Amino Acids & Proteins (Lec) Flashcards by Yna Book

most abundant biomolecule in the cell

Proteins

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polymers made of monomers

amino acids

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atoms or small molecules that bond together to form more complex structures such as polymers

Monomers

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four main types of monomer

sugars, amino acids, fatty acids, and nucleotides

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a process by which a polypeptide chain folds to become a biologically active protein in its native 3D structure.

Protein folding

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T/F - Proteins may be rigid or flexible to various degrees as required for optimum function

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Number of peptides possible for a chain of n amino
acids

20^n (ex. 100 residue protein has 20^100)

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Hierarchy of Protein Structure

the amino acid sequence

primary structure

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Hierarchy of Protein Structure

frequently occurring substructures
or folds

secondary structure:

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Hierarchy of Protein Structure

three-dimensional arrangement of all
atoms in a single polypeptide chain

tertiary structure

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Hierarchy of Protein Structure

overall organization of non-covalently
linked subunits of a functional protein.

quaternary structure

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tendency for non-polar solutes to aggregate in
aqueous solution to minimize the hydrocarbon-water
interface

Hydrophobic Effects [important in the binding of substrates (ligands) into protein receptors and enzymes]

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RATIONALE BEHIND PROTEIN FOLDING

Proteins fold to minimize their surface contact with wate

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hydrocarbon on the inside, polar group on the outside

micelle structure

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unfolding of the native three-dimensional structure of a protein by chemical influences

Protein Denaturation

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unfolding of the native three-dimensional structure of a protein by chemical influences

Protein Denaturation

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Common secondary structures:

α-helix (amino acids wound into a helical structure)
β-sheet
β-turn
disulfide bonds

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hydrophobic sidechains form an interface between
α-helices (de novo protein design)

Helical Bundles

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covalent structural scaffolds, redox active, reversible

Disulfide bonds

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FUNCTIONS OF PROTEIN (8)

Structural – for support (ex. collagen, elastin)

Catalytic – for hastening biochemical reactions (ex. amylase)

Storage – for storage of amino acids (ex. casein, ovalbumin)

Transport – for transport of other substances (ex. hemoglobin)

Regulation – for regulation of bodily activities (ex. insulin, glucagon)

Receptor – for response of cell to external stimuli (ex. neuron receptors)

Contractile – for movement (ex. myosin, actin)

Defensive – for protection against disease (ex.
antibodies)

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a specific three-dimensional conformation that is essential for the biological function in proteins

Native conformation (3-D folded conformation with active function)

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T/F - Loss of structure 🡪 loss of biological function

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spatial arrangement of atoms in a protein

Conformation

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building blocks or unit of proteins

amino acids

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FOUR FEATURES OF AMINO ACIDS

1. central/ α carbon atom linked to an amino group 2. carboxyl group 3. hydrogen atom/Amino group 4. side chain (R group)

gives the amino acid a unique identity and property

R group

T/F - Amino acids are chiral

T (chirality - existing in left and right-handed forms)

T/F - Amino acids can exist as either the D or the L isomer (orientations that are mirror image of each other)

T (Most amino acids exist in nature in the L isomer.)

the only cyclic amino acid

Proline (Usually a D isomer; does not have both free α-amino and free α-carboxyl groups)

the only achiral amino acid

Glycine (has a hydrogen atom as its sidechain)

T/F - Proteins can be differentiated and classified according to type of side chain, R group

T (it specifies which class of amino acids it belongs to)

Non-polar amino acids (9): - hydrophobic

glycine (Gly; G) alanine (Ala; A) leucine (Leu; L) isoleucine (Ile; I) proline (Pro; P) tryptophan (Trp; W) valine (Val; V) phenylalanine (Phe; F) methionine (Met; M)

Polar amino acids (6): - hydrophilic

serine (Ser; S) threonine (Thr; T) cysteine (Cys; C) tyrosine (Tyr; Y) asparagine (Asn; N) glutamine (Gln; Q)

Basic amino acids (3): - positively charged, hydrophilic amino acids

lysine (Lys; K) arginine (Arg; R) histidine (His; H)

