Proteins Flashcards
What do you call the structural protein present in plants? The chief structural proteins in animals, which are constituents of hair, skin, nails, etc., are?
- Cellulose
- Collagen & Keratin
Two proteins that are responsible for our movement?
muscle expansion and contraction are involved in every mvmnt
actin & myosin
What do you call the protein that transports oxygen from lungs to other cells and CO2 from the cells to the lungs?
hemoglobin
what do you call the proteins from a foreing substance that enters the body? Similarly, what do you call the proteins that the body makes to counteract the foreing molecule?
Antigen; Antibody
what do you call the protein which has a protective function (blood clotting)?
Fibrinogen
what do you call the storage protein that stores nutrients in milk? what abt in eggs?
casein; albumin
what do you call the protein in liver that stores iron?
Ferritin
what are the two major types of proteins?
- Fibrous
- Globular
Among the two major types of proteins, which is used mainly for structural proteins and is generally insoluble? What about the one that has a functional (nonstructural) purpose and is more soluble in water?
Fibrous; Globular
The R groups of amino acids have four types of side chains based on polarity:
- Nonpolar
- Polar neutral
- Acidic
- Basic
Can you classify them based on hydrophobicity/hydrophilicity?
- Nonpolar = hydrophobic
- Polar, Acidic, Basic = hydrophilic
Looking at the general formula of amino acids, all but one are chiral with carbon stereocenters, ano yung isang iyon?
Glycine
Glycine = 2 H+ sa alpha carbon
what do you call the two possible configurations which is based on the enantiomers of amino acid given that it is a chiral molecule?
this configuration refers to the rotation of plane-polarized light
enantiomers = molecules that are non-superimposable mirror images of one another (do not overlap when placed on top of each other); inversion of the whole molecule
D and L configuration
Among the two isomers of amino acids, which of the two isomers does our body have?
L-isomer
D-amino acids are rare in nature (sometims nasa wall ng ibang bacteria)
when assigning D or L, remember that amine group is always on the left. You may also note that in line structure, follow CORN rule to see if counterclockwise ang priority grps (L)
can water be a strong enough base or acid to cause the dissociation COOH to COO- and protonation of NH2 to NH3+?
Yes.
An amino acid has COOH (can’t exist w/ presence of weak base) and NH2 (can’t exist w/ presence of weak acid) groups in the same molecule. Therefore, in water solution, the COOH donates a proton to the NH2
Compounds that have a positive charge on one atom and a negative charge on another are called what?
Zwitterions
German zwitter meaning “hybrid”
amino acids are zwitterions not only in H2O but also in solid state
When acids are added to amino acids, what happens to its zwitterion?
protonation (in COO- group)
from COO- to COOH; and NH3+ same lang din
When bases are added to amino acids, what happens to its zwitterion?
deprotonation (in NH3+ group)
from NH3+ to NH2; and COO- remains d same
What do you call the pH when a molecule have equal positive and negative charges?
Isoelectric point
3 basic = higher pI; 2 acidic = lower pI
At or near the isoelectric point, amino acids exist in aqueous solution largely or entirely as?
eto yung (+) on one atom & (-) on one atom
zwitterions
If amino acids can accept and donate protons, we call that compound as?
Amphoteric
Amino acids also are amphiprotic
Since amino acids in a solution can accept or donate protons, it can neutralize both acids and bases and their solutions are known as?
buffers
Amino acids are therefore amphiprotic compounds, and aqueous solutions of them are buffers (Bettelheim)
Why is it that amino acid is never found in this form: RCH(NH2)COOH?
(mahaba ans ko hehe)
Carboxylic acids are stronger acids than water. amines are stronger bases than water (weaker acids). Therefore, since COOH is more acidic, it should donate protons and then the amino group will accept that proton. It isnt possible to find this amino acid form because acids are technically proton donors and bases (weaker acids) are proton acceptors
The carboxyl has a hydrogen to donate, and the amino group can accept a hydrogen. In very un-scientific terms, the hydrogen is not going to be found on the
stronger acid and removed from the stronger base. That is why the zwitterion predominates
The combination of a carboxylic acid and an amine is called an?
