mRNA and Protein Synthesis

mRNA and Protein Synthesis - Monday 23, 2025

Stranded Messenger RNA

  • mRNA corresponds to a specific gene.

  • mRNA serves as a template for translation into proteins.

Genetic Code

  • DNA is arranged in triplets: three nucleotides correspond to one amino acid.

  • This triplet code accounts for the complexity difference between proteins (20 amino acids) and DNA/RNA (4 nucleotides).

  • Using a triplicate code increases the number of possible variations for each position.

Linearity of Molecules

  • DNA, mRNA, and proteins are linear chains.

  • They are polymers connected in sequence.

  • No branching occurs.

  • The linear sequence is crucial for how the genetic code functions.

DNA Structure and Information

  • DNA is a linear sequence of deoxyribonucleotides containing all genetic information.

  • DNA is arranged as a double helix, but information is primarily derived from one strand during any process.

  • The double-stranded nature provides stability to the DNA molecule.

  • Only one strand provides information at a time.

Complementarity of DNA

  • DNA's double-strandedness allows it to serve as a template.

  • mRNA generated is complementary to the template strand.

  • mRNA sequence is identical to the non-template (complementary) DNA strand.

  • Transcription uses a DNA template to generate mRNA.

  • Due to complementary base pairing, the mRNA sequence mirrors the nucleotide sequence of the DNA's complementary strand.

Role of Ribosomes

  • mRNA moves through ribosomes to produce proteins.

  • Ribosomes are the sites of protein synthesis.

Exam Information

  • Next exam is on Wednesday.

  • The exam covers chapter 12: genetic code and transcription.

  • Chapter 13 on translation (proteins) will be on the subsequent exam.

  • Transcription and translation are tested separately.

  • Eukaryotes perform transcription in the nucleus and translation in the cytoplasm.

  • Bacteria can perform both processes almost simultaneously, but they will be tested separately.

Analogy to Languages

  • Nucleotides and amino acids can be treated as functional letters.

  • The genetic code can be thought of as a language.

  • Ribonucleotide bases serve as letters but are used in triplets called codons.

Nucleotide Combinations

  • Codons are always three nucleotides long.

  • Single or double nucleotide codons are insufficient to cover all 20 amino acids.

  • With single nucleotides, only four amino acids can be represented.

  • Duplicate nucleotides provide 4^2 = 16 combinations, which is still not enough.

  • Triplicate nucleotides yield 4^3 = 64 combinations, providing extra coverage.

Extra Codons

  • There are 64 codons for about 20 amino acids, resulting in redundancy.

  • Each codon corresponds to an amino acid, but there are more codons than needed.

Linear Chains

  • DNA, RNA, and proteins are linear chains.

  • Proteins and RNAs can fold, but their basic structure is a linear sequence of monomers.

Linear Form of Information

  • The genetic code is written and perceived in a linear form.

  • Each "word" consists of three ribonucleotide letters (a codon).

  • The code is consistent with triplets, and there are no overlaps or spaces.

  • The number of nucleotides in a codon doesn't change; it's always three with no gaps or overlaps.

Unambiguous Code

  • Each triplet codon specifies only one amino acid.

  • For example, UUU always codes for phenylalanine.

  • CCU always codes for proline.

Universality of the Genetic Code

  • The genetic code is nearly universal across species.

  • CAG codes for lysine, and GAG codes for glutamic acid in almost all organisms.

  • This applies to various organisms, including chickens, trees, and bacteria.

Stop Codons

  • There are codons that do not code for an amino acid called stop codons.

  • They signal the end of protein synthesis.

  • Three stop codons: UAA, UAG, and UGA.

Degeneracy of the Genetic Code

  • The code is unambiguous, but it is degenerate.

  • A single amino acid can be encoded by multiple triplet codons.

  • For example, threonine is encoded by ACU, ACC, ACA, and ACG.

  • Knowing there is threonine in a protein, one cannot determine the exact codon on the mRNA.

