From gene to protein Flashcards
What is the problem with the molecular language
There are 4 nucleotides vs 20 amino acids
How do you go from 4 nucleic acids into specifying the protein?
Different codons
Nucleic acids
- Composed of nucleotides
- Codons are based on 3 nucleotides that can be put into different combos to produce the 20 diff amino acids
Genes
Info in DNA that specifies what the sequence of amino acids will be
Proteins are specified by
Our genes that are composed of codons
Protein Functions
- Takes things out of the environment:
-> Sugars, fats, other things one can consume/synthesize from different metabolites - Builds membranes, glycogen, other structure (working molecules)
DNA main function
stores all the info for every protein in the cell
How can an “alphabet” of A, T, C and G give rise to millions of proteins?
The Codon - the unit of information
Singlet DNA code
4 possible amino acids
Doublet DNA code
4^2 = 16 possible amino acids
Triplet DNA code
4^3 = 64 possible amino acids (CODON)
How are codons translated into amino acids?
A genetic code for protein synthesis
Genetic Code
Set of rules by which info encoded in genetic material (DNA or RNA) is translated into proteins or amino acid sequences
- Consists of Codons: sequences of three nucleotides (Triplet DNA code) that specify a particular amino acid or signal the end of protein synthesis.
The genetic code is degenerate
- Amino acids can be specified by more than one codon
-> bc there are more amino acids than codons - TRP (UGG) = special bc it’s unique
-> It has giant side chains
The genetic code is universal
- Same GFP (Green Fluorescent Protein) gene in all cells
- If you take fluorescent gene from jellyfish and put it into bacteria, yeast, or mouse
- Putting a specific wavelength of light will excite the protein, it goes to a high energy state which makes a chemical reaction that produces light
Because DNA is degenerate:
- The DNA sequence can determine the polypeptide (protein) sequence
- But polypeptide sequence cannot determine DNA sequence
Why are codons mRNA
They have uracil instead of thymine
3 Stop Codons
- Make sure that there are no random ends of proteins by telling the system that is building the protein where to stop
- Stop codons don’t specify amino acids
How are the 64 codons organized
16 blocks
What does each block specify
Each block specifies the 1st and the 2nd letter of the codon
- There is variation in the 3rd
Why don’t some mutations in a gene change the protein sequence
Bc mutation in the third letter of the codon may still code for the same amino acid.
Sense (coding) strand vs. Template (antisense) strand
Sense: 5’ - 3’
Template: 3’ - 5’
What is the first codon in the sense strand
ATG/AUG in mRNA = Met Amino Acid
Why do we look at the sense strand
It is where mutations are - so when we look at DNA, we look at sense strand to find out if there are mutations that change the protein
How do you build sense strand from template strand
- Substitute T for A
- Substitute C for G
How do you make an mRNA sequence
- The mRNA sequence is a perfect copy of the DNA sense sequence except T is substituted with U (uracil)
- SO: Substitute the T’s in DNA sense strand with U
What happens to mRNA sequence of codons
They are translated into an amino acid sequence
Why is Amino Acid Met special
- all genes have the first codon as being AUG or ATG
- first amino acid in every protein is always Met
Gene Structure
- Promotor: initiates transcription of a particular gene
- Start codon = ATG/AUG (1 or more)
- Transcribed gene (will be transcribed into RNA)
-> sequence of nucleotides when broken up into 3 nucleotides represent the codons that get translated to protein sequence - Stop codon = 1 of 3
- Terminator = rich in Adenines
-> Adenine tail makes sure that when mRNA is translated, the RNA also has Adenine tail, won’t be digested from the back to the front
Promotors
- Make sure RNA polymerase finds the right place: It has specific sequences that act like the substrates of an enzyme
- Promoter binds to RNA polymerase (Enzyme that makes a copy of the sense strand with U instead of T)
- Promoter and start codon control where RNA polymerase will start transcribing the DNA sequence into an mRNA transcript
- As soon as RNA polymerase starts to build mRNA, it releases from the promoter and works its way down the sequence, building the RNA
- Promotor does not specify amino acids
Transcription/sigma factor:
- Recognizes the regions on the DNA where transcription should start (1st and 2nd sites) and makes sure a gene turns on
-> Where it starts will change the primary sequence of the protein and its function - Transcriptions factors also recruit RNA polymerase (specifies where RNA polymerase sits down
- There are 2 regions so it’s more specific and stays in the right place
- These steps control gene expression and can produce alternative yet functional proteins that are highly specialized for a cell type/stage in development
Transcription vs Translation
Transcription: DNA to RNA
Translation: RNA to Protein
Protein synthesis (Translation)
- Dynamic process
- Translation machine = Ribosome
Ribosome
- Has large and small subunits
- Giant series of enzymes that has 3 active sites
- Link the sequences associated with nucleic acids and proteins mechanistically
tRNA (transfer RNA)
- Transfers amino acids to a mRNA molecule bound to a ribosome
- Recognizes the mRNA /start codon AUG that corresponds to Anticodon (UAC)
- It binds to mRNA long enough to allow a peptide bond to form, then it has to release
A (Aminoacyl) site
- Where the mRNA codon is recognized
- tRNA and amino acid enter Active site
- Amino acid charges tRNA
-> Aminoacyl-tRNA syntheses catalyzes covalent bonding btw amino and tRNA
P (Peptidyl) Site
- Where peptide bonds are formed
- Requires energy (ATP) to overcome the energy barrier so it can make a covalent bond between adjacent amino acids to form a peptide chain
-> Does this by bringing in tRNA that is bound to an amino acid
E (Exit) Site
- Where you go indexing across
- Complete polypeptide
- tRNA that was used to recognize the codon is released
- New tRNA enters
Releasing the Polypeptide
- Ribosome reaches a stop codon (UAG, UAA, UGA) on the mRNA
- Release factor (bound to GTP) facilitates Hydrolysis of GTP
-> Hydrolysis reaction provides energy needed for the release factor to catalyze the release of the polypeptide chain from tRNA - Free polypeptide
- Ribosome subunits and other components dissociate
Why can Ribosome dissociate
Because it is an enzyme
A polypeptide must be folded correctly for the protein to function
- Polypeptides fold with help from helper proteins so they make less mistakes
-> If it makes too many mistakes early on: proteins tends to be degraded bc there are sites that are exposed on it that can be digested by enzymes - Need to fold to get their hydrophobic areas away from water and their hydrophilic areas closer to water
-> NOTE: this is how secondary structure occurs
Where does the folding of a polypeptide happen
- Cytoplasm (aqueous part of the cell)
OR - Inside of a Membrane Compartment
How a single mutation in DNA can change the shape and function of a protein - Point Mutations
1) Silent: change in third codon
- Has no effect on protein sequence
2) Missense: results in amino acid substitution
- Acidic to Basic/Uncharged to Charged so Protein function might change
3) Nonsense: substitutes a stop codon for an amino acid
- Protein truncated, loss of function
Frameshift mutations
- Different protein, or a truncated protein
- Loss or Gain of function
- Cause of many diseases
- Because DNA sequence read from 5’ to 3’, everything past that mutation will be wrong (lost or a different sequence)
