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.