Amino Acids and Proteins Flashcards
Who discovered the central dogma?
Watson and cricks
Who was Marshell Nirenberg?
He won the noble prize said DNA to RNA to Protein
What are DNA and RNA made up of?
Made of nucleic acid
What is a protein made up of?
Amino acids
What is the process called DNA copy to DNA?
Replication
What is DNA to RNA called?
Transcription
What is RNA to Protein called?
Translation
What does it mean that DNA, RNA, and Protein are linear polymers?
This means that each individual monomer attached to 2 units
What does DNA stand for?
Deoxyribonucleic acid
What does RNA stand for?
Ribonucleic acid
Why does new discovery contradicts Central Dogma?
1) Reverse transcription: Information from RNA to DNA backward
- Reverse transcription: is an enzyme generates complementary DNA or cDNA from RNA
- Retrovirus- HIV
- Retrovirus reverse transcribe RNA to DNA and integrate into host genome violates entral dogma
2) Retrovirus:
info stored as RNA have genome directly by host cell machinary as if they were messenger RNA and translate into proteins
-serve as RNA template for another RNA
-Example CORONAVIRUS: responsible for SARS, influenza,
3) Discovery of noncoding RNA: (ncRNA)
- noncoding RNA is a functinal RNA molecule that skip last step of being translated into protein and can directly perform function within cell as RNA molecules
What are the two examples of function RNA are?
1) Transfer RNA and ribosomal RNA both used for translation of messenger RNA into Protein.
What is Epigenetics?
Study of heritable changes in gene activity that are caused by changes in DNA sequence
-Same DNA sequence, so DNA does not change but modified.
What mechansim produce changes in epigenetics?
1) DNA methylation and Histone modification
- DNA expression is modified by epigenetic mechanism these epigenetic mechanism allow the transcription of only gene in genome depend on type of cell.
How is the peptide bond formed and cleavage?
proteins are formed from the folding of polypeptide chains formed by linking amino acids together these links called a peptide bond.
What is the mechanism in which the peptide bonds are formed?
Formed by nucleophilic addition- elimination reaction between the carboxyl group of one amino acid and the amino group of another amino acid.
Why is the peptide/amide bond rigid and planar?
That is because it is stabilized by resonance delocalization of nitrogen electron to this carbonyl oxygen. A peptide with resonance delocalization of electrons has a double bond character no rotation of this bond but the alpha carbon atom can rotate.
What is the order of amino acids binding to another amino acid?
Start with Amino of N terminal and ends with C terminal
N-C-C-N-C-C
What is the process of breaking the amino acid called?
Hydrolysis reaction: breaks the amino acids
Hydrolysis works because it is helped along by 2 commo means:
1) with help of strong acids
2) With proteolytic enzyme
What is acid hydrolysis?
It is a form of hydrolysis that breaks amino acids by using a strong acid, combine with heat is a nonspecific way of cleaving peptide bonds.
-Example: throw something at the pot and get individual peptide bond cleaved.
What is proteolysis?
A form of hydrolysis, it is a specific cleavage of peptide bond with the help of special proteins enzyme called protease.
What is protease trypsin?
Trypsin cleaves only on the carboxyl side of basic amino acids like arginine and lysine
-same enzyme produced by our pancreas to help digest food
Example: When you add trypsin cleaves on C terminus of arginine and lysine
N-Thr-Arg-His-Pro-Lys-Val-C
N-Thr-Arg-Cleave-His-Pro-Lys-Cleave-Val-C
Why are histidine, proline, glycine, and cysteine special cases of amino acids
These are 4 amino acids have side chains that set it apart from the rest
What is special about histidine?
- Histidine side chain has Pka at around 6.5 close to psychological pH around 7.4
- Psychological pH is PH of fluids within our own bodies therefore histidine will exist in both protonated and deprotonated form
- Histidine useful to have at active site of a proton that can stabilize and destabilize a substrate/
What state will the amino acid exist in if PH below amino acid Pka?
Amino acid will exist in protonated or positively charged form.
What state will amino acid exist in if PH above amino acid Pka?
It will exist in deprotonated form
What is special about proline?
- The proline side chain is an alkyl group wrap around and forms the second covalent with a nitrogen atom in the backbone.
- Proline has a secondary alpha-amino group means the side chain forms a second bond with the alpha nitrogen.
What is special about glycine?
It is simplest of all side chains this carbon no longer a chiral carbon, meaning optical activity under plane polarized light, glycine flexible free-roration alpha carbon
Why are proline and glycine amino acids grouped together?
They both play a role in disrupting a particular protein found in a secondary protein structure called an alpha helix.
- both introduce kinks into the alpha helix
- These two are known as alpha-helix breakers
What is special about cysteine?
- Has thiol groups (SH)
- cysteine in close proximity forms a bond together between the two sulfur atom called disulfide bridge
- thiol in reducing form has the hydrogen
- thiol gets in the oxidized form gets in oxidized environment see a loss of these hydrogens form sulfur bonds.
When is cysteine in a reduced or oxidized form?
- Turns out exterior of the cell (extracellular space is an oxidizing environment, will favor the formation of disulfide bridges
- Intracellular space is more likely to find a reducing environment. intracellular has little antioxidants stifle any oxidizing reactions keep intracellular space in a reducing environment
- Two-way cystine spelled
1) Cysteine- reduced form
2) Cystine- When oxidized
What is hemoglobin?
-Found within red blood flow all through our bloodstream
Hgb- responsible for picking up oxygen when red blood cell flow through the vessels and the lungs pick up O2 and transport this O2 to various tissues within our bodies
-Each cell in tissues take O2 and use it to ATP energy source for all various metabolic process
-Amino acid is the building block of hemoglobin proteins
What is an amino acid include? what is chirality?
- Different in R groups
- Chiral carbon has 4 unique groups bound to it
- Chirality refers to optical activity
- One exception to chirality is amino acid glycine (R group is just hydrogen)
What type of amino acid is found in the human body?
L amino acid is the only form you will find within the human body
What is an isoelectric point PI?
Isoelectric point is the point along the PH scale at which a molecule- in this case amino acid exist in neutral charge (not + or -)
-is PH at which amino goes from either positive, negative or neutral state.
What is a zwitterion?
It has a + on NH3 and - on O this gives an overall charge of 0.
What happens if we put a neutral amino acid at a low PH like 1?
-At very low PH say PH 1 acidic solution think of lots of excess proton around and anthing that protonated will be protonated the NH3 become NH2+ and O- become OH, PH is 1
What happens if we put amino acid at High PH let says at like around 12?
-At high PH say 12 will be basic solution having excess hydroxide anions around so now we have NH2 and and O-
What is the average amino group PKa?
9
What is the average carboxylic acid group PKa?
2
How do we calculate PI (isoelectric point of generic amino acid?
Take average PKa for amino group /average Pka divide by 2
Pka1+Pka2/2
example 9+2/2=11/2=5.5
How are amino acid grouped?
- Charge
- H-bonding ability
- Acidic vs Basic
