PROTEINS Flashcards
Comes from the Greek word “proteios” = primary importance
Molecules were first described and named by the Swedish chemist Jöns Jakob Berzelius in 1838.
Naturally occurring, unbranched polymers
Monomer unit: amino acid (Made up of about 20 common amino acids)
Proteins
Most abundant molecules in the cells after water
15% protein, 70-75% water, 2% CHO
Elemental composition: C,H,O,N
All proteins have N in their structure
Most also contain S but not all (methionine, cysteine)
There are some specialized proteins that contain Phosphorus, Fe etc…
Ex: P-Casein: major protein of milk, Fe- Hgb
Average nitrogen content of proteins is 15.4%
We have more than 700 hundred proteins
Building Block of Proteins:
Amino acid
(have amino, acid group and H in structure)
Amino group: NH2, NH3 (charged)
Acid/ carboxyl group: COOH
H group in structure
Side group varies: responsible for size, shape, charge, pH, H bonding ability, and chemical reactivity
Group of Amino Acids according to Polarity:
insoluble to water
Hydrophobic or water fearing
Tryptophan: polar neutral; has weak interaction to H2O: borderline nonpolar
When present in proteins, they are located in the interior of protein where there is no polarity
Interior: no polarity, for proteins to be water soluble
H2O: polar solvent
Non-Polar Amino Acids (VILMAPGF)- VILMA PaGrab Food
Valine, Isoleucine, Leucine, Methionine, Alanine, Proline, Glycine, Phenylalanine (aromatic)
8 Standard amino acids are non-polar
Some are 9 (Tryptophan)
Group of Amino Acids according to Polarity:
7 amino acids
One carboxyl and one amino group, and side chain that is polar but neutral
Polar Neutral Amino Acids (CNQSTWY)- CoNQueST With You
Cysteine, Asparagine, Glutamine, Serine, Threonine, Tryptophan (aromatic), Tyrosine (aromatic)
Group of Amino Acids according to Polarity:
2 carboxyl and one amino group. 2nd carboxyl group being part of the side chain
Carboxyl group: gives the acidity and negative charge
One that loses H+
Polar Acidic Amino Acids (DE)- Don’t Eat
Aspartate/ Aspartic acid ad Glutamate/ Glutamic acid
Group of Amino Acids according to Polarity:
One carboxyl and two amino groups. 2nd amino group is a part of the side chain
Positive charges, accepts H+
Side chain (NH2): responsible for the basic
Polar Basic Amino Acids (HRK)- Hello Rich Kid
Histidine, Arginine, Lysine
TRUE OR FALSE:
Glycine is the only achiral amino acid because of the 2 H molecules attached to it
TRUE
Identify the Amino Acid:
not true amino acid bcs of side chain propyl, bonded on both alpha C and N of amino group forming closed cyclic side chain
Imino acid: C-N-C-C=O
Proline (P)
Identify the Amino Acid:
alanine bonded w/ benzene, non-polar: phenyl benzene + alanine
Phenyl: side chain benzene
Phenylalanine (F)
Identify the Amino Acid:
borderline member of no polar
Contains indole ring as side chain (heterocyclic), has specific test for its identification
Has a benzene ring and an NH group
Tryptophan (W)
Identify the Amino Acid:
both have NH2 but is neutralized by C=O = uncharged
Related to polar acidic amino group
Asparagine and Glutamine (N and Q)
Identify the Amino Acid:
acidic because of COO-/ COOH (carboxylate ion)
Diff bet asparagine and glutamine is because of side chain
Glutamate: CH3-CH2-COOH side chain (propanoic acid)
Aspartate and glutamate (D and E)
amino group responsible for basic charge
Has NH2 or NH3: + charge; basic
Lysine, Histidine, Arginine (K, H, R)
How many?
a. Essential amino acids in children
b. Essential amino acids in adults
a. 10 (10th is Arginine)
b. 9
Essential amino acids: HILKMVRWTF
(HILiK Mo VRo What The Fun) Histidine Isoleucine Leucine Lysine Methionine Valine Arginine Tryptophan Threonine Phenylalanine
A if only the first statement is true
B if only the second statement is true
C if both of the statements are true
D if neither of the statements is true
- One checked for handedness is carboxyl group (NH2 or NH3; used during reactions)
- Natural occurring and biochemically important proteins or amino acids are all left (L)
B
Acid-Base Behavior or Amino Acids :
a dipolar ion having both a formal positive and formal negative charge (overall charge neutral, no charge = 0)
double ion; amino (+) and carboxyl (-) group
NH2 —> NH3 & COOH —> COO-
Zwitterion
Acid-Base Behavior or Amino Acids:
react as either an acid or a base.
