Chapter Four: Protein Structure

Primary Structure: Secondary Structure: Tertiary Structure: Quaternary Structure:

1:Amino Acid Sequence 2:Secondary Structural Elements (alpha helix/ beta sheet) 3: functional; structural; Domains, Proteins 4: Multimeric Complex

There are ____ alpha-L- amino acids found in proteins and they fall into ____ groups. Name the groups

20, 4 Polar Amino Acids with negatively charged side chain Polar Amino Acids with positively charged side chain Polar Amino Acids with uncharged polar side chain Non-Polar Amino Acids with non-polar side chain

Secondary Structure: the alpha Helix ____ ____ per _____ (amount of ______ in ______ of a_____) Amino acid _____ directed _____ Stabilized by ______ [between ____ (__) & _____ (___)] Can have ______ character ( has both _____ and _____ parts) _____ alpha helix is most ______ ______-______ fold __-__ amino acids are sufficient to ______ the _______

3.6, residues, turn, amino acids, one turn, helix side chains, outward hydrogen bonds, amide, NH, carbonyl, CO amphipathic, hydrophilic, hydrophobic Hydrophobic, common, membrane, spanning 18, 22, traverse, plasma membrane

Types of Bonds A B 1 2 3 An _____ bond is an _________ between two _________ atoms.

A: Covalent B: Non-Covalent 1. Ionic Bond 2. Hydrogen Bond 3. Van der Waals ionic bond, electrostatic attraction, fully charged

Alpha Amino Acids Imagine a Carbon atom surrounded by four molecules, at the top is a Hydrogen atom, to it's right COOH, beneath it, CH3, to it's left H2N. Match the molecule to it's name! A: Amino Group B: Carboxyl Group C: Side Chain (R) D: alpha-Carbon This stucture is in a(n) ______ form

A: H2N B: COOH C: CH3 D: Carbon atom in center non-ionized

Name the amino acids that are non-polar and have a non-polar side chain (10)

Alanine, Glycine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Methionine, Tryptophan, Cysteine

Which amino acids have side chains that are primarily responsible for conformational stability? (10)

Alanine, Glycine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Methionine, Tryptophan, Cysteine

Christian _______ studied the ____ of ______. ______ required for proper _____ of ____ is _____ in the _________. Proper _____ is ________ driven, resulting in the ______ of ________ energy. _____ is a _______ process that gives rise to distinct _______ (e.g. _____) A->B->C

Anfinsen, folding, ribonuclease A, Information, folding, proteins, encoded, amino acid sequence, folding, thermodynamically, conformation, lowest, Folding, step-wise, intermediate structures, molten globule A: Unfolded; B: molten globule; C: Native (Folded)

Name the amino acids that are polar and have a positive side chain (3)

Arginine Lysine Histidine

Name the amino acids that are polar and have a uncharged polar side chain (5)

Asparagine Glutamine Serine Threonine Tyrosine

Which amino acids have side chains that are available for glycosylation? (4)

Asparagine Serine Threonine Tyrosine

Name the amino acids that are polar and have a negative side chain (2)

Aspartic Acid Glutamic Acid

Name the amino acids involved in ligand binding and catalysis (10)

Aspartic Acid, Glutamic Acid, Arginine, Lysine, Histidine, Asparagine, Glutamine, Serine, Threonine, Tyrosine

Coiled-coil: ______ of two alpha helices ______ together by ________ interactions between ______ amino acid present long _____ of each helix. Stabilizes _______-_____ interactions. Commonly found in ________ domains of ________ proteins such as _____ Conserved ______ sequence

Associations, bound, hydrophobic, nonpolar, one side, protein, protein, dimerization, DNA binding, c-Jun heptad

______ proteins ______ proper ______. ______ proteins can _____ the _____ of a _____ _______ chain. The _______ bind to _______ or _______ chains and _____ them to _____ along the most __________ pathway. Association of these _________ with the ______ protein requires an _____ of ________ from _________.

Chaperone, assist, folding, Chaperone, guide, folding, newly synthesized, polypeptide, chaperones, bind, newly synthesized, partially folded, help, fold, energetically favorable, chaperones, target, input, energy, ATP hydrolysis

______ and _____ are abundant extracellular _____ proteins. A ______ molecule is a ______ formed by _____ _____ protein chains that ___ around _______. Many ____ ______ molecules are ______together in the ________ to form ________ , which have the tensile _____ of _____. The _____ on the ______ is caused by the regular_____ arrangement of the _____ molecules within the ____.

