MCAT Biochemistry: Molecular Genetics Part 2

Hydrophilic

"water loving," pertains to polar (charged) molecules

classifications of AA's

(1) acidic/basic

post-translational modifications include:

(1) covalent modifications: -->electron sharing, intermolecular bonding, permanent bonded changes --> peptide bonds, N-terminus, C-terminus and amino acid residues. ex: insulin (remove something in the middle and disulfide bonds bring the ends back together) (2) non-covalent modifications: -addition of cofactors -folding

basic amino acids

-a lot of amine groups -positive charge -lysine, arginine, histidine

20 amino acids need to know

-are the ones used to make proteins -are α-amino acids meaning that carboxyl group, amino group, R group are all on the α -carbon

Quaternary structure of proteins

-multiple proteins put together -multiple subunits -example: hemoglobin -2 subunit protein: Dimer -3 subunit proeftin: Trimer -3 of the same subunit: homotrimer -3 different subunits: heterotrimer -4 subunits: tetramer

Translation step:

1. mRNA arrives in the cytoplasm 2. small ribosomal subunit binds to the 5'cap 3. small subunit will move in the 5'--> 3' direction until it encounters the start codon (AUG) 4. Once the small subunit finds AUG, the large subunit is brought in and binds to the mRNA. 5. Initiator tRNA binds to the P site of the large subunit. this tRNA carries methionine. 6. the Aminyl acyl tRNA comes in and binds to the A site. (we need GTP and elongation Factors in order to start elongation) 7. we bind the P site methionine AA and the A site AA with a peptide bond, using peptidyltransferase 8. after this bond is formed the methionine on the initiator tRNA Is transferred to the A site tRNA chain and is released form the initiator chain. 9. after this occurs, the ribosome shifts down -> 3' direction. And the A site tRNA -with AAs attached is shifted to the P site and the P site tRNA is shifted to the E site. And the A site is then available for another tRNA to come in and scan the mRNA and add another Amino acid 10. This occurs until the A site binds a STOP codon. 11. a release factor is signaled and they let go of the mRNA 12. after the peptide chain is released from the Ribosome complex, it must undergo post-translational modifications (to ensure that we have a fully functioning protein and to regulate the protein)

Secondary structure of proteins

Localized folding H-bonding -->alpha-helices -->Beta-sheets

codon:

a sequence of three nucleotides that together form a unit of genetic code in a DNA or RNA molecule -Triplet reading frame -64 possible choices for codons -61 code for amino acids (20 amino acids are represented by 61 codons) -the other 3 are STOP codons *CODONS TO KNOW: AUG: start codon UAA/ UAG, UGA: stop codons*

acidic amino acids

apart acid ---> aspartate glutamic acid ---> glutamate negative charge (acidic)

Zwitterion

at pH near the pI of the amino acid, the amino acid is a neutral ph ===> Acidic : protonation (+) ph ===> PI : neutral [Zwitterion] ph ===> basic : deprotonation (-)

Q: Codons that specify the same AA can differ only in the: a. First base b. Second Basde c. Third base d. ALL of the above

c. Third base -wobble factors is the third base in the codon.

Q: which of the following is true concerning the genetic code? a. there are more amino acids than codons b. any change in the nucleotide sequence of a codon must result in a new amino acid. c. the genetic code varies from species to species d. There is no codon that can code for more than one amino acid.

d. there is no codon that can code for more than one AA -one codon codes for one amino acid.

Tertiary structure of proteins

gives 3D structure of protein --> fold the alpha-helices and beta-sheets even more. -salt bridges -H-bonding -disulfide bonds (S-S) Produces a loop. -hydrophobic interactions

Hydrophobic

hates water non polar lots of hydrocarbons "water fearing" non-polar molecules which do not dissolve in water

primary structure of protein

linear sequence of AAs, no folding N-term to C-term

key players in translation: RNA structure

mRNA 5' cap 5' UTR START codon Coding sequence (CDS) STOP codon 3' UTR PolyA tail

redundancy/ degeneracy

of codons is the redundancy of the genetic code. ---> multiple codons coding for the same amino acid. -this allows for mistakes. -if we have certain mutation we will still get an unaffected protein in the end.

peptide bond

the covalent linkage between two amino acid units in a polypeptide; formed by dehydration synthesis

tRNA

transfer RNA; job is to bring amino acids from the cytosol to the ribosomes, has a four leaf clover shape -Amino acid is attached to the tRNA

Translation

translate a strand of mRNA into a polypeptide.

Denaturation

unfolding, breaking apart taking apart secondary, and tertiary structures. (breaking down bonds) -caused by high temperatures or extreme pH