Week 1 - from Pset

Question 1

True or False: The DNA floats freely in the cytoplasm.

Answer 1

F - in eukaryotic organisms, the dna floats freely within the nucleus, which contains nucleoplasm, not cytoplasm. The nucleus is separated from the cell’s cytoplasm

Question 2

True or False: The central dogma of molecular biology holds that RNA is transcribed into DNA which is then translated into proteins.

Answer 2

F - quite the contrary. The central dogma stats that DNA is transcribed to RNA which is then translated into Amino Acid chains (polypeptide chains), also known as “proteins”. Reverse transcription via reverse transcriptase is present in retroviruses, and some non-retro viruses, and in certain retrotransposons, as well as telomeres, but not in most of our DNA or cells.

Question 3

True or False: Enhancers bind to DNA at specific sequences to upregulate the expression of genes.

Answer 3

Enhancers are regions/sequences of DNA that attract and are bound to by activators, which then upregulate the expression of genes

Question 4

What do enhancers do?

Answer 4

regions/sequences of DNA that attract and are bound to by activators, which upregulate the expression of genes

Question 5

Are enhancers always in close proximity to the genes that they affect?

Answer 5

No, enhancers can be very far away, and still serve to activate certain genes as the cromatin folds upon itself

Question 6

How do you determine valence electrons?

Answer 6

Counting the number of electrons in a valence (outer) shell.

Question 7

what is a polypeptide bond?

Answer 7

A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O).

Question 8

is a peptide bond covalent?

Answer 8

yes!

Question 9

The phosphoanhydride bonds between three phosphates in ATP are what types of bonds?

Answer 9

covalent

Question 10

The glycosidic bond between glucose and galactose in lactose is what type of bond?

Answer 10

covalent

Question 11

amphipathic

Answer 11

structure/molecule with both hydrophobic and hydrophilic properties

Question 12

polar amino acids are ______

Answer 12

hydrophilic

Question 13

nonpolar amino acids are______

Answer 13

hydrophobic

Question 14

A phospholipid molecule consists of a ______ head and two _______ fatty acid tails. Because of their composition, phospholipids are considered _______ and will spontaneously form bilayers or micelles in water.

Answer 14

polar, non-polar, amphipathic

Question 15

phospholipid _______

Answer 15

bilayer

Question 16

3 parts of hydrophilic head of phospholipid molecule

Answer 16

polar group(choline), phosphate, glycerol

Question 17

ATP stands for

Answer 17

adenoshine triphosphate

Question 18

what is the basis for a van der Waals attraction

Answer 18

form of electrical attraction caused by fluctuating electric charges whenever two atoms are a vier short distance apart

Question 19

3 functions of the plasma membrane (phospholipid bilayer)

Answer 19

receiving information (communication), import and export of molecules, cell growth and motility

Question 20

most common phospholipid in most molecules

Answer 20

phosphatidylcholine

Question 21

proteins account for ___ of the mass of most plasma membranes

Answer 21

50%

Question 22

are transmembrane proteins hydrophobic?

Answer 22

they’re amphipathic

Question 23

a polypeptide chain will usually cross the bilayer as what secondary structure?

Answer 23

Alpha helix

Question 24

T/F - Energy from ATP is required to repair membrane tears.

Answer 24

False - membrane is self repairing/sealing

Question 25

T/F? - The fluidity of a membrane does not depend on temperature, but it does depend on the structure of the hydrocarbon tails.

Answer 25

False - depends on temp and structure

Question 26

T/F ? - Bilayers that contain a large proportion of unsaturated hydrocarbon tails are more fluid than those with lower proportions.

Answer 26

False - the opposite is true. cholesterol adds rigidity and structure

Question 27

T/F? - Phospholipids are more likely to move laterally within their monolayer than to flip to the other side of the bilayer.

Answer 27

T - they're highly unlikely to flip, and are much more likely to re-arrange

Question 28

T/F? - The cell membrane allows for the internal and external cellular environments to accumulate different charges.

Answer 28

True

Question 29

3 Stages of cellular metabolism

Answer 29

1: Breakdown of large macromolecules to simple subunits. 2: Breakdown of simple subunits to Acetyl CoA, plus production of small amounts of ATP and NADH 3: Complete oxidation of acetyl CoA to H2o and Co2, making large amounts of ATP in mitochondria

Question 30

What does ADP stand for?