Collagen, elastin, fibrous, collagen, triple helix, three, extended, wrap, one another, rodlike, collagen, cross-linked, extracellular space, collagen fibrils, strength, steel, striping, collagen fibril, repeating, collagen, fibril

Strength of Bonds (both in vacuum and in water): Strongest -> Weakest

Covalent Bonds Ionic Bond Hydrogen Bond van der Waals

Tertiary Structure: ______ are _____ regions of a ______ consisting of groups of ___________. As ______ polypeptide ______ from the ______ : 1. _______ form; 2. ________ fold. ______ is completed after "_____" of ______ from _______. Ex: _________ : a "_____"

Domains, stable, protein, secondary structural elements, nascent, emerges, ribosome, secondary structures, domains, Folding, release, protein, ribosome Green Flourescent Protein, beta Barrel

____ molecules are ______ together by _____ bonds to form rubberlike, ______. Each ____ polypeptide chain ______ into a more ________ when the ______ is _______, and _______ spontaneously as soon as the _________ is ______.

Elastin, cross-linked, covalent, elastic fibers, elastin, uncoils, extended conformation, fiber, stretched, recoils, stretching force, relaxed

______ proteins can ____ into ______ structures. ________ between _______ determines ______.

Globular, assemble, complex, Relationship, binding domains, shape

_______ α helices can form a stiff _________. A single α helix has ______ amino acid ________ labeled in a sevenfold _______ sequence "abcdefg." Amino acids "__" and "__" in such a sequence lie _______ on the ________, forming a ______ that winds slowly around the α helix. Proteins that form ________ typically have _______ amino acids at positions "__" and "__." Consequently, two α helices can _______ each other, with the _______ side chains of one α helix _______ with the _______ side chains of the other, while the more _______ amino acid side chains are left _______ to the ________ environment

Intertwined, coiled-coil, successive, side chains, repeating, a, d, close together, cylinder surface, stripe, coiled-coils, nonpolar, a, d, wrap around, nonpolar, interacting, nonpolar, hydrophilic, exposed, aqueous

Leucine Zipper 7 letters | 7 letters | 1 letter The leucine zipper is a common three-dimensional _____ motif in ______ and it has that name because ______ occur every ______ amino acids in the _________ domain. The _______ of the ______ are ______ for the __________ to the proteins.

LASTANM, LREQVAQ, L structural, proteins, leucines, seven, dimerization, localization, leucines, critical, DNA binding

_______ may be subject to, ______, ______, _____, and _______

Lysine, methylation, acetylation, ubiquitination, sumoylation

Quaternary Structures: ______ Complex Neuraminidase forms a _________ protein complex which is a protein complex made up of ______ _____ subunits (_____) which are _______ but not __________ . Neuraminidase _______ is formed by _____ between two _______ ______ sites on each ______ Domain A and Domain B ____: determines ______

Multimeric homotetrameric, four, identical, monomer associated, covalently bound, tetramer, interactions, nonidentical, binding, monomer bind, geometry

Alanine

Non- Polar Amino Acid Non-polar Side Chain Ala; A

Cysteine

Non- Polar Amino Acid Non-polar Side Chain Cys; C

Glycine

Non- Polar Amino Acid Non-polar Side Chain Gly; G

Isoleucine

Non- Polar Amino Acid Non-polar Side Chain Ile;I

Leucine

Non- Polar Amino Acid Non-polar Side Chain Leu; L

Methionine

Non- Polar Amino Acid Non-polar Side Chain Met;M

Phenylalanine

Non- Polar Amino Acid Non-polar Side Chain Phe; F

Proline

Non- Polar Amino Acid Non-polar Side Chain Pro;P

Tryptophan

Non- Polar Amino Acid Non-polar Side Chain Trp; W

Valine

Non- Polar Amino Acid Non-polar Side Chain Val; V

______ (_______) side chains tend to _____ in the _____ of the ______ protein (just as ______ oil droplets ______ to form _________). Tucked away inside the ______ protein, ______ side chains can avoid ______ with the _______ ________ that surrounds them ______ a cell. In contrast, _______ side chains tend to arrange themselves near the _______ of the_________, where they can form ________ with ______ and with other _____ molecules. The ______ of _____ (_______) moleculess or regions of molecules is ______ favored.