Amide
The bond which is the product of the combination of COOH and NH3+ of amino acids is called?
peptide bond
2 amino acids = dipeptide
If there are more than 15 (30 sa book) amino acids in a protein, its chain is called?
polypeptide
What do you call the amino acids in a peptide chain?
residues
What do you call the amino acid at the end of a peptide that has a free alpha-carboxyl group?
C-terminus
What do you call the amino acid at the end of a peptide chain that has a free alpha-amino group?
N-terminus
Because of the presence of the carboxylate, the side chains of these two amino acids (D & E) are ____ charged at neutral pH.
negatively charged
There are two carboxylic acids present in D and E. Thus, at neutral pH, these two carboxylic acids (since stronger acids than water) donate their H+, making the overall charge of the amino acid negative
The side chains of lysine and arginine are ____ charged at or near neutral pH
positively
In lysine, the aliphatic hydrocarbon tail is bonded to a side-chain what group?
amino group
In arginine, the side-chain basic group, the ____ group, is more complex in structure than the amino group and also bonded to an aliphatic hydrocarbon tail.
guanidino
What functional group in histidine makes it basic?
Imidazole group
Histidine is also found in enzymes since its pH is around 6.0 which is not far from physiological pH
What are the 3 amino acids that demonstrate aromaticity in their side chains?
- Phe
- Trp
- Tyr
Aromatic amino acids absorb UV light at ____ nm
280
Considering that F, W, and Y are precursors to neurotransmitters, what is d descendant of W?
Serotonin
5-hydroxytryptamine
Considering that F, W, and Y are precursors to neurotransmitters, what is d product of Y & F?
norepinephrine & epinephrine
what do you call the process characterized by the modification of the parent amino acid after the protein is synthesized? This process is involved in the production of uncommon amino acids.
post-translational modification
Identify the two uncommon amino acids characterized by their hydroxyl groups on their side chains?
- Hydroxylysine
- Hydroxyproline
This uncommon amino acid has an extra iodine-containing aromatic group on its side-chain, what is it?
Thyroxine
what do you call the horizontal line of atoms representing the repeating structure of proteins?
N-C-C-N-C-C
peptide backbone
The pI of a protein is the pH where there is an equal number of positive and negative charges. If pH is above the isoelectric point, the overall charge of the protein is?
negative
The pI of a protein is the pH where there is an equal number of positive and negative charges. If pH is below the isoelectric point, the overall charge of the protein is?
positive
When pH is greater or lesser than the isoelectric point of a protein, charges will be present, these charges will cause the proteins too demonstrate what?
Attraction or Repulsion
Repulsion
repulse protein molecules when there is a difference between the pH and the isoelectric point
When there are no repulsive forces, protein molecules clump together to form ____ of two or more molecules to reduce their solubility.
aggregates
thus, at isoelectric point, proteins are least soluble and can be precipitated from their solutions
the primary structure of proteins describes the ____ of amino acids in the polypeptide chain.
linear sequence
The secondary structure refers to certain ____, such as the a-helix conformation or the B-pleated sheet conformation or the absence of a repeating pattern, as with the random coil
repeating patterns
or repetitive conformations of the protein backbone
The tertiary structure describes the overall ____ of the polypeptide chain.
3D conformation
The ____ structure applies mainly to proteins containing more than one polypeptide chain (subunit) and deals with how the different chains are spatially related to one another
Quaternary
As with naming peptides, the assignment of positions of the amino acids in the sequence starts at the ____ end.
N-terminal
The primary structure of a protein determines to a large extend the ____ 2ndary and tert structures.
blank is also defined as “most frequently occurring”
native
what structure pertains to the repetitive conformations of the protein backbone?
secondary structure
what structure pertains to the overall 3D conformation of a polypeptide chain, including the interactions of the side chains and the position of every atom in the polypeptide?
