Biol 141 Chapter 3 Flashcards


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1

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

2

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
3

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

4

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
5

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
6

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
7

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