Proteins

The beta turn it accomplished over (?) proteins; The turn is stabilized by a hydrogen bond on the carbonyl carbons oxygen to the amide proton three residues down the sequence.

4

(?) -- are formed from the side chains of amino acids that are ionized at physiological pH (name them). These oppositely charged amino acids interact to form these bonds.

Electrostatic Interaction or 'salt bridges' Arginine (+), Lysine (+), Glutamate (-) and Aspartate (-)

(?) -- are formed between specific cysteine residues on a peptide chain. These are found (?) or (?).

Disulfide bonds on proteins on the outer surface of the cell in secretory proteins.

Cellular responses to maintain homeostasis are controlled and regulated by the largest groups of proteins, the (?) and the (?) proteins. These proteins control and regulate the activities of the cell: metabolism, transcription and translation, replication and apoptosis.

Signal Transduction receptors cellular cascade

ϕ (phi) angle: angle around the α-carbon—(?) bond

amide nitrogen

(?) transporters that move two or more molecules across the membrane in opposite directions

antiporters

Motifs can be found as recurring structures in numerous proteins. Proteins made of different motifs folded together to form (?).

domains

There are two major classes of proteins: ? & ?

fibrous and globular

These quaternary structures can be (?) identical protein sub-units bonded together. Or they can be (?)different polypeptides bonded together.

homomeric heteromeric

This native configuration is held in position by weak interactions such as

hydrogen bonding, salt bridges and in specific protein subsets such as secreted proteins that contain disulfide bonds.

The (?) is necessary to drive the formation of the peptide bond in a biological system.

hydrolysis of an ATP

All peptide bonds in the α helix have a similar orientation which results in the α helix having a (?).

large macroscopic dipole moment

The electron, shared between the carbonyl of the first amino acid in the peptide bond and the bonded N of the amine will make the peptide bond exhibit a large dipole moment in the favored (?) configuration. Rotation around the peptide bond is not permitted

trans the partial double bond of the peptide bond inhibits the ability for rotation around this bond to occur.

This figure shows the globular proteins troponin I, T and C which form a complex bound to the fibrous proteins (? and ?), blocking the myosin binding site.

tropomyosin and actin

Rotation around bonds connected to the α-carbon are permitted In a fully extended polypeptide, both ϕ and Ψ are (?).

180°. Some ϕ and Ψ combinations are very unfavorable because of steric crowding of backbone atoms with other atoms or side chains. Some ϕ and Ψ combinations are more favorable because of the possibility to form H-bonds along the backbone.

In immunoglobulin, the binding region is formed from A. Beta basket and large turns B. Beta sheet turn alpha helix C. Alpha helix turn alpha helix D. Beta basket, large turns and alpha helix

A

The three-dimensional structure of a protein depends on A. Specific gene codes B. Random binding of amino acids into a peptide chain C. What amino acids are numerous and available D. The ribosome, selecting the amino acid order

A

What amino acids are most prevalent in both type 1 and type 2 beta turns? A. Proline and glycine B. Aspartate and glutamate C. Proline and threonine D. Serine and glycine

A

Which of the following is true about a peptide bond A. Because of its resonance the N has a partial positive charge B. Because of its resonance the N has a partial negative charge C. Because of its resonance the N has no charge D. Depends on the pKR for what charge the N has

A

Cascade of events A transmembrane receptor binds an extracellular chemical signal, causing a conformational change in the receptor which propagates through the membrane. The intracellular domain of the receptor is bound to an intracellular heterotrimeric G protein in the cell. The G protein dissociates and one subunit interacts with and activates an enzyme called (?), which converts ATP into a second messenger - cyclic AMP (cAMP) - in the cell. cAMP activates protein (?), which phosphorylates proteins at specific serine or threonine side chains.

Adenylate Cyclase kinase A (PKA) The figure below shows a scheme of a receptor binding a ligand and the activation of several protein kinase enzymes that then phosphorylate specific proteins that form what is an amplification cascade of activated proteins to cause changes in cellular responses.

In the peptide chain the R groups A. Are always cis of each other B. Are always trans of each other C. Can be either cis of trans D. Are long stretches of cis, then alternate to trans

B

The unique beta barrel motif is found to predominantly form in A. Enzymes that are membrane bound in the endoplasmic reticulum B. Mitochondrial membrane transporters C. Enzymes that are membrane bound in the mitochondria D. Transporter of the plasma membrane

B

What are the strongest bonds holding a peptide into tertiary structure? A. Hydrogen bonds B. Disulfide bonds C. Hydrophobic effect D. Electrostatic interactions

B

Where are the Φ and ψ angles of rotation found on the amino acid in a peptide chain? A. Between the amine N and the C of the carbonyl group of the peptide bond B. Between the N and alpha carbon bond, and the bond between the carbonyl carbon bond to the alpha carbon. C. Between the alpha carbon and the N of the amine group D. Between the R group and the alpha carbon

B

All amino acids in a peptide are trans to each other EXCEPT (it can be either cis or trans) A. Glycine B. Alanine C. Proline D. Serine

