Module 03: Proteins (Stoker) Flashcards
This is a naturally-occurring, unbranched polymer in which the monomer units are amino acids. Moreover, these are most abundant molecules in the cells after water – account for about 15% of a cell’s overall mass
Proteins
What elements are primarily present in proteins?
Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), most also contain Sulfur (S)
How many is the average nitrogen content of proteins by mass?
15.4%
This is an organic compound that contains both an amino (-NH2) and carboxyl (-COOH) groups attached to same carbon atom
Amino Acid
This is the compound where the amino group (NH2) and the carboxyl group is bonded)
Alpha Carbon
Based on common “R” groups, there are how many standard amino acids?
20 amino acids
Standard amino acids are divided into four groups based on the properties of R-groups, which are namely:
(1) Non-polar amino acids
(2) Polar amino acids
(3) Polar-neutral
(4) Polar-basic and Polar-acidic
These are amino acids constituted with R-groups that are non-polar or amino acids are hydrophobic-water fearing (insoluble in water)
Non-polar amino acids
Where are Non-polar amino acids located?
When present in proteins, they are located in the interior of protein where there is no polarity
How many non polar amino acids are there?
8 to 20 standard amino acids
This amino acid contains R-groups that are polar.
Polar Amino Acids
This amino acid contains polar but neutral side chains
Polar-neutral amino acids
This amino acid contain carboxyl group as part of the side chains
Polar acidic amino acids
This amino acid contain amino group as part of the side chain
Polar basic amino acids
What are the different non-polar amino acids?
(1) Glycine
(2) Alanine
(3) Proline
(4) Valine
(5) Isoleucine
(6) Leucine
(7) Methionine
(8) Phenylalanine
(9) Tryptophan
What are the different Polar Neutral Amino Acids?
(1) Serine
(2) Threonine
(3) Asparagine
(4) Cysteine
(5) Glutamine
(6) Tyrosine
What are the different Polar Basic Amino Acids?
(1) Lysine
(2) Arginine
(3) Histidine
What are the different Polar Acidic Amino Acids?
Glutamic and Aspartic Acids
Four different groups are attached to the a-carbon atom in all of the standard amino acids except ____________________.
Glycine
How many standard amino acids contain a chiral center?
19 to 20
These exhibit enantiomerism (left- and right-handed forms)
Chiral Centers
Where are L-isomers present?
Proteins
Where are D-isomers present?
bacteria
What is the rules for drawing Fischer projection formulas for amino acid structures
The — COOH group is put at the top, the R group at the bottom to position the carbon chain vertically
This is an ion with + (positive) and – (Negative) charges on the same molecule with a net zero charge
Zwitterion
In Zwitterions, what do carboxyl groups do?
Carboxyl groups give-up a proton to get negative charge
In Zwitterions, what do amino groups do?
Amino groups accept a proton to become positive
What is the state of amino acids and carboxyl groups at low pH?
At low pH, amino groups and carboxyl groups are protonated (gained H+)–> NH3+ and –COOH
What is the state of amino acids and carboxyl groups at pH 7?
carboxyl group –COOH is ionized to –COO-
What is the state of amino acids and carboxyl groups at high pH?
At high pH, the protonated amino –NH3+ is deprotonated –> -NH2
This is the pH at which the concentration of Zwitterion is maximum –> net charge is zero
Isoelectric point (At isoelectric point - amino acids are not attracted towards an applied electric field because they net zero charge.)
This is the only amino acid that has the standard amino acid with a sulfhydryl group ( — SH group).
Cysteine
What happens to cysteine in the presence of mild oxidizing agents?
Cysteine in the presence of mild oxidizing agents dimerizes to form a cystine molecule.
What comprises a cystine?
two cysteine residues linked via a covalent disulfide bond.
This pertains to a chain of covalently-linked AAs.
peptide.
The covalent bonds between amino acids in a peptide are called ____________
peptide bonds.
What are the properties of a peptide bond?
(1) It is formed between –COOH of one amino acid and the –NH2 of the next amino acid
(2) It is a strong bond with partial double bond character due to resonance. It resists rotation, thereby stabilizing protein structures.