Answer 30

Adenosine diphosphate

Question 31

ATP ____ energy in _____ to become ADP

Answer 31

loses , hydrolysis

Question 32

ADP goes through a ______________ reaction to become ATP

Answer 32

phosphorylation

Question 33

Because ATP loses energy while becoming ADP, it is energetically ________________

Answer 33

favorable

Question 34

ATP hydrolysis is _______ with non-favorable reactions

Answer 34

coupled

Question 35

Any reaction that involves the xfer of a phosphate group to a molecule is called a _______ reaction

Answer 35

phosphorylation

Question 36

phosphorylation is a ________ reaction

Answer 36

condensation

Question 37

Pi

Answer 37

inorganic phosphate

Question 38

ATP hydrolysis yields between ___ and ___kcal/mole of usable energy

Answer 38

11 and 13

Question 39

ADP + Pi =

Answer 39

ATP

Question 40

ADP + Pi to ATP is energetically_________

Answer 40

unfavorable

Question 41

ADP to ATP is a _______ reaction

Answer 41

condensation

Question 42

by itself, is ATP hydrolysis fast or slow

Answer 42

slow, it needs a catalyst to overcome the activation barrier

Question 43

T/F - our cells generate and store large amounts of ATP

Answer 43

False - it is continuously regenerated

Question 44

the opposite of a condensation reaction

Answer 44

hydrolysis

Question 45

heat is energy in its most ________ form

Answer 45

disordered

Question 46

oxidation

Answer 46

addition of oxygen atoms, removal of electrons

Question 47

reduction

Answer 47

addition of electons

Question 48

T/F - The products of ATP hydrolysis are more stable than the reactants because they possess a more positive Gibbs free energy

Answer 48

False, the delta G is negative in this reaction, as the conversion of ATP to ADP + Pi is favorable

Question 49

equation for delta G

Answer 49

G products - G reactants = delta G

Question 50

3 ways that an enzyme serves as a catalyst

Answer 50

1. binding with two molecules and encouraging a reaction. 2. Changing positive/negative charges which results in a reaction. 3. bending or contorting a molecule into a state / structure that favors a reaction

Question 51

An active site in an enzyme includes the _________ and the __________

Answer 51

binding site and catalytic site

Question 52

an enzyme bonds with a ________

Answer 52

substrate

Question 53

allosteric regulation

Answer 53

regulation of protein by the binding of an "effector" to the allosteric site, which is NOT the active site

Question 54

T/F The binding of the regulatory ligand always decreases the catalytic activity of the enzyme.

Answer 54

False - this isn't always the case. The regulatory ligand my increase or decrease the catalytic activity, operating as either activators or inhibitors.

Question 55

T/F - The regulatory ligand binds directly to the active site.

Answer 55

F - the regulatory ligands will bind to the allosteric, or regulatory site.

Question 56

where does glycolysis take place?

Answer 56

the cell cytoplasm

Question 57

which comes first, glycolysis or the citric acid cycle?

Answer 57

glycolysis

Question 58

where does the citric acid cycle take place?

Answer 58

in mitochondria

Question 59

where is acetyl coa produced?

Answer 59

in mitochondria

Question 60

what is used to produce acetyl coa?

Answer 60

pyruvate

Question 61

put these in the correct order: citric acid cycle, pyruvate--> acetyl coa , glycolysis

Answer 61

glycolysis, pyruvate-->acetyl coa, citric acid cycle

Question 62

where does fermentation take place?

Answer 62

the cell's cytoplasm

Question 63

T/F - Many citric acid cycle intermediates are also crucial in producing amino acids, lipids, and nucleotides.

Answer 63

True - it provides the building blocks for many important molecules

Question 64

T/F - The CO2 made from the CAC comes directly from O2.

Answer 64

F - the Co2 will occur in anaerobic conditions, as the CAC turns carbon atoms of the acetyl groups into Co2

Question 65

T/F - The common entry point for both sugars and fatty acids is acetyl CoA.

Answer 65

True

Question 66

What are the products of the CAC?

Answer 66

ATP (GTP), Co2,NADH,FADH2

Question 67

Does the CAC result in Pyruvate?

Answer 67

no