Amino Acids & Proteins (Lec) Flashcards
most abundant biomolecule in the cell
Proteins
polymers made of monomers
amino acids
atoms or small molecules that bond together to form more complex structures such as polymers
Monomers
four main types of monomer
sugars, amino acids, fatty acids, and nucleotides
a process by which a polypeptide chain folds to become a biologically active protein in its native 3D structure.
Protein folding
T/F - Proteins may be rigid or flexible to various degrees as required for optimum function
T
Number of peptides possible for a chain of n amino
acids
20^n (ex. 100 residue protein has 20^100)
Hierarchy of Protein Structure
the amino acid sequence
primary structure
Hierarchy of Protein Structure
frequently occurring substructures
or folds
secondary structure:
Hierarchy of Protein Structure
three-dimensional arrangement of all
atoms in a single polypeptide chain
tertiary structure
Hierarchy of Protein Structure
overall organization of non-covalently
linked subunits of a functional protein.
quaternary structure
tendency for non-polar solutes to aggregate in
aqueous solution to minimize the hydrocarbon-water
interface
Hydrophobic Effects [important in the binding of substrates (ligands) into protein receptors and enzymes]
RATIONALE BEHIND PROTEIN FOLDING
Proteins fold to minimize their surface contact with wate
hydrocarbon on the inside, polar group on the outside
micelle structure
unfolding of the native three-dimensional structure of a protein by chemical influences
Protein Denaturation
unfolding of the native three-dimensional structure of a protein by chemical influences
Protein Denaturation
Common secondary structures:
α-helix (amino acids wound into a helical structure)
β-sheet
β-turn
disulfide bonds
hydrophobic sidechains form an interface between
α-helices (de novo protein design)
Helical Bundles
covalent structural scaffolds, redox active, reversible
Disulfide bonds
FUNCTIONS OF PROTEIN (8)
Structural – for support (ex. collagen, elastin)
Catalytic – for hastening biochemical reactions (ex. amylase)
Storage – for storage of amino acids (ex. casein, ovalbumin)
Transport – for transport of other substances (ex. hemoglobin)
Regulation – for regulation of bodily activities (ex. insulin, glucagon)
Receptor – for response of cell to external stimuli (ex. neuron receptors)
Contractile – for movement (ex. myosin, actin)
Defensive – for protection against disease (ex.
antibodies)
a specific three-dimensional conformation that is essential for the biological function in proteins
Native conformation (3-D folded conformation with active function)
T/F - Loss of structure 🡪 loss of biological function
T
spatial arrangement of atoms in a protein
Conformation
building blocks or unit of proteins
amino acids
FOUR FEATURES OF AMINO ACIDS
- central/ α carbon atom linked to an amino group
- carboxyl group
- hydrogen atom/Amino group
- side chain (R group)
gives the amino acid a
unique identity and property
R group
T/F - Amino acids are chiral
T (chirality - existing in left and right-handed forms)
T/F - Amino acids can
exist as either the D or the L isomer (orientations that are mirror image of each other)
T (Most amino acids exist in nature in
the L isomer.)
the only cyclic amino acid
Proline (Usually a D isomer; does not have both free α-amino and free α-carboxyl groups)
the only achiral amino
acid
Glycine (has a hydrogen atom as its sidechain)
T/F - Proteins can be differentiated and classified according to type of side chain, R group
T (it specifies which class of amino acids it belongs to)
Non-polar amino acids (9): - hydrophobic
glycine (Gly; G)
alanine (Ala; A)
leucine (Leu; L)
isoleucine (Ile; I)
proline (Pro; P)
tryptophan (Trp; W)
valine (Val; V)
phenylalanine (Phe; F)
methionine (Met; M)
Polar amino acids (6): - hydrophilic
serine (Ser; S)
threonine (Thr; T)
cysteine (Cys; C)
tyrosine (Tyr; Y)
asparagine (Asn; N)
glutamine (Gln; Q)
Basic amino acids (3): - positively charged, hydrophilic amino acids
lysine (Lys; K)
arginine (Arg; R)
histidine (His; H)
Acidic amino acids (2): - negatively charged, hydrophilic amino acids
aspartic acid (Asp; D)
glutamic acid (Glu; E)
Amino acids that the body can synthesize
nonessential amino acids (11)
amino that the body cannot synthesize either at all or in sufficient amounts, must also be obtained from the diet.
essential amino acids (9)
T/F - The nutritional value of a protein is dependent on what amino acids it contains and in what quantities.
