Chapter 3

Question 1

Define metabolism

Answer 1

the sum total of all the chemical reactions a cell needs to carry out to survive, grow, and reproduce

Question 2

Define catabolism

Answer 2

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

Question 3

Define anabolism

Answer 3

using the energy harnessed by catabolism to drive the synthesis of the many molecules that form the cell

Question 4

Define enzyme

Answer 4

a protein that accelerates a reaction by lowering the activation energy

Question 5

Describe competitive inhibitor and give the effect of more substrate

Answer 5

bind to the same site as the substrate, competes directly with it

can be overcome with additional substrate

Question 6

Describe noncompetitive inhibitor and give the effect of more substrate

Answer 6

bind where the end product binds (allosteric site)

cannot be overcome with additional substrate

Question 7

Define biosynthesis

Answer 7

an enzyme-catalyzed process by which complex molecules are formed from simple substances by living cells (also called anabolism)

Question 8

Define a coupled reaction

Answer 8

linked pair of chemical reactions in which free energy released by one reaction

Question 9

What are the two ways an unfavorable reaction can occur?

Answer 9

coupling with a second, highly negative reaction

overabundance of reactant

Question 10

Compare the effects of enzymes and thermal activation

Answer 10

enzymes lower the activation energy and thermal activation increases the energy of the reactant ((enzymes are specific, thermal activation is not))

Question 11

What determines the rate at which an enzyme will interact with its substrate?

Answer 11

concentration of the substrate

rate at which substrate undergoes its reaction is the limit of the rate of the reaction as a whole

Question 12

Define Km

Answer 12

the concentration of substrate at which the enzyme works at half its maximum speed

directly proportional to strength of binding (lower is better)

Question 13

Define Vmax

Answer 13

((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

Question 14

Describe a michaelis-menton graph

Give its strengths and weaknesses

Answer 14

plots substrate concentration against reaction speed in a hyperbolic line

shows how many enzymes are occupied at any time, but Vmax is estimated

Question 15

Describe a double-reciprocal or lineweaver-burk graph

Give its strengths and weaknesses

Answer 15

plots reciprocal of substrate concentration against reciprocal of reaction speed in a straight line

can easily tell Vmax

Question 16

Compare condensation reactions and hydrolysis reactions

Answer 16

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

Question 17

Define activated carrier

Answer 17

a small molecule that stores energy or chemical groups in a form that can be donated to many different metabolic reactions

Question 18

What is the most common activated carrier and how does it work?

Answer 18

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

Question 19

Describe the synthesis of a polynucleotide such as RNA or DNA

Answer 19

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

Question 20

Describe the activated carriers NADH and NADPH

Answer 20

carry energy in the form of 2 high energy electrons and a proton (forms a hydride ion, H-)

Question 21

Describe the four parts of an amino acid

Answer 21

Unionized: C attached to H, COOH, R group, and NH2

Ionized: C attached to H, COO-, R group, and NH3

Question 22

Describe the parts of a protein (chain of amino acids)

Answer 22

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))

Question 23

Give the four types of amino acids

Answer 23

acidic, basic, uncharged polar, nonpolar

Question 24

Which of the 4 types of amino acids is hydrophillic or hydrophobic?

Answer 24

nonpolar is hydrophobic

acidic, basic, uncharged polar are hydrophilic

Question 25

Which of the 4 types of amino acids can form ionic bonds?

Answer 25

acidic (negative charge) and basic (positively charged)

Question 26

Which of the 4 types of amino acids can only form electrostatic bonds (as opposed to ionic)?

Answer 26

uncharged polar

Question 27

Which of the 4 types of amino acids can form H-bonds?

Answer 27

uncharged polar

Question 28

Which of the 4 types of amino acids are part of lipid bylayers?

Answer 28

nonpolar

Question 29

What type of isomers make up proteins?

Answer 29

the l-isomers of the acids

Question 30

How are amino acids bonded together?

Answer 30

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

Question 31

What are the noncovalent bonds that held proteins together?

Answer 31

H-bonds, electrostatic attractions, van der waals, and side chains are joined by hydrophobic interaction

Question 32

What are the covalent cross-linkages that help proteins fold?

Answer 32

disulfide s-s bonds that form from two cysteine side chains

Question 33

Describe what primary structure, secondary structure, tertiary structure, and quaternary structure means in relation to proteins.

Answer 33

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

Question 34

What are the two main secondary structures in proteins?

Answer 34

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

Question 35

Describe the use of X-Rays to determine the structure of proteins

Answer 35

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.

Question 36

Describe the use of NMR to determine the structure of proteins

Answer 36

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.

Question 37

Describe globular proteins

Answer 37

have a polypeptide chain that folds up into a compact shape like a ball with an irregular surface

Question 38

Describe fibrous proteins

Answer 38

have a relatively simple, elongated 3D structure