SEM 2 EXAM Flashcards
(14 cards)
- Know Common Functional Groups
- Hydroxyl Group (-OH)
Found in alcohols.
Structure: An oxygen atom bonded to a hydrogen atom.
Example: Ethanol (C₂H₅OH). - Carbonyl Group (C=O)
Found in aldehydes and ketones.
Structure: A carbon atom double-bonded to an oxygen atom.
Aldehyde: The carbonyl group is at the end of the carbon chain (e.g., formaldehyde, CH₂O).
Ketone: The carbonyl group is within the carbon chain (e.g., acetone, CH₃COCH₃). - Carboxyl Group (-COOH)
Found in carboxylic acids.
Structure: A carbonyl group (C=O) and a hydroxyl group (-OH) attached to the same carbon atom.
Example: Acetic acid (CH₃COOH). - Amino Group (-NH₂)
Found in amines and amino acids.
Structure: A nitrogen atom bonded to two hydrogen atoms.
Example: Glycine (an amino acid), H₂NCH₂COOH. - Phosphate Group (-PO₄³⁻)
Found in nucleotides (like DNA) and ATP.
Structure: A phosphorus atom bonded to four oxygen atoms, one of which has a double bond.
Example: Adenosine triphosphate (ATP), which stores energy in cells. - Sulfhydryl Group (-SH)
Found in thiols.
Structure: A sulfur atom bonded to a hydrogen atom.
Example: Cysteine (an amino acid), HSCH₂CH(NH₂)COOH. - Methyl Group (-CH₃)
Found in alkyl chains.
Structure: A carbon atom bonded to three hydrogen atoms.
Example: Methane (CH₄).
- Understand the Spectrum of Bonding Between Purely Covalent and Purely Ionic Bonds
Pure Covalent (Nonpolar): Electrons are shared equally between atoms with similar electronegativity (e.g., H₂).
Polar Covalent: Electrons are shared unequally, with one atom pulling the electrons closer (e.g., H₂O).
Purely Ionic: Electrons are transferred from one atom to another, creating ions that attract each other (e.g., NaCl).
Think of it as a spectrum:
Pure Covalent ↔ Polar Covalent ↔ Ionic
- Recognize Addition, Elimination, Substitution, and Rearrangement Reactions
Addition: Combine two molecules into one (add atoms).
Elimination: Remove atoms to create a double or triple bond.
Substitution: Swap one group for another.
Rearrangement: Change the structure, but not the composition.
- Understand the Concept of pH, pKa, and the Henderson-Hasselbalch Equation
pH measures how acidic/basic a solution is.
pKa tells you how strong an acid is (lower pKa means stronger acid).
Henderson-Hasselbalch equation links pH, pKa, and the ratio of protonated/deprotonated forms of an acid.
- Know the Structures and Functions of All 20 Amino Acids
Nonpolar (Hydrophobic) Amino Acids:
Glycine (Gly, G): Simplest amino acid, R group is H.
Alanine (Ala, A): R group is a methyl (-CH₃).
Valine (Val, V): R group is -CH(CH₃)₂.
Leucine (Leu, L): R group is -CH₂CH(CH₃)₂.
Isoleucine (Ile, I): R group is -CH(CH₃)CH₂CH₃.
Methionine (Met, M): R group contains sulfur, -CH₂CH₂SCH₃.
Proline (Pro, P): R group forms a ring with the amino group, causing a rigid structure.
Phenylalanine (Phe, F): R group contains a benzene ring.
Tryptophan (Trp, W): R group contains a double-ring structure (indole).
Polar (Hydrophilic) Uncharged Amino Acids:
Serine (Ser, S): R group contains a hydroxyl (-OH).
Threonine (Thr, T): R group contains -CH(OH)CH₃.
Asparagine (Asn, N): R group contains -CH₂CONH₂ (amide group).
Glutamine (Gln, Q): R group contains -CH₂CH₂CONH₂.
Tyrosine (Tyr, Y): R group contains a phenol (-OH on a benzene ring).
Cysteine (Cys, C): R group contains a sulfhydryl (-SH), can form disulfide bonds.
Positively Charged (Basic) Amino Acids:
Lysine (Lys, K): R group contains -CH₂CH₂CH₂CH₂NH₂.
Arginine (Arg, R): R group contains -CH₂CH₂CH₂NHC(NH₂)NH₂ (guanidinium group).
Histidine (His, H): R group contains an imidazole ring, which can accept or donate protons (acts as a buffer).
Negatively Charged (Acidic) Amino Acids:
Aspartic Acid (Asp, D): R group contains -CH₂COOH (carboxyl group).
Glutamic Acid (Glu, E): R group contains -CH₂CH₂COOH (carboxyl group).
Functions of Amino Acids:
Structural roles: Amino acids combine to form peptides and proteins, which are essential for cell structure (e.g., collagen).
Enzyme catalysis: Amino acids are the building blocks of enzymes, which catalyze biochemical reactions.
Cell signaling: Amino acids like glutamate and glycine act as neurotransmitters in the brain.
Immune response: Arginine plays a role in the immune system by producing nitric oxide.
Energy: Some amino acids can be used as fuel by being converted into glucose or ketone bodies.
- Understand Protein Primary,
Primary
- The linear sequence of amino acids in a polypeptide chain
- Amino acids are linked by peptide bonds (covalent bonds)
- the sequence determines the proteins shape and function
- Describe the Roles of DNA and RNA
DNA = The blueprint for life; stores and transmits genetic information.
RNA = The worker that helps read and execute DNA’s instructions, specifically in protein synthesis.
- Define and Recognize Conjugation and Resonance in Organic Molecules
Conjugation: Alternating single and double bonds that allow electron delocalization, increasing stability.
Resonance: Different ways to draw the structure of a molecule, showing electron delocalization over multiple forms, making the molecule more stable.
General structure of an amino acid
General Structure of an Amino Acid:
A central carbon (called the alpha carbon) bonded to:
An amino group (-NH₂),
A carboxyl group (-COOH),
A hydrogen atom (H),
And an R group (side chain), which differs for each amino acid.
Amino Acid Groups:
The 20 common amino acids can be grouped based on the properties of their R groups:
Secondary
- The local folding of the polypeptide structures into 2 types
- alpha helix - a coiled structure stabilized by hydrogen bonds between the carbonyl group of one amino acid and the amide group of another four residues down the chain
- beta sheet - a sheet like structure formed by hydrogen bonds between strands of amino acids
Function - secondary structres provide stability and are commonly found in many proteins
Tertiary structure
- overall 3d shape of a single polypeptide chain
- polypeptide fold into a specific 3D shape, driven by interactions between the side chains of the amino acids.
- hydrophobic interactions
- hydrogen bonding between the polar side chains
- ionic bonds between charged side chains
- disulfide bridges - covalent bonds beteween cystein and residues
Function - critical for protein function as it determines how the proteins interact with other molecules
Quartenary structure
- the arrangement of multiple polypeptide chains in a protein
- example: HAEMOGLOBIN - 4 subunits - 2 alpha, 2 beta, that work together to carry oxygen
function - allows proteins to function cooperatively
Summary of Primary, Secondary, tertiary and quartenary
Amino Acids: There are 20 common amino acids, grouped by properties (nonpolar, polar, acidic, basic). Each has a distinct R group that affects its function in proteins.
Protein Structures:
Primary: The sequence of amino acids.
Secondary: Local structures like alpha helices and beta sheets.
Tertiary: The overall 3D shape of a polypeptide.
Quaternary: The arrangement of multiple polypeptide chains.
