TBL 1 Cells and Organelles

Question 1

Eukaryotic cell size is limited by a minimum and maximum.

The lower limit is __________; whereas the upper limit is __________.

Answer 1

Lower limit: Least cell volume required to fit all organelles

Upper limit: Maximum volume such that the surface area-to-volume ratio for exchange of substances is not compromised.

Question 2

The cell ________ (organelle) is responsible for the control of cellular organisation and all cellular activities.

Answer 2

nucleus

Question 3

The nucleus is embedded with specialised pore complexes, _________, allowing for the movement of resources to and from the nucleus.

Answer 3

Nuclear pores

Question 4

The nucleus has a DOUBLE membrane (__________) that becomes continuous with the __________(organelle), allowing for continuous passage of mRNA to ribosomes embedded in the membrane of the ER.

Answer 4

nuclear envelope; rough ER

Question 5

Endosymbiotic theory: _________ and ________ (organelles in eukaryotes) are believed to be derived from the incorporation of prokaryotic cells.
Both of them have their own _______ DNA.

Answer 5

mitochondria and chloroplast; circular DNA

Question 6

Conventional light microscopes allow us to see up to ___ (units); whereas electron microscope allows us to see up to ___.

Answer 6

Light - micrometres

Electron - nanometres

Question 7

________ motion is the spontaneous movement of molecules into and out of the cells, and is what allows molecules to diffuse freely.

Answer 7

Brownian motion

Question 8

__________ converts angiotensin I to bioactive angiotensin II which helps to (increase/decrease) blood pressure.

Answer 8

Angiotensin Converting Enzyme (ACE)

Question 9

___________ is responsible for the removal of phosphate from glucose-6-phosphate to increase the bioavailability of glucose. It cleaves phosphate to allow the release of glucose into the bloodstream when the blood glucose level is low.

Answer 9

Glucose-6-phosphatase

Question 10

__________ (Clinical condition) is an autosomal recessive disorder resulting from G6PD deficiency. (low levels of glucose-6-phosphatase enzyme –> hypoglycaemia)

Answer 10

Von Glerke’s disease

Question 11

Enzymes act by _________ that impede chemical reactions from happening.

Answer 11

lowering activation energy

Question 12

The first law of thermodynamics states that

Answer 12

Energy can neither be created nor destroyed. (only converted)

Question 13

The second law of thermodynamics states that

Answer 13

Any isolated system tends towards entropy/disorderliness. (i.e. degree of disorder can only increase)

Question 14

Biological systems are very well-ordered - they follow the second law of thermodynamics by taking energy from the _________ surrounding the cell and investing it in chemical reactions which maintain order.

Answer 14

take energy from surrounding environment

=> increased disorder as a whole system

Question 15

________ is the amount of energy within the molecule that can perform useful work at a constant temperature.

Answer 15

Gibbs free energy

Question 16

delta(G) =

Answer 16

free energy of products - free energy of reactants

Question 17

Change in Gibbs free energy is a measure of the change in order within the cell and change in entropy of the system.

Answer 17

-

Question 18

Reactions are spontaneous if delta(G) <0 (exergonic) or >0 (endogenic)?

Answer 18

delta(G) < 0

i.e. free energy of reactants > free energy of products

Question 19

Do enzymes change the delta(G) of the reaction?

Answer 19

No. Spontaneous reactions (i.e. delta(G) <0) might not proceed due to slow kinetics, so enzymes are used to speed up the rate without changing delta(G) of the reaction.

Question 20

Anabolic reactions are generally energetically unfavourable (i.e. delta(G) <0), so how do cells overcome this problem?

Answer 20

Couple anabolic reactions to energetically favourable reactions like ATP hydrolysis –> delta(G overall) > 0 and is therefore spontaneous.

Question 21

In ATP hydrolysis, energy is released through the hydrolysis of __________ bonds.

Answer 21

Phosphoanhydride bonds

Question 22

__________ is the minimum amount of energy that reactants need to possess before the reaction can proceed.

Answer 22

Activation energy

Question 23

Catalytic amino acid residues within the enzyme participate in the creation/breaking of bonds of substrates by ______________.

Answer 23

altering electron arrangement (redox reactions)

Question 24

Stressing bonds i.e. ________ of substrate molecules into a certain shape causes them to resemble the _________, which is a particular conformation where atoms are rearranged geometrically and electrically so they are more susceptible to reaction.

