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
PROTEIN MISFOLDING
Misfolded proteins are usually tagged and corrected by ? or degraded in the cell by ?.
HOWEVER, quality control systems are not ?, and intracellular or extracellular misfolded proteins can accumulate, especially as individuals ?.
Deposits of misfolded proteins are associated with ?
prions related to which disease?
Transthyretin amyloidosis related to transthyretin
PROTEIN MISFOLDING
Misfolded proteins are usually tagged and corrected by chaperones or degraded in the cell by proteosomes
HOWEVER, quality control systems are not perfect, and intracellular or extracellular misfolded proteins can accumulate, especially as individuals age.
Deposits of misfolded proteins are associated with disease
prions related to which disease? = mad cow disease
PRION DISEASE
- Prion diseases are ?, ? disorders that occur worldwide in both humans and animals.
- Prions are ? proteins that can transmit their ? shape onto normal variants of the same protein.
- Toxic misfolding and ? – Proteinopathies
- Bovine spongiform encephalopathy (BSE) in cattle - ‘Mad Cow’ disease
PRION DISEASE
- Prion diseases are fatal, degenerative brain disorders that occur worldwide in both humans and animals.
- Prions are misfolded proteins that can transmit their misfolded shape onto normal variants of the same protein.
- Toxic misfolding and clumping of the prion n protein – Proteinopathies
- Bovine spongiform encephalopathy (BSE) in cattle - ‘Mad Cow’ disease
PROTEIN DENATURATION
? and ? of secondary and tertiary structures of a protein.
Primary structure (generally) remains ? - NO ? of peptide bonds
May be ?, so the protein refolds once the ? agent is removed
Mostly proteins, once denatured, remain ? (insoluble, precipitate)
Denaturing agents include: list 5
All physiological change is mediated by ?!
* Function depends on protein ? and ?
* Proteins can bind to other molecules very specifically,
* Proteins change shape, which in turn alters their ? properties and their ?.
** The ? of a protein (its conformation), determines protein ?. **
PROTEIN DENATURATION
unfolding and disorganization of secondary and tertiary structures of a protein.
Primary structure (generally) remains intact - NO hydrolysis of peptide bonds
May be reversible, so the protein refolds once the denaturing agent is removed
Mostly proteins, once denatured, remain permanently disordered (insoluble, precipitate)
Denaturing agents include:
strong acids and bases
detergents
heat
organic solvent
heavy metal ions (lead)
All physiological change is mediated by ?!
* Function depends on protein shape and shape changes
* Proteins can bind to other molecules very specifically,
* Proteins change shape, which in turn alters their binding properties and their function.
** The 3D shape of a protein (its conformation), determines protein function**
Classification Based on ?
* Fibrous Proteins
* Globular Proteins
* Intermediate Proteins
Classification Based on ?
* Simple Proteins
* Conjugated Proteins
Classification Based on ?
* Structural Proteins, Enzymes, Hormones
* Pigments, Transport Proteins, Contractile Proteins
* Storage Proteins, Toxins
Classification Based on struc.
* Fibrous Proteins
* Globular Proteins
* Intermediate Proteins
Classification Based on composition
* Simple Proteins
* Conjugated Proteins
Classification Based on function
* Structural Proteins, Enzymes, Hormones
* Pigments, Transport Proteins, Contractile Proteins
* Storage Proteins, Toxins
Fibrous (ask if u have to know this)
* Linear
* Tough & Strong
* Long parallel polypeptide
chains cross linked at regular
intervals
* Perform structural functions in
the cell
* Usually do not have a
(complex) tertiary structure
Solubility in Water: Insoluble
Most Important Structure: secondary struc.
Examples
Collagen, Elastin, Myosin, Keratin, Silk
Globular
* Spherical/globular shape * Polypeptide chain tightly
folded into spherical shapes * Physically softer
* Most proteins in cells are
globular proteins
* Functions: form enzymes,
antibodies and some hormone
Solubility in Water: Readily Soluble
Most Important Structure: tertiary struc.
