Proteins definitions

Question 1

define amino acid

Answer 1

the building blocks of proteins or monomers from which proteins are made. they have amino acid and carboxyl groups attached to the carbon atom

Question 2

define polar amino acids

Answer 2

those with side chains that prefer to reside in an aqueous environment, i.e. ones with hydroxyl or amide groups in their variable side chain

Question 3

define peptide bond

Answer 3

chemical bond formed btwn 2 amino acids when the carboxyl group of one reacts with the amino group of the other amino acid, releasing a molecule of water

Question 4

define “alpha helix”

Answer 4

common secondary structure folding pattern in proteins in which a linear sequence of amino acids folds into a helix stabilised by internal hydrogen bonds spaced 4 amino acids apart

Question 5

define “beta pleated sheets”

Answer 5

common secondary structure formed by hydrogen bonds btwn amino acids in adjacent strands. they can form either from neighbouring polypeptide chains that run in the same orientation (parallel chains) or from a polypeptide chain that folds back and forth upon itself, with each section of the chain running in the direction opposite to that of its immediate neighbours (antiparallel chains)

Question 6

define domain

Answer 6

portion of a protein that has a 3d structure of its own. large proteins have many domains each with different fnxns

Question 7

define pro protein/peptide

Answer 7

protein precursor that is an inactive protein (or peptide) that can be turned into an active form by post-translational modification, such as breaking off a piece of the molecule or adding on another molecule

Question 8

define phosphorylation

Answer 8

a reaction in which a phosphate group is covalently attached to a molecule such as an amino acid of a protein

Question 9

define methylation

Answer 9

reaction in by which methyl groups are added to a molecule such as an amino acid of a protein or deoxyribose of DNA

Question 10

define acetylation

Answer 10

reaction that attaches an acetylene functional group (COCH3) to a chemical compound such as a protein

Question 11

define homeostasis

Answer 11

maintenance of a constant or suitable environment

Question 12

define autophagy

Answer 12

the natural, regulated mechanism of the cell that disassembles unnecessary or dysfunctional components. it allows the orderly degradation and recycling of cellular components.

Question 13

define protease

Answer 13

enzyme which breaks down proteins

Question 14

define ubiquitous

Answer 14

present everywhere - protein found in all cells/everywhere in body

Question 15

define SDS

Answer 15

sodium dodecyl sulfate, an anionic detergent used for denaturing and attaching negative charges to proteins which then have a similar mass to charge ratio

Question 16

define PAGE

Answer 16

Polyacrylamide gel electrophoresis; an analytical technique widely used in biochemistry, forensics, genetics, molecular biology, biotechnology - to seperate components of a protein mixture based on their size, length, conformation & charge. technique based upon the principle that a charged molecule will migrate in an electric field towards an electrode with opposite sign

Question 17

define SDS PAGE

Answer 17

polyacrylamide electrophoretic technique where the sample proteins are treated with SDS & thus denatured & have negative charges attached to give a similar mass to charge ratio. used to determine the molecular weight of separated proteins in a sample.

Question 18

define isoelectric focusing

Answer 18

technique for separating charged molecules, usually proteins or peptides, on the basis of their isoelectric point (pI) or charge

Question 19

define isoelectric point

Answer 19

the pH at which the overall charge of the protein is zero (neutral charge) and thus unable to migrate

Question 20

define 2D-gel electrophoresis

Answer 20

technique used to analyse and separate proteins from complex mixtures such as samples from tissues. they are separated into 2 sequential steps, 1st isoelectric focusing & then SDS PAGE

Question 21

define molecular weight

Answer 21

weight of a protein determined by its amino acid composition & additional post translational modifications

Question 22

define column chromatography

Answer 22

a chromatography technique used to separate a mixture of chemical substances into its individual compounds. It is often used to purify specific proteins from a mixture

Question 23

define affinity chromatography

Answer 23

chromatographic technique based on highly specific biological interactions btwn 2 molecules that have an affinity for one another. one component of the pair is immobilised on the beads (support) of the column. if the other component is present in the sample added to the column, it will bind and all the other proteins would wash through.

Question 24

define size-exclusion chromatography/molecular sieve chromatography

Answer 24

chromatographic method in which molecules in solution are separated by size. beads with pores used I column. smaller proteins trapped in pores and move through column more slowly. large proteins would move through the column more quickly as they are unable to enter (excluded from) the pores

Question 25

define ion exchange chromatography

Answer 25

method for the purification of proteins & other charged molecules. cation-exchange chromatography: positively charged molecules (cations) attracted to negatively charged solid support/bead (anionic) Anion-exchange chromatography: negatively charged molecules (anions) attracted to positively charged solid support/bead

Question 26

define recombinant protein

Answer 26

proteins which are produced as a result of the expression of recombinant DNA (rDNA) within a cell free system or mammalian, insect, and bacterial cells

Question 27

define restriction enzymes

Answer 27

enzyme (endonuclease) produced mainly by the bacteria that cleave (cut) a DNA molecule at a specific site determined by the specific sequences of nucleotides at that site

Question 28

define plasmid vector

Answer 28

small circular molecules of dsDNA derived from plasmids that occur naturally in bacterial cells, widely used for gene cloning

Question 29

define recombinant DNA

Answer 29

DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in the genome

Question 30

define transformation

Answer 30

genetic alteration of a bacterial cell resulting from the transfer of foreign DNA or rDNA into it

Question 31

define transfection

Answer 31

the introduction of foreign DNA into eukaryotic cells either by physical (electroporation) or chemical (cation lipid or calcium phosphate reagents) methods

Question 32

define expression system

Answer 32

cell free system or mammalian, insect, yeast and bacterial cells used to express the recombinant protein

Question 33

define inclusion bodies

Answer 33

nuclear or cytoplasmic insoluble aggregates of proteins due to incorrect folding of rProteins expressed in E coli or non-eukaryotic expression systems

Question 34

define selectable marker gene

Answer 34

a gene introduced into a vector that allows the researcher to identify those bacterial cells that have taken up the plasmid during the transformation process.

Question 35

define gene expression

Answer 35

the process by which information from a gene is used in the synthesis of a functional gene product. these products are often proteins, but in non-protein coding genes such as tRNA or snRNA genes, the product is a fnxnal RNA

Question 36

define bacteriophage

Answer 36

a virus that infects and replicates within bacteria

Question 37

define expression vector

Answer 37

self-replicating DNA molecules used to transfer foreign DNA btwn host cells. e.g. plasmids, bacteriophages, cosmos