  • Francis Crick noted you cannot work backward to determine the original codon from an amino acid.

Start Codon

  • A start codon is needed to initiate protein synthesis.

  • The start codon is usually methionine (AUG in RNA, ATG in DNA).

  • Most proteins begin with methionine unless modified.

  • AUG is the primary start codon, but there are exceptions.

Start and Stop Codons

  • AUG is the start codon. Methionine.

  • There are three stop codons that do not encode any amino acids.

  • Sequences are read three units (codons) at a time.

  • There are no gaps, no skipping, and no overlaps.

  • The code is coalescent; translation starts and goes without breaks.

  • Everything happens in units of three, affecting everything downstream (like a train on a track).

Non-Overlapping and Collinear Code

  • The code is non-overlapping and doesn't shift backward or have gaps.

  • The code is collinear; different genes can exist on different DNA strands.

  • Information on one DNA strand can be for one gene, while the other strand could be for a different gene.

  • Once within a gene, reading is in units of three.

Universality of the Code Revisited

  • The code is nearly universal with rare exceptions typically in organelles.

  • Exceptions, like in mitochondria, do not disprove the rule.

  • Jacques Monod's quote: "What happens in E. Coli happens in the elephant."

  • Insulin is produced using bacteria, demonstrating this universality.

  • Enzymes are synthesized in bacteria using the universal genetic code.

Role of Messenger RNA

  • DNA stores genetic material, converted into RNA.

  • mRNA is the focus because it is the sequence for proteins.

  • Genes are DNA genetic information converted into proteins using mRNA.

  • mRNA carries information from DNA to build a protein.

  • mRNA is an intermediate in transferring genetic information from DNA to proteins.

Other Types of RNA

  • For other RNAs (tRNA, ribosomal RNA), the RNA itself is the product.

  • mRNA is a transient intermediate between DNA and protein.

  • mRNA translates nucleotide information from DNA into amino acids.

Triplet Code

  • There are 64 codons encoding 20 amino acids.

  • mRNA makes use of this triplet code without commas or overlaps.

  • Codon information (from 64 codons) corresponds to an amino acid that is added to the polypeptide.

Early Understanding of the Code

  • Early researchers determined that the code must be at least a triplet to cover all amino acids.

  • Sydney Brenner proposed the triplicate code.

  • Initially, it was unknown whether the code was linear and consistent or varied.

  • Biology often takes the easiest, most consistent path.

Experimental Validation

  • Francis Crick used phages to study frameshift mutations and validated Brenner's idea.

  • Insertion or deletion of one or two nucleotides messes up all amino acids due to the shift in the reading frame.

  • Adding or deleting multiples of three nucleotides results in extra or deleted amino acids without affecting the overall sequence.

  • Results strongly supported the triplet nature of the code.

Frameshift Mutations

  • Inserting or deleting a non-multiple of three nucleotides causes a frameshift mutation.

  • Frameshift mutations alter the entire amino acid sequence downstream.

  • The code is contiguous and non-overlapping, ensuring the effects of frameshift mutations.

Non-Overlapping Reading

  • The sequence is non-overlapping, implying continuous reading.

  • Reading does not bounce backward; it is continuous once on track.

Codon Degeneracy

  • Most amino acids are encoded by more than one codon.

  • Leucine has six codons.

  • Alanine has four codons.

Start Codon and Methionine

  • The start codon, AUG, codes for methionine.

  • Methionine and tryptophan are encoded by a single codon each.

Order in the Genetic Code

  • There is order in the genetic code; the first and second nucleotides matter more than the third.

  • For serine, having U in the first position and C in the second position always results in serine regardless of the third nucleotide.

  • For many amino acids, the third position doesn't matter.

Grouping of Similar Amino Acids

  • Similar types of amino acids are grouped together such that if the third codon is messed up, the change is minimal.

  • For example, aspartic acid and glutamic acid are both acidic amino acids.

