Protein Synthesis and Bacterial Transfer of DNA Flashcards
Gene
segment (sequence) of DNA that is transcribed into an mRNA that may or may not be translated into a polypeptide
(Genes are recipes for proteins)
(a sequence of DNA that codes for a protein)
Where does transcription take place?
inside the nucleus for eukaryotic cells
in the cytoplasm for prokaryotic cells
what is the central dogma
the concept that cells are governed by a cellular chain of command:
DNA –> RNA –> protein
Why is there only 20 amino acids when it seems like there would be 64 based on the amount of codons?
Its a redundant code:
different codons can code for the same amino acid
What codon means start?
AUG
Gene expression
the process by which DNA directs protein synthesis,
includes two stages: transcription and translation
What is transcription
the synthesis of messenger RNA (mRNA) from a segment (template strand) of DNA
What is translation
the synthesis of a polypeptide, using information in the mRNA
Template strand
On of the two DNA strands in transcription,
provides a template for ordering the sequence of complementary nucleotides in an RNA transcript
always the same strand for a given gene
codons
mRNA base triplets that are read in the 5’ to 3’ direction during translation
RNA polymerase
The enzyme that catalyzes RNA synthesis:
pull the DNA strands apart (breaking hydrogen bonds) and joins together the RNA nucleotides
Does RNA polymerase need a primer?
no
Where does RNA polymerase bind?
an area on the DNA called the promoter
Promoter
Sequence of DNA upstream of the transcription unit (part that will ultimately get translated into a string of amino acids)
What are the steps of transcription (what does RNA polymerase do)?
- binds to promoter
- pulls apart the two different strands of DNA
- Reads DNA from 3’ to 5’ direction, builds RNA in 5’ to 3’ direction
- enzyme pops off at area called terminator leaving piece of RNA (pre-mRNA since still has to be processed)
What happens in RNA processing
The 5’ end receives a modified guanine nucleotide 5’ cap
the 3’ end gets a poly-A tail (extra adenine nucleotides added to the 3’ end)
What are the functions of the modifications that occur in RNA processing?
they help mRNA get out of the nucleus and into the cytoplasm
They protect mRNA from hydrolytic enzymes (enzymes that destroy mRNA)
They help ribosomes attach to the 5’ end
(both the 5’ tail and poly-A tail help with all 3 of these things)
Once the mRNA gets into the cytoplasm where it will be transferred into the protein, why would you want to destroy that mRNA (hydrolytic enzymes)?
Just because the cell wants to make a protein right now, doesn’t mean it wants to make it forever
hydrolytic enzymes help minimize this
introns
long noncoding stretches of nucleotides that lie between coding regions
(they are in the way, so you cut them out and throw them away, and then splice back together the exons)
exons
all regions that aren’t introns
Spliceosomes
consist of a variety of proteins and several small snRNPs that recognize the splice sites
What are snRNPs made up of
proteins and a special kind of RNA called snRNA
What is the role of the snRNP?
decide what is the intron, cut it out, and splice back together the exons
Three properties of RNA that enable it to function as an enzyme
- it can form a three-dimensional structure because of its ability to base-pair with itself
- some bases. in RNA contain function groups that may participate in catalysis
- RNA may hydrogen-bond with other nucleic acid molecules
tRNA and what it does
a type of RNA that functions as an interpreter in translation
Each tRNA molecule has a specific anticodon, picks up a specific amino acid, and conveys the amino acid to the appropriate codon on mRNA
how do tRNAs figure out what their appropriate amino acid is?
they look at their Anticodon and figure out based on what the nitrogenous bases would bond to
E.G
in picture it would be UUC (amino acid Phe) because A(U)A(U)G(C)
Name 3 ways in which bacteria can perform horizontal gene transfer
- transformation
- transduction
- conjugation
Transformation (1 way that genes can move from one bacterial cell to another)
the incorporation of foreign DNA from the surrounding environment (in the form of a fragment from another bacterial cell)
Transduction (1 way that genes can move from one bacterial cell to another)
The transfer of bacterial genes by a phage:
when new viruses are being assembled in an infected bacterial cell, a fragment of DNA belonging to the host cell may be mistakenly packaged within the phage’s coat along with the phage’s own DNA.
When the phage infects a new bacterial cell, the DNA stowaway from the former host cell is injected into the new host.