C

In quaternary structure identical peptides are called? A. Isopeptides B. Heteropeptides C. Homodimers D. Hetrodimers

C

What are secondary peptide structures? A. Extended chains and alpha helix B. Extended chains and beta pleated sheets C. Alpha helix and beta pleated sheets D. Random coils and extended regions

C

Whether a Φ or ψ is favored can be found on a A. RicTic plot B. Linweaver-Burk plot C. Ramachandran plot D. Arrhenius plot

C

Which functional groups on the first and second amino acid form the peptide bond? A. They are randomly assembled B. The peptide bonds are formed by the R groups of the first and second amino acids C. The carboxylic acid of the first and the amine group of the second D. The amine group of the first and the carboxylic acid of the second

C

When the troponin complex binds (?) it moves to unblocks the site from myosin to bind to actin and to cause muscle contraction.

Ca2+

Peptide bonds are formed and broken by the reverse processes dehydration synthesis and hydrolysis. What is being taken away or added back in these reactions? A. R groups are added or removed B. Protons are added or removed C. The amine and carboxylic acid groups are added or removed D. Water molecules are added or removed

D

Why is the peptide bond planar? A. Because there's no possible rotation around bonds between N and C atoms B. Because rotation only happens around atoms bonded to alpha C C. Because the carboxylic acid cannot rotate D. Because of the resonant double bond between the C of the carbonyl group and the N of the peptide bond

D

Proteins give structure to the cell, are receptors on the surface of the cell along with transporters and the extracellular matrix proteins, the proteoglycans.

Fnxs of proteins

(?) -- interaction of N-H and C=O of the peptide bond leads to local regular structures such as α-helices and β-sheets.

Hydrogen bonds These amino acids are found exposed to water on the surface of the protein and form H bonds with water molecules solvating the protein. H bonds are not exclusive to the surface but are also found in the interior region as well, stabilizing the folded structure.

Breaking of a peptide bond into the individual amino acids with the addition of a water molecule across the peptide bond is a process know as (?)

Hydrolysis

(?) -- A primary force for folding of a polypeptide is to remove hydrophobic amino acids from interactions with water; the need to remove these amino acids from solvation is why they are sequestered into the interior region of the folded protein. The interior forces called (?), are the interactions of these hydrophobic amino acid side chains. These forces AKA (?) -medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein.

Hydrophobic effect Van der Waals forces London dispersion

Peptides fold up into secondary and finally tertiary structure by being held together by specific weak forces. Name 4

Hydrophobic effect Hydrogen bonds Electrostatic Interaction or 'salt bridges' Disulfide bonds

(?) are another type of cell surface protein that functions along with the signal transduction receptors. It plays a central role during the adhesion of cell to cell and cell to extracellular matrix.

Integrins It can transduce signals bidirectionally, into and out of the cell. It is already known that a lot of cellular proteins can bind the cytoplasmic tail of integrins and these proteins that then transduce the activating signal from integrins to other cellular proteins or cytoskeleton.

When myoglobin binds oxygen it is held in position in the oxygen binding crevice bound to both (?) and a (?) In hemoglobin when the first oxygen binds, it causes a rotation of the 4 peptides. This conformational change allows the next 3 oxygen molecules to bind with a 1000 fold greater affinity. When you look at the graph of oxygen binding, myoglobin has a (higher/lower) affinity for oxygen (rectangular hyperbolic curve), than that of hemoglobin (sigmoidal curve.) Hemoglobin's binding of oxygen is also pH dependent. Oxygen is released by hemoglobin due to a small (increase/decrease) in pH, to be bound by myoglobin. This is what has been called the (?) effect. It is due to increase in H+ ions and CO2 that cause this pH drop in the capillaries of tissues. This effect changes the tetramer binding, it does not affect myoglobin since it is a monomer.

Iron + Imidazole ring (histidine) higher decrease Bohr

Specific arrangements of several elements of secondary structure: α-helix, β-sheet or a mix of both alpha-helices and beta-sheets is known as?

Motifs

(B) The α helix viewed from one end, looking down the longitudinal axis.

Note the positions of the R groups, represented by green spheres. This ball-and-stick model, which emphasizes the helical arrangement, gives the false impression that the helix is hollow, because the balls do not represent the van der Waals radii of the individual atoms.

(?) acts as a helix breaker because the rotation around the N-Ca bond is impossible. (?) acts as a helix breaker because the tiny R-group (H) supports other conformations. The negatively charged R groups (glutamate) or positively R groups such as arginine and lysine are strong (?)-forming amino acids. In the antibody molecule (?) play an essential role in the function of this protein.

Proline Glycine helix-forming beta loops

large biological molecules, or macromolecules, consisting of one or more long chains of amino acid residues.

Proteins

(?) structure is formed by the assembly of individual polypeptides into a larger functional cluster.

Quaternary These proteins dock to one another at specific orientation, with various types of bonds holding them together. The bonds that hold them together are the same bonds that hold protein in tertiary structure.

