Cell bio amino acids 3 Flashcards
PROTEIN PRIMARY STRUCTURE
Unique sequence of amino acids in polypeptide chain
o Amino acids are linked by ?
between ? and ? groups
- Peptide bonds are
o ? bonds
o ? to conditions that denature proteins
(i.e. heating & high concentrations of urea) - Prolonged exposure to a ? or ? at elevated temperature is ? to break these bonds non-enzymatically
PROTEIN PRIMARY STRUCTURE
Unique sequence of amino acids in polypeptide chain
o Amino acids are linked by peptide bonds
between a-carboxyl and a-amino groups
- Peptide bonds are
o strong covalent bonds
o resistant to conditions that denature proteins
(i.e. heating & high concentrations of urea) - Prolonged exposure to a strong base or acid at elevated temperature is necessary to break these bonds non-enzymatically
- How many polypeptide chains and how many AA in each chain?
- What bonds are linking A and B chain? 3. Where is Insulin produced?
- How many polypeptide chains and how many AA in each chain? 2 chains and
- What bonds are linking A and B chain? disulfide bridge (cysteine forms disulfide bridge)
- Where is Insulin produced? pancreas
PROTEIN SECONDARY STRUCTURE
? in space of adjacent amino acid residues in a polypeptide chain.
Examples of common secondary structures of proteins:
?
?
? (reverse turns, β-turns)
Both structures are held in shape by ? bonds, formed between the carbonyl-O group of one AA and the amino-H group of another
PROTEIN SECONDARY STRUCTURE
regular recurring arrangments in space of adjacent amino acid residues in a polypeptide chain.
Examples of common secondary structures of proteins:
a-helix
beta-sheet
beta-bends (reverse turns, β-turns)
Both structures are held in shape by H bonds, formed between the carbonyl-O group of one AA and the amino-H group of another
(H bonds (weaker than peptide bonds) and they hold secondary structure)
alpha-helix
- sturcture: ?
- Side chains of component amino acids extend ? to avoid ? with each other
- Hydrogen bonds between carboxy O groups and amino H groups are #? AA away – ? structure.
αKeratins: ? protein component of ?, nails (hoof) and ?, rigidity determined by number of ** ? ** bonds between α-Helix structures
alpha-helix
- sturcture: spiral structure, tightly packed, coiled polypeptide chain core
- Side chains of component amino acids extend outward to avoid interfering with each other
- Hydrogen bonds between carboxy O groups and amino H groups are #4 AA away – spiral structure.
αKeratins: fibrous protein component of hair, nails (hoof) and skin, rigidity determined by number of ** disulfide** bonds between α-Helix structures
PLEATED BETA SHEET
H bond is stronger in antiparallel or parallel? (green things are H bonds)
PLEATED BETA SHEET
H bond is stronger in antiparallel or parallel? - stronger in antiparallel as they are closer to each other
PLEATED BETA SHEET
- Beta ? are the backbone of the beta-sheets, typically 3 to 10 AAs long (don’t memorize #)
- Beta sheets consist of various beta strands linked laterally by at least ? or ? ? bonds.
- Antiparallel beta-sheets are slightly more ? because of the more ? bonding structure.
Both (parallel and antiparallel structures) are ? in nature
** ? ** an insoluble protein present in silk.
Made by ? and certain ? (‘silkworm’ is larvae of moth Bombyx ?).
Layers of antiparallel β- sheets
PLEATED BETA SHEET
- Beta strands are the backbone of the beta-sheets, typically 3 to 10 AAs long (don’t memorize #)
- Beta sheets consist of various beta strands linked laterally by at least 2 or 3 H bonds.
- Antiparallel beta-sheets are slightly more stable because of the more optimum H bonding structure.
Both (parallel and antiparallel structures) are common in nature
** Fibroin ** an insoluble protein present in silk.
Made by spiders and certain moth (‘silkworm’ is larvae of moth Bombyx mori).
Layers of antiparallel β- β-sheets
β-bends characteristics:
o ? the direction of a polypeptide chain,
helping it form a compact, ? shape
o Generally composed of 4 amino acids, one of which is often ** ? ** (this causes a kink in the polypeptide chain)
o Critical for the protein ? and ?, generally occur when the protein chain needs to ? direction in order to ? two other elements of secondary structure.