Conjugation (1 way that genes can move from one bacterial cell to another)
when two bacterial cells “mate” and transfer DNA:
there is a gene called an F factor, and if a bacterial cell has this gene, it enables it to grow a conjugation tube that connects to another cell, and allows some of the original DNA to go through and into the other cell
ribosomes
a cell structure consisting of RNA and protein organized into two subunits and functioning as the site of protein synthesis in the cytoplasm
Plasmid
a small circular DNA molecule separate from the bacterial chromosome
F Factor
A piece of DNA that can exist as a bacterial plasmid
What are the steps of translation in order?
- The small ribosomal subunit binds to the mRNA in a region that encompasses the start codon
- The first tRNA with the complementary anticodon (UAC), which is already carrying a methionine (met amino acid), will come in and hydrogen bond with the codon
- The large ribosomal subunit comes in with 3 sites: A site, P site, E site
builds amino acid chain (reads 5’ to 3’) anticodon builds 3’ to 5’
How does the amino acid chain get built (during translation)?
There is already a tRNA with the anticodon UAC hydrogen bonded to the start codon (AUG) at the P site.
The next 3 nucleotides after AUG are the next codon. A tRNA with the appropriate anticodon will come and hydrogen with that next codon at the A site.
The amino acid on the first tRNA will pop off and connect to the amino acid on the new tRNA at the A site (forming chain).
The whole mRNA shifts (including the tRNAs).
The tRNA that no longer has an amino acid will then be in the E site (Exit site), and it will pop off and leave.
The tRNA with the growing chain of amino acids will now be in the P site, and the A site will be empty waiting for a tRNA with the appropriate anticodon for the NEXT codon.
The process repeats
(GTP powers this)
When does the process of building the amino acid chain stop? what happens when it stops?
It stops when it reaches a stop codon
release factor comes in (not a tRNA) and goes into the A site and breaks whole thing apart
leaves free polypeptide which can then fold and become a protein
What proteins have to be made in the Rough ER?
proteins that have to be packaged into a vesicle
How are proteins made in the rough ER?
first several amino acids in the chain will be called signal peptides
signal peptide is recognized by a protein called SRP (signal recognition particle), grab onto the signal peptide and drag it to the rough ER
(will bring to one of the pores in the membrane of the rough ER)
the ribosome will be making the polypeptide chain but feeding it into the lumen of the rough ER
when the whole thing breaks apart (reaches stop codon), the polypeptide will end up inside the rough ER (in the lumen)
Mutations
changes in the genetic material of a cell or virus
Point mutations/base pair mutations
the wrong nitrogenous base is put in: change in just one base pair of a gene
can be good, bad, or indifferent
indifferent - SILENT MUTATION if the code is redundant (if you change one letter it might end up coding for the exact same amino acid)
Good - change amino acid so that the protein is slightly different and better than it used to be (at whatever it’s job is)
Bad - change amino acid and make protein slightly different but worse than what it used to be at its job
Silent mutation (type of point mutation)
when a mutation is indifferent: the change of the codon (or the base of the codon) codes for the same amino acid (redundant code)
Frame-shift mutation
removing or inserting a base (or any amount that isn’t 3) a whole: changes whole reading frame and screws up everything after the removed base (changes all the amino acids)
Which would matter more: a mutation during DNA replication or a mutation during protein synthesis (transcripiton)? why?
the one during DNA replication would be much worse.
If it happens during the making of mRNA (protein synthesis), its not really a big deal because that one protein will be bad, but when you try to make protein again, the original recipe (the DNA) is fine, and you could copy it correctly the next time
if it happens during DNA replication then the mutation is in the recipe, meaning every time you try and make protein using that DNA it will make the wrong recipe
Missense mutation (type of point mutation)
The mutation still codes for an amino acid, but not the correct one
Nonsense mutation (type of point miutation)
the mutation changes the amino acid codon to a stop codon, nearly always leading to a nonfunctional protein
Advantage of horizontal gene transfer
genetic diversity
When do mutations occur?
it occurs during transcription but could also occur during DNA replication
What mutations are most impactful?
one that happens during S phase of DNA replication before meiosis
or very early on in embryonic development when the first cell will start dividing (before mitosis during S phase)
when are mutations least impactful?
when they effect the 99% of DNA that doesn’t code for anything
when the mutation doesn’t affect the amino acid sequence of the protein (redundant code)