Acidic amino acids (2): - negatively charged, hydrophilic amino acids

aspartic acid (Asp; D) glutamic acid (Glu; E)

Amino acids that the body can synthesize

nonessential amino acids (11)

amino that the body cannot synthesize either at all or in sufficient amounts, must also be obtained from the diet.

essential amino acids (9)

T/F - The nutritional value of a protein is dependent on what amino acids it contains and in what quantities.

nonessential amino acids (11)

alanine arginine asparagine aspartic acid cysteine glutamic acid glutamine glycine proline serine tyrosine

essential amino acids (9)

histidine isoleucine leucine lysine methionine phenylalanine threonine tryptophan valine

T/F - With the exception of Glycine, all protein-derived amino acids have at least one stereocenter (the α-carbon) and are chiral

uncommon amino acids (2)

Hydroxylysine hydroxyproline

aromatic amino acids (3)

phenylalanine tryptophan tyrosine

T/F - Amino acids are AMPHOTERIC

T - they can either accept or donate a proton.

T/F - Amino acids may act as weak acids and bases within an aqueous environment

how they react depends on the pH of their environment

T/F - at low pH, ionizable groups tend to be protonated; at high pH, they tend to be deprotonated

a number that shows how weak or strong an acid is

pKa (The lower the value of pKa, the stronger the acid and the greater its ability to donate its protons)

T/F - Under the physiological pH range (6.8-7.4), amino acids are zwitterions, or dipolar ions.

hybrid, neutral molecule with positive and negative charges

zwitter

Net charge of the molecule

zero [attained when they reach the ISOELECTRIC pH (pI)]

pH at which zwitterion form predominates

Isoelectric point

Acidity and Basicity of Amino Acids Ex. Alanine

Acid solution less than 2 = net charge: +1 Neutral solution pH approximately 6 = net charge: 0/isoelectric form Basic solution pH greater than 10 = net charge: -1

Dissociation of the hydrogen:

at low pH, both of the amino and carboxyl groups are fully protonated. As the pH of the solution is raised, the –COOHgroup of Form I can ionize and donate H+ to the medium. The release of the proton results to carboxylate group, -COO-. The Form II then has a net charge of zero.

The workhorses of biological systems

peptide bonds (amide bonds that join amino acids together)

Peptide bond formation is accompanies by the loss of

H2O

formed between the carboxyl group of an amino acid and the amino group of another

Peptide bonds

planar, rigid and have partial double bond character.

Peptide bonds

By convention, peptides are written from what direction

left to right (N to C)

beginning of the protein where the free –NH3 + group is located

N-terminal end

end of the protein where the –COO group is located

C-terminal end

Levels of structural organization of proteins (4)

Primary Secondary Tertiary Quaternary

T/F - Most natural polypeptide chains contain between 50 and 2000 amino acid residues and are commonly referred to as proteins.

the amino acid sequence of a protein from N to C-terminal that determine the 3-D structures

Primary Structure

primary structure can be obtained through a lab technique called

Sequencing

changes to an amino acid with similar properties

Conservative replacement

ex. of diseases with alterations of the primary structure leading to abnormal protein function

Sickle Cell Disease (abnormal form of hemoglobin)

The local structure of neighboring amino acids

Secondary Structure (ordered arrangements in localized regions)

the result of intramolecular hydrogen bonding

Secondary Structure

Refers only to interactions of the peptide backbone.

Secondary Structure

Most common secondary structures

a-helix and b-pleated sheet

Formed and stabilized by _____ bond between the amide proton and carbonyl oxygen

hydrogen bond

CHARACTERISTICS OF ALPHA-HELIX

Spiral structure Structural features: C=O of each peptide bond is hydrogen bonded to the N-H of the fourth amino acid away; there are 3.6 aa/turn Pitch: 0.54nm All R groups point outward from helix Example: Keratin Bulkiness (steric strain) between adjacent R-groups Coil is clockwise

introduces kinks/bends to the structure, restricted movement, no H bonding

Helix Destabilizers - Proline and Glycine

strong helix formers

small hydrophobic residues (e.g. Ala, Leu)