T
nonessential amino acids (11)
alanine
arginine
asparagine
aspartic acid
cysteine
glutamic acid
glutamine
glycine
proline
serine
tyrosine
essential amino acids (9)
histidine
isoleucine
leucine
lysine
methionine
phenylalanine
threonine
tryptophan
valine
T/F - With the exception of Glycine, all protein-derived amino acids have at least one stereocenter (the α-carbon) and are chiral
T
uncommon amino acids (2)
Hydroxylysine
hydroxyproline
aromatic amino acids (3)
phenylalanine
tryptophan
tyrosine
T/F - Amino acids are AMPHOTERIC
T - they can either
accept or donate a proton.
T/F - Amino acids may act as weak acids and bases within an
aqueous environment
how they react depends on the pH of
their environment
T/F - at low pH, ionizable groups tend to be protonated; at high pH, they tend to be deprotonated
T
a number that shows how weak or strong an acid is
pKa (The lower the value of pKa, the stronger the acid and the greater its ability to donate its protons)
T/F - Under the physiological pH range (6.8-7.4), amino acids are
zwitterions, or dipolar ions.
T
hybrid, neutral molecule with positive and
negative charges
zwitter
Net charge of the molecule
zero [attained when they reach the ISOELECTRIC
pH (pI)]
pH at which zwitterion form predominates
Isoelectric point
Acidity and Basicity of Amino Acids
Ex. Alanine
Acid solution less than 2 = net charge: +1
Neutral solution pH approximately 6 = net charge: 0/isoelectric form
Basic solution pH greater than 10 = net charge: -1
Dissociation of the hydrogen:
at low pH, both of the amino and carboxyl
groups are fully protonated. As the pH of the solution is raised, the –COOHgroup of Form I can ionize and donate H+
to the medium. The release of the
proton results to carboxylate group, -COO-. The Form II then has a net charge of zero.
The workhorses of
biological systems
peptide bonds (amide bonds that
join amino acids together)
Peptide bond formation is
accompanies by the loss of
H2O
formed between the carboxyl group of an amino acid
and the amino group of another
Peptide bonds
planar, rigid and
have partial double bond character.
Peptide bonds
By convention, peptides
are written from what direction
left to right (N to C)
beginning of the protein where the free –NH3 + group is located
N-terminal end
end of the protein where the –COO group is located
C-terminal end
Levels of structural organization of proteins (4)
Primary
Secondary
Tertiary
Quaternary
T/F - Most natural polypeptide chains
contain between 50 and 2000 amino
acid residues and are commonly
referred to as proteins.
T
the amino acid sequence of a protein
from N to C-terminal that determine the 3-D structures
Primary Structure
primary structure can be obtained through a lab
technique called
Sequencing
changes to an amino acid with similar properties
Conservative replacement
ex. of diseases with alterations of the primary structure leading to abnormal protein function
Sickle Cell Disease (abnormal form of hemoglobin)
The local structure of neighboring
amino acids
Secondary Structure (ordered arrangements
in localized regions)
the result of intramolecular
hydrogen bonding
Secondary Structure
Refers only to interactions of the
peptide backbone.
Secondary Structure
Most common secondary structures
a-helix and b-pleated sheet
Formed and stabilized by _____
bond between the amide proton and
carbonyl oxygen
hydrogen
bond
CHARACTERISTICS OF ALPHA-HELIX
Spiral structure
Structural features: C=O of each peptide bond is
hydrogen bonded to the N-H of the fourth amino acid
away; there are 3.6 aa/turn
Pitch: 0.54nm
All R groups point outward from helix
Example: Keratin
Bulkiness (steric strain) between adjacent R-groups
Coil is clockwise
introduces kinks/bends to the structure, restricted movement, no H bonding
Helix Destabilizers - Proline and Glycine
strong helix formers
small hydrophobic residues (e.g. Ala, Leu)
CHARACTERISTICS OF BETA-PLEATED SHEETS
- form when two or more polypeptides line up side-by-side
stabilized by hydrogen bonds of adjacent polypeptide
chains (interchain or intrachain) - β-strands are extended into a zigzag
- All R groups extend above or below the sheet in an
alternating up and down direction
TYPES OF BTA-PLEATED SHEETS (2)
PARALLEL β-Pleated Sheets
- Run in same directions
- Forms bent H-Bonds (weaker)
ANTI-PARALLEL β-Pleated Sheets
- Run in opposite directions
- Forms linear H-Bonds (stronger)
3-D arrangement of all atoms
Tertiary Structures
T/F - Noncovalent interactions stabilize
the higher levels of protein structure.
