Week 4 Day 1 Molecular Biology Flashcards
Nonpolar Amino Acids pneumonic
Grandma
C
Always
Visits
London
In
May
Por
Tio’s
Party
Glycine (Gly)
Cysteine (Cys)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Methionine (Met)
Proline (Pro)
Tryptophan (Trp)
Phenylalanine (Phe)
Acidic Amino Acids (polar)
Glutamic Acid (Glu)
Aspartic Acid (Asp)
Basic Amino Acids pneumonic (polar)
Are
Liars
High
Arginine (Arg)
Lysine (Lys)
Histidine (His)
Polar uncharged amino acids pneumonic
Asparagus
Gets
Sweeter
Through
Time
Asparagine (Asn)
Glutamine (Gln)
Serine (Ser)
Threonine (Thr)
Tyrosine (Tyr)
What determines the identity of an amino acid?
it’s side chain
Which amino acid is not chiral?
Glycine, it’s side chain is an H
Which end of the zwitterion is the conjugate base of a weak acid…the carboxylate end or the ammonium-ion-end?
carboxylate-ion-end
Which end of the zwitterion is the conjugate acid of a weak base…the carboxylate end or the ammonium-ion-end?
the ammonium-ion-end
Stated from the book:
The net electrical charge on an AA is a function of pH, and this has both critical and useful implications. At very low pH, an AA is primarily in its fully protonated form (H2A+), and the net charge on an AA is positive. As pH increases, the cationionic form is gradually converted to the zwitterionic for (HA), and the net charge approaches zero. As we continue to increase the pH to strongly basic conditions, the ammonium group surrenders the second proton, converting the amino acid into its fully deprotonated form (A-), and the net charge on an AA is negative.
Primary structure of proteins
linear sequence of amino acids in a peptide chain
Secondary structure of proteins
indicates local spatial arrangement of polypeptide backbone yielding alpha helical or beta pleated sheet structure
Hydrogen bonds between the ‘backbone’ amide -NH- and
-CO-
Tertiary structure
how the alpha helices and beta sheet portions of a polypeptide chain are folded into a compact globular structure
Quanternary structure
indicates the assemply of multiple polypeptide chains into an intact, tetrameric protein
i.e. hemoglobin
Elements of tertiary structure of proteins
- disulfide bonds (covalent bond) - strongest, but we don’t have a lot, they tend to have special/specific uses (think hair)
- hydrogen bonds - weak, easy to break, but we have A LOT
- salt bridges (much like an ionic bond) - stronger than hydrogen bond, less frequent
- hydrophobic interactions
What is the purpose of RNA polymerase?
Binds to the DNA strand to “unzip” or “split up” the double strand of DNA
After the RNA copy is made in the nucleus, what are some modifications we need to do before sending it out to the cytoplasm?
Put a cap on the 5’ end
cut out the introns
finish with a poly A tail
T or F: The process of making an RNA copy from DNA is called trancription.
True
this is called mRNA synthesis
Where does mRNA synthesis occur?
The nucleus
What is the purpose of RNAase
To degrade the mRNA once the mRNA is done making proteins.
When RNAase begins degrading the protein, which end of the RNA does it start on, or does it even matter? If so, why?
The RNAase begins degrading the protein at the poly A tail. This is important because not all poly A tails are the same lengh. When the mRNA copy is made, the length of the poly A tail is designated by how many types of this protein will be needed. If a lot will be needed, the poly A tail will be long and this protein will take longer to degrade. If a small amount of this type of protein is needed, the poly A tail will be shorter and the poly A tail will degrade quicker.
Another word for protein synthesis.
Translation
In regards to base pairs, If the DNA has a C, G, T or A base, what will corresponding pair be for RNA
DNA base RNA base
C G
G C
T A
A U
A codon has how many nucleotides?
3
What is the nucleotide arrangement of the start codon and stop codon of the mRNA?
Start codon: AUG
Stop codon: UGA
If the protein being synthesized is meant to remain in the cell in the cytoplasm, where will it finish translation?
On free ribosomes in the cytoplasm, then it will remain in the cytoplasm.
If a protein being synthesized needs to be sent out of the cell, where will it finish synthesis and which organelle will “ship it out of the cell?”
Synthesis will finish on the rough ER and then the golgi will take proteins from the rough ER and either ship them to organelles within the cell or ship them out of the cell.
**Think of the golgi like the post office of the cell.**
Would unzipping of the DNA likely start at an A&T bond or C&G bond, why?
The DNA unzipping would likely start where there are A&T bonds becasue these are only bound by 2 hydrogen bonds whereas C&G bonds are bound by 3 hydrogen bonds. So all together the A&T bonds are weaker.
In which direction is DNA read?
from the 5’ end to the 3’ end
Describe a nucleic acid.
A nucleic acid is a polymer consisting of a 5 carbon sugar (ribose in RNA, deoxy ribose in DNA) lined together by phosphate groups. Each sugar molecules carries a nitrogenous base.
The phosphate groups attach to which 2 carbons of the DNA’s 5 carbon sugar molecule?
3 carbon and 5 carbon - hence, 3’ and 5’
Which carbon does the nitrogenous base of the DNA 5 carbon sugar molecule attach to?
Carbon 1
We use the DNA template strand to make the RNA transcript. The RNA transcipt which will match the ____ _______ ______.
DNA coding strand.
The RNA transcript is created from the ____ prime end to the _____ prime end. This means that the DNA template strand runs from the _____ prime end to the ______ prime end.
RNA transcript created from 5’ to 3’
DNA template strand runs from 3’ to 5’
Name 3 major ways in which RNA differs from DNA.
- RNA is single stranded (DNA double stranded)
- Made of ribose (not deoxyribose)
- Made with U’s instead of T’s
What gives DNA the name of deoxy?
The 2 carbon is attached to a Hydrogen, not an oxygen. The oxygen has been removed, making it deoxyribonucleic acid.
Where are the genes for rRNA contained?
The nucleolous of the nucleus
Name the two subunits of rRNA. Which is larger?
40S subunit, 60S subunit.
60S subunit is larger.
What are the 40S and 60S subunits made of?
rRNA + “a bunch of little proteins”
T or F: Multiple ribosomes can bind to an mRNA strand.
True
AUG is the start codon. Which AA does AUG code for?
Methionine.
**This does not mean that every polypeptide chain begins with methionine. This is sometimes chopped off in post translational modification.**
UGA is the stop codon. Which AA does this code for?
UGA just tells the ribosome to stop. UGA does not code for any specific AA.
5 major stages of protein synthesis.
1. Activation of tRNA
2. Initiation
3. Elongation
4. Termination
5. Folding and post-translational processing
Which enantiomers will we focus on for AA: D or L?
L-Amino Acids
Of the 20 AA acids we focus on, do they all contain a chiral carbon?
All but glycine, the simplest amino acid. Glycine has a side chain of H, making it not chiral because it will be bound 2 Hs. (Only 3 different side chains vs 4)
Describe the structure of an AA.
INFO CARD
How do we make a peptide bond?
