peptide formation + structure Flashcards
stereochemistry of peptide bond
trans
true structure of peptide bond
resonance hybrid
which is stronger, peptide or single bond
peptide
which is longer, peptide or single bond
single
protein function
proteins accelerate thousands of biochemical reactions in the cell
catalysis
examples of proteins involved in catalysis
rubisco (photosynthesis)
hexokinase (first enzyme in glycolysis)
most abundant protein in earth
rubisco
first enzyme in glycolysis
hexokinase
protein function
some proteins provide protection and support
structure
ex of proteins for structure
collagen (connective tissue), elastin (elastic fibers), keratin (hair)
protein function
proteins are involved in all cell movements and muscle contraction
movement
– movement of sperm and protozoa
*dynein
protein function
various proteins have protective functions
Defense -
ex proteins for defense
keratin
immunoglobulins
protein function
various proteins regulate cellular processes
- Regulation –
ex proteins for transport
glucose transporter
hemoglobin
LDL and HDL
transferrin
storage proteins containing 20 AA
Casein and ovalbumin
example of proteins for toxin
plant lectins, venom of snake
protein structure
the order or sequence of amino acids in the polypeptide chains
*Peptide bond is a covalent bond
primary
protein structure
conformation of the polypeptide backbone
2ndary
protein structure
arrangement in space of all atoms in the polypeptide chain
tertiary
protein structure
describes the interaction of the subunits in an oligomeric protein
*stabilized by both covalent & non-covalent forces
quaternary
levels of protein structure stabilized by covalent and non-covalent forces
quaternary and tertiary
has *intersubunit interaction
quaternary
has intrasubunit interaction
tertiary
what proteins have quaternary structure
only oligomericproteinswith ≥ 2 subunits
e.g. dimer
stabilizing force of secondary structure
H-bonding between the amide proton and carboxyl oxygen
the sequence of amino acids linked by peptide bonds.
▪ The backbone of a peptide chain or protein.
primary structure
Proteins are composed of ___ only
L-amino acids
conformation of the polypeptide backbone (stabilized by H-bonding) without side chains
secondary
which is stronger? H bond or peptide
Peptide bonds
– combination of α-helix & β-pleated sheet
random coil
The backbone can change direction by making __
reverse turn and loops.
type of secondary structure
Backbone coils into a periodic/repeating, compact structure (rigid)
alpha-helix
H-bonds of alpha helix are typically ____ (olarity)
amphiphilic
is alpha helix left-handed or right handed
right handed
is a “helix-breaker”
- no more H in Nitrogen of _____; no more H-bonding
- cannot rotate freely at ф
proline
a helix breaker
due to too much flexibility of H atom in _ H atom is too small
glycine
- Polypeptide backbone is almost fully extended.
β-pleated sheet (Zigzag)
≥ 2 backbones aligned for H-bonding
β-pleated sheet (Zigzag)
Backbones are aligned side by side leading to formation of H-bonds between carbonyl O of one chain & -NH group of the adjacent chain
β-pleated sheet (Zigzag)
maybe parallel or antiparallel orientation
- more stable than α-helix
β-pleated sheet (Zigzag)
these AA make reverse turns
Proline & glycine
this type of 2 structure is typical of fibrous proteins such as silk
β-pleated sheet (Zigzag)
– combination of coils; higher form of secondary structure
SUPERSECONDARY STRUCTURE
bonding with the side chain creates a specific overall shape (3-D structure) of the protein
“arrangement of all the atoms”
tertiary structure
type of conformation wherein Polypeptides fold into its 3-D structure
(native conformation)
Covalent & Non-covalent Interactions in the 30 Structure
H-bonding
- hydrophobic interaction
- π- π complexation reaction (specifically for aromatic rings)
- salt bridge/ionic/electrostatic
- metal-ion coordination bond (hemoglobin, myoglobin) for transition metal (Fe)
- oxidation of two cysteine to form cystine
- combination of large number of βαβ motifs
*β-barrelor superbarrel
– composed of 4 amino acids; due to glycine & proline
bends
– they do not have regular, periodic structures
loop
– denaturation of proteins
unfolding
types of tertiary structure
globular
disordered
fibrous
type of tertiary structure
interacts well with water and takes a random config
disordered
type of tertiary structure
many insoluble amino acids
proteins tend to minimize surface to volume ratio
globular
type of tertiary structure
strong secondary structure allows protein to retain a nonspherical shape
fibrous
type of protein structure
aggregates of two or more protein chains connected by weak non-covalent interactions
quaternary
examples of tetramers
alcohol dehydrogenase
hemoglobin
example of dodecamer
glutamine synthetase
– has only 10, 20 & 30 structures
*MONOMERIC PROTEINS
– has 10, 20, 30 & 40 structures
*OLIGOMERIC PROTEINS
▪ rod-like forming fibers; elongated
▪ insoluble in H2O (because they are structural proteins)
▪ usually has structural functions
▪ e.g. keratin, collagen, elastin
Fibrous Proteins
▪ spherical shaped
▪ soluble in H2O
▪ mostly functions as enzymes; for catalysis (non-structural functions)
▪ the interior is highly hydrophobic; amino acids are nonpolar inside
▪ the surface of the globular protein has polar amino acids
▪ e.g. casein, albumin, hormones
Globular Proteins
approximately spherical in shape; consist of several different lobes called domains
◦ hydrophobic core; hydrophilic external surface that reacts with water
◦ highest level maybe 30 or 40
Globular Proteins`
◦ elongated molecules in which the 20 structure (either α-helices or β-pleated sheets) is the dominant structure.
