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110 terms

protein structure

protein
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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