What are the parts of an operon?
1) regulatory gene
2)operon, which consists of:
What does the regulatory gene in operons do?
This gene is constitutive, which means it's expressed all the time. It's constantly active to make the instructions fr the repressor protein. What is this gene called?
What does the promoter do?
This is where RNA Polymerase sits when it's ready to transcribe. What is this?
What does the operator do?
This is where the repressor binds to. It stops RNA Polymerase from reading the reset of the genes. What is this?
What do the structural genes do?
These genes encode for enzymes that do are implemented in whatever pathway they're used for. What are these genes?
What is an inducible system?
In this system, the default position is off, so the repressor is always bound until something induces it to turn on.
Microbes get the most energy out of what?
Glucose. Microbes utilize glucose before any other sugar molecule. They get more energy out of glucose.
What is Cyclic AMP (cAMP)?
It is a molecule that acts as an alarm signal that tells the cell there is no more glucose present. It binds to the CAP.
As glucose goes down, cAMP goes?
cAMP goes up as glucose goes down.
What is a Catabolic Activator Protein (CAP)?
CAP is a protein that binds to a molecule of cAMP. When bound with cAMP it sits on the promoter of an inducible operon and allows RNA Polymerase to sit down on the promoter as well. WIthout CAP w/ cAMP attached to it, RNA Polymerase can't transcribe.
What two things needs to happen in order for RNA Polymerase to transcribe an inducible operon such as lactose?
Lactose needs to be present to bind to the repressor off the operator and Glucose needs to be in low supply because when glucose is low then the signal molecule cAMP will be released and help RNA Polymerase.
What is catabolite repression?
The phenomenon that glucose can stop any other catabolic pathways with it's presence is known as what?
Why is the total energy output for lactose lower than glucose?
The total energy output for lactose is lower than glucose because bacteria will want to primarily use glucose if it is available and they will stop themselves from using any other sugars as long as glucose is present.
Why do we have glucose in a TSI plate along with another sugar such as lactose/ sucrose?
We have glucose in a TSI plate because we want the bacteria to use up all the glucose first and then release the signal molecule cAMP, wich then activates one of the two sugar pathways (glucose/ sucrose).
What is epigenetic control?
This is another way of controlling transcription by means of decorating nucleotides of DNA with methyl groups (CH3's)
How does decorating nucleotides of DNA with methyl groups in epigenetic control affect transcription?
The methyl groups black the ability of RNA Polymerase to go through and transcribe the rest of the gene because the methyl group is so big.
How are these methyl group chemical decorations in epigenetic control passed on through generations?
These chemical decorations can be passed vertically through generations. If a bacterium chemically decorates it's DNA to inactivate a gene it can pass it on to the next generation.
If bacteria can pass on the methyl groups of epigenetic control, can humans do it too?
Yes, as humans we can also add methyl groups to our genes to shut them down so they are no longer active. Any chemical decorations on our DNA will be passed on to our children.
Are these methyl group decorations reversible or irreversible?
These decorations are reversible and they are constantly being added and removed.
What is it called when the RNA message has been made through transcription but we control how much proteins are made from it?
When we control how much proteins are made after the RNA message has been made we call this Post-Transcriptional Control.
How does post-transcriptional control work?
Following transcription, mRNA molecules can be destroyed before translation is allowed to happen. Even if we've made our mRNA message, if that ribosome doesn't get the chance to translate that message into protein, you won't get that protein. Just because it's gone through transcription doesn't necessarily mean it'll get a protein at the end.
What are the two ways that mRNA be destroyed?
1) by microRNA's
2) by RNases
How do microRNA's destroy mRNA messages?
microRNA's are able to destroy mRNA messages by using base pairs. They bind to the mRNA and pair with that part of the mRNA. Normally RNA isn't seen in double strands, so enzymes are able to destroy that RNA molecule once it's been seen.
How many base pairs does microRNA have?
microRNA is only 22 bases long.
How do RNAses destory mRNA?
RNAses job is to degrade mRNA. They eat up enzymes. And most of the time it's very quickly.
What are RNAses?
They're enzymes/ proteins.
How do you dictate how long mRNA is present?
How long mRNA is present is dictated by how much protein can be made from it.
What is the goal of transcription?
The goal of transcription is to make mRNA from a strand of DNA.
What is the goal of translation?
