UAMS COP Biochem Quiz 1 (All of Aykin-Burns' section)

amino acids, genes, activity

Proteins differ in their sequence of ____________, determined by the nucleotide sequence of their ______, which usually results in folding of the protein into a specific three-dimensional structure that determines its _________.

peptide bonds

Proteins are linear polymers consist of monomer units called amino acids, which are linked by ____________.

primary structure

determined by the sequence of linked amino acids

secondary structure

determined by 3D structure formed by H-bonds between amino acids in close proximity

tertiary structure

is formed by folding of secondary structural elements into three-dimensional conformation due to long-range interactions between amino acids

quarternary structure

the three-dimensional structure of proteins with more than one subunit and how the subunits fit together

Acidic carboxyl group, basic amino group, hydrogen

Amino acids have three common functional groups attached to the α-carbon (Proline is the exception):

chiral

All amino acids are _________ (except Glycine).

L

Only __-amino acids are incorporated into proteins.

hydroxyl group

In biology the important role of these groups mostly has to do with their ability to form hydrogen bonds. The polarity of the functional group and the ability to form two simultaneous H-bonds increase the water solubility of any molecule that has this group attached to it.

Phosphate group

These groups are vital structural units for nucleic acids, and biological membranes; they have a perfectly balanced reduction potential to make them excellent intermediaries in redox reactions; Their large size, and electronegativity can cause deformations in the 3D structure of proteins which make them the primary way to control enzymatic function, and cell signaling.

Carboxyl Group (Carboxylic Acid)

These acids are ubiquitous in biology and include amino acids, fatty acids, acetic acid, and many others. These groups are also susceptible to nucleophilic attack, especially when modified in an enzymatic pocket. This is what allows amino acids to chain together into proteins.

amino group

These function as bases by accepting protons and important for maintaining the structure of many macromolecules through electrostatic interactions and H-bonding.

Thiol Group

This group is nucleophilic and readily undergo redox reactions, giving it a variety of biological functions. The most common place students will see thiols is in the amino acid cysteine. Two cysteines can form a sulfur-sulfur bonds which give additional 3D structure to the protein.

carbonyl group

These groups have a large partial positive charge on the carbon attached to the oxygen which makes it susceptible to nucleophilic attack.

Peptides

Amino acids polymerize to form ___________.

buffers

All free amino acids, plus charged amino acids in peptide chains, can serve as __________.

ionizable protons

Amino acids contain at least two __________, each with its own pKa.

Zwitterion

__________ is a neutral molecule with both positive and negative electrical charges.

dipolar ions

Under the physiological pH range (6.8-7.4), amino acids are zwitterions, or ____________.

isoelectric point (pl)

the pH at which a molecule carries no net electrical charge

protons (H+)

The net charge on the molecule is affected by pH and can become more positively or negatively charged due to the gain or loss, respectively, of _________.

Aliphatic hydrocarbon group

the absence of a benzene ring

Gly, Ala, Val, Leu, Ile

Which AA belong to a Aliphatic hydrocarbon group?

Phe, Trp

Which AA have an aromatic side group?

Met (Methionine)

Which AA has a sulfur-containing group?

Pro (Proline)

Which AA has an aliphatic side group?

nonpolar

In proteins found in aqueous solutions--a polar environment--the side chains of the _________ amino acids tend to cluster together in the interior of the protein

hydrophobic effect

In proteins found in aqueous solutions--a polar environment--the side chains of the nonpolar amino acids tend to cluster together in the interior of the protein. What is this phenomenon called?

R-groups

The hydrophobic effect is the result of the hydrophobicity of the nonpolar _________.

3D shape

The nonpolar R-groups fill up the interior of the folded protein and help give it its ___________.

membrane, outside

Proteins that are located in a hydrophobic environment, such as a __________, the nonpolar R-groups are found on the _______ surface of the protein, interacting with the lipid environment.

Proline

________ differs from other amino acids in that its side chain and α- amino N form a rigid, five-membered ring structure.

secondary amino, collagen

Proline has a __________ group. The unique geometry of proline contributes to the formation of the fibrous structure of ________, and often interrupts the α-helices found in globular proteins.

Polar (hydrophilic) amino acids

electrically neutral (uncharged) at pH 7.4

functional side chains

Polar (hydrophilic) amino acids' __________ are often involved in the catalytic mechanism of enzymes and in drug-receptor binding.

Hydroxyl (-OH) group

Serine and Threonine have an _____ group attached to an aliphatic side chain

aromatic ring

Tyrosine has -OH group attached to an ____________.

oxidation

Cysteine has -SH which can react with other thiol group to forms disulfide (-S-S-) bridges in protein in an __________ reaction.

Disufide

_________ bonds are important for protein structure, metal ion binding, antioxidant capability of the peptides/proteins

Cys (cysteine)

Disulfide bonds between cysteine residues stabilize the structures of many proteins, may act as a redox sensor.

phosphate group

The polar hydroxyl group of serine, threonine, and, rarely, tyrosine, can serve as a site of attachment for structures such as a ____________.

oligosaccharide chains

The polar hydroxyl group of serine, threonine, and, rarely, tyrosine, can serve as a site of attachment for ___________ in glycoproteins.

Amide

______ group is derived from carboxyl groups, in their side chains.

ionize

Amide bonds do not usually _______ in the range of pH encountered in biochemistry.

Asp (asparagine/Aspartic Acid)

Amide group of _______ can serve also serve as a

oligosaccharide chain attachment site.

carboxyl, glutamate and aspartate

Aspartic acid and glutamic acid, have ______ groups in their side chains in addition to the one present in all amino acids. A carboxyl group can lose a proton, forming the corresponding carboxylate anion, _______ and __________, respectively.

asp (Aspartic acid) and glu (glutamic acid)

___________ and __________ are fully ionized and negatively charged at the physiological pH of 7.4.

Protons

The side chains of basic amino acids accept _________.