Wobble Hypothesis

  • The initial two ribonucleotides in the triple codon are more critical than the third.

  • Not every cell produces every single tRNA; they often have preferences for codons.

  • Codon bias refers to the fact that organisms favor a single codon.

  • The third position of a codon is less spatially constrained, allowing for some ambiguity if the first two are correct.

Implications of the Wobble Hypothesis

  • Point mutations in the first two nucleotides of a codon are more likely to have an effect than in the third.

  • This allows for more efficient translation since cells do not need to carry as many versions of tRNA.

  • Codon bias affects protein production and folding.

  • This creates a buffer against mutations that tend to make mutations less impactful depending on where they occur.

Methionine as Start Codon

  • Methionine is the initial amino acid in most proteins.

  • In bacteria, when methionine is the start codon, it is modified to N-formal methionine.

  • Eukaryotes do not modify the methionine when it's the start codon.

Stop Codons (Terminators)

  • Stop codons are called terminator sequences or termination codons: UAG, UAA, and UGA.

  • They do not code for anything and are not recognized by any tRNA.

  • When encountered, these signal to stop building the protein.
    *

Stop Codons Frequency

  • The chance of getting a stop codon is about 1 in 20, but reading frames are usually far longer, around 1000-3000 amino acids.

Mutation & Stop Codons

  • When you create a frameshift mutation it leads to a premature stop codon, coding in an aberrant and incorrect amino acid.

Nonsense Mutations

  • A premature stop codon causes a nonsense mutation.

  • A nonsense mutation produces a stop codon somewhere in the gene which terminates translation, producing nonsense.

Universality - Exceptions & Organelles

  • Universal code is nearly universal ,but there are exceptions in organelle DNA.

Overlapping Genes & Reading Frames

  • DNA enconded in codons and triplicates, there are three diff reading frames.
    *

  • DNA has 3 reading famres where it enncodes and there are anitparellel strains from 5 to 3 prime. So the strand hae three reading frames and means this strand has three reading frams.
    *

  • Six Reading Frames - you have the possibility of having six genes in this region.

  • Multiple genes overlapping - can synthesize that one, and then you'd have to finish and start to synthesize a different one if the overlap.
    *

  • With overlapping genes you had a single mRNA that actually has multiple initiation points.

The Human Genome Project

  • Humna genomes have more reading frams and diferent intron points so they can add or delete the protien, rather than having a single protein

Virus & Frame Shifts

  • Different viruses throw of all kinds of diff sorts with different truncted lengths

Transcription

RNA and Transcription

  • Genetic information in DNA is transferred to RNA through transcription.

  • RNA acts as an intermediate molecule.
    Analogy: DNA is like a reference book, mRNA is like a photocopy, and protein is like the built object.

mRNA and tRNA

  • mRNA is each triplet codon complement is on to an anticodon of tRNA

RNA polymerase

  • DNA replication, DNA polymerase.

  • synthesis of RNA, RNA polymerase.

  • Catalyzes RNA synthesis using DNA as a template.

  • Produces a sequence complementary to DNA using ribonucleotides.

  • RNA polymerase has high advantage over DNA polymerase, it can synthesize de novo.

  • RNA polymerase can't excisse or proof read in place activity, lacks three prime hydroxyl group to initiate RNA polymerization

  • Does not require a primer, is huge advantages, no need for primer sequence.
    *

  • Advantage because there no need for terminal primers but it also doesnt prootread the rna so if makes a mestake dont worry.

  • The findla rpdocut is going a seng;e stranded.

Start Site Transcription

  • Need upstream of the start codon, RNA polymerase has to line up.
    *

  • RNA polymerase lines up on the region called the promoter region, ususallly up stream.
    *

  • Promoter - sequence upstream.

  • RNA polymerase is a holoenzyme, composed of individual polypeptides.

  • Holoenzyme includes subunit called sigma
    Subunit sigma directs RNA polymerase to land.

  • Sigma subunite does no involve polymerase at all.
    *Once the subunit is done it dissicoates.

