- Enzyme structure and function questions
- Enzyme structure and function
- Introduction to enzymes and catalysis
- Enzymes and activation energy
- Induced fit model of enzyme catalysis
- Six types of enzymes
- Co-factors, co-enzymes, and vitamins
- Enzymes and their local environment
Enzymes are proteins that facilitate chemical reactions in living organisms. There are six different types of enzymes. Oxidoreductases manage redox reactions, transferring electrons between molecules. Transferases are responsible for moving functional groups from one molecule to another. Hydrolases are able to break chemical bonds, while lyases create new bonds by removing or adding functional groups. Isomerases rearrange atoms within a molecule, and ligases help join two separate molecules together. Created by Ross Firestone.
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- the order of enzyme classification isn't this
6 ligases(33 votes)
- It's a standard convention. If a biochemist refers to an enzyme belonging to Group 3, for example, it's internationally understood that she is talking about a hydrolase.(8 votes)
- What type of enzyme is catalase?(12 votes)
- Since the breakdown of hydrogen peroxide into water and oxygen is an oxidation-reduction reaction, I think that catalase would most appropriately be categorized as an oxidoreductase enzyme.(24 votes)
- What exactly is tRNA? I've never heard of it before. I'm asuming its 'transfer' due to it's interaction, but I'm not exactly a chemist.(4 votes)
- I like to think of tRNA as a shuttle.
The "t" is for "transfer" because tRNA transfers an amino acid to a growing polypeptide (i.e future protein).
This occurs during the Translation ( another "t" word ;) ) of mRNA into a string of amino acids that will make up a polypeptide strand.
mRNA, like DNA, is made up of nucleotide sequences called codons.
Each codon is three nucleotide characters long.
So an mRNA strand, the strand being translated from nucleotide into amino acid string (aka polypeptide), is made up of a string of codons.
Here's an example:
think of AUGCUAUAA as AUG - CUA - UAA ,
where AUG, CUA, and UAA are each individual codons which code for one of the 20 standard amino acids that comprise the proteins of all living species (spp).
(Neat fact: There are actually over 400 naturally occurring amino acids, though you will only see the standard 20 making up living spp here on earth.)
UAG is the only START codon of these 20.
In some classes you may need to be able to recognize this.
The 3 STOP codons that you may also be expected to recognize are UAG , UGA , and UAA .
Each tRNA has an anticodon which bonds to a specific codon found along an mRNA strand.
mRNA strands are comprised of a string of codons.
Whereas, tRNA molecules poses complimentary anticodons along their coiled up RNA strands (which are actually coiled up into the general shape of a letter "t").
So the tRNA anticodon sequenc for the AUG codon will be UAC.
This tRNA molecule with the UAC anticodon will carry a specific amino acid to the AUG codon, found on the mRNA molecule that's being translated.
Similarly, the tRNA molecule with the GAU anticodon will carry a specific amino acid that matches with the CUA codon.
And the tRNA with the AUU anticodon will carry a specific amino acid to the UAA codon.
Think of the top of the "t" as carrying the amino acid and the bottom of the "t" as carrying the complimentary anticodon sequence that will bond to a specific codon sequence on an mRNA strand.
When DNA strands bond to other DNA strands,
as seen in DNA replication:
T bonds to A (via 2 hydrogen bonds) and
G bonds to C (via 3 hydrogen bonds).
However, it is important to remember that RNA has a U in place of a T.
So when a DNA strand bonds to an RNA strand,
as seen in transcription from DNA to mRNA,
the A from a DNA strand will bond to a U (instead of T) on an RNA strand.
Also, when a RNA strand bonds to another RNA strand,
as seen here in translation,
the A from one strand bonds to the U on another, and vise versa.
This is why the A from the mRNA strand bonds to the U from the RNA strand in the tRNA molecule.
Notice, this is because tRNA and mRNA are both RNA molecules.
And this is how specific codons code for / call for specific amino acids.
i.e. this is how the mRNA language is "translated" into the amino acid language.
It is worth knowing that each codon codes for only one amino acid.
For example: UGA will only ever code for one specific amino acid.
And you will usually be given a chart for figuring out which amino acid that is.
Yet some amino acids are actually coded for by multiple codons.
More important related information:
Translation takes place at the ribosome in the cytoplasm.
There are free ribisomes as well as ribosomes bound to endoplasmic reticulum (ER).
ER with bound ribosomes is called rough endoplasmic reticulum (RER).
With the help of tRNA molecules, mRNA, which was transcribed from DNA in the nucleus, is translated into a polypeptide chain at a ribosome found in the cell's cytoplasm.
