protein structure

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protein

primary structure

The first level of protein structure; the specific sequence of amino acids making up a polypeptide chain.

primary structure

sequence of amino acids

primary structure

the unique sequence in which amino acids are joined

primary structure

linear sequence of amino acid residues, covalent bonding including disulfide bonds -SS-

amino acid residues

an amino acid in a polypeptide that is not the N or C terminal AA

polypeptide bond

a long chain of amino acids

primary structure

equivalent to specifying the sequence of its monomeric subunits, e.g., the nucleotide or peptide sequence

nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base

nucleotide

building block of a nucleic acid (DNA and RNA)

nucleotide

composed of a nucleobase (nitrogenous base), a five-carbon sugar (either ribose or 2'-deoxyribose), and one to three phosphate groups

five carbon sugar

ribose is a ______.

ribose

a pentose sugar important as a component of ribonucleic acid

deoxyribose

five-carbon sugar that is a component of DNA nucleotides

nitrogenous base

carbon ring structure found in DNA or RNA that contains one or more atoms of nitrogen; includes adenine, guanine, cytosine, thymine and uracil

adenine

purine base found in DNA and RNA; pairs with thymine in DNA and with uracil in RNA

purines

adenine and guanine are what

purine

One of two families of nitrogenous bases found in nucleotides. Adenine (A) and guanine (G) are ______

thymine

The base that pairs Adenine in DNA

thymine

a base found in DNA (but not in RNA) and derived from pyrimidine

pyrimidine

a nitrogenous base that has a single-ring structure; one of the two general categories of nitrogenous bases found in DNA and RNA; thymine, cytosine, or uracil

cytosine

a base found in DNA and RNA and derived from pyrimidine

cytosine

a base found in DNA and RNA and derived from pyrimidine; pairs with guanine

uracil

a nitrogen-containing base found in RNA (but not in DNA) and derived from pyrimidine

uracil

one of the four bases that combine with sugar and phosphate to form a nucleotide subunit of RNA; uracil pairs with adenine

amino end

N-terminus

amino end

the end of a protein having a free amino group

carboxyl end

C-terminus

carboxyl end

the end of a protein having a free carboxyl group. The carboxyl end is encoded by the 3' end of the mRNA and is the last part of the protein to be synthesized in translation.

5' to 3'

replication, transcription, and translation are carried out in this direction

motif

a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance

secondary structure

The result of hydrogen bonds between the repeating constituents of the polypeptide backbone

secondary structure

main chain H-bonding (alpha helix, b sheet, b turn)

alpha helix

A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure.

alpha helix

common motif in the secondary structure of proteins

alpha helix

is a right-handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier ( hydrogen bonding).

alpha helix

a delicate coil held together by hydrogen bonding between every fourth amino acid

beta sheet

consist of beta strands connected laterally by at least two or three backbone hydrogen bonds

beta sheet

made up of beta strands. in antiparallel, hydrogen bonding is straight across, parallel is two residues farther along the opposite chain.

beta sheet

, ).is a stretch of amino acids typically 5-10 amino acids long whose peptide backbones are almost fully extended. The association of beta sheets has been implicated in the formation of protein aggregates and fibrils observed in many human diseases, notably the amyloidoses.

beta sheet

the second form of regular secondary structure in proteins consisting of beta strands connected laterally by five or more hydrogen bonds

alpha helix

forming a generally twisted, pleated sheet (the most common form of regular secondary structure in proteins is the

beta sheet

is the β hairpin, in which two antiparallel strands are linked by a short loop of two to five residues, of which one is frequently a glycine or a proline

turn

is an element of secondary structure in proteins

α-turn

is characterized by (a) hydrogen bond(s) in which the donor and acceptor residues are separated by four residues (

β-turn

the most common form) is characterized by (a) hydrogen bond(s) in which the donor and acceptor residues are separated by three residues ().

hairpin

is a special case of a turn, in which the direction of the protein backbone reverses and the flanking secondary structure elements interact. For example, a β-hairpin connects two hydrogen-bonded, antiparallel β-strands

tertiary structures

proteins assume complex, three dimensional [ ] that determine the final configuration of the polypeptide, the most important influence on this is its cellular environment - whehter its in the watery cytoplasm of a cell, in the lipids of cellular membranes or spanning a cell membrane, thus straddling two environments

tertiary structures

three-dimensional structure

Tertiary structure

_________is considered to be largely determined by the biomolecule's primary structure, or the sequence of amino acids or nucleotides

side chain interactions

what are the interactions that form the tertiary structure

hydrophobic interactions

The alpha-helices and beta-sheets are folded into a compact globule.

hydrophobic interactions

amino acids with nonpolar side chains end up in clusters at the core of the protein, out of contact with water; caused by the action of water molecules, which exclude nonpolar substances as they form hydrogen bonds with each other and with hydrophilic parts of the protein

Quaternary structure

The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.

Quaternary structure

The overall protein structure that results from the aggregation of these polypeptide subunits.

Quaternary structure

is a larger assembly of several protein molecules or polypeptide chains, usually called subunits in this context

tertiary structure, quaternary structure

what are stabalized by the same non-covalent interactions and disulfide bonds

non-covalent interactions

van der waals, hydrogen bonds, ionic bonds, hydrophobic interactions

van der waals

Weak interactions that occur when atoms and molecules are very close together; based on the fact that because electrons are in constant motion, they may accumulate by chance in one part of the molecule or another, thus creating a charge for that instant

hydrogen bonds

very weak bonds; occurs when a hydrogen atom in one molecule is attracted to the electrostatic atom in another molecule

Primary Structure

amino acid sequence (covalent, peptide bonds)

H-bonding Ionic Hydrophobic Van der Waals Covalent

Interactions that hold proteins together

alpha helix

right-handed coiled or spiral conformation

alpha helix

in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier ( hydrogen bonding).