◦ muscle movement and cilliary proteins
◦ insoluble in water; structural functions
◦ often have repeating structures
◦ generally have 10 and 20 structures only
FIBROUS PROTEINS
amide linkages between the α-carboxyl group of one amino acid and the α-amino group of another
-not broken by conditions that denature proteins, such as heating or high concentrations of urea
peptide bonds
each component amino acid in a polypeptide
-named as such because it is the portion of the amino acid remaining after the atoms of water are lost in the formation of peptide bond.
Residue –
Bonds between ___ can be freely rotated (which allows the polypeptide chain to assume a variety of configurations
α-carbons and the α-amino or α-carboxyl groups
_____ of the peptide bond are uncharged, polar, and involved in hydrogen bonds
-C=O and –NH groups
– sequence of amino acids
- order in which amino acids are covalently linked by peptide bonds; one dimensional
- important to understand because many genetic diseases result in proteins with abnormal amino acid sequences
- dictates the secondary structure
primary structue
- folding of the backbone
- regular folding
- have repetitive interactions resulting from hydrogen bonding
- conformations of the side chain are not part of —– structure
SECONDARY STRUCTURE
- spatial arrangement of the atoms in a polypeptide chain
- interaction: H-bond between the amide proton and carbonyl oxygen
SECONDARY STRUCTURE
- spiral structure consisting of a tightly packed, coiled polypeptide backbone core
- side chains extend outward to avoid steric interference
alpha helix
• stabilized by extensive hydrogen bonding between peptide-bond carboxyl oxygens and amide hydrogens
- hydrogen bonds extend up and are parallel to the spiral
- intramolecular H-bonds
alpha helix
disrupts the helix because its secondary amino group is not geometrically compatible with the right-handed spiral of the helix
-inserts a kink in the chain
Proline –
disrupt the helix by forming ionic bonds or by repelling each other
Charged amino acids
all of the peptide bond components are involved In the hydrogen bonding
-surfaces appear pleated
β-sheet
have hydrogen bonds perpendicular to the polypeptide backbone, instead of parallel.
β-sheet
– when hydrogen bonds are formed between the polypeptide backbones of separate polypeptide chains
Interchain bonds
when a β-sheet is formed by a single polypeptide chain folding back on itself
Intrachain bonds
– usually produced by packing side chains from adjacent secondary structural elements close to each other
-combinations of alpha and beta strands
Supersecondary Structures
– repetitive supersecondary structure
Motif
Other secondary structures (3)
- Other helix structures
- Random coils
- Reverse turns or β-bends
– almost similar with β-pleated sheet but there are bends
-glycine and proline are frequently encountered in reverse turns
Reverse turns or β-bends
– refers to both folding of domains and final arrangement of domains in the polypeptide
- three-dimensional arrangement
- important aspect: arrangement of side chains as AA residues
Tertiary
– covalent linkage formed from the sulfhydryl group of each of two cysteine residues
Disulfide bond
- spatial arrangement of polypeptide subunits
- interactions: same with tertiary structure
quaternary
- unfolding of a protein
- loss of high-level of structural organization of protein except for primary structure
DENATURATION
-denaturing agents (6)
- Heat – increase in temp
- Change in Ph – high or low extremes of ph
- Organic solvents (alcohol, urea) – urea may form stronger H-bonds and can disrupt hydrophobic interactions
- Detergents (SDS) – disrupt hydrophobic interactions
- Salts of heavy metals
- Performic acid and 2-mercaptoethanol
Β-mercaptoethanol – reduce disulfide bridges to two sulfhydrryl groups
- may be acid, base, neutral hydrolysis
- breakdown of peptide bond or the primary structure
HYDROLYSIS
leads to unfolding of protein and subsequent loss of biological function
denaturation
remains of hydrolysis
individual aa
remains of denaturation
group of aa
physical agents of protein denaturation
Heat or temperature
Mechanical agitation or stress
by applying __, bubbles will form (foam) which signifies denaturation
e.g. Bradford assay
stress
a chemical agent which targets the salt bridges in the protein.
Strong acid
Chemical agents
target ionic interactions with protein
Strong acids and bases
Most common reducing agents are for breaking ____ bonds
disulfide
reducing agents
- β-mercaptoethanol
2. Dithiothreitol (DTT)
▪ target proteins in the body particularly the enzymes
▪ target cysteine side chain (-SH) which is very important in protein
-SH + Hg → -SHg
▪ target charged interaction
heavy metal ions
