Chapter 3 Flashcards
Define metabolism
the sum total of all the chemical reactions a cell needs to carry out to survive, grow, and reproduce
Define catabolism
breaking down foodstuffs into smaller molecules, thereby generating both a useful form of energy for the cell and some of the small molecules the cell needs as building blocks
Define anabolism
using the energy harnessed by catabolism to drive the synthesis of the many molecules that form the cell
Define enzyme
a protein that accelerates a reaction by lowering the activation energy
Describe competitive inhibitor and give the effect of more substrate
bind to the same site as the substrate, competes directly with it
can be overcome with additional substrate
Describe noncompetitive inhibitor and give the effect of more substrate
bind where the end product binds (allosteric site)
cannot be overcome with additional substrate
Define biosynthesis
an enzyme-catalyzed process by which complex molecules are formed from simple substances by living cells (also called anabolism)
Define a coupled reaction
linked pair of chemical reactions in which free energy released by one reaction
What are the two ways an unfavorable reaction can occur?
coupling with a second, highly negative reaction
overabundance of reactant
Compare the effects of enzymes and thermal activation
enzymes lower the activation energy and thermal activation increases the energy of the reactant ((enzymes are specific, thermal activation is not))
What determines the rate at which an enzyme will interact with its substrate?
concentration of the substrate
rate at which substrate undergoes its reaction is the limit of the rate of the reaction as a whole
Define Km
the concentration of substrate at which the enzyme works at half its maximum speed
directly proportional to strength of binding (lower is better)
Define Vmax
((The maximum rate of the reaction, where an increased concentration of substrate no longer can increase the rate)) NOT - the concentration of substrate at which the reaction is at its maximum
Describe a michaelis-menton graph
Give its strengths and weaknesses
plots substrate concentration against reaction speed in a hyperbolic line
shows how many enzymes are occupied at any time, but Vmax is estimated
Describe a double-reciprocal or lineweaver-burk graph
Give its strengths and weaknesses
plots reciprocal of substrate concentration against reciprocal of reaction speed in a straight line
can easily tell Vmax
Compare condensation reactions and hydrolysis reactions
Condensation reactions are energetically unfavorable (require energy from sunlight or food) reactions that produce water when two molecules combine. Hydrolysis reactions are energetically favorable reactions that release energy when a molecule divides
Define activated carrier
a small molecule that stores energy or chemical groups in a form that can be donated to many different metabolic reactions
What is the most common activated carrier and how does it work?
ATP
single hydrolysis reaction results in a donation of a P group, creation of ADP
double hydrolysis results in a donation of 2 P groups (P-P, then break apart), creation of AMP
Describe the synthesis of a polynucleotide such as RNA or DNA
nucleoside monophosphate reacts with 2 ATP molecules to get two P groups, then reacts with the end of the DNA/RNA with its extra energy and releases the P groups
Describe the activated carriers NADH and NADPH
carry energy in the form of 2 high energy electrons and a proton (forms a hydride ion, H-)
Describe the four parts of an amino acid
Unionized: C attached to H, COOH, R group, and NH2
Ionized: C attached to H, COO-, R group, and NH3
Describe the parts of a protein (chain of amino acids)
Amino (N-) terminus, amino acid, peptide bond, amino acid, carboxyl (C-) terminus ((The H in the NH2 is removed and bonded to the C in the Carboxyl group, which is now C=O))
Give the four types of amino acids
acidic, basic, uncharged polar, nonpolar
Which of the 4 types of amino acids is hydrophillic or hydrophobic?
nonpolar is hydrophobic
acidic, basic, uncharged polar are hydrophilic
Which of the 4 types of amino acids can form ionic bonds?
acidic (negative charge) and basic (positively charged)
Which of the 4 types of amino acids can only form electrostatic bonds (as opposed to ionic)?
uncharged polar
Which of the 4 types of amino acids can form H-bonds?
uncharged polar
Which of the 4 types of amino acids are part of lipid bylayers?
nonpolar
What type of isomers make up proteins?
the l-isomers of the acids
How are amino acids bonded together?
covalent peptide bonds linking the C of the carboxyl group of one amino acid with the N from the amino group of the other amino acid
Its formation releases water
add onto the carboxyl sideov
What are the noncovalent bonds that held proteins together?
H-bonds, electrostatic attractions, van der waals, and side chains are joined by hydrophobic interaction
What are the covalent cross-linkages that help proteins fold?
disulfide s-s bonds that form from two cysteine side chains
Describe what primary structure, secondary structure, tertiary structure, and quaternary structure means in relation to proteins.
1=amino acid sequence (determines folding)
2=folds in certain segments of the chain, domains
3=3D conformation
4=protein is made of more than one chain
What are the two main secondary structures in proteins?
alpha helices: chain turns around itself and forms H-bonds between every 4th amino acid, C=O to N-H
beta sheets: H-bonds form between segments of a chain lying side by side, forming a rigid, pleated structure
Describe the use of X-Rays to determine the structure of proteins
X-ray beams pass through a protein crystal, producing a diffraction pattern that can be converted into a shape. It is more difficult, but provides high resolution data.
Describe the use of NMR to determine the structure of proteins
NMR observes local magnetic fields around atomic nuclei. It only requires that the protein can be soluble, but can only directly determine the structure of proteins less than 50 kilodaltons.
Describe globular proteins
have a polypeptide chain that folds up into a compact shape like a ball with an irregular surface
Describe fibrous proteins
have a relatively simple, elongated 3D structure