Antiparallel

A characteristic of the DNA double helix; one strand runs in the 5' to 3' direction while the other runs 3' to 5'

antiparallel beta sheet

what are antiparallel, and can be close on the protein

parallel beta-sheet :

all bonded strands have the same N to C direction, separated by long sequence distances

beta sheet

connected laterally by at least two or three backbone hydrogen bonds

beta strand

is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an almost fully extended conformation

antiparallel beta sheet

arrangement, the successive β strands alternate directions so that the N-terminus of one strand is adjacent to the C-terminus of the next

parallel beta sheet

all of the N-termini of successive strands are oriented in the same direction

parallel beta sheet

this orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern

a beta turn

is a short secondary structure, which enables the structure to have a 180° turn

pro

is common in beta turns

proline

An amino acid that causes kinks/bends in protein structures.

myoglobin, hemoglobin

Examples of a Alpha Helix

5.4 Angstroms

Complete turn in an alpha helix is

Fibrous proteins

keratin and collagen and elastin

Fibrous proteins

Alpha helics & Beta (pleated) sheets

Chains of beta pleated sheets

antiparallel (most stable) and parallel

collagen

The fibrous protein constituent of bone, cartilage, tendon, and other connective tissue.

Primary Structure

The sequence of amino acids in a protein or polypeptide is known as the primary structure. The primary structure will determine how the polypeptide will fold. There are twenty different amino acids and they can be combined in different ways to produce many different proteins

Tertiary structure

The three-dimensional structure of a protein. A polypeptide is a molecule made from a large number of amino acids joined by condensation. This polypeptide is folded to form a protein. Some sections of the polypeptide coil and fold to produce the secondary structure of the protein. The whole protein then folds into a specific three-dimensional shape known as the tertiary structure. The tertiary structure of a protein is very important in determining its function.

Alpha Helix

Hydrogen bonds form between the C=O and -NH of the amino acids to form a spiral. Secondary structure of protein

Secondary Structure

Where the polypeptide chain forms either an alpha helix or a beta sheet

Tertiary structure of Globular Proteins

hydrophobic AA generally on the inside, hydrophilic AA generally on outside

Alpha helix bonds

each C=O forms bond with amide hydrogen of residue n+4

Beta Strands

polypeptide chains that are almost fully extended stabalized by hydrogen bonds between C=O and NH on adjacent strands

Loops and Turns

connect alpha helices and B strands and allow a peptide chain to fold back on itself to make compact structure

3D structure

determines function

Tertiary

3D, functional form

cysteine

disulfide bonds; strongest nucleophile of amino acid residues; two could come together to form a cysteine bridge

glycine

only A-chiral amino acid residue, in places where you need a lot of flexiblity

proline

rarely forms intermolecular interactions just there for protein structure

3D structure

defined by the primary structure

H-bond

weak and allow DNA to zip and unzip. Hold nitrogen bases together.

Watson and Crick

• got Nobel prize for building a model of and describing the structure of DNA as a double helix• got Nobel prize for building a model of and describing the structure of DNA as a double helix

secondary

The _______ structure: or the way that this strand of amino acids orients itself in the protein structure: these are the alpha helix and beta strand structure that you may have heard about in earlier classes

tertiary

The _______ structure of a protein is the way that the entire polypeptide folds to form a unit of protein, a monomer. Tertiary structures can be globular, fibrous or barrel proteins of one or more secondary structure types

amino

The primary structure is numbered from the _______ end of the polypeptide to the carboxyl end

proximal

cysteines can form disulfide bonds when they are _______ to each other.

fibrous

one of the three protein structures: the _______ protein, where monomers can interact to form long thin proteins, such as we see with collagen and myosin.

globular

One of three protein structure: Proteins can also be_______, and this class of protein structure is the most common with soluble proteins, that is, proteins that exist free in the cytosol or other biological fluids.

beta

The primary sequence of proteins can form two major secondary structures: the _______ strand, which often forms into a super-secondary structure of sheets, thus called _______ sheets, and the alpha helix.

bonds

Why does a primary sequence form a beta strand or an alpha helix? The folding of proteins into these two secondary structures depends on the freedom of movement of the _______ within the peptide chain.

phi

The _______ bond is between the nitrogen and alpha carbon.

psi

the _______ bond is between the alpha carbon and the carbonyl carbon.

right

in secondary structures: For the most part, alpha helices are going to be _______ handed, that is, as the helix extends from the N-terminus of the polypeptide to the C-terminus, the turn of the helix will be counterclockwise, or if you hold out your right hand with the thumb up, indicating the elongation axis of the helix, then your fingers curve in the direction of the helix.

hydrogen

Along the alpha helix, there is _______ bonding between the carbonyl oxygen of the backbone with the backbone nitrogen of the residue that is four positions ahead.

3.6

It takes _______ residues to make a single turn in an alpha helix, so you can see how the residues would be aligned to allow this hydrogen-bonding.

isoelectric point

pI- the pH at which the net charge is zero

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