Biol 141 Chapter 3 Flashcards

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What role do condensation and hydrolysis reactions play in biological processes?

Condensation reaction -> produce H2O molecule

  1. make a long chain of amino acids
  2. gives primary structure
  3. gives function to protein
  4. essentially makes large macromolecules used in biological processes

Structure of amino acids and R groups

  1. Carboxyl and amino group
  2. Structure is correlated to function
  3. Biggest factor is size and shape

Hydrolysis -> gain H2O molecule, breaks up polymers

  1. water comes in and protein gets cut into pieces

Monomers form polymers which form proteins which help cells


What determines the properties of a particular amino acid?

  • Non-polar = Carbon and Hydrogen on R group
  • Polar = Oxygen molecule on R group
  • Acidic = Side chain has negative charge
  • Basic = Side chain has positive charge

Draw the chemical structure of the polypeptide Ile-Gln-Tyr-Lys. Label the side chains and peptide bonds. Explain the terms N- and C-termini, and indicate each on your drawing.

Distinguish what makes a side chain polar, non-polar, charged or non-charged.

  1. Does the side chain have a negative charge? If so, it has lost a proton, so it must be acidic.
  2. Does the side chain have a positive charge? If so, it has taken on a proton, so it must be basic.
  3. If the side chain is uncharged, does it have an oxygen atom? If so, the highly electronegative oxygen will result in a polar covalent bond and thus is uncharged polar.

N-terminus: The beginning of a polypeptide has the amino group which is NH3

C-terminus: The ending of a polypeptide chain, has the carboxyl group which is OH.

Peptide bond: The C-N covalent bond that results from a condensation reaction, is planar and limits movement of the atoms participating in the peptide bond, amino acids linked by a peptide bond are referred to as residues to distinguish them from free monomers


Explain how secondary, tertiary, and quaternary levels of structure depend on primary structure. Give an example of a how a change in amino acid sequence can alter protein structure and function.

  • Primary structure: the unique sequence of amino acids in a protein
  • Secondary structure: created by hydrogen bonding between the oxygen on the C=O group of one amino acid residue and the hydrogen on the N-H groups of another, although these hydrogen bonds are relatively weak, their large number makes them highly stable
    • Alpha helix: the polypeptide backbone is coiled, hydrogen bonds form between residues that are just four linear positions apart in the polypeptide‚Äôs primary sequence
    • Beta-pleated sheet: segments of a peptide chain bend 180 degrees and then fold in the same plane
  • Tertiary: overall shape of a polypeptide, results from the interaction between R-groups or between R-groups and the backbone, each contact between the R-groups causes the peptide-bonded backbone to bend and fold which results in the distinctive three dimensional shape of a polypeptide, these side chains can be involved in a wide variety of bonds
  • Macromolecular machines: groups of macromolecules that assemble to carry out a particular function
  • Hydrogen bonding: in the peptide backbone or the R-groups
  • Hydrophobic interactions: water molecules interact with the hydrophilic polar side chains and force the hydrophobic nonpolar side chains into globular masses
  • van der Waals interactions: further stabilizes their association once hydrophobic side chains are close together
  • Covalent bonding: occurs between two cysteines through a reaction between the sulfhydryl groups
  • Ionic bonding: between groups that have full and opposing charges such as ionized acidic and basic side chains
  • Quaternary: when polypeptides (subunits) come together to form new proteins, held together by the same type of bonds that tertiary structures contain
  • In some individuals, hemoglobin has a valine instead of glutamate and this produces hemoglobin molecules that stick to one another and form fibers when oxygen concentrations in the blood are low

Give three examples of proteins, and state the function of each. How can proteins serve such diverse functions?

  • Channel proteins - facilitate the movement of substances with the gradient
  • Carrier proteins - facilitate movement of substances through membrane can be facilitated diffusion or active transport
  • Enzymes - catalyze reactions
  • Motor proteins - moving cell + large molecules

Is protein shape fixed? Explain, citing at least one example.

  • Proteins do not have a fixed shape. Specific molecules can bind to a protein to change its shape.
    • Potassium-sodium pump, phosphate group from ATP binds to pump to change shape and allow the K+ ions to pass through.
    • The inactive form of calmodulin has a disordered shape but when the concentration of calcium ions increases in the cell, it binds these ions, folds into an ordered, active conformation, and sends a signal to increase the diameter of blood vessels

What is an enzyme? What is an active site?

  • An Enzyme is a protein that speeds up /catalyzes chemical reactions
  • An active site is the location where substrates bind and where the catalysis actually occurs