T
T/F - Secondary, tertiary, and quaternary
structure of proteins is formed and
stabilized by weak forces
T
T/F - Hydrophobic residues prefer to be on
the interior of proteins, which reduces their
proximity to water
T
T/F - globular proteins fold with a hydrophobic core and a hydrophilic exterior.
T
the interactions of these drive
protein folding
Tertiary Structure:
Hydrophilic &
Hydrophobic
Interactions
Acid-base interactions
between amino acids with
charged groups can occur,
also known as salt bridges
Tertiary Structure
Electrostatic
Interactions
Cysteine residues can
undergo oxidation to
form disulfide bridges, or
cystine. They create
loops in protein chains
and dictate how curly
hair is.
Tertiary Structure
Covalent
Bonding
Tertiary Structure
Contain polypeptide chains
organized approximately parallel
along a single axis
Fibrous Proteins
Consists of long fibers or large
sheets, tend to be mechanically
strong
Fibrous Proteins
Insoluble in water and dilute salt
solutions, and play important
structural roles
Fibrous Proteins (ex. Keratin is found in hair, wool, and
nails. Collagen is found in cartilage,
bones, and skin)
Tertiary Structure
Proteins that are folded into a spherical
shape
Globular Proteins
Most of its polar side chains are on the
outside; nonpolar side chains buried
inside the structure
Globular Proteins
Soluble in water; Function: metabolic (catalytic,
transport, etc.)
Globular Proteins
Nearly have all substantial sections
of α-helix and β-sheet
Globular Proteins
association of polypeptide chains into
aggregations
Quaternary Structure
formed by the assembly of individual polypeptides
(subunit/monomer) into a larger functional cluster
Quaternary Structure
its subunits are stabilized by non-covalent interactions (like
tertiary structure)
Quaternary Structure
ROLES OF THE FORMATION OF QUARTERNARY STRUCTURES
- more stable (by further reducing the surface area of the protein complex)
- reduce the amount of DNA needed to encode the protein complex
- bring catalytic sites close together (allowing intermediates from one reaction to be directly shuttled to a second reaction)
- can induce cooperativity, or allosteric effects
Disrupts the secondary, tertiary, and quaternary structures
Denaturating Agents (Physical Agents & Chemical Agents)
Physical Agents (4)
High temperature
Vigorous shaking or agitation
Hydrostatic pressure
UV radiation
Chemical Agents (6)
Change in pH
Change in ionic strength
Organic solvents (e.g. urea, alcohol)
Reducing agents (e.g. performic acid and mercaptoethanol)
Detergents
Salts of heavy metals
Hydrogen bonds are most important in this type of structure in proteins:
a. primary structure
b. secondary structure
c. tertiary structure
d. quaternary structure
e. all of these
b. secondary structure
derive part of their function from covalently-attached molecules called prostehtic groups
Conjugated Proteins
proteins with
lipid prosthetic groups
Lipoproteins
proteins with
carbohydrate prosthetic
groups
Glycoprotein
proteins
with nucleic acid prosthetic
groups
Nucleoprotein
Cell to cell recognition, depending on blood type of prosthetic groups
Glycoproteins
ability for all quaternary structures to help or work each other/together
Cooperativity
Helix Destabilizers (3):
Presence of helix breakers
(Proline and Glycine)
* However, small hydrophobic
residues (e.g. Ala, Leu) are strong
helix formers
- Electrostatic repulsion (or
attraction) between successive
charged aa residues. - Bulkiness (steric strain)
between adjacent R-groups
T/F - Amino acids cannot share one letter codes.
T
T/F - Amino acids cannot share one letter codes.
T
T/F - Trypsin is NOT an amino acid, it is a protein with an enzymatic function
T