The mRNA strand is translated in the 5' ---> 3' direction.
mRNA: 5' - AUG - CUA - UAA - 3'
AUG will translate the first amino acid, CUA the second, and UAA the third.
The polypeptide chain only constitutes the primary (1') structure of a protein.
So polypeptide strand folding into secondary (2'), tertiary (3') and quaternary (4') protein structures takes place after translation.
Here's a great Khan video about "The four levels of protein structure":
Hm... We really need a detailed video to sum all of this up...
Just found Khan video about protein translation!
Biomolecules: DNA: Protein Translation:
Haven't watched this yet. I'm sure it's excellent. Good luck! :)(21 votes)
- At7:10Why does lyase need to generate a double bond or ring structure to break apart a bond?(8 votes)
- The answer to your question is because that is how this class of enzymes work. When they catalyze the lysis reaction they catalyze the removal of a group from a molecule to form a double bond, or they add a group to a double bond.
If you are asking how they do it, then that is a more complicated question where you would need to look at the active site of the enzyme, the substrate being reacted upon, and the reaction mechanism of the particular reaction to determine how exactly the double bond or ring structure is being formed to break apart the molecule.(4 votes)
- aren't arginine and fumarate the products of arginiosuccinate lyase?(5 votes)
- According to the Lehninger Principles of Biochemistry Textbook, you are correct Argininosuccinase catalyzes the reaction where Argininosuccinate is cleaved into L-Arginine and Fumarate.
You should raise this point under the Report a Mistake section instead of the Questions. Good Catch!(6 votes)
- When he references A and B and then draws an arrow with another combination of A and B after the arrow, is he referring to reactants and products?(3 votes)
- I think the answer to your question is "yes".
Not sure if you are referencing the use of "A" and "B" in ALL of the reactions (rxn) or if you are specifically referencing the lygase reaction example given at2:15. Either way the answer is the same.
The ARROW (--->) denotes the direction that the rxn follows.
The LEFT side of the arrow represents the REACTANTS.
Whereas, the RIGHT side of the arrow represents the PRODUCTS.
For example: reactants ---> products
~ rxn goes from the left to right ~ from reactants to products
Or: reactants <=> products
~ rxn goes both ways ~ from reactants to products and from products to reactants
(<=> : equillibriam symbol: arro pointing to the right above an arrow pointing to the left)
Note when one of the arrows are longer/larger than the other. ;)
In the video, when A or B are seen on the LEFT side of the rxn arrow (--->), they represent the REACTANTS, not matter what their combinations may be.
When A or B are seen on the RIGHT side of the rxn arrow (--->), they represent the PRODUCTS, again, no matter what their combinations may be.
As in the Lygase example: A + B ---> AB
A and B, found on the left side of the rxn arrow, are both individual reactants.
AB, found on the right side of the rxn arrow, is the product - which just so happens to be the result of the combination of A and B.
You may also see this: AB ---> A + B
Notice that AB is on the reactants' side of the equation and A + B are now on the right side of the equation.
So AB is not always the symbol denoting product.
And this last rxn example is similar to/basically the same sort of rxn as the hydrolase catalyzed rxn found at about4:48in this video.
Great question!(2 votes)
- What language does the suffix "-ase" come from?(2 votes)
- This suffix "-ase" comes from the greek word ἄσις (διαστασις), which means slime or mud, due to the way that an enzymes attaches itself to the substance it is helping break down.(3 votes)
- what is a 'serine residue'?(2 votes)
- Residue is how we refer to an amino acid after it has been incorporated into the chain of a (poly)peptide.
Thus a 'serine residue' means the part of the amino acid serine that is found in a protein.