The goal of translation is to convert the information in the nucleotide sequence of the RNA into amino acid sequences of proteins.
What is mRNA composed of?
mRNA is composed of 3-letter codons, with each codon coding for a particular amino acids.
mRNA is going to always start with which three letter codon?
mRNA is always going to start with AUG.
What does AUG code for?
AUG codes for methionine.
What are the three stop codons that don't code for any amino acids?
How many codons are possible to make given what you know about nucleotides.
There are 64 possible codons based on the fact that we know there's A,T,C, and G in nucleotides.
How many amino acids are there?
There are 20 amino acids.
If there are only 20 amino acids but we have 64 ways of making amino acids, then what does this mean?
This means that a lot of amino acids are coded by more than one codon.
What does it mean that our genetic code has degeneracy?
This is the concept that multiple codons can code for the same amino acid
What is the wobble position?
This is when in our DNA code, if a mistake happens and the mistake is in the third letter of the codon, then the likelihood of a mutation happening is slim. That third position is a little flexible in terms of allowing for some mutations.
What are the two different kinds of codons?
1) sense codons
2) nonsense codons
What do sense codons do?
sense codons are the codons which code for amino acids.
What do nonsense codons do?
Nonsense codons are the three stop signals UAA, UAG, and UGA. They don't code for any amino acids as well.
How are codons read in translation?
They're read from the 5' to 3' .
What is the purpose of tRNA (transfer RNA)
tRNA is another type of RNA which bring with them the amino acids and tell what codon is coming next. They add the on the appropriate amino acido acids.
What happens to the mRNA when we reach a stop codon/ nonsense codon?
once we reach a stop codon/ nonsense codon mRNA floats off to be used by another ribosome or to be eaten up by enzymes.
the physical structure of the ribosome is dictated by what?
the physical structure of a ribosome is dictated by:
1) the protein
2) Ribosomal RNA (rRNA)
Why can prokaryotic cells couple transcription and translation together and why can't eukaryotic cells do this?
In prokaryotes, you can couple transcription and translation because their DNA sn't bound inside the nucleus. The DNA is together with the ribosomes in the cytoplasm, so coupling is possible, unlike in eukaryotes where the DNA is bound inside a nucleus. We have to first transfer the mRNA into the cytoplasma so that the ribosomes can access them.
specifically, what are mutations?
Mutations are permanent changes to the base pair sequences in the nucleotides of DNA.
How do mutations work?
Mutations work by changing the letter sequences which can affect what the protein is going to look like at the end, because if we've made a change to that codon, instead of one amino acid we may be adding a different amino acid instead.
What does it mean that mutations are deleterious?
This means that mutations can knock out the function of an important protein and cause the cell to either grow slowly/ die or be beneficial. (Beneficial mutations are extremely rare events.)
What are the different types of mutations?
1) there are point mutations, which include:
2) frameshift mutations
What happens in point mutations?
In point mutations we have base substitutions where a single base in DNA is changed into another base.
What are silent mutations and how do they work?
Silent mutations are a type of point mutation where you change the DNA base sequence and it does nothing to change the amino acid. It is usually in the last letter of the codon, which is the wobble position.
What are missense mutations and how do they work?
We have a missense mutation when we make a one-letter change that is going to insert the wrong amino acid. Having a different amino acid will change the properties of what is being expressed and it can change how the protein folds up, which could affect the function.
What is a nonsense mutation and how do they work?
A nonsense mutation occurs when we change the DNA base sequence and it leads to a premature insertion of a stop codon.
So how are silent, missense, and nonsense mutations related to each other?
These three mutations arise when we change a SINGLE letter.
What happens in frameshift mutations?
When we have a frameshift mutation we add or subtract one more more nucleotides from the DNA strand making it longer or shorter. Frameshift's usually lead to a number of incorrect amino acids added until a stop codon is reached.
Why are frameshift mutations so bad?
Frameshift mutations are bade because you might be putting stop codons where they shouldn't be or you're making the wrong amino acids all together.
What are mutagens?
Mutagens are agents in the environment that can directly or indirectly bring about mutations?
What are some examples of mutagens?
radiation and chemical changes are examples of mutagens because they can change the DNA sequences.
What are spontaneous mutations and are they common or rare?
Spontaneous mutations are mutations that occur as errors durring DNA replication due to DNA Polymerase misreading. These mutations are very rare.