Sigma Subunit

Sigma subunit that tells where to go
Then dissacoates and tellas the rna polymerase where to go.
Then you got the elogatnioin process to build.
Once sigma sbbunit direct the enzyme to where it should land.

Responsible for recognition by RNA polysmerase.
Sites just upstrea of the transcriptional start site.

Begin transacription at the transcriptional start site.
MRNA generated has a little bit of extra RNA that gets attached
Think of it like it s alittle of handle for mmRNA.

Transcriptinal start site is up stream of the coding itself
So from the gene from start to stop.
Then we attacth our RNA polymerates to the promoter region where the RNA polymearase is going to sit.

Promoter Region

  • is upstream of the the transatiop start site with comsesnsuq sequence

  • has consensus sequense where tend to have two seqences upstrea, onme from primal box a tgttac, -35, -10. So upstrea from transciptinal start at siw.
    Bioinformatician aeqwncing genome, would see likely these promoter seqeunce that inicaited gene
    Non idneitcl, you have son changes, but the most nccleotides will be the same at minus 35 and minus 19 .
    Will tellyou you how well the RNA polymerases
    So for lots and lots gene lots these.
    Less important, likely to have more deviaitions to that consensus sequence.

Cs aciting DNA element

Cs means the same same chomosome. Bacetira is porb small upstream the start.
Trans acting factors are at a distant and not even DNA.

Chain Elongation Initiation

Initiate Chain Elongation - that we when when we actually polymeraste RNA.

Riboncueliotdies are added to the RNA chain

Signa subb unites is where rna polyserase to lad
Signa dissacoates

Termination

Know when to stop and wont build indeffinietly.

Enzymes is the that polysmeraizaitos n is anitated with
RNA polymerase to build entire gene ,reaches the termination sites and break off with the mRNA.
unttul it reaches a teermination nucelotide sequence
RNA polymerase break the enyzme ends transcription

Bacterial Termination

in bacteria determination, transcribed into RNA and
as it commeing off DNA.
as its comming off it floping around where it makes air pin loop structure and that is going to slow down rna polymerase has ro dependent is ro termination factor as well. , This protein called ron helps help release RNA, DNA base.
and allows the mernenger RNA the to transolate is elwswher
air pin loop recruisment, ro and ro go to the site and separates teh two.

Operons in polcysthroic messenger RNA

  • Under normal conditiosn for three diff genes yodl have to have geneo ne gen two and genere three.

  • Three separate messenger RNA that has to take to acound.

  • Bactiera doenst aalys do thta and enconde thme.

  • Where al th genes are together acs to each othe
    For vitamin path wya we just have an opean that drie all ths three

Vitamin PathWays

Is is what i if do you have this path wya and make protein one and not two or three

  • They all need tpbe encoded together bevuas ey all one big group
    Because they shar one promoter region are all comnteced, one rna produved,
    what if the rna has mulitpl genes encded on one m rna multiple sythrons.

Eukaryotoe Transcription Notes

Comapre these notes to eukaryotic

Is just diff
eukaryotic alwasy is teh nuclues
doe nbot occurs in nuclues, bacteria because

Doesnt have the yoccurs, it occurs in cytoplasm

  • Transcription inside nuclues.

Chommatin - dynamic, has histones and the have unwoind for hisotne, unqind the DNa, this chroamitin is so dyanic

  • Transciption factors play a bigger role eukaryotes
    *Enahance or decrease transciption
    Add transcription factors - incremental increase or decrease

The amount that is going a consensus ,is ngoing to incremenetla increased

Rarely is there a gene is completely off, at leaast some transcripts.
Particualyreukeartes ahteay alot or trancprtions factors, enhancers that they fine turn the dynaity

Eukryotic RNA Polymearse

euaktorese possess RNA forms polymerases diff types for diff genes
1) RNA polysmerae two , focusing, mernenger RNA
2) RNA polymerase one -ribosmal,
3) RMA polymesar three -trNAs and located in different area, nucleus the ribomal and also nuclues not with in nucluese, not nuclopleasam
if toght nuclues lke a spare, that also anout couoparetmene whtitin
that means to syntheis m m rna

Cis Acting V Tras Acting

Its has the elmenents or trnas trancsrtipn faactots,
Cs actign is DNA that is a sequence of dna utpstream of gene that tells the rna
DNA with the protein that what transect
That protein other and and is more and more tranlactig
There are the taata box for enhanchser or for
Trans elmanet.