Tertiary structure
What structure determines the spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain?
Quaternary structure
what are the two most common secondary structures found in a protein? what do you call protein conformations that do not exhibit a repeated pattern?
a-helix & B-pleated sheet; random coils
A secondary structure where the protein folds into a coil held together by hydrogen bonds parallel to the axis of the coil
a-Helix
In the ____ form, a single protein chain twists in such a manner that its shape resembles a right-handed coiled spring.
alpha-helix
what holds the shape of the helix and it exists between the backbone -C=O and NH groups?
hydrogen bonds
In an alpha helix, a hydrogen bond between the oxygen of a carbonyl group and the hydrogen of an amine group is formed how many amino acids away? This cyclic pattern creates a helix of how many amino acids per turn?
4 amino acids away; 3.6 amino acids per turn
In an alpha-helix, the amine group points where? what abt the carbonyl grp? the side chains point where?
upward or downward or inward or outward
- upward
- downward
- outward from the helix
what do you call the secondary structure that can occur between molecules when polypeptide chains run parallel or antiparallel from each other?
B-pleated sheet
In all secondary structures, the hydrogen bonding is between backbone -C=O and H-N- groups, a characteristic that distinguishes between secondary and tertiary structures. In the latter, as we shall see, the hydrogen bonding can take place between ____.
R-groups
or interactions of side chains (not just the peptie backbone)
What forms when a cysteine residues between two different chains meet?
formation of disulfide bond
which is a covalent bond
What structures are stabilized by hydrogen bonding between polar groups on side chains or between side chains and the peptide backbone?
Tertiary structures
Other term for salt bridges?
electrostatic attractions
This occur between two amino acids with ionized side chains—that is, between an acidic amino acid (-COO-) and a basic amino acid (-NH3+ or =NH2+) side chain.
Salt bridges
or electrostatic attractions (held together by ion-ion attraction)
In aqueous solutions, globular proteins usually turn their ____ groups outward, toward the aqueous solvent and their ____ groups inward, away from H2O molecules.
polar; nonpolar
Two side chains with the same charge would normally repel each other, but they can also be linked via a what?
metal ion
For example, two glutamic acid side chains (-COO-) would both be attracted to a magnesium ion (Mg2+), forming a bridge.
What do you call proteins that help other proteins to fold into the biologically active conformation and enable partially denatured proteins to regain their biologically active conformation?
chaperones
As a result of noncovalent interactions in a quaternary structure, subtle changes in structure at one site on a protein molecule may cause drastic changes in properties at a distant site. Proteins that exhibit this property are called ____.
allosteric
Protein conformations are stabilized in their native states by secondary and tertiary structures and through the aggregation of subunits in quaternary structure. Any physical or chemical agent that destroys these stabilizing structures changes the conformation of the protein and this process is called?
denaturation
what cleaves hydrogen bonds, so boiling a protein solution destroys the a-helical and b-pleated sheet structure?
heat
what denaturating agent causes the unfolding of the polypeptide chains wherein precipitation or coagulation then takes place?
heat
what denaturating agent, besides heat, causes the breakage of H-bonds and cause the unfolding of globular proteins?
6M Urea
____ change protein conformation by opening up the hydrophobic regions.
Surface-active agents (detergents)
What denaturating agents are responsible for affecting (or breaking) the salt bridges and H-bonds?
- Acids & Bases = salt bridges & H-bonds
- Salts = salt bridges lng
What denaturating agent is responsible for breaking the disulfide bonds that results to the reduction to -SH groups?
Reducing agents
Heavy metal ions (for example, Pb2+, Hg2+, and Cd2+) also denature protein by attacking the ____. They form salt bridges, as in -S-Hg2+-S-
-SH groups
____ changes secondary, tertiary, and quaternary structures. It does not affect primary structures
Denaturation
When the amino group of one amino acid condenses with the carboxyl group of another amino acid, an ____ (peptide) bond is formed, with the elimination of water.
amide