Examples
Insulin, Hemoglobin, Albumin, DNA Polymerase and RNA Polymerase
Intermediate
* Intermediate shape, mostly linear
Solubility in water: soluble
Most Important Structure:
e.g. Blood clotting proteins
Simple proteins
Composed of only ?, relatively simple structure *
Examples: ?
Conjugated proteins:
Complex proteins contain one or more *? components called ? groups, essential for biological function:
Usually ? and ?
* ? * are conjugated proteins
Further classification based on the nature of the ? (p.g.):
a) Phosphoproteins: p.g. is phosphoric acid (Casein/milk, vitellin/egg)
b) Glycoproteins: p.g. is carbohydrate (membrane proteins)
c) Nucleoproteins: p.g. is nucleic acid (proteins in chromosomes, ribosomes)
d) Chromoproteins: p.g. is pigment or chrome (Hemoglobin)
e) Lipoproteins: p.g. is lipid (chylomicrons)
f) Flavoproteins: p.g. is FAD- Flavin Adenine Dinucleotide (proteins of electron transport system)
g) Metalloproteins: p.g. is metal ions (Hemocyanin – copper containing protein, transport of O2 in crustaceans)
Simple proteins
Composed of only AAs, relatively simple structure *
Examples: myosin, keratin, collagen, insulin
Conjugated proteins:
Complex proteins contain one or more *non-amino acid components called prosthetic groups, essential for biological function:
Usually globular and soluble in water
* most enzymes * are conjugated proteins
Further classification based on the nature of the prosthetic groups (p.g.):
a) Phosphoproteins: p.g. is phosphoric acid (Casein/milk, vitellin/egg)
b) Glycoproteins: p.g. is carbohydrate (membrane proteins)
c) Nucleoproteins: p.g. is nucleic acid (proteins in chromosomes, ribosomes)
d) Chromoproteins: p.g. is pigment or chrome (Hemoglobin)
e) Lipoproteins: p.g. is lipid (chylomicrons)
f) Flavoproteins: p.g. is FAD- Flavin Adenine Dinucleotide (proteins of electron transport system)
g) Metalloproteins: p.g. is metal ions (Hemocyanin – copper containing protein, transport of O2 in crustaceans)
FUNCTION
- Structural proteins:
Components of connective tissue, bone, ?, skin, ?, nail, ?, horn
Mostly ? proteins, ? in water
Examples: ?, ?, Elastin - Enzymes
* Biological catalysts, reduce the activation energy of reactants and speed up reactions
* Can be ?, ?,
* Examples: ? - Hormones:
* Peptide hormones
Examples: ?, ?, ?, CCK - Respiratory pigments:
Colored, conjugated proteins with a pigment
(chrome) as their p.g.
Examples: Hemoglobin, ? - Transport proteins:
? materials in cells and form channels,
Example: ? - Contractile proteins:
Can contract muscles with the expense of energy from ?,
Examples: Actin, Myosin - Storage proteins:
Store ? ions and ? in cells, found in seeds and pulses, egg and milk Examples: ? (iron), Casein, ?, Gluten - Immunoglobulins
* ? - Toxins
* Toxic proteins
Example: ?
FUNCTION
- Structural proteins:
Components of connective tissue, bone, hair, skin, feathers, nail, hair, horn
Mostly fibrous proteins, insoluble in water
Examples: collagen, keratin, Elastin - Enzymes
* Biological catalysts, reduce the activation energy of reactants and speed up reactions
* Can be globular, conjugation proteins
* Examples: DNA pol, lipase - Hormones:
* Peptide hormones
Examples: insulin, glucagon, gastrin, CCK - Respiratory pigments:
Colored, conjugated proteins with a pigment
(chrome) as their p.g.
Examples: Hemoglobin, myoglobin - Transport proteins:
transport materials in cells and form channels,
Example: serum albumin - Contractile proteins:
Can contract muscles with the expense of energy from ATP
Examples: Actin, Myosin - Storage proteins:
Store metal ions and AAs in cells, found in seeds and pulses, egg and milk Examples: Ferritin (iron), Casein, Ovalbumin, Gluten - Immunoglobulins
* Antibodies - Toxins
* Toxic proteins
Example: snake venom
