proteins Flashcards
thyrotropin is an example of what size peptide
a tiny peptide, has 3 amino acid residues
cytochrome is an example of what size peptide
a medium peptide, 104 amino acid residues
Tyrosine kinase is an example of what size peptide
a large peptide, 1200 amino acid residues
RNA polymerase is an example of what size peptide
an Extra large peptide, has 4158 aa residues
TRUE or FALSE proteins only contain one peptide chain
FALSE
the bond that forms peptide bonds is known as
condensation reaction, when bonding it release H2O and when unbonding it gains this back
when is a protein most thermodynamically stable?
when it has a spatial arrangement of atoms
what type of favourable bonds does a native fold try to have as many of
multiple weak, non-covalent bonds and covalent (such as disulfide non-peptide)
TRUE or FALSE: alpha-helices and beta-sheets are both held in place by hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another
TRUE
in an alpha-helix, the carbonyl (C=O) of one amino acid is ??? bonded to the amino H (N-H) of an amino acid that is ??? down the chain. (E.g., the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.)
hydrogen bonded to the amino H of an amino acid that is FOUR down the chain.
in a Beta-sheet, +2 segments of a polypeptide chain line up ???, forming a sheet-like structure held together by ??? bonds. These bonds form between carbonyl and amino groups of ???, while the R groups extend above and below the plane of the sheet
line up next to each other to form a sheet-like structure held together by HYDROGEN bonds that form between carbonyl and amino groups of the BACKBONE
an antiparallel beta-sheet the strands run in opposite directions, resulting in ??? bonds which provide strength—> N-terminus of one strand is positioned next to the C-terminus of the other, very strong
linear hydrogen bonds
??? residues are buried in the protein interior. This occurs frequently
Hydrophobic residues
number of hydrogen bonds and ??? interactions within protein are maximised to reduce unfavourable/ unsuitable pairing between H-bonding and ???-groups
ionic interactions
ionic-groups
RESONANCE bond is an ??? sharing of electrons between carbonyl O and amide N. This causes peptide bonds to be less reactive than esters, and exhibit a large ??? moment in favoured ???-configuration
unequal sharing
large dipole moment
trans-configuration
what causes primary structure of peptide bonds to be very rigid and nearly planar?
the resonance bond
secondary structure of a peptide refers to the ??? arrangement of polypeptide backbone
local spatial arrangment
irregular arrangement of secondary structure is also known as
random coil
alpha-helix is a ??? helix with 3.6 amino acid residues per turn
right-handed helix
what offers stability in alpha-helix secondary structure?
amino acid sequence
TRUE or FALSE: how far apart amino acid residues are can determine if a helix can form or if beta-sheet occurs instead
TRUE
strong helix formers include ??? and ??? because they are small, hydrophobic
alanine and leucine
proline acts as a ??? breaker because rotation around its N-C bond is impossible (because of its ??? structure)
helix breaker
ring structure
Glycine acts as a helix ??? because its tiny r-group gives ??? flexibility
breaker
too much flexibility
parallel beta sheets have the ??? bonded strands running in the same direction = ???-bonds are bent, causing ???
H-bonded strands
H-bonds are bent, causing weakness
TRUE or FALSE: an alpha-helix has covalent bonds between amino acids near each other
FALSE they have non-covalent bonds
do many proteins require chaperones to assist them with their folding?
yes
Fibrous proteins are polypeptide chains arranged in long ??? made from the same/single type of secondary structure
long strands/sheets
fibrous proteins provide ???, shape, external protection
support
Globular proteins often contain both ??? and ??? secondary structures as they can interact together. these proteins tend to be enzymes and regulatory proteins
alpha and beta secondary structures
Globular proteins are water soluble and lipid-soluble ??? proteins
lipid soluble membrane proteins
Proteome refers to:
the entire complement of proteins expressed by a cell, tissue, organ
cation exchange chromatography refers to when buffer is ??? , it binds ??? / ??? charged ions and will elute anions (negatively charged ions)
acidic/anionic
cations/positively charged ions
gel filtration column (size exclusion) will elute the ??? proteins first because these sized proteins cannot enter
larger
salting out separation of proteins: proteins precipitate depending on their ??? and can then be isolated with centrifugation
solubility
column chromatography: for anion exchange, column is positive and binds ???
anions
2D gel electrophoresis combines isoelectric focusing and SDS-PAGE so that
1st dimension seperates proteins by ???
2nd dimension separates proteins by ???
pI
molecular weight