Lys, Arg, His

For amino acids with a basic side chain, at pH 7.4 the side chains of _________ and _____ are fully ionized and positively charged. __________ is weakly basic, so mostly uncharged in its free amino acid form at pH 7.4.

Lys, Arg

_______ is capped by a primary group and ______ is capped by a guanidinium group.

His

_______ contains an imidazole group, which can bind and release protons during enzymatic reaction.

ionic

Although it is mostly neutral as a free amino acid, when histidine is incorporated into proteins, its side chain can be positively charged or neutral depending on the _____ environment of the polypeptide chain of that particular protein.

Phosphorylation

the most common type of regulatory modification

Essential Amino Acid

an amino acid that cannot be synthesized de novo (from scratch) by the organism being considered, and therefore must be supplied in its diet. If they are not taken through diet, they will not be available for protein synthesis.

conditionally essential

Some amino acids are considered ________. Under certain conditions like illness or stress the body might not be able, or might be limited in the ability, to synthesize them.

Arg

may or may not be considered as essential, depending on certain conditions; there's not enough production of it, it needs to be supplemented through the diet.

hydrophobic effect

The release of water molecules from the structured salvation layer around the molecule as protein folds increase the net entropy.

Ionic bonds

The bonds form via electrostatic attraction between oppositely charged ions.

Hydrogen bonds

interaction of N-H and C=O of the peptide bond leads to local regular structures such as alpha-helices and beta-sheets. They can also form within alpha-helices and beta-sheets.

disulfide bonds

the covalent bonds that are derived from two thiol (-SH) groups

London Dispersion

Medium-range weak attraction between between all atoms contributes significantly to the stability in the interior of the protein.

electrostatic interactions

Long-rage strong interactions between primarily charged groups (e.g. H-bonds); salt bridges, especially those buried in the hydrophobic environment, strongly stabilize the protein.

peptide bond (also called amide bond), condensation (dehydration)

A _______ is formed by linking the α-carboxyl group of one amino acid to α-amino group of another amino acid via the release of a H2O molecule, thus it is a _______ reaction.

Amino acids linked by a peptide bond

What do polypeptides consist of?

main chain (or backbone)

The polypeptide chain consists of a repeating part called the _________

and a variable part consisting of the distinctive amino acid side chains

50-2000

Proteins - most natural polypeptide chains contain between________ amino

acid residues.

amino group (N-terminus) to Carboxyl group (C-terminus)

The primary structure of an AA is always written from?

H-bonding

The backbone has _______ potential because of the carbonyl groups and hydrogen atoms that are bonded to the nitrogen of the amine group.

dalton

How is the mass of a protein measured?

free energy

Synthesis of protein primary structure require input of __________.

amino acid sequence

The final structure of the protein chain is determined by its ________.

resonance, rotate

Each peptide bond has some double-bond characteristics due to _____ and cannot _______.

Between the carboxylic and amino group

Where does the peptide bond occur?

double bond characteristic, C-N, transconfiguration

A polypeptide has a partial ___________, because there is resonance between _______, this causes the peptide bond to have a rigid structure and majority will favor ___________.

The secondary structure of the protein

The organization around the peptide bond, paired with the identity of R groups, determines what?

local spatial arrangement

Secondary structure refers to a ________ of the polypeptide backbone formed by hydrogen bonds between peptide NH and CO groups of amino acids that are near one another in the primary structure.

alpha-helix and Beta-stands/sheets

(QUIZ QUESTION) Prominent examples of the secondary structure

Loops and coils

Other regions of the polypeptide chain form non-regular, non-repetitive secondary structures such as ________.

Helical

In the secondary structure of a protein, because of the carboxylic group, each amino acid wants to dorm a H-bond to the amine group of the other one, and brings them closer to each other, forming a _______ shape.

3.6 amino acid residues

The amino acids for each turn in the alpha-helix are about ________ apart.

Dipole movement

The peptide bond has a strong _________.

orientation

All peptide bonds in the α helix have a similar _______.

positive

(QUIZ QUESTION)Negatively charged residues often occur near the ______ end of the helix dipole.

right-handed

Essentially all α helices found in proteins are ____________.

energetically more favorable

Right-handed helices are ________ because there is less steric clash between the side chains and the backbone.

Ferritin and Collagen

The majority of amino acids give a nice, helical shape except:

Ferritin

Major iron-storage protein

Ala (Alanine) and Leu (Leucine)

Helix formers

Pro (Proline) and Gly (Glycine)

Helix Breakers

Beta-strand

Polypeptide chains running side-by side

Beta-sheet

stabilized by hydrogen bonding between polypeptide strands (inter- strand).

3.5

The distance between adjacent amino acids along a β-strand is approximately _____Å

opposite directions

The side chains of adjacent amino acids point in _________.

beta-sheet

β-strands are rare because they are conformationaly less stable. However, when two adjacent β strands line up they can form hydrogen bonds. This creates a ______.

less stable

Parallel sheets are ________ than antiparallel sheet, possibly because the hydrogen bonds are distorted.

bent (weaker)

In parallel β-sheets, the H-bonded strands run in the same direction, thus hydrogen bonds between strands are _______.

linear (stronger)

In anti-parallel β-sheets, the H-bonded strands run in opposite directions., thus hydrogen bonds between strands are ________.

Beta-sheets

β turns occur frequently whenever strands in _______ change the direction.

180, 4

The beta-turn is ______ degrees and is accomplished over ___ amino acids.