The Triple Threat Test AP Biology (Chapters 13,14,15)😅💀
The Structure of DNA
Composed of three parts;
Formed in G1 Stage
Each above nucleotide is structured in a latter
Each side runs antiparallel to one another, the 3 prime and 5 prime ends on opposite sides of each other
The phosphate group is aligned with the 5’ end and the hydroxyl group (OH) is aligned with the 3’ end
Each nitrogen base has a matching pair
A→T, share two bonds
G→C, share three bonds
DNA Replication
DNA Polymerase; an enzyme that copies DNA
Rules of Replication
has to build off something already there (which is why we have primer)
can only add to the 3’ end of new DNA strand (5’ → 3’)
Steps of Replication
Helicase unzips DNA in two directions
Important reminder, there will now be two pieces of DNA being replicated. One goes from 5’ → 3’ and the other goes from 3’ → 5’. It can get really confusing so draw it out.
Primase, an enzyme, adds a primer to the template. This allows build-off
Once there is a primer, DNA Polymerase can add bases
Only can add bases from the 5’ end towards the 3’ end.
When it is being added, both strands add bases in the same direction, so even if it looks like one is going left and the other right, think about the rotation and how one is upside-down.
This creates a leading and a lagging end
The leading strand is the one where primer is added and the bases can be add continuously from the 3’ to 5’ end.
The lagging strand occurs when the part that is being unzipped is behind the adding of bases. Since there will be a gap, more primer is added and polymerase is added in chunks.
DNA Polymerase “1” replaces RNA w/DNA after an exonuclease enzyme removes the primer but double check cause this is only written once in my notes.
Once DNA polymerase has fully copied, DNA Ligase forms covalent bonds (Ch2) between the hydroxyl (OH) groups and the phosphate groups.
Protein Synthesis
Protein Synthesis allows cells to produce proteins that the organism needs using existing DNA codes to do so.
Protein synthesis can be broken into three parts “TRT”
Transcription
RNA Processing
Translation
Transcription
“The process of making an RNA in order to build proteins”
In order to code for protein, RNA Polymerase needs a landing strip
This TATAAA box is a sequence of bases that provides a starting base.
When transcription factors are presently landed on the base, they are basically telling the cell “hey we need more of this protein!”
RNA Polymerase lands on the transcription factors and begins to assemble RNA
Single strand of DNA which codes for proteins
Instead of Thymine base, RNA uses Uracil base which is a very similar compound.
Like DNA synthesis, it can only add to the 3’ end of DNA, resulting in a strand of RNA that goes from left to right 5’ → 3’
Works in there stages (I know there stages within three stages its crazy)
Initiation- When TF factors land on promoter TATAAA box
Elongation- When RNA Polymerase begins to code for RNA
Termination- When transcription stops and RNA is formed
Fun Fact: when a protein needs to be made quickly, there can be multiple strands being made at the same time.
RNA Processing
“When the RNA comes from transcription, it is pre-mRNA, and RNA processing takes it into mRNA”
Only takes place in Eukaryotes
pre-mRNA is made of introns and exons
Introns: sequence(s) which does not code for a protein
Exons: sequence(s) which
The process of changing pre-mRNA can be explained in the acronym “ACT”
Altercation
The removal of introns
Removed using spliceosome enzyme
Capping
The addition of a guanine nucleotide (G-P-P-P)
Added to the 5’ end
Tailing
attach Poly-A-Tail to the 3’ end
Poly-A-Tail is made of 50-250 adenine nucleotides (AAA…)
Used to push the RNA out of the nucleus
Translation
“The addition of matching bases using an enzyme to create an amino acid chain”
Each 3 bases becomes a codon, or a set which codes for an amino acid
It is read 5’ → 3’
Important codons
AUG = start codon, methionine
UAA,UAG,UGA = stop codon
Think every good party starts with meth and ends when it gets too ugly
The steps for making an amino acid chain
ribosome attaches to the mRNA
tRNA lands on a AUG codon for meth
3 inner sections (EPA)
Left side = E for exit site. When a tRNA is present her that means it has used its codon and can leave
Middle = P for polypeptide. This is where the tRNA drops off its amino acid
Right side = A for arrival site. When tRNA matches the next set, it lands here and prepares to drop off its codon
tRNA lands on A site
met tRNA drops off its amino acid
2nd tRNA moves into P site, first tRNA moves to E site, and a new tRNA lands on the A site
steps 4-6 repeat until they reach a stop codon and everything disassembles, leaving a completed amino acid
Both the RNA and the enzyme move
Amino acids are also made in rough ER, so the first couple peptides can cause the ribosome to dock to the ER
Important Acronyms
TRT
Transcription, RNA Processing, Translation
IET
Initiation, Elongation, Termination
ACT
Altercation, Capping, Tailing
APE
Arrival, Polypeptide, Exit
Control of Gene Expression
Operon: gene controlled by one promoter
Operator: on/off switch for transcription of gene
Regulatory Gene: codes for a repressor protein
Repressor Protein: binds to operator and stops transcription of the gene
There are two types of operons
Repressible
produces a protein (like -trp)
-trp is made in its inactive form, so it does not bind to the repressor
when -trp does bind to the repressor, it can fit to the operator and stop the production of more -trp
It is naturally ON until something comes to turn it OFF which means it is able to be REPRESSED
Inducible
when no lactose is present, the repressor is bound to the operator
when lactose is present, it needs to be broken down by the protein lactate, and thus the lactose will bind to the repressor, changing its shape to detach it
RNA polymerase can translate now.
It is naturally OFF until something comes to turn it ON which means it is able to be INDUCED
Additional Lab Notes
Frameshift Mutations
Removes or changes amino acids which changes the actual changes the protein making it nonfunctional
Missense Mutations
A single nucleotide is changed, which resulted in a different amino acid
Nonsense Mutations
A change to a codon which makes it a stop codon, which can make the protein nonfunctional
Silent Mutations
A nucleotide is changed, however it still code for the same amino acid and has little no no effect on the organism
Placeholder
Conversation Log:
User: if you have a piece of dna, where the top piece goes from 5' towards 3' and a given sequence of TAGCATCACCGT, and a complementary 3' towards 5' piece with a given sequence of ATCGTAGTGGCA, which will get coded for a RNA, for protein synthesis
Assistant: The DNA sequence provided is:
Top Strand (5' to 3'): TAGCATCACCGT
Complementary Strand (3' to 5'): ATCGTAGTGGCA
To determine the RNA coded from the DNA, we need to transcribe the template strand, which is the bottom strand (3' to 5'). The transcription process uses the base pairing rules where Adenine (A) pairs with Uracil (U), Thymine (T) with Adenine (A), Cytosine (C) with Guanine (G), and Guanine (G) with Cytosine (C).
Following this rule, the RNA sequence synthesized from the complementary DNA strand (3' to 5') will be:Template (3' to 5'): ATCGTAGTGGCA
RNA Transcript (5' to 3'): UAGCAUCAACGU
This mRNA (UAGCAUCAACGU) will then be used in the process of protein synthesis (translation).
User: So the take away from this is that when RNA is being synthesized, it always codes for the 3' towards 5' piece of DNA?
Assistant: When RNA is being synthesized, it is transcribed from the template strand of DNA, which runs in the 3' to 5' direction. RNA polymerase reads this template strand and synthesizes the RNA molecule in the 5' to 3' direction, complementing the bases according to pairing rules: (A) pairs with (U), (T) pairs with (A), (C) pairs with (G), and (G) pairs with (C). Thus, the RNA transcript directly complements the DNA template strand, effectively coding for the information stored in the DNA.