Chapter 1 Foundations of Biochem

Question 1

What are the 3 domains of life?

Answer 1

Bacteria, Archea, Eukarya

these domains are based off of differences at the cellular and molecular level

Question 2

What are the 6 kingdoms of life?

Answer 2

Archea - unicellular prokaryote 
Bacteria - unicellular prokaryote 
Protista - unicellular eukaryote
Fungi - uni or multi cellular eukaryote
Plantae - multicellular eukaryote 
Animilia - multicellular eukaryote

Question 3

What are the structures of a bacterial cell?

Answer 3

Nucleiod - contains bacterial dna
Pili -provide points of adhesion to surface of other cells
Flagella - propels cells thru environment
Ribosomes - protein synthesis from an RNA messenger
Cell envelope - varies with type of cell

Question 4

What are the structures of an animal cell?

Answer 4

Ribosomes - protein synthesis 
Peroxisomes - oxidizes fatty acids 
Cytoskeleton - supports cell 
Lysosome - degrades intercellular debri 
Transport vesicles -
Golgi
Smooth ER - lipid synthesis 
Rough ER - protein synthesis 
Mitochondria - produce ATP 
Plasma membrane - separates cell from environment and regulates things in and out of cell 
Nucleolus - ribosomal mRNA synthesis 
Nuclear envelope 
Nucleus

Question 5

Can atoms rotate around a double bond?

Answer 5

no molecules can’t rotate around a double bond so they reside in the same plane

Question 6

Define stereoisomer

Answer 6

molecules with the same chemical bond and formula but differ in configuration (space)

Question 7

The function of molecules are strongly dependent on what?

Answer 7

3D structure

• double bonds
• chiral center

Question 8

Define geometric isomers

Answer 8

differ in arrangement of substituent groups with respect to a non rotating double bond
-cis/trans

Question 9

Cis vs Trans

Answer 9

cis - Z = “zame” groups are on the same side

Trans- E = “epposite” on opposite side

Question 10

Chiral carbon

Answer 10

carbon with 4 different substituents

Question 11

Enantiomers

Answer 11

mirror images of each other but not superimposable

- different R and S and each chiral center

Question 12

Diasteriomers

Answer 12

not mirror images but superimposable
-they do not have opposite (R) and (S) confirmations at each chiral center, but the confirmations are different at two or more chiral centers.

Question 13

How do enzymes speed up chemical reactions?

Answer 13

1. change the rxn by coupling to a fast one

2. lower the activation barrier by catalysis

Question 14

Do enzymes change gibbs free energy?

Answer 14

no. only stabilize the transition state

Question 15

Endergonic rxn?

Answer 15

• rxn that require energy
• thermodynamically unfavorable (+ delta G)
• rxn have too high of an energy barrier

Question 16

Exergonic

Answer 16

-give off energy
-thermodynamically favorable (- delta G < 0)
-

Question 17

Energy coupling

Answer 17

-coupling of exergonic and endergonic rxn allows otherwise unfavorable

Question 18

what is the pathway flow of genetic information?

Answer 18

DNA -> RNA -> protein

DNA- stores information
RNA - transmits information
protein - function manifests information

Question 19

Does natural selection favor mutations?

Answer 19

yes

Question 20

What are the different ways of categorizing life?

Answer 20

1. rRNA sequences
   -  phylogenetic tree->  3 domains of life
2. Visual features and organization of cells/organisms
   -  6 kingdoms of life
3. Energy and carbon sources

Question 21

Which of the following is NOT a unique feature of bacteria?
A. Pili
B. Flagella
C. Cell envelope  
D. Ribosomes

Answer 21

D.

Structures of Bacteria

• ribosomes
• cell envelope
• flagella
• pilli
• nucleoid

Question 22

What is a nucleiod?
A. Animal cellular structure where proteins are synthesized
B. Bacterial cellular structure that contains chromatin
C. Animal cellular structure where rRNA is synthesized
D. Animal cellular structure that contains chromatin
E. Bacterial cellular structure that contains DNA

Answer 22

E.

contains bacterial DNA

Question 23

Which of the following pairs is incorrect?
A. Nucleus - contains chromatin
B. Lysosome - oxidizes fatty acids
C. RER -  site of protein synthesis
D. Mitochondrion -  ATP production 
E. Nucleolus - rRNA synthesis

Answer 23

B.

peroxisomes - oxidize fatty acids

lysosomes - degrade intercellular debris

Question 24

How do you distinguish between gram + and gram – bacteria?
A. Gram positive bacteria have a cell envelope, gram negative bacteria do not.
B. Gram negative bacteria have a cell envelope with an outer membrane, gram positive bacteria have a cell envelope without an outer membrane.
C. Gram negative bacteria have a cell envelope with an inner membrane, gram positive bacteria have a cell envelope without an inner membrane.
D. Gram negative bacteria have a cell envelope with a peptidoglycan layer, gram positive bacteria have a cell envelope without a peptidoglycan layer.

Answer 24

B.

Gram neg.
- outer membrane

Gram pos
- no outer membrane

Both have peptidoglycan layer

Question 25

``` Which of the following element is not a divalent ion? A. Na B. Ca C. Zn D. Fe E. Mg ```

Answer 25

A. Na K+, Ca++, Mg++, Zn++, Fe++

Question 26

What is the definition of a covalent bond?

Answer 26

bond that involves the sharing of electron pairs between atoms

Question 27

Alkane/alkene/alkyne – what is the difference?

Answer 27

``` Alkane = saturated hydrocarbons (they have only carbon-carbon single bonds) Alkene = unsaturated hydrocarbon that contains one or more carbon-carbon double bonds Alkyne = unsaturated hydrocarbon that contains one or more carbon-carbon triple bonds ```

Question 28

Which of the following indicate how enzymes speed up reactions? A. By coupling to a fast one B. By lowering the activation energy by catalysis C. By causing the reaction to be exergonic instead of endergonic D. A and B E. A, B, and C

Answer 28

D

Question 29

What is ΔG?

Answer 29

free energy change = free energy of products – free energy of reactants

Question 30

Why would a reaction be endergonic? A. The products’ free energy is higher the reactants’ free energy B. The reaction is thermodynamically unfavorable C. The energy barrier is too high D. The reactants are kinetically stable E. All of the above

Answer 30

CORRECT ANSWER: E How do you write out that the energy barrier is too high? Answer: ΔG‡ > 0

Question 31

Why would a reaction be Exergonic? A. The products’ free energy is higher the reactants’ free energy B. The products are kinetically unstable C. The cellular concentrations of the metabolites are far higher than their equilibrium concentrations D. The reaction is catalyzed by an enzyme

Answer 31

C

Question 32

HOW exactly can endergonic and exergonic reactions be coupled?

Answer 32

1. Phosphorylation of enzyme - can activate enzymes for example by changing their shape => enhances catalysis 2. Phosphorylation of substrate - Phosphorylation => can activate enzymes for example by changing their shape => enhances catalysis 3. Adenylylation of enzyme - AMP is then a good leaving group 4. Adenylylation of substrate - AMP is then a good leaving group

Question 33

``` What do catalysts alter? A. The free energy change of a reaction B. The activation free energy change of a reaction C. The rate of the reaction D. A and C E. B and C ```

Answer 33

E