Answer 24

Contortion; transition state

Question 25

The _________ hypothesis states that the 3D conformation of the substrate is completely and exactly complementary to that of the enzymatic active site.

Answer 25

lock-and-key | => only bind to one substrate and catalyse one reaction (Substrate specificity)

Question 26

The ________ hypothesis suggests that the 3D conformation of the substrate is not completely complementary to that of the enzymatic active site.

Answer 26

induced fit => accounts for the ability of enzymes to bind to substrates which are structurally/chemically similar (group specificity)

Question 27

_______ is a component of tears and nasal secretions and serves as a first line of defence against bacterial infections.

Answer 27

Lysozyme

Question 28

Lysozyme functions to catalyse ________.

Answer 28

catalyse the hydrolysis of sugar molecules within the bacterial cell walls (cells are induced to undergo lysis and die).

Question 29

Substrate of lysozyme:

Answer 29

Alternating polysaccharide co-polymers of N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM) - unit structure of bacterial cell walls.

Question 30

Lysozyme cleaves at the __________ connecting C_ of NAM to C_ of NAG.

Answer 30

cleaves at the B(1,4) glycosidic linkage connecting C1 of NAM to C4 of NAG

Question 31

Lysozyme (protein enzyme) secondary structure:

Answer 31

both alpha helical and B pleated sheets

Question 32

Lysozyme (acidic/basic) catalytic amino acid residues:

Answer 32

Glutamate-35 and Aspartic acid-52

Question 33

Structure and function of lysozyme: _____ (AA) protonates oxygen in the glycosidic bond, breaking the bond holding the sugar molecules together. Water molecule enters and is deprotonated by _____. _____ (AA) stabilises the positive charge in the transition state, while the OH- ion attacks the ____ carbocation to add a -OH group.

Answer 33

Glu-35 protonates oxygen, breaking bond. Glu-35 accepts H+ from H2O, forming OH-. Asp-52 stabilises positive charge, while -OH ion attacks the NAM carbocation to add a OH group.

Question 34

The optimum pH for lysozyme enzyme is ___, when Glu-35 is (unionised/ionised) and Asp-52 is (unionised/ionised).

Answer 34

pH 5.0 | Glu-35 is unionised; Asp-52 is ionised

Question 35

Proteins are a group of organic compounds that is composed of ___% of our human body.

Answer 35

20%

Question 36

Amino acids with positively-charged R groups are (acidic/basic).

Answer 36

Basic (i.e. can accept H+)

Question 37

Amino acids with negatively-charged R groups are (acidic/basic). e.g. Asp and Glu (lysozyme)

Answer 37

Acidic (i.e. can donate H+ to form negative charge)

Question 38

______ (AA) has a 5-membered ring involving backbone N atom, causing steric hindrance in the backbone --> kinks.

Answer 38

Proline

Question 39

Amino acids can act as buffers (resist small changes to pH) by forming _________.

Answer 39

zwitterions

Question 40

______ is the only amino acid that is non-chiral.

Answer 40

Glycine

Question 41

All natural endogenous amino acids are of the ___-form.

Answer 41

Laevorotary (L)-form: i.e. rotates plane polarised light to the left.

Question 42

Polypeptide chains are formed from the _______ of amino acids. A covalent peptide bond is formed between __________.

Answer 42

condensation of amino acids covalent peptide bond formed between the amine group of one amino acid and the carboxyl group of the other amino acid

Question 43

Proteins will assume a conformation where the folding is of ________ energy, by maximising _______ and _________ bonds.

Answer 43

lowest energy; maximising hydrogen and covalent bonds

Question 44

_______ bind to partially folded polypeptide chains to ensure that folding continues along the most energetically feasible pathway.

Answer 44

Chaperones

Question 45

Why are C=O and N-H bonds of each peptide always on the same plane?

Answer 45

Because the C=O bonds on amino acids restrict free rotation

Question 46

Proteins can be denatured using _____ to break the H bonds in the secondary, tertiary and quaternary structures.

Answer 46

urea

Question 47

Proteins can be denatured using 2-mercaptoethanol, which breaks _______ bonds.

Answer 47

disulphide bonds

Question 48

a-helices have hydrogen bonds formed between amino acid residues ___ positions apart. One turn spans ___ amino acid residues, with side chains projecting outwards.

