Protein Structure
Peptide bonds are ___ to environmental changes such as ___ and ___
resistant pH Temp
peptide bonds are so stable because of
resonance
B sheet is made by H bonding between
amino and carboxyl group on adj strands
Quaternary structure hetero =
different subunits
Quaternary structure 2 subunits called 3 subunits called 4 subunits called
dimer trimer tetrameter
Quaternary subunits held together by same type of interactions that maintain tertiary. structure (3)
H bonds, salt bridges, disulfide
Condensation reaction means ___ is expelled
water
Hydrolysis involves
water adding across
Alpha Helixes are __ to __ amino acids long
4-40
resonance structure of peptide bond O has ___ charge N has ___ charge structure = ___ Covalent = ____
- + planar strong
what are two main local protein folding
1. alpha helix 2. beta sheets
1 amino acid is ___ Da
110
Average alpha helix is ___ turns
3 turns
Average protein size is ___ KDa
50
Average protein has ___ amino acids
500
Secondary structure is stabilized by ___ between amino and acid groups
H bonding
Amyloid fibrils can cause (2) diseases
Alzheimers and parsons disease
Primary structure has directionality; new amino acids always add to ___ terminus
C terminus
Alpha helix are common in ___ binding proteins that fit into ___
DNA, grooves of DNA double helix
Alpha helix are formed by amino ___ and carbonyl ____ __ # residues down same chain
H O 4
Primary structure is made starting with ___ to ___-
N to C
Proteins are synthesized from N to C terminus C to N terminus
N to C
Protein X is a monomer that contains numerous antiparallel strands stabilized by hydrogen bonds that are enriched in lysine and aspartate. Based on this information, which of the following statements are likely true? Select all that apply. Protein X contains multiple polypeptide chains. Protein X is an integral membrane protein. Protein X contains at least one beta pleated sheet. Protein X contains at least one alpha helix.
Protein X contains at least one beta pleated sheet.
Some but not all proteins have ___ structure
Quaternary
Which of the following statements are true of alpha helices? Select all that apply. They are an element of secondary structure. They are commonly found in membrane-spanning proteins. They typically contain a high proportion of lysine, alanine, and proline residues. Misfolding and aggregation of alpha helices can give rise to amyloid fibrils.
They are an element of secondary structure. They are commonly found in membrane-spanning proteins.
True or false: Disulfide bonds are a type of covalent bond that is created and broken through redox reactions.
True
Dipetide
Two amino acids bonded together
Some amino acids favor __ or ___ while some ___ secondary structure
alpha helix or beta sheet disrupt secondary structure
Proline is rarely found in ___ but is often found in ____
alpha helix, turns of beta sheet
Peptide bonds form an
amide
Tertiary structure results from __ interactions
amino acid side chain
Back bone interactions are not the same as ___
attractive forces between side chains
Alpha helix and B sheets occur through ___ interactions
back bone
Side Chain Interactions Based on Charge:
basic amino acid interacting with acidic amino acid
Beta Sheets are formed by
beta strands
Peptide bond forms via a ___ reaction between ___ and ____
condensation reaction between carboxyl group of one with amino group of other
peptide bond is a ___ type bond
covalent
Side Chain Interactions Covalent disulfide bonds of two ___ formed via ____ broken bay ____
cystine amino acids, formed by oxidation, broken by reduction
Only way to free a peptide bond is via
hydrolysis
Hydrolysis is energetically ___ and occurs _____ but is very _____
favorable, spontaneously slow
Primary structure influences protein ___-
folding
Tertiary structure determines
fully folded state and function of protein
Hemoglobin is a
hetero tetramer
Under normal conditions peptide bonds are ___ stable
highly stable
Secondary structure is stabilized by: hydrogen bonds between side chain atoms. covalent bonds between side chain atoms. hydrogen bonds between backbone atoms. covalent bonds between backbone atoms.
hydrogen bonds between backbone atoms.
Amyloid fibrils
improperly folded beta sheets that aggregate
Quaternary structure results from
interactions between multiple subunits
Proline does what to secondary structure
kinks
Quaternary structure involves the assembly of protein subunits into ____ each with their own
larger complex own primary, secondary, and tertiary structure
polypeptide
larger than 20 amino acids
Primary is classified based on
length of backbone
oligopeptide
less than 20 amino acids
polypeptide is ___ amino acids
less than 50
Primary structure
linear chains of amino acids that form the backbone of a protein
Secondary structure refers to ___ regions of protein folding
local
A protease is an enzyme that: lowers the energy barrier to peptide bond synthesis so that this already spontaneous reaction occurs more quickly inside cells. lowers the free energy of peptide bond synthesis so that this normally nonspontaneous reaction occurs spontaneously inside cells. lowers the energy barrier to peptide bond hydrolysis so that this already spontaneous reaction occurs more quickly inside cells. lowers the free energy of peptide bond hydrolysis so that this normally nonspontaneous reaction occurs spontaneously inside cells.
lowers the energy barrier to peptide bond hydrolysis so that this already spontaneous reaction occurs more quickly inside cells.
What two amino acids are often found in alpha helix?
lysine alanine
Polypeptide
made up of amino acid monomers
Alpha helix are common in ___ spanning proteins
membrane
Protein can be ___ large polypeptide or ___
one or more than one
Peptide hydrolysis is catalyzed by ___ or ___ which lowers ____
peptidases or proteases, lowers AE
Indvidual amino acids are linked by ___ bond
peptide bond
Amino acid side chain interactions are driven by ___ or ___
polarity or charge
Protein = one or more
polypeptides
Heat shock proteins are chaperone enzymes that facilitate proper folding and assembly of other proteins. Based on the general principles of protein folding, chaperones most likely: prevent protein aggregation during the folding process. catalyze peptide bond synthesis to promote rapid polypeptide assembly. remove the free energy barrier that prevents proteins from folding spontaneously. reduce disulfide bridges to promote subunit aggregation and attachment.
prevent protein aggregation during the folding process.
Secondary structure is the first layer of
protein folding
Alpha helix looks like a ____ handed ____
right handed spiral
Quaternary structure homo =
same subunits
many proteins have areas without any well defined ___
secondary structure
Beta strands are
segments of polypeptide chain that line up next to each other in either parallel or antiparallel fashion
How is 3D structure determined
simulating endless folding patterns to find the most stable/lowest energy
Protein folding is ___ and ___
spontaneous and thermodynamically favorable
Side Chain Interactions based on polarity: hydrophobic interactions also known as ___
tendency for non-polar amino acids to group together away from polar molecules also known as salt bridges
Tertiary structure is driven by all of the following interactions EXCEPT: the formation of salt bridges between charged residues. the tendency of nonpolar amino acids to group together. hydrogen bonding between polar side chains. the reduction of cysteine residues to form disulfide bonds.
the reduction of cysteine residues to form disulfide bonds.