little chance of encountering the substrate and colliding with it.
- enzyme also becomes more flexible as solution temperature increases which aids in induced fit
- at super high temperatures, the molecules move too much. hydrogen bonds become weak because of heat. this causes the structure to unfold and even though the collision rate is higher, the structure doesn’t allow it to bond
enzyme concentration
- graph looks like a line more enzymes is more rate of reaction - more stuff so more collisions - it is a linear relationship - when and if a reaction plateau’s , that means that the substrate is all fully reacted
As the enzyme concentration increases, the rate of reaction will increase. This is due to a greater number of collisions
substrate concentration
- graph looks like a line then it reaches a point of saturation and plateaus
excess enzyme then you start increasing the substrate concentration - 100 substrates and 50 enzymes is still 50 enzymes!
- it plateaus at the point of saturation until the enzyme is saturated by the substrate and the rate will no longer increase despite further increase in substrate.
what affects the rate of reaction
substrate and enzyme concentration
pH vs enzyme activity
- There is a bell curve graph with the top being the “optimum pH”
Enzymes have an optimum pH
- Increase or decrease in pH changes ion concentration in solution
- Ions alter structure of the enzymes or substrate
- Additional hydrogen ions (positively charged, acidic) interact with negatively charged parts of enzymes
- Additional hydroxide ions (negatively charged, basic) interact with positively charged parts of enzyme
- Disrupt balance of forces that maintain specific shape
- If the active site is deformed then the substrate can’t bind to the enzyme
nucleic acid function
- making the proteins that are inside the cell
- make up the genes
- also work in transfers of energy. DP is when one phosphate is hydrolyzed. only adenine and guanine do this
directions to make proteins
DNA
making proteins
RNA
nucleic acid polymer
nucleic acid
nucleic acid monomer
nucleotide
nucleotide structure
CHONP
- phosphate group
- 5 carbon sugar (pentose. in RNA it is ribose sugar. DNA is deoxyribose sugar. It has the oxygen removed)
- nitrogenous base (called that because it has nitrogen. this is the one thing that varies in nucleotides)
DNA Nucleotides
- Adenine (2 rings therefore purine)
- cytosine (1 ring therefore pyramidine)
- guanine (2 rings therefore purine)
- thymine (1 ring therefore pyramidine)