FYI
- carbonyl ? of one residue is ? bonded (which bond) to the ? proton of a residue 3 residues away
- ? and ? are prevalent in beta turns
β-bends characteristics:
o reverses the direction of a polypeptide chain, helping it form a compact, globular shape
o Generally composed of 4 amino acids, one of which is often ** PROLINE ** (this causes a kink in the polypeptide chain)
o Critical for the protein structure and function, generally occur when the protein chain needs to change direction in order to connect two other elements of secondary structure.
FYI
- carbonyl O of one residue is H bonded (which bond) to the amide proton of a residue 3 residues away
- proline and glycine are prevalent in beta turns
PROTEIN TERTIARY STRUCTURE
TERTIARY refers to
** ? **
** ? ** in the polypeptide
** ? ** of the polypeptide chain in space
- ? * are the fundamental functional & three-dimensional structural units of ?
Polypeptide chains ≥ 200 amino acids consist of #? or ? domains
- The tertiary structure will have a ? polypeptide chain “?” with one or more ? structures -> the protein domains *
** The tertiary structure is the structure at which polypeptide chains become ?.
At this level, every protein has a specific ? and presents ? groups on its ? surface, allowing it to interact with other ?, and giving it its ? function. **
PROTEIN TERTIARY STRUCTURE
TERTIARY refers to
** folding of domains **
** final arrangement of domains ** in the polypeptide
** 3-dimensional arrangement ** of the polypeptide chain in space
- DOMAINS * are the fundamental functional & three-dimensional structural units of proteins
Polypeptide chains ≥ 200 amino acids consist of 200 or more domains
- The tertiary structure will have a single polypeptide chain “?” with one or more protein secondary structures -> the protein domains *
** The tertiary structure is the structure at which polypeptide chains become functional.
At this level, every protein has a specific 3D shape and presents functional groups on its outer surface, allowing it to interact with other molecules, and giving it its unique function. **
which AA go in hydrophobic interactions?
BOND TYPES
hydrophobic interactions: these AAs orient themselves toward the ? of the polypeptide to avoid the ?
Disulphide bridges: The AAs ? forms a bond with another ? through its ? group
Hydrogen Bonds: Polar ? groups on AAs form bonds with other ?
Hydrophilic interactions: these AAs orient themselves outward to be ?
Ionic Bonds: ? charged R groups bond together
BOND TYPES
hydrophobic interactions: these AAs orient themselves toward the center of the polypeptide to avoid the water
Disulphide bridges: The AAs cysteine forms a bond with another cysteine through its R group
Hydrogen Bonds: Polar R groups on AAs form bonds with other polar R groups
Hydrophilic interactions: these AAs orient themselves outward to be close to the water
Ionic Bonds: positively charged R groups bond together
PROTEIN QUARTERNARY STRUCTURE
- Association of ? protein chains or ? into a closely packed arrangement.
1 Example of a quaternary structure ?
- ? has its own primary, secondary, and tertiary structure.
Subunits are held together primarily by ? interactions such as ? list 3 bonds
Subunits may function ?
i.e hemoglobin(Hb), where binding of ? to one subunit ? the affinity of other subunits for oxygen.
PROTEIN QUARTERNARY STRUCTURE
- Association of several protein chains or subunits into a closely packed arrangement.
1 Example of a quaternary structure = hemoglobin
- each of the subunit has its own primary, secondary, and tertiary structure.
Subunits are held together primarily by non-covalent interactions such as hydrogen bonds, ionic bonds and hydrophobic interactions
Subunits may function independently of each other or work cooperatively
i.e hemoglobin(Hb), where binding of oxygen to one subunit increases the affinity of other subunits for oxygen (attachment of heme group changes shape of entire junction)
Hemoglobin (Hb) molecule
- A ? protein formed as a symmetric assembly of #? subunits
- Contains two copies of ? and 2 copies of ?