Does that help?(3 votes)
So today, we're going to talk about enzymes and all the different kinds of reactions that enzymes can catalyze. But before we do that, let's review the idea that enzymes make biochemical reactions go faster. And if you look at a reaction coordinate diagram, you'd notice that enzymes speed up reactions by lowering their activation energy. Now, enzymes are generally named for their reactions, which is convenient because it makes it a lot easier to remember what an enzyme does if someone gives you its name. And a great example of this is that one of the enzymes involved in DNA replication is called DNA polymerase, which is named as such because it acts on DNA and specifically makes polymers of DNA. Now, the suffix "ase" is usually just one that you find at the end of most enzyme names. Now, another great example is that the enzyme that catalyzes the first step of glycolysis, which you may remember is the reaction between glucose and ATP to form glucose-6-phosphate and ADP, is called hexokinase. And "hexo" refers to the number 6, which is a reference to glucose being a six-carbon sugar. And "kinase" is a term referring to enzymes that add phosphate functional groups to different substrates. So overall, hexokinase adds phosphates to six-carbon sugars like glucose. Now generally, every enzyme has a very specific name that gives insight into the specific reaction that that enzyme can catalyze. So we can actually divide most enzymes into six different categories based off the kinds of reactions that they catalyze. Now, our first group is the transferase group. And the basic reaction that transferases catalyze are ones where you move some functional group, X, from molecule B to molecule A. And a great example of one of these reactions occurs during protein translation, where amino acids bound to tRNA molecules are transferred over to the growing polypeptide chain. So in this case, A refers to our amino acid chain, B refers to our tRNA, and X refers to this lysine residue, which is being transferred from B to A. And this reaction in particular is catalyzed by an enzyme called peptidyl transferase, which is an appropriate name since it is a transferase involved in making peptides. Next we have the ligase group, which catalyzes reactions between two molecules, A and B, that are combining to form a complex between the two, or AB. And an example of a reaction using a ligase that you might be familiar with occurs during DNA replication, where two strands of DNA are being joined together. So in this reaction, A and B represent the two separated DNA polymers, which are being joined to form a single strand. And this reaction in particular is catalyzed by an enzyme called DNA ligase, which is named since it's a ligase that works on DNA strands. Now our third group as the oxidoreductase group, which is a little different from the others since it actually includes two different types of reactions. And these reactions involve transferring electrons from either molecule B to molecule A or from molecule A to molecule B. Now, we say that an oxidase is directly involved in oxidizing or taking electrons away from a molecule, while a reductase is involved in reducing or giving electrons to a molecule. And we call these enzymes oxidoreductases together because they can usually catalyze both the forward and reverse reactions, which is why I used equilibrium arrows here instead of just a normal single-headed arrow. Now a great example of an oxidation reduction reaction occurs during lactic acid fermentation, where electrons are either passed from NADH to pyruvate or from lactic acid to NAD. Now, this reaction is catalyzed by an enzyme called lactate dehydrogenase. Remember that the word "dehydrogenase" refers to the removal of a hydride functional group. And that's the same as saying the removal of electrons, since hydrides are basically just hydrogen atoms with two electrons on them instead of just one. Now, this enzyme is given its name since it's able to remove a hydride, or remove electrons, from a molecule of lactic acid. Next, we have the isomerase group. And enzymes in this group are typically involved in reactions where a molecule, like molecule A, is being converted to one of its isomers. And an example of this type of a reaction is the conversion of glucose-6-phostate to fructose-6-phosphate, which is one of the steps of glycolysis that you may remember. Now, this reaction is catalyzed by an enzyme called phosphoglucose isomerase, which is appropriately named since it creates isomers of glucose molecules that are phosphorylated. Now, our next category is the hydrolase category. And hydrolases use water to cleave a molecule, like molecule A, into two other molecules, B and C. And a great example of one of these reactions is the hydrolysis reaction that can occur to peptide bonds. And if we have this lysine-alanine dipeptide here, it could be reacted with water to form two individual amino acids that are no longer bound. And this particular hydrolysis reaction can be catalyzed by a class of enzymes that we call serine hydrolases, which some people call serine proteases. And they are named this way because they are hydrolases that use a serine residue as the key catalytic amino acid that is responsible for breaking the peptide bond. Now, our last category is a little more complicated than the others. And it's the lyase group. Now, lyases catalyze the dissociation of a molecule, like molecule A, into molecule B and C, without using water like hydrolases would, and without using oxidation or reduction like an oxidoreductase would. And one example of a reaction catalyzed by a lyase is the cleavage of argininosuccinate into arginine and succinate. And this reaction takes place during the urea cycle, which you also might be familiar with. Now this specific reaction is catalyzed by an enzyme called argininosuccinate lyase, which is appropriately named because it is a lyase that catalyzes the breakdown of an argininosuccinate molecule. Now, it's important to recognize that since lyases don't use water or oxidation to break a bond, they need to generate either a double bond between two atoms or a ring structure in a molecule in order to work. So what did we learn? Well, first we learned that enzymes are sometimes named for their reactions. And next we learned about the six different types of enzymes. We have transferases, which transfer functional groups from one molecule to another; ligases, which ligate or join two molecules together; oxidoreductases, which move electrons between molecules; isomerases, which convert a molecule from one isomer to another; hydrolases, which break bonds using water; and lyases, which break bonds without using water and without using oxidation.