unit 6 Flashcards
central dogma
The flow from DNA to RNA to Proteins (The workers of the Body)
Types of RNA- Know functions and how RNA is different from DNA
mRNA, tRNA, rRNA
mRNA
Structure/Function:
This is a single stranded molecule that writes down the DNA instructions (sequence)
Created during transcription and is the messenger from DNA to the cytoplasm (carries message to ribosomal RNA
Base Pairing Rules
There is no Thymine in RNA instead it uses Uracil
A=U
C=G
T (If showing on DNA strand) turns to A on the RNA strand
Be able to write mRNA out based on DNA
Example: DNA reads: ATGACT
RNA reads: UACUGA
tRNA (Transfer RNA)
Structure/Function
This is shaped like a “t” and contains an anticodon at the bottom and holds the amino acid at the top
Brings amino acids to the ribosomes based on the mRNA strand
anticodons
The “bottom” of the tRNA has three nucleotides that form the anticodon, a three base triplet that can base pair with the specific codon on the mRNA
The purpose of this is to ensure accuracy of the strand being read and the amino acid that is being added to the polypeptide chain.
accuracy
Anticodons ensures that the adding of amino acids will be accurate and correct.
Accurate translation comes from correct match between tRNA and amino acid and also between tRNA anticodons and mRNA codons
rRNA (Ribosomal RNA)
Structure/Function
Responsible for reading the mRNA and creating the polypeptide strand that will eventually become a protein (Protein Factory)
Is made up of a small subunit and a large subunit. The small subunit reads the mRNA and the large subunit is responsible for connecting amino acids with the help of tRNA
protein factory
rRNA is often referred to as the protein factory due to it being responsible for creating the polypeptide chain that will be folded into a functional protein.
Sites: A site P site and E site
A site - holds the tRNA that carries the next amino acid to be added to the chain
P side - holds the tRNA that carries the growing polypeptide chain
E site - exit site; where discharged tRNA’s leave the
Types of ribosomes
Free ribosomes: Found in the cytoplasm and makes proteins for the cytoplasm
Bound ribosomes: Found in the rough ER and makes proteins for the endomembrane system and those destined to leave the cell
transcription
This process takes place inside the nucleus. The DNA cannot leave this structure but mRNA can by using the nuclear pores to move in and out of the nucleus.
Transcription step 1: initiation
Promoters (TATA sequence) signal the start point and extends several nucleotide pairs upstream of the gene trying to be transcribed
Transcription factors mediate the biding of RNA p[polymerase
When you combine the promoter, transcription factors, and RNA polymerase this is called a transcription initiation complex.
Transcription step 2: elongation
RNA polymerase moves along the DNA and untwists the double helix 10 to 20 bases at a time
RNA polymerase builds using the template of DNA based on base pairing rules.
Transcription step 3: termination
RNA polymerase will continue to build until it reaches a polyadenylation sequence (sequence with at least 6 adenine in a row)
RNA polymerase II
Responsible for building mRNA based on the template strand of DNA
promoter
DNA sequence that tells RNA polymerase II where to bind to begin building mRNA
Examples
TATA sequence
Transcription Factors
A group of proteins that work together to mediate the binding of RNA polymerase and the initiation of transcription
mRNA processing ONLY IN EUKARYOTES (What must happen to the pre-mRNA before it can be translated into a functional protein?)
pre-mRNA, post-mRNA
pre-mRNA
mRNA is considered pre- until its been processed; 5’ end gets a 5’ cap and the 3’ end gets a poly-A-tail….Introns cut out and exons spliced (glued) together.
post-mRNA
This is the mature or functional mRNA this is after all the processing has taken place
Introns vs exons
Introns - noncoding regions that are cut out of the mRNA
Exons - Coding regions that will be spliced together to make mature mRNA
Alternative RNA splicing
Removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence…This is important because we can use the same stretch of DNA to create several different proteins by changing what are introns and what are exons in a single stretch of DNA
mRNA Lifespan
The lifespan of a mRNA is based on how long the poly-A-tail is. The longer the poly-A-tail the longer it will live and the shorter it is the shorter life span it has. This ultimately determines how many times the mRNA can be translated in the cytoplasm.
mRNA degradation
mRNA begins to break down as soon as it enters the cytoplasm to get translated. This is why it is important to add the 5’ cap and poly-A tail to protect it from degrading to fast.
1st picture on study guide (labeling)
A = Promoter; B= RNA Polymerase II; C = mRNA (pre-mRNA); F = Transcription factors
Base pairing rules of DNA and RNA
DNA: A=T; T=A; G=C; C=G
RNA: A=U; T=A; G=C; C=G
Translation
mRNA leaves the nucleus through the nuclear pore and enters the cytoplasm to start translation.
translation step 1: initiation
Brings together mRNA, a tRNA with the first amino acid and the two ribosomal subunits.