Nonpolar, hydrophobic, cluster, interior, folded, hydrophobic, coalesce, one large drop, inside, folded, hydrophobic, contact, aqueous, cytosol, inside, polar, near, outside, folded protein, hydrogen bonds, water, polar clustering, nonpolar, hydrophobic, thermodynamically

______ protein can, on occasion, adopt an _____, _____ _____ form. The _____ form of the protein can _____ to the ______ form, inducing _____ to the _______ conformation. -________ ______ proteins ________ and ______ to form _______

Normal, abnormal, misfolded, prion, prion, bind, normal, conversion, abnormal Abnormal, prion, propagate, aggregate, amyloid fibrils

Linus ______: Father of _________ Proposed the _____ of both the _____ and ________ Only person to receive both the _______ (_____; _____) and the _______ (___). Was the first to propose a ______ structure for _____ but got the ______ wrong

Pauling, Structural Biochemistry structures, alpha helix, beta "pleated" sheet Nobel Prize, Chemistry, 1954, Nobel Peace Price, 1963 helical, DNA, details

Secondary Structure: the beta "_______" Sheet Composed of "____ _____" arranged in either ______ or ______ orientation. _____ are _______ by ________. Amino acid ________ project from ________ _____ of the sheet. Can have ______ character

Pleated beta, strands, parallel, anti-parallel, Strands, stabilized, hydrogen bonds, side chains, alternate, faces, amphipathic

Aspartic acid

Polar Amino Acid Negative Side Chain Asp; D

Glutamic Acid

Polar Amino Acid Negative Side Chain Glu; E

Arginine

Polar Amino Acid Positive Side Chain Arg; R

Histidine

Polar Amino Acid Positive Side Chain His; H

Lysine

Polar Amino Acid Positive Side Chain Lys; K

Asparagine

Polar Amino Acid Uncharged Polar Side Chain Asn; N

Glutamine

Polar Amino Acid Uncharged Polar Side Chain Gln; Q

Serine

Polar Amino Acid Uncharged Polar Side Chain Ser; S

Threonine

Polar Amino Acid Uncharged Polar Side Chain Thr; T

Tyrosine

Polar Amino Acid Uncharged Polar Side Chain Tyr; Y

________ involves _________ about ____- _____ & ____- ___ _____ ________ is _______ by _________ bonds.

Protein folding, rotation, N, alpha C, Alpha C, CO, bonds Protein conformation, stabilized, non-covalent

Name the Amino Acid with side chains available for phosphorylation (3)

Serine, Threonine, Tyrosine

Elements of Secondary Structure: (5)

alpha helix, beta sheet, disulfide bridge, loops, turns

Immunoglobulin Model: Both _____ contribute to the ______ binding ______. The immunoglobulin is composed of ____ polypeptide chains (___ identical ___ chains and ___ identical and ____ ____ chains), held together by _____ bonds. Each chain is made up of several similar ______. The antigen-binding site is formed where a _____-chain _____ domain (__) and a _____-chain _____domain (__) come _______. These are the ______ that ______ most in their _______ sequence in ______ immunoglobulins.

chains, antigen, domain, four, two, heavy, two, smaller, light, disulfide, domains, heavy, variable, Vh, light, variable, Vl, close together, domains, differ, amino acid, different

Secondary Structure: : Local _______ ________ Together the _____ and _____ account for _____ percent of the secondary structure of ______. These ______ are ______ through ________.

conformational stability alpha helix, beta sheet, 60, polypeptides, structural elements, stabilized, hydrogen bonds

Beta sheets come in two _____ - both are _______ A: ---> <--- ---> B: ---> ---> --->

conformations, common A: anti-parallel sheet B: parallel sheet

A _______ _______ bond forms when the ____ atom of the ______ group of one ______ (such as glycine) shares _____ with the ______atom from the ______ group of a second _______ (such as alanine). Because a _____ of ______ is _______, ____________ is classifed as a ________ reaction. The deltaG0 for the reaction described is _____ ___/___

covalent, peptide, carbon, carboxyl, amino acid, electrons, nitrogen, amino, amino acid, molecule, water, eliminated, peptide bond formation, condensation 2.2, kcal, mol

The fact that a ________ can, on its own, ______ into the __________ indicates that _____ the _________ necessary to __________ the _______________ of a ________ is _________ in its __________. _____ of the ______ required to direct proper _______ is contained in the _______.

denatured protein, refold, correct conformation, all, information, specify, three- dimensional shape, protein , contained, amino acid sequence Alll, information, protein folding, primary structure

Extracellular ____ of proteins are often ______ by _______. ______ ______ bonds help _____ a ____ protein _____. These ______ can _____ either _____ of the _____ polypeptide chain (_____ ____ bond) or ______ polypeptide chains (____ ____ bond). Because the ____ required to ___one ____ bond is much _____ than the ______ required to _____ even a ______ of _______ bonds a ______ bond can have a major ________ effect on a protein's __________.

domains, stabilized, disulfide bridges, Covalent, disulfide, stabilize, favored, conformation, bridges, join, two parts, same, intrachain, disulfide two different, interchain, disulfide energy, break, covalent, larger, energy, break, whole set, noncovalent, disulfide, stabilizing, folded structure

The Hydrophobic Effect: _______ driven _____ of ______ _____ from _____ media. In an ______ environment, ______ molecules, including the _________ of particular _________, tend to be ________ to _______ their ______ effect on the _______ network of the surrounding _____ molecules.