A (?), gives the distribution of the dihedral ϕ and Ψ that are found in a protein

Ramachandran plot

(D) Space-filling model

The atoms in the center of the α helix are in very close contact; there are no water molecules in this space.

(A) showing the intrachain hydrogen bonds.

The repeating unit is a single turn of the helix, 3.6 residues.

(C) Helical wheel projection of an α helix.

The yellow residues, for example, are hydrophobic amino acids. The green circles represent residues that are polar non-charged amino acids. Theses amino acids for instance in a membrane integral protein would interact with the fatty acid chains of the phospholipids. The pink and grey circles represent residues with the potential for interaction of negatively and positively charged side-chains on the alpha helix. In the transmembrane protein these residues would be located towards the interior of, for example a transport, to interact with the anion being transported.

Cellular transporters belong to two major families: passive facilitated transport and active transport

Those were the transporter is moving molecules with the concentration gradient the energy of transport is from the gradient, and is called passive. On the other hand if these small molecules are being transported against the concentration gradient, then cellular energy is required to carry them across the membrane by these active transporters.

Proteins are bonded together by

a covalent peptide bond

Proteins are bonded together by (?) bond

a covalent peptide bond

Sheet-like arrangement of the backbone is held together by hydrogen bonds between the (?) in different strands, connected by extended chains.

backbone amines

Ψ (psi) angle: angle around the α-carbon—(?) bond

carbonyl carbon

The formation of a peptide bond is a (?) with the release of water

dehydration synthesis

The amino acid sequence could not support an alpha helix and the structure collapses into beta sheet. The beta sheet arrangement is held together by the (?) between the backbone amine and carbonyl oxygen of a lateral strand.

lateral hydrogen bonds

The specific 3-dimensional shape is called the (?) of the protein.

native configuration

The α helix is stabilized by hydrogen bonds between (?), and the β sheet stabilized by hydrogen bonds between (?)

nearby residues adjacent segments that may not be nearby The alpha-helical backbone is held together by hydrogen bonds between the carbonyl group of the n amino acid and the n+4 amine of that amino acid; the right-handed α helix with 3.6 amino acid residues (5.4 Å) per turn of the helix (see above figure).

Tertiary structure refers to the overall spatial arrangement of atoms in a protein that is stabilized by (?) between (?); largely hydrophobic and polar interactions and can be stabilized by (?)

numerous weak interactions amino acid side chains disulfide bonds.

Alpa Helix: Peptide bonds are aligned roughly (?) to the helical axis. Side chains point out and are roughly (?) with the helical axis.

parallel perpendicular The inner diameter of the helix is too small for anything to fit "inside".

Those were the transporter is moving molecules with the concentration gradient the energy of transport is from the gradient, and is called (passive/active). On the other hand if these small molecules are being transported against the concentration gradient, then cellular energy is required to carry them across the membrane by these (passive/active) transporters.

passive active

The (?) of the peptide bond and the (?) geometry of the α-carbon create a β-pleated sheet-like structure.

planarity tetrahedral

The (?) consists of a sequence of amino acids linked together by peptide bonds, which is a (?) and includes any disulfide bonds between adjacent cysteine amino acids of proteins on the cell surface and proteins secreted from the cell.

primary structure covalent bond

All peptide bonds in proteins occur in the trans configuration. The exception to this is (?), which energetically can be in either the cis or trans configuration.

proline The cis-trans isomerization is actually carried out by the enzyme peptidyl prolyl isomerase in biological systems.

Beta Turn: The presence of (?) in position 2 of an amino acid sequence forming a beta turn or (?) in position 3 are commonly found. Type 1 beta turns occur (?) than Type 2.

proline glycine 2 times more frequently

The structure of the protein is partially dictated by the (?)

properties of the peptide bond

Irregular arrangements of polypeptide chains are called the (?)

random coil or extended chain

The resulting polypeptide can be arranged into units of (?); these are α-helix and β-pleated sheets and/ or extended chains of amino acids connecting these secondary structures.

secondary structure

(?) move two or more molecules simultaneously across a membrane in the same direction;

symporters

The α-helix, β-sheet and extended chain are also part of the folding to form the of the native polypeptide.

tertiary structure The tertiary structure itself can be one of the subunits that make up the quaternary structure of the multi-subunit protein, as in this case of the oxygen carrier protein found in red blood cells, hemoglobin.

The glucose transporter is an example of a (uniport/symport/antiport) transporter found on mammalian cells, it transports glucose into the cell. The bacterial sodium galactose is an example of a (uniport/symport/antiport). It transports 2 sodium ions to each galactose molecule not the cell. Although not cellular energy is expended in this process it is active transport since the transport of galactose is dependent on the sodium gradient.

uniport symport

(?) are those that transport a small molecule across a membrane

uniporters

Side chains (R groups of amino acids) protrude from the sheet alternating in (?)-configuration.

up and down directions (trans configuration).

In parallel β sheets, running in the same direction, the H-bonded strands of parallel strands resulting in bent H-bonds that are (?) In the anti-parallel β sheets, H-bonded strands run in opposite directions, resulting in linear H-bonds that are (?)

weaker stronger