A small ribosomal subunit binds with mRNA and reads the mRNA unit lit reaches the start codon (AUG) which establishes the reading frame of mRNA
Once the start codon is found the large subunit will bind to form the ribosomes
Protein factors are responsible for bringing all these components together
translation step 2: elongation
Reading the mRNA in groups of three and adding the correct amino acids to create a polypeptide chain.
translation step 3: termination
Occurs when a stop codon is reached resulting in the addition of water. The water molecule cleaves (cuts) the mRNA strand from the ribosome and the two subunits of the ribosome come apart.
How is translation ended?
When a stop codon is reached signaling the addition of water which cleaves (cuts) the mRNA strand from the ribosome and the two subunits of the ribosome come apart
2nd labeling diagram
A = Polypeptide chain; B = tRNA; C = Large subunit; D = Small subunit; E = Poly-A-Tail; F= mRNA
NOTE: You should be able to look at the DNA and Transcribe it and Translate it into proteins - I will provide the codon/amino acid key sheet.
Proteins
Building Blocks
They are built from amino acids
What codes for proteins
DNA bases - the middle portion of DNA that make up the rungs of the ladder
Why are proteins important/ Function?
Carry out all of the function sin your body including how you express traits
Are they fully functional after translation/What happens to them after translation?
The amino acid sequence (polypeptide chain) is not function until it has been folded (talked about this in unit 1)
Universal code
DNA which is the genetic code and is universal because all known living organisms use the same genetic code
Reading frame
(Correct Groupings) codons must be read in reading form in order for the specified polypeptide to be produced. It will be read in groups of three bases that code for the amino acid until all the amino acids needed for that polypeptide chain are present.
Missense mutations
Still codes for an amino acid but not the correct one.
Nonsense mutations
Changes amino acid codon into a stop codon
Point Mutations (Substitution)
Substitution of a single nucleotide for another nucleotide
Frameshift Mutations
Changes the way we read the mRNA by shifting reading frame
Insertion
Addition of a nucleotide
Deletion
Deletion of a nucleotide
Silent mutations
Does not have an effect on the amino acid produced either because it occurs in a noncoding region or because the change codes for the same amino acid called for
Operon
The entire stretch of DNA that includes the operator, the promoter, and the genes that they control (A group of genes that can be transcribed together)
Operator
Found in the promoter and turns the transcription on and off (acts like a light switch)
Promoter
DNA sequence where RNA polymerase attaches…. more specifically where the transcription initiation complex forms.
Example: TATA sequence
Repressor Protein (What produces this?)
Prevents gene transcription by binding to the operator and blocking RNA polymerase (This means the operon would be off)
Can be in an inactive or active for, depending on the presence of other molecules.
Created by the regulator gene upstream from the promoter region
Corepressor
A molecule that cooperates with the repressor protein (to activate the repressor protein) to switch an operon off.
In the case of the trp operon, “Trp” is the corepressor and when it binds to the repressor protein it makes it active. This will then let it bind and switch the operon off
Negative Gene Regulation
a type of gene regulation that is focused on how to turn translation of genes off. For example, how repressor protein is used to stop expression of proteins
Repressible Operon
Always on until a repressor protein binds to switch and switches operon off
Trp Operon and how it works
Always on and when enough trp has been made the operon will be repressed by activating the inactive repressor protein. When the protein and corepressor bind to the operator the operon switches off and no mRNA can be made
Levels of tryptophan?
THEREFORE, if the level of tryptophan is high then the trp operon is off
Inducible Operon
Always off due to the repressor protein being active. When an inducer molecule binds to the repressor protein it inactivates it switching the operon on.
Inducer
Inactivates the repressor to switch the operon on.
Lac Operon and how it works
Lac operon is inducible and contains genes that code for enzymes that function to break down lactose. By default, it is off because the repressor protein is active. An inducer (allolactose) inactivates the repressor and turns transcription on
Levels of Cyclic AMP (cAMP) and Lactose?
High levels of these two molecules would cause the operon to be switched on by making the repressor protein inactive
When an inducer molecule attaches to the repressor protein what happens to the repressor protein
Changes the shape of the repressor protein making it NOT possible to bind to the operator
Which type of operon, an inducible one or an repressible one, would an organism likely use to produce enzymes and other proteins required to metabolize a nutrient in its environment?
Inducible
Which type of operon, an inducible one or an repressible one would an organism likely use to produce enzymes and other proteins required for cell to manufacture a molecule needed from smaller molecules in the environment
Repressible
Diagrams for both types of operons ….Be able to explain what is happening each diagram.