entropically, exclusion, non-polar, solutes, aqueous. aqueous, hydrophobic, nonpolar side chains, amino acids, forced together, minimize, disruptive, hydrogen-bonded, water

The final ______ structure, or ______, adopted by any ______ chain is determined by ________ considerations: a protein generally _____ into the ______ in which its _______ (__) is ______. The ______ process is thus energetically ______, as it releases ______ and increases the ______ of the _____ (_____).

folded, conformation, polypeptide, energetic, folds, shape, free energy, G, minimized, folding, favorable, heat, disorder, universe, entropy

Proper _____ of proteins brings into position ______ _______ that participate in _____ function such as: (3)

folding, non-adjacent, amino acids, protein Enzyme active sites Receptor binding sites Protein-protein interaction surfaces

Many proteins have a "______ _____" _____ _____ region contains _________ side chains. ______ bonds can ____ between ____ and the _____ side chains on the ______ of the protein. _____ begins as _______ ______ emerges from the_______.

hydrophobic, core, Hydrophobic, core, nonpolar, Hydrogen, form, water, polar, outside Folding, nascent, polypeptide, ribosome

Upon being _____ this structure transforms and becomes a ______ What becomes of the amino group? What becomes of the carboxyl group?

ionized, zwitterion H3N+ COO-

A close examination of a single _____ chain reveals that the most _____ parts of the polypeptide chain extend as _____ at one ____ of the _______ domain (__) to form ______ of one ___________ of the immunoglobulin molecule. Both the ______ and ______ domains are _______ of a _____ of two _______ __________ connected by a _____ bond. Immunoglobulin Model: Both _____ contribute to the ______ binding ______

light, variable, loops, end, variable, Vl, half, antigen-binding site, constant, variable, composed, sandwich, antiparallel, beta sheets, disulfide, chains, antigen, domain

Proteins are ______ _____ of ___- _________ joined by __________. ________ are formed when the __ ______ group of one ______ _____ with the __ _____ group of another to form a _______.

linear, polymers, alpha, amino acids,peptide bonds Peptide bonds, alpha, carbonyl, amino acid, condenses, alpha, amino, substituted amide

Protein _____ are ______ that _____ in many different proteins. Protein _____ appears to involve _______ of ______ to yield proteins with new _______.

mpdules, domains, appear, evolution, recombination, modules, functionality

The ___________ is formed from a ________ of the __________ (-__-__-__-) found in _____ amino acid. Because the two _____ of each amino acid are __________—one sports an ______ group (___, also written ____) and the other a ______ group (____, also written ___)—each _______ has a _________: the end carrying the _____ group is called the _______ , or ________, and the end carrying the free _______ group is the ________, or ________.

polypeptide backbone, repeating sequence, core atoms, N, C, C, every, ends, chemically different, amino, NH3+, NH2, carboxyl, COO-, COOH, polypeptide chain, directionality, amino, amino terminus, N-terminus, carboxyl, carboxyl terminus, C-terminus

Tertiary structure is _______ within protein ______. Each ______ of a protein _____ have an ________ sequence and a ________ conformation that closely ______ those of the other ________.

preserved, families, member, family, amino acid, three-dimensional, resembles, family members

Primary structures are a source of tremendous ________ Somehow, a ______ manages to fold into a _______ _______ ______. It is these ______ that are _____. There are numerous _____ _____ ______.

structural diversity protein, single, stable, conformation stable conformations, active unstable inactive conformations.

There are _____ amino acids with side chains primarily responsible for _______. These side chains ______ _________ via _________ ______. _________ are so ______ that ______ must be very _______ to _______ to ______ through this _______.

ten, conformational stability, stabilize, protein conformation, non-covalent van der Waals attractions, weak, atoms, close, one another, interact, mechanism

A protein can be ______, or ________, by treatment with _______ that disrupt the ________ interactions holding the __________ together. This treatment converts the protein into a __________ that has lost its ________. Under the right conditions, when the denaturing ______ is ________, the protein often ________ spontaneously into its ___________—a process called _______.

unfolded, denatured, solvents, noncovalent, folded chain, flexible polypeptide chain, natural shape, solvent, removed, refolds, original conformation, renaturation

Length of Bonds: Longest -> Shortest

van der Waals Hydrogen Bonds Ionic Bonds Covalent Bonds

A ______ is a _____ or _____ having separate ______ and ________ _____ groups. Only ___- ____- Amino Acids are incorporated into ______ Amino acids can occur in ____ and ____ forms but only ____ forms are ____ by _____.

zwitterion, molecule, ion, positively, negatively, charged alpha, L, proteins L-, D-, L-, used, cells