PROTEINS Flashcards by Ady Cabalquinto

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

How well did you know this?

Not at all

Perfectly

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

How well did you know this?

Not at all

Perfectly

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)

How well did you know this?

Not at all

Perfectly

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)

How well did you know this?

Not at all

Perfectly

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

How well did you know this?

Not at all

Perfectly

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

How well did you know this?

Not at all

Perfectly

TRUE OR FALSE:

Glycine is the only achiral amino acid because of the 2 H molecules attached to it

TRUE

How well did you know this?

Not at all

Perfectly

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)

How well did you know this?

Not at all

Perfectly

Identify the Amino Acid:
alanine bonded w/ benzene, non-polar: phenyl benzene + alanine
Phenyl: side chain benzene

Phenylalanine (F)

How well did you know this?

Not at all

Perfectly

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)

How well did you know this?

Not at all

Perfectly

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)

How well did you know this?

Not at all

Perfectly

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)

How well did you know this?

Not at all

Perfectly

amino group responsible for basic charge

Has NH2 or NH3: + charge; basic

Lysine, Histidine, Arginine (K, H, R)

How well did you know this?

Not at all

Perfectly

How many?

a. Essential amino acids in children
b. Essential amino acids in adults

a. 10 (10th is Arginine)

b. 9

How well did you know this?

Not at all

Perfectly

Essential amino acids: HILKMVRWTF

(HILiK Mo VRo What The Fun)
Histidine
Isoleucine
Leucine
Lysine
Methionine
Valine
Arginine
Tryptophan
Threonine
Phenylalanine

How well did you know this?

Not at all

Perfectly

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)

How well did you know this?

Not at all

Perfectly

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

How well did you know this?

Not at all

Perfectly

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

How well did you know this?

Not at all

Perfectly

determine pH of amino acid

Isoelectric point (pl)

How well did you know this?

Not at all

Perfectly

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

How well did you know this?

Not at all

Perfectly

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

How well did you know this?

Not at all

Perfectly

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)

How well did you know this?

Not at all

Perfectly

unbranched polymers
Used for structural purposes
Branching: only happens when 2 specific proteins/ amino acids bond

Polypeptide

How well did you know this?

Not at all

Perfectly

happen bet 2 cysteine amino acids
Responsible for hardness of keratin
The more the harder, the less the brittle

Disulfide bonds

How well did you know this?

Not at all

Perfectly

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 1. Protein structure determines protein function 2. Denaturation or inhibition which may change protein structure will change its function

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 1. Proteins are not denatured if subjected in high temperature 2. Coenzymes and cofactors in general may enhance the protein's structure

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

PROTEINS Flashcards

(60 cards)