CHARACTERISTICS OF BETA-PLEATED SHEETS

- form when two or more polypeptides line up side-by-side stabilized by hydrogen bonds of adjacent polypeptide chains (interchain or intrachain) - β-strands are extended into a zigzag - All R groups extend above or below the sheet in an alternating up and down direction

TYPES OF BTA-PLEATED SHEETS (2)

PARALLEL β-Pleated Sheets - Run in same directions - Forms bent H-Bonds (weaker) ANTI-PARALLEL β-Pleated Sheets - Run in opposite directions - Forms linear H-Bonds (stronger)

3-D arrangement of all atoms

Tertiary Structures

T/F - Noncovalent interactions stabilize the higher levels of protein structure.

T/F - Secondary, tertiary, and quaternary structure of proteins is formed and stabilized by weak forces

T/F - Hydrophobic residues prefer to be on the interior of proteins, which reduces their proximity to water

T/F - globular proteins fold with a hydrophobic core and a hydrophilic exterior.

the interactions of these drive protein folding

Tertiary Structure: Hydrophilic & Hydrophobic Interactions

Acid-base interactions between amino acids with charged groups can occur, also known as salt bridges

Tertiary Structure Electrostatic Interactions

Cysteine residues can undergo oxidation to form disulfide bridges, or cystine. They create loops in protein chains and dictate how curly hair is.

Tertiary Structure Covalent Bonding

Tertiary Structure Contain polypeptide chains organized approximately parallel along a single axis

Fibrous Proteins

Consists of long fibers or large sheets, tend to be mechanically strong

Fibrous Proteins

Insoluble in water and dilute salt solutions, and play important structural roles

Fibrous Proteins (ex. Keratin is found in hair, wool, and nails. Collagen is found in cartilage, bones, and skin)

Tertiary Structure Proteins that are folded into a spherical shape

Globular Proteins

Most of its polar side chains are on the outside; nonpolar side chains buried inside the structure

Globular Proteins

Soluble in water; Function: metabolic (catalytic, transport, etc.)

Globular Proteins

Nearly have all substantial sections of α-helix and β-sheet

Globular Proteins

association of polypeptide chains into aggregations

Quaternary Structure

formed by the assembly of individual polypeptides (subunit/monomer) into a larger functional cluster

Quaternary Structure

its subunits are stabilized by non-covalent interactions (like tertiary structure)

Quaternary Structure

ROLES OF THE FORMATION OF QUARTERNARY STRUCTURES

- more stable (by further reducing the surface area of the protein complex) - reduce the amount of DNA needed to encode the protein complex - bring catalytic sites close together (allowing intermediates from one reaction to be directly shuttled to a second reaction) - can induce cooperativity, or allosteric effects

Disrupts the secondary, tertiary, and quaternary structures

Denaturating Agents (Physical Agents & Chemical Agents)

Physical Agents (4)

High temperature Vigorous shaking or agitation Hydrostatic pressure UV radiation

Chemical Agents (6)

Change in pH Change in ionic strength Organic solvents (e.g. urea, alcohol) Reducing agents (e.g. performic acid and mercaptoethanol) Detergents Salts of heavy metals

Hydrogen bonds are most important in this type of structure in proteins: a. primary structure b. secondary structure c. tertiary structure d. quaternary structure e. all of these

b. secondary structure

derive part of their function from covalently-attached molecules called prostehtic groups

Conjugated Proteins

proteins with lipid prosthetic groups

Lipoproteins

proteins with carbohydrate prosthetic groups

Glycoprotein

proteins with nucleic acid prosthetic groups

Nucleoprotein

Cell to cell recognition, depending on blood type of prosthetic groups

Glycoproteins

ability for all quaternary structures to help or work each other/together

Cooperativity

Helix Destabilizers (3):

Presence of helix breakers (Proline and Glycine) * However, small hydrophobic residues (e.g. Ala, Leu) are strong helix formers * Electrostatic repulsion (or attraction) between successive charged aa residues. * Bulkiness (steric strain) between adjacent R-groups

T/F - Amino acids cannot share one letter codes.

T/F - Trypsin is NOT an amino acid, it is a protein with an enzymatic function