Ammonium ion acts as an acid and Carboxylate as a base
If in solution or solid state: exist as zwitterion (- and +)
Amphoteric
determine pH of amino acid
Isoelectric point (pl)
covalently linked amino acid
Peptides
Oligopeptide: 10-20 amino acid residues
A.A residue: portion of A.A structure that remains when water is released
Amino Acid + Amino Acid —> Dipeptide
2 amino acid responsible for peptide chain
Amino Acid + Dipeptide —> Tripeptide
A.A + A.A + … + Tripeptide —> Polypeptide
happens bet amino group and carboxyl group: horizontal position
Covalent bond bet amino acids in a peptide
1 amino acid uses NH2 while the other uses C=O
C=OOH + NH2 = peptide
Peptide bond
A if only the first statement is true
B if only the second statement is true
C if both of the statements are true
D if neither of the statements is true
- Hydrolysis reaction is responsible for peptide bond formation wherein H2O is released during formation
- Every peptide has N-terminal end and C-terminal end (end of peptide chain)
B
unbranched polymers
Used for structural purposes
Branching: only happens when 2 specific proteins/ amino acids bond
Polypeptide
happen bet 2 cysteine amino acids
Responsible for hardness of keratin
The more the harder, the less the brittle
Disulfide bonds
Protein Classification Based on Chemical Composition:
A protein in which only amino acid residues are present:
More than one protein subunit may be present but all subunits contain only amino acid
Ex: Protein only has amino acid residue
Simple protein
Protein Classification Based on Chemical Composition:
A protein in which only amino acid residues are present:
A protein that has one or more non-amino acid entities (prosthetic groups) present in its structure:
One or more polypeptide chains may be present
Non-amino acid components: organic or inorganic: prosthetic groups
Ex: Lipoproteins; Glycoproteins (has CHO); Metalloproteins (inorganic)
Conjugated protein
must have 40 amino acid residues present in peptide chain, less than is just peptide chain
Protein
Levels of Organization of Proteins:
Amino acid sequence of the protein
Primary structure of protein refers to the order in which amino acids are linked together in a protein
What amino acid it has
Every protein has its own unique amino acid sequence
:
Primary structure Frederick Sanger (1953): Sequenced and determined the primary structure for the first protein Insulin: first sequence and determined Primary structure: One-letter code ex: MERRY
Levels of Organization of Proteins:
H bonds formed in the peptide chain backbone
Refers to the regular geometric pattern along a polypeptide brought about by hydrogen bonding
Peptide chains bonded thru H
Secondary structure
2 Arrangements of secondary structure proteins:
A single protein chain adopts a shape that resembles a coiled spring (helix)
H-bonding between same amino acid chains: intramolecular
R-group outside of the helix: not enough room for them to stay inside
Ex: fibrous protein
α-helix (alpha)- spiral
2 Arrangements of secondary structure proteins:
Completely extended amino acid chains
H-bonding between two different chains: inter- and/or intramolecular
Side chains below or above the axis
Ex: globular protein
β-sheets/ pleated sheet (beta)- folded
Levels of Organization of Proteins:
Non-covalent interactions bet the R groups w/in the protein
3-D folding of polypeptide to form a complex molecular shape
Globular, irregular, ball shaped twisted form, has rods, chain
Ex: Chain B of Protein Kinase C
Tertiary structure
Levels of Organization of Proteins:
Interaction between 2 polypeptide chains
2 secondary structure are together to form structure
Combi of sub-units
Refers to the organization among the various peptide chains in a multimeric protein: Highest level of protein organization
Some proteins are made of several polypeptide subunits
Ex: hemoglobin has 4 beta sheets, protein kinase C, myoglobin
Quaternary structure
Present only in proteins that have 2 or more polypeptide chains (subunits) associate closely together to form multi chain complex
Subunits are generally independent of each other- not covalently bonded
Proteins often referred to as oligomeric proteins (combination of sub-units)
Contain even number of subunits
Types of Proteins:
Tend to have simple, regular, linear structure
Tend to aggregate together to form macromolecular structures
Insoluble, elongated shape, single type of alpha-secondary
Ex: hair, nails
Fibrous Proteins
Involved in structure: tendons, ligaments, blood vessels, teeth and skin
