Proteins Flashcards
The only amino acids with secondary a-amino group
Proline
Amino acid without stereocenter (not chiral)
Glycine
Two amino acids with two stereocenters
Isoleucine and threonine
Proposed that proteins are long chains of amino acids joined by amide bonds
Emil Fischer (1902)
A short polymer of amino acids joined by peptide bond; they are classified by the number of amino acids in the chain
Peptide
A molecule containing two amino acids joined by peptide bonds
Dipeptide
A molecule containing three amino acids joined by peptide bonds
Tripeptide
A macromolecule containing many amino acids joined by peptide bonds
Polypeptide
A biological macromolecule containing at least 30 to 50 amino acids joined by peptide bonds
Protein
Individual amino acid units
Residues
Discovered that there is about 40% double-bonded character to the C-N bond and that a peptide bond between two amino acids is planar
Linus Pauling
Pauling explained the double-bonded character to the C-N bond through the concept of _____
Resonance
The amino acid at the end of the chain having the free -COO- group
C-terminus
The amino acid at the end of the chain having the free -NH3+ group
N-terminus
How do you read the amino acids?
Left-right (N-terminus to C-terminus)
The sequence of amino acids in a polypeptide chain
Primary structure
Conformations of amino acids in localized regions of a polypeptide chain
Secondary structure
Examples of secondary structure
a-helix, b-pleated sheet, random coil
Complete three-dimensional arrangement of atoms of a polypeptide chain
Tertiary structure
Spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain
Quaternary structure
Antidiuretic hormone
Vasopressin
Affects the contractions of the uterus in childbirth and muscles of the breast in secretion of milk
Oxytocin
Differences in the structure of vasopressin and oxytocin
Vasopressin: Arg & Phe
Oxytocin: Leu & Ile
A type of secondary structure in which a section of polypeptide chain coils into a spiral, most commonly a right-handed spiral
a-helix
A type of secondary structure in which two polypeptide chains or sections of the same polypeptide chain align parallel to each other; the chains may be parallel or antiparallel
b-pleated sheet
In a-helix, there are ____ amino acids per turn of the helix
3.6
The six atoms of each peptide bond in a-helix lie in the _____ plane
same
The N-H groups point in the _____ direction, roughly _____ to the axis of the helix (a-helix)
same, parallel
The C=O groups point in the _____ direction, roughly _____ to the axis of the helix (a-helix)
opposite, parallel
All R-groups of a-helix point _____ from the helix
outward
A polypeptide derived entirely from alanine, where the intrachain hydrogen bonds that stabilize the helix are visible as the interacting C-O and N-H bonds
polyalanine, a-helix
In b-pleated sheet, the six atoms lie in the _____ plane
same
The C=O and N-H groups of the peptide bonds (b-pleated sheet) from _____ chains point _____ each other and in the ____ plane
adjacent, toward, same
All R-group (in b-pleated sheet) on any one chain ___ of the sheet
alternate (above, then below)
The overall conformation of an entire polypeptide chain
tertiary structure
Four ways of stabilization of tertiary structure
Covalent, hydrogen, salt bridges, hydrophobic interactions
Example of tertiary structure stabilization: formation of disulfide bonds between cysteine side chains
Covalent bonds
Example of tertiary structure stabilization: between the -OH groups of serine and threonine
Hydrogen bonding
Example of tertiary structure stabilization: the attraction of the -NH3+ group of lysine and the COO- group of aspartic acid
Salt bridges
Example of tertiary structure stabilization: nonpolar side chains of phenylalanine and isoleucine
Hydrophobic interactions
The arrangement of polypeptide chains into noncovalently bonded aggregation
Quaternary structure
Adult hemoglobin: two alpha chains of ____ amino acids each, and two beta chains of _____ amino acids each
141, 146
Fetal hemoglobin: _____ alpha chains and _____ gamma chains
2, 2
The process of destroying the native conformation of a protein by chemical or physical means
Denaturation
Denaturating agent: can discrupt hydrogen bonding; in globular proteins, it can cause unfolding of polypeptide chains with the result that coagulation and precipiation may take place
Heat
Denaturating agent: disrupts hyrdogen bonding
6M aqueous urea
Denaturating agent: detergents such as sodium dodecylbenzenesulfate (SDS) disrupt hydrogen bonding
Surface-active agents
Denaturating agent: 2-Mercaptoethanol cleaves disulfide bonds by reducing -S-S- groups to -SH groups
Reducing agents
Denaturating agent: transition metal ions form water-insoluble salts with -SH groups
Heavy metal ions
Denaturating agent: penetrates bacteria and kills them by coagulating their proteins
Alcohol
Where will the equilibrium shift if pI>pH?
Left
Where will the equilibrium shift if pI<pH
Right
Net charge if pH>pI
Negative
Net charge if pI>pH
Positive
A sugar alternative that is 200x sweeter than sucrose
Aspartame
Present amino acid in aspartame
Phenylalanine
Effect of configuration in aspartame
D-configuration will lead to a bitter taste (it should be sweet)
Three physiologically important amino acids especially as neurotransmitters
tyrosine, tryptophan, phenylalanine
Low level of L-dopa will lead to ______
Parkinson’s disease
Two amino acids associated with L-dopa
Tyrosine and phenylalanine
Serotonin is converted from what amino acid?
Tryptophan
Low levels of serotonin leads to ____
Depression
Extremely high levels of serotonin leads to ______
Manic-depressive schizophrenia (Or bipolar disorder)
Water insoluble complexes from heated test tube (from glycation process)
Advanced glycation end-products (GAE)
pH of hemoglobin
6.8
pI of albumin
4.9
Difference between normal hemoglobin and sickle cell hemoglobin (HbS)
Valine replaces Glutamic Acid in the sixth position
_____ prompts bone marrow to manufacture fetal hemoglobin for sickle cell anemia
Hydroxyurea
True or false. Denaturation affects all structures of proteins
False. Primary structures are not affected, only to a small extent if ever, and it can be reversed
Some denaturation caused by heat can be reversed by _____. They help a partially heat-denatured protein to regain its native secondary, tertiary, and quaternary structures
Chaperones
