Topic 2C Flashcards
what determines a protein’s shape and function?
the exact order of amino acids
what does an amino acid molecule consist of?
an alpha carbon (central), an amino group (NH2), a carboxyl group (COOH) and a side chain/R group
at cellular pH, what happens to the amino acid molecule?
amino group gains a proton (NH3+) and carboxyl group loses a proton (COO-)
what shape is an amino acid?
tetrahedron
what determines the amino acid’s different chemical/physical properties?
the R group
how does the R group determine the structures of the protein?
it influences how a polypeptide fold and hence the 3D shape and properties of a protein
what do hydrophobic amino acids consist of?
nonpolar R groups composed of hydrocarbon chains or uncharged carbon rings
where are most hydrophobic amino acids located?
in the interior of folded proteins (away from water)
amino acids with polar R groups tend to form…
hydrogen bonds with each other or with water molecules (hydrophilic)
where are charged R groups of amino acids located?
on the outside surface of a folded molecule
peptide bond
a covalent bond that links the carbon atom in the carboxyl group of one amino acid to the nitrogen atom in the amino group of another amino acid
amino end
the end of a polypeptide chain that has a free amino group
carboxyl
the end of a polypeptide chain that has a free carboxyl group
polypeptide
a polymer of amino acids connected by peptide bonds
protein
the key structural and functional molecules that do the work of the cell, providing structural support and catalyzing chemical reactions. The term “protein” is often used as a synonym for “polypeptide”
residue
any of the amino acids that is incorporated into a protein
primary structure
the sequence of amino acids in a protein
secondary structure
the structure formed by interactions between stretches of amino acids in a protein
tertiary structure
The overall three-dimensional shape of a protein, formed by interactions between secondary structures.
quaternary structure
The structure that results from the interactions of several polypeptide chains.
secondary structure results from
hydrogen bonding in the polypeptide backbone
what are the two types of secondary structure found in proteins?
alpha helix and beta sheet
tertiary structures result from
interactions between amino acid side chains
denaturation
the unfolding of proteins by chemical treatment or high temperature
chaperone
a protein that helps shield a slow-folding protein until it can attain its proper three-dimensional structure
translation
synthesis of a polypeptide chain corresponding to the coding sequence present in a molecule of messenger RNA
messenger RNA (mRNA)
the RNA molecule that combines with a ribosome to direct protein synthesis; it carries the genetic “message” from the DNA to the ribosome
ribosome
a complex structure of RNA and protein, bound to the cytosolic face of the RER in the cytoplasm, on which proteins are synthesized
what are the three binding sites for tRNA on the large subunit of a ribosome?
animoacyl (A) site, peptidyl (P) site, and exit (E) site
codon
a group of three adjacent nucleotides in RNA that specifies an amino acid in a protein or that terminates polypeptide synthesis
reading frame
following a start codon, a consecutive sequence of codons for amino acids
anticodon
the sequence of three nucleotides in a tRNA molecule that base pairs with the corresponding codon in an mRNA molecule
what is the nucleotide sequence for each tRNA on its 3’ end?
CCA
where does the corresponding amino acid to the anticodon on tRNA attach?
the 3’ hydroxyl of the A in CCA sequence on 3’ end
aminoacyl tRNA synthetase
an enzyme that attaches a specific amino acid to a specific tRNA molecule
genetic code
the correspondence between codons and amino acids, in which 20 amino acids are specified by 64 codons
What was Khorana’s experiment?
using synthetic RNAs of known sequence to decipher the standard genetic code
initiation
the stage of translation in which methionine is established as the first amino acid in a new polypeptide chain
elongation
the process in protein translation in which successive amino acids are added one by one to the growing polypeptide chain
termination
in protein translation, the time at which the addition of amino acids stops and the completed polypeptide chain is released from the ribosome.
initiation factor
a protein that binds to mRNA to initiate translation
elongation factor
a protein that breaks the high-energy bonds of the molecule GTP to provide energy for ribosome movement and elongation of a growing polypeptide chain
release factor
a protein that causes a finished polypeptide chain to be freed from the ribosome
describe translation initiation in eukaryotes:
initiation complex forms at the 5’ cap and scans along the mRNA until the first AUG is encountered
describe translation initiation in prokaryotes:
the mRNA molecules have no 5’ cap, initiation complex is formed at one or more internal sequences present in the mRNA known as a Shine-Dalgarno sequence
polycistronic mRNA
a single molecule of messenger RNA that is formed by the transcription of a group of functionally related genes located next to one another along bacterial DNA
operon
a group of functionally related genes located in tandem along the DNA and transcribed as a single unit from one promoter; the region of DNA consisting of the promoter, the operator, and the coding sequence for the structural genes