- Each of four polypeptide chains contains a ? molecule (red)
- This is the site where ? is bound
- Each molecule of Hb in blood carries #? molecules of O2
Hemoglobin (Hb) molecule
- A polymeric protein formed as a symmetric assembly of #4 subunits
- Contains two copies of alpha-globin and 2 copies of beta-globin
- Each of four polypeptide chains contains a heme molecule (red)
- This is the site where oxygen is bound
- Each molecule of Hb in blood carries #4 molecules of O2
IMPORTANT CHEMICAL BONDS
Primary Structure AA’s are joined by ? bonds which are ? bond
* 2 atoms sharing electrons between C-atom of ? group of 1 AA and N-atom of ? of another AA.
* ? bond -> molecule backbone
Secondary Structure 3D shaping (β-sheet, α-helix, β-bends) held in place by → ? bonds
* ? interaction between a hydrogen H atom and an electronegative atom, such as N or O.
* Hydrogen bonds are strong or weak bonds?
IMPORTANT CHEMICAL BONDS
Primary Structure AA’s are joined by peptide bonds which are covalent bond
* 2 atoms sharing electrons between C-atom of carboxyl group of 1 AA and N-atom of amino group of another AA.
* strong bond -> molecule backbone
Secondary Structure 3D shaping (β-sheet, α-helix, β-bends) held in place by → H bonds
* dipole-dipole interaction between a hydrogen H atom and an electronegative atom, such as N or O.
* Hydrogen bonds are strong or weak bonds
IMPORTANT CHEMICAL BONDS
Tertiary Structure
Hydrogen bonds between the side chains of the individual amino acids are weak or strong?
Ionic bonds between ? charged ions (anions - and cations +) - STRONGER THAN which ? bonds
Disulfide bridges ? bond between 2 ?groups (S-H) - STRONG BOND
Hydrophobic interactions between hydrophobic (nonpolar) AA-side chains - CAN BE ?
Hydrophilic interactions usually on the ? part of the protein structure, towards the aqueous environment
Quaternary Structure is stabilized by ?-bonds and ? and ? interactions between amino acids side chains (R groups) of each subunit
IMPORTANT CHEMICAL BONDS
Tertiary Structure
Hydrogen bonds between the side chains of the individual amino acids are weak
Ionic bonds between oppositely charged ions (anions - and cations +) - STRONGER THAN H bonds
Disulfide bridges S-S bond between 2 thiol groups (S-H) - STRONG BOND
Hydrophobic interactions between hydrophobic (nonpolar) AA-side chains - CAN BE STRONG
Hydrophilic interactions usually on the OUTER part of the protein structure, towards the aqueous environment
Quaternary Structure is stabilized by H-bonds and hydrophobic and hydrophillic interactions between amino acids side chains (R groups) of each subunit
FYI SLIDE
PROTEIN STRUCTURE
A collection of protein molecules, shown at the same scale
Hemoglobin, catalase, porin, alcohol dehydrogenase, and aspartate transcarbamoylase are formed from multiple copies of subunits -> THUS THEY ARE polymeric
(polymer = a substance that has a molecular structure consisting chiefly or entirely of a large number of similar units bonded together, e.g., many synthetic organic materials used as plastics and resins.)
PROTEIN FOLDING
Many proteins don’t fold by themselves, but instead get assistance from ? or ? proteins
(Hsp)
Quality control: protein folded improperly will not leave the ?
Chaperones
? proteins
? at high temperatures
?
?l
Hsp70: ? and ? damaged proteins, corrects misfolding, prevent protein ?, facilitates ? of aggregates.
PROTEIN FOLDING
Many proteins don’t fold by themselves, but instead get assistance from chaperones or heat-shock proteins
(Hsp)
Quality control: protein folded improperly will not leave the ER
Chaperones
heat-stable proteins
high acitivity at high temperatures
ATPases
Quality control
Hsp70: repairs and refolds damaged proteins, corrects misfolding, prevent protein aggregates, facilitates degradation of aggregates.
PROTEIN FOLDING – Folding cycle
- Chaperone is bound to ?
- ?/Chaperone-complex has a high affinity for ? proteins
- After binding, ? is released
- After ATP binding and protein folding, the complex ?, and the correctly folded protein is ?
PROTEIN FOLDING – Folding cycle
- Chaperone is bound to ADP
- ADP/Chaperone-complex has a high affinity for unfolded proteins
- After binding, ADP is released
- After ATP binding and protein folding, the complex dissociates, and the correctly folded protein is released