Thataat boy is whithin the promoer the seqeucne and also re
RNA polysamrae alds, It helps regulaes RNA the polyamerasse
If ever were professor thant box is what he did because he used a personliazd laicense plate box from tata for taatta

Tata and Biding

  • Tatab box t bindin protein and if biding protein a big bump in incread

  • Dirct the trna polyaemrase where to land it to setted up.

  • Transcript facot bind and upregulate or dow nergeulate gene express and usualy foudn upstrea, sometiems willin or downbut sually near.
    These aEnhacnser and silences so trwans cting
    dna somewhere esl, trancription into protien and then cme bcka and regaulate
    dow neeguation and how much proint the cell needs.

More Euklryotic Cells

wew can doo some modifcations to teh cells more
And one of the reasons why its emboled the nucleis, waitng room
So do make them good before to rbisomose.

Eukaroti Cell Modfication and the Five Prime

  • the is s addito of the cap and the tale- additional wat sto regulate and morre staebile and more likely transatalte.

  • Five prime end of a mssenger rna, you have the enxumes is add of serben methyguanisine.

  • Essntially the is the same for the Nucelotied and it gat attahe dot
    To the the the five rpme the a end of ptorein,
    Three Prime End
    Thre Prime and of m RNA you got a poly a tales, just a bunch of atouns

Extsion of Inrontds for mRNA

  • In eukartict m rna can include more nucletidoes than what is going to ultiamtely, going tot eh genges.

  • WIthint eukaroatict transctips yo have these called the interveining sequnecs, introons, and thse cant cut out.
    these that remain are acoond as exscond, the actual protine is expresed with exons and interventing a seqeucens, a junky well cut out.
    So in yaucarote but buield messanger you have alot biigger than what it shoutd alwyst but it all about teh inforatojn.

what happnes bulding messaenger , 7 methylgruinosine at the five prime and at teh poyl,
Cut this otu, then the exoes are riggght next to each otehr .
So now its ready it cane live the nucleis and instiat translatio , hwich s the next proeess.
Talk aotbt this interveinign a lit.

Introns for the Human Genome Protien

  • MESSANGER A MRNA FRoM the ssame transcprit, increase gneretic diversity.
    Introoon in onne context and ytou acna ut is otud to dthe normal, that innrtoonn brcomes an exoton . you ca nn what is allternattibve slicing.
    you are able the mutpl e diff m erna and singal per, so in spimplest from

Alternative Splicing and Related

We wanna build the mrna to build thisprotien, need t ocut out t he intro
the intro are intwrvining where seqeucne and

Prokaryoic and Eukarotic Gene and MRNA Splicing (Continuation of notes)

  • So when transcribe it trscirbe fullel that sequence.
    Intoricts, intervention secuence, thsoe gat cut out

  • Prokayrtes dont do this , dont wast time or the energy
    Loves becuas as increase genreticc diviersity, eukarte the t extra regulare and regulation and have
    How much of the messanger intervernting seqne and what to do. Mouse, rabbit, and human.
    There is a lot intrerention there interevinted sequence.

  • There were cut out reasemble exons , inrtosn are removed but there splicing and exon are join bact tiohether that build the mesaaurer and RNA.
    So yoru prem ma is slonget has more infomratoin then needs.
    And splice everything , you gwt hsti shorter molecuelles will bemco e mature mRNA and a little bit with the insulin.
    Insterulin has the two introns the and 50 one introns.