(3) Can not be broken by denaturing agents but by prolonged exposure to acids or bases at elevated temperatures
(4) Usually in transconfiguration
(5) C=O and N-H can participate in H-bonding
This is a bond between two amino acids
Dipeptide
This is a bond between ~ 10 - 20 amino acids
Oligopeptide
This is a bond between large number of amino acids
Polypeptide
What are some examples of small peptides that are biochemically active?
(1) Hormones
(2) Neurotransmitters
(3) Antioxidants
These are examples of small peptide hormones
oxytocin and vasopressin
Where are small peptide hormones formed?
the pituitary gland
What constitutes a nonapeptide
(nine amino acid residues) with six of the residues held in the form of a loop by a disulfide bond formed between two cysteine residues
The is called the ‘love hormone’ because of its role in various behaviors, including orgasm, social recognition, bonding, and maternal behavior. It is released in response toactivation of sensory nerves during labor, breastfeeding and sexual activity.
Oxytocin
These are pentapeptide neurotransmitters produced by the brain and bind receptor within the brain help to reduce pain.
Enkephalins
Where to Enkephalins bind to?
Opiate receptors
What are the types of enkephalins?
Met-enkephalin: Tyr–Gly–Gly–Phe–Met
Leu-enkephalin: Tyr–Gly–Gly–Phe–Leu
This is a tripeptide – is present is in high levels in most cells
Glutathione
What amino acids constitute a Glutathione?
Glycine, Glutamine, Cysteine (where Glu is bonded to Cys through the side-chain carboxyl group.)
What is the role of Glutathione?
(1) Regulates oxidation-reduction reactions
(2) Is an antioxidant and protects cellular contents from oxidizing agents such as peroxides and super oxides
This is a dipeptide or an artificial non-saccharide sweetener 200 times sweeter than sucrose and is commonly used as a sugar substitute in foods and beverages.
Aspartame
What amino acids constitute aspartame?
Asparagine and Phenylalanine
This is a peptide in which at least 40 amino acid residues are present
Protein
Common proteins contain_______________amino acid residues
400–500
Small proteins contain _________amino acid residues
40–100
This protein contains one peptide chain
Monomeric
This contains more than one peptide chain
Multimeric
This is a protein in which only amino acid residues are present:
More than one protein subunit may be present but all subunits contain only amino acids
Simple proteins
This is a protein that has one or more non-amino acid entities (prosthetic groups) present in its structure. In this, one or more polypeptide chains may be present
Conjugated protein
These type of proteins contain lipid prosthetic groups
Lipoproteins
These type of proteins contain carbohydrate groups,
Glycoproteins
These type of proteins contain a specific metal as prosthetic group
Metalloproteins
what are the four types of structure
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
This protein structure refers to the order in which amino acids are linked together in a protein
Primary Structure
He sequenced and determined the primary structure for the first protein - Insulin
Frederick Sanger (1953)
This protein structure refers to the regular arrangement of amino acids closed to one another in the linear sequence.
Secondary Structure
The Secondary Structure is stabilized by what?
Stabilized by H-bonding between peptide bond component: carbonyl oxygen and amide H.
This structure has a spiral structure, consisting of tightly packed, coiled polypeptide, pp backbone core:
Alpha-helix (-helix)
All the peptide bonds in an alpha helix is linked to each other through?
Interchain Hydrogen Bonds
What are the amino acids that disrupt an alpha helix?
(1) Proline because it is not geometrically compatible with the right handed spiral of the alpha helix
(2) Glutamate, Aspartic, Lysine, Arginine and Histidine because they electrostatically repel one another
(3) Tryptophan, Valine, and Isoleucine because they are bulky and present in large numbers
These structure are completely extended amino acid chains, the surfaces appear pleated, composed of 2 or more pp chains or 2 segments of a pp, H-bonding is perpendicular to the polypeptide backbone
Side chains below or above the axis
Beta-Pleated Sheets
This structure reverses the direction of a polypeptide chain, helping it form compact and globular shape
Beta-turns or Bends
This protein structure pertains to the overall three-dimensional shape of a protein and results from the interactions between amino acid side chains (R groups) that are widely separated from each other.