Ex: collagen and keratin
Contractile proteins in movement: muscle, microtubules (cytoskeleton, mitotic spindle, cilia, flagella)
_____: rich in proline (20%); imino acid, most abundant protein in humans
_____: 30% of proteins, alpha keratin, hydrophobic A.A residue, hardness depends on the disulfide bond of cysteine
Collagen
Keratin
Types of Proteins:
Most proteins which move around (albumin, casein in milk)
Proteins molecules w/ peptide chains are folded into spherical or globular
Proteins with binding sites: enzymes (largest type), haemoglobin, immunoglobulins, membrane receptor sites
Globular Proteins
_____: oxygen carrier molecule in blood; transports O2 from lungs to tissues
Tetramer: 4 peptide chains (each subunit has a heme group)
2 α globin subunits and 2 β globin subunits
Heme group: where O2 binds to the protein; can bind 4 O2
_____: oxygen storage molecule in muscles; binds one O2 molecule
Monomer: single peptide chain with one heme unit
Higher affinity for O2 compared to hemoglobin
Hemoglobin
Myoglobin
A if only the first statement is true
B if only the second statement is true
C if both of the statements are true
D if neither of the statements is true
- Protein structure determines protein function
- Denaturation or inhibition which may change protein structure will change its function
C
A if only the first statement is true
B if only the second statement is true
C if both of the statements are true
D if neither of the statements is true
- Proteins are not denatured if subjected in high temperature
- Coenzymes and cofactors in general may enhance the protein’s structure
B
Protein classified by Function:
enzymes: used as catalyst: speeds up reaction
Almost biochemical reaction needs enzymes
CATALYTIC
Protein classified by Function: Immunoglobulin/ antibodies, fibrinogen, blood clotting factors Immunoglobulin: IgG, IgM, IgA, IgE, IgD IgG: past/ chronic infection IgM: recent/ acute infection IgA: found in milk IgE: allergic reactions IgD: signal B cells to activate
DEFENSE/PROTECTIVE Fibrinogen: clotting factor I Formation of clot during hemostasis Activated: fibrin clot Polymers of fibrin: mesh of fibrin
Protein classified by Function:
hemoglobin, transferrin, HDL, LDL
Transferrin: main protein of the blood that binds in Fe
Liver —> bone marrow
HDL, LDL: lipoproteins, carrier of cholesterol in blood stream: good CHO
High Density Lipoproteins
Low Density Lipoproteins
TRANSPORT
Protein classified by Function:
hormones (ex: insulin) and neurotransmitters
MESSENGER/ COMMUNICATION
Protein classified by Function:
actin, myosin, dynein (microtubules)
Actin, myosin: muscles
CONTRACTILE
Protein classified by Function:
cell membrane proteins, keratin (hair), collagen
STRUCTURAL
Protein classified by Function:
Control of ions or molecules thru cell membrane
Passage of molecules: what could enter and exit
Selective in molecules and ions that could pass in cell membrane
TRANSMEMBRANE
Protein classified by Function:
myoglobin: stores O2 in muscles
STORAGE
Protein classified by Function:
insulin
Regulates glucose
Hormone that could lower blood glucose level
REGULATORY
Protein classified by Function:
ovalbumin (egg white), casein (milk), zein (maize; corn)
NUTRIENT
Protein classified by Function: hemoglobin Transport of O2 O2 concentration/ saturation plays a role on buffer system of body Bicarbonate carbonic acid buffer system Make sure blood pH is normal (7.35-7.45)
BUFFER
Protein classified by Function:
albumin and globulin
Intestine w/ total protein for kidney and liver function
FLUID BALANCE
Protein classified by Function:
commonly found in snake venom
TOXINS
Peptides: Variety of Functions:
Insulin (sugar)
Oxytocin (childbirth, labor): contraction
Sex-peptide (fruit fly mating): Pheromones: attracting opposite sex
Hormones and Pheromones
Peptides: Variety of Functions: Substance P (pain mediator)
Neuropeptides
Peptides: Variety of Functions:
Polymyxin B (Gram – bacteria)
Bacitracin (Gram + bacteria)
Antibiotics
Peptides: Variety of Functions:
Amanitin (mushrooms)
Conotoxin (cone snails)
Chlorotoxin (scorpions)
Protection: ex: toxins
Functional non-amino acid component; proteins are binded w/ non-amino acids (conjugated proteins)
Metal ions or organic molecules
Metal: prosthetic groups, inorganic
Cofactors
Organic cofactors
NAD+ in lactate dehydrogenase: utilize in biochemical process (ex: lactate dehydrogenase)
Nicotinamide adenine dinucleotide
Coenzymes
Covalently attached cofactors
Heme in myoglobin
Prosthetic groups
like metal ions, CHO, or lipids
Other modifications