Tertiary Structure
This type of interaction pertains to the covalent, strong, between two cysteine groups, contributes to stability of 3-dimensional structure of protein
Disulfide bond
This type of interaction pertains salt Bridge between charged side chains of acidic and basic amino acids
-OH, -NH2, -COOH, -CONH2
Electrostatic interactions
This type of interaction pertains between polar, acidic and/or basic R groups, enhances increase in the solubility of protein with polar solvents. For H-bonding to occur, the H must be attached on O, N or F
H-Bonding
This type of interaction Between non-polar side chains of amino acids, found in the interior of globular proteins interacting with other nonpolar amino acids.
Hydrophobic interactions
This structure of protein refers to the organization among the various peptide chains in a multimeric protein. Moreover, this is highest level of protein organization and is only present only in proteins that have 2 or more polypeptide chains (subunits)
Quaternary structure
Proteins with quartenary structure are often referred to as ________________
oligomeric proteins
These protein molecules with elongated shape and are generally insoluble in water. They tend to have simple, regular, linear structures and aggregate together to form macromolecular structures, e.g., hair, nails, etc.
Fibrous proteins
What kind of structures do fibrous proteins have?
Secondary Structures
These protein molecules with peptide chains folded into spherical or globular shapes. They are generally hydrophobic amino acid residues in the protein core. Moreover, they function as enzymes and intracellular signaling molecules
Globular proteins
These proteins are associated with cell membranes and are insoluble in water – hydrophobic amino acid residues on the surface. They help in transport of molecules across the membrane
Membrane proteins
What is the structure of alpha keratin?
Helical in structure and 4o structure is association of alpha helices into coiled coil
What is the structure of beta keratin?
4o is stacked -pleated sheets
What is the entailed for collagen in terms of maintaining its structure?
Proline (20%)
These are best known for their catalytic role.
Catalytic Proteins (Enzymes)
These are central to functioning of the body’s immune system.
Defense proteins: Immunoglobulins or antibodies
These bind small biomolecules, e.g., oxygen and other ligands, and transport them to other locations in the body and release them on demand.
Transport proteins
These transmit signals to coordinate biochemical processes between different cells, tissues, and organs.
Messenger proteins
These amino acid regulate carbohydrate metabolism
Insulin and glucagon
These are necessary for all forms of movement.
Contractile proteins
These are contractile proteins that constitute a muscle.
actin and myosin
They confer stiffness and rigidity
Structural proteins
These span a cell membrane and help control the movement of small molecules and ions. Moreover, they have channels that help molecules can enter and exist the cell. In this, transport is very selective - allow passage of one type of molecule or ion.
Transmembrane proteins
These bind (and store) small molecules.
Storage proteins
This is an iron-storage protein - saves iron for use in the biosynthesis of new hemoglobin molecules
Ferritin
This is an oxygen-storage protein present in muscle
Myoglobin
These are often found “embedded” in the exterior surface of cell membranes - act as sites for receptor molecules. Moreover, often the molecules that bind to enzymes (catalytic proteins), thereby turning them “on” and “off,” and thus controlling enzymatic action.
Regulatory proteins
These proteins are particularly important in the early stages of life - from embryo to infant.
Nutrient proteins
This is the amino acid abundant in milk.
Casein
This is the amino acid abundant in eggs.
ovalalbumin
This is known as the reverse of peptide bond formation: This results in the generation of an amine and a carboxylic acid functional groups.
Hydrolysis
This form of hydrolysis pertains to the digestion of ingested protein.
enzyme-catalyzed hydrolysis
Collagen is rich in?
Rich in 4-hydroxyproline (5%) and 5-hydroxylysine (1%) — derivatives
Immunoglobulin bonding to an antigen via variable region of an immunoglobulin occurs through what interactions?
through hydrophobic interactions, dipole – dipole interactions, and hydrogen bonds.
This is a conjugated protein that contains lipids in addition to amino acids
Lipoproteins
What is the primary role of lipoproteins?
They help suspend lipids and transport them through the bloodstream
These lipoproteins transport dietary triacyclglycerols from intestine to liver and to adipose tissue.
Chylomicrons
These lipoproteins transport triacyclglycerols synthesized in the liver to adipose tissue.
Very-low-density lipoproteins (VLDL):
These lipoproteins transport cholesterol synthesized in the liver to cells throughout the body.
Low-density lipoproteins (LDL):
These lipoproteins collect excess cholesterol from body tissues and transport it back to the liver for degradation to bile acids.
High-density lipoproteins (HDL)