Answer 48

bind to amino acid residues 4 positions away | each span 3.6 AA residues

Question 49

Amino acids a-helices are ____-handed.

Answer 49

right-handed a-helices (due to L-form AA)

Question 50

Proline residues terminate the a-helix due to:

Answer 50

large 5-membered ring structure that restricts the C-N bond rotation and prevents hydrogen bond formation ---> kink is inserted and helix is terminated.

Question 51

Disulfide bonds are formed from the _______ of ______ side chains.

Answer 51

oxidation of 2 cysteine amino acid side chains

Question 52

Many blood clotting factors contain N-terminal glutamate residues that must be modified by __________ via a carboxylation reaction to form ________ which enhances the calcium-binding capabilities of the factor.

Answer 52

N-terminal glutamate residues to be modified by vitamin K-dependent carboxylase to form y-carboxyglutamate

Question 53

For vitamin K to be functional (for vitamin K-dependent carboxylase to work and produce suitable blood clotting factors), it must be reduced by __________.

Answer 53

vitamin K epoxide reductase

Question 54

_______ is an anti-coagulant drug which prevents blood from clotting.

Answer 54

Warfarin

Question 55

What is the main mechanism of action of Warfarin?

Answer 55

It inhibits vitamin K epoxide reductase, thereby reducing the levels of functional Vitamin K, impairing the function of vitamin K-dependent carboxylase. The enzyme therefore cannot carboxylate glutamate to form y-carboxyglutamate, reducing calcium-binding capability and reduced blood clotting.

Question 56

Phospholipids are ______ (contain both hydrophilic and hydrophobic groups).

Answer 56

amphiphilic

Question 57

All phospholipids contain __________.

Answer 57

1 glycerol connected to 2 fatty acid chains and 1 phosphate group

Question 58

Saturated fatty acid chains are (less/more) densely packed.

Answer 58

more densely packed (membrane less fluid)

Question 59

Phosphatidylcholine (also known as _______) is a common phospholipid in the membrane bilayer. It is found as a lung surfactant to reduce surface tension of small alveoli.

Answer 59

lecithin

Question 60

_________ is a membrane constituent which regulates membrane fluidity and permeability depending on the temperature and nature of the membrane.

Answer 60

Cholesterol

Question 61

The short hydrophobic tail of cholesterol functions to __________.

Answer 61

anchor the cholesterol to the lipid bilayer

Question 62

The planar steroid ring of cholesterol causes __________.

Answer 62

stiffening of the cell membrane

Question 63

The polar head of cholesterol functions to ________.

Answer 63

anchor cholesterol to the lipid bilayer via hydrogen bonds with the phospholipid heads.

Question 64

At low temperatures, cholesterol will (increase/decrease) membrane fluidity by _________.

Answer 64

Increase membrane fluidity by preventing the phospholipids from packing too closely by intercalating between them.

Question 65

At high temperatures, cholesterol (increases/decreases) membrane fluidity by ___________.

Answer 65

Cholesterol decreases membrane fluidity at high temperatures by forming hydrophobic interactions with the hydrophobic tails of the phospholipids --> interfering with chain flexing and lateral diffusion

Question 66

Cholesterol (reduces/increases) membrane permeability.

Answer 66

Reduces membrane permeability. It plugs transient pores between phospholipids.

Question 67

Membranes are asymmetrical in nature.

Answer 67

- Glycolipids are on the extracellular side of membrane. | - Negative charges are inside the cell.

Question 68

________ of phospholipids is when lipids diffuse within the monolayer (i.e. swap places).

Answer 68

Lateral diffusion (frequent)

Question 69

_______ is the process of lipids switching sides in the bilayer.

Answer 69

Flip-flop (rare)

Question 70

The fluid mosaic model suggests that:

Answer 70

the presence of integral proteins (unilateral/transmembrane) or peripheral proteins which will increase membrane fluidity as it breaks the orderly fashion of the membrane

Question 71

Fence & Picket model: Membrane proteins were found to be constrained in their movement. Proteins were constrained by fences (__________).

Answer 71

Membrane cytoskeleton | => Actin filaments on cytosolic side of membrane form spaces where proteins can move freely.

Question 72

DNA is (more/less) stable then RNA due to the ________.

Answer 72

DNA is more stable than RNA due to the lack of -OH group on C2. (less reactive, and allows for closer packing of molecule)

Question 73

Purines include ______ and ______. They have a __-ringed structure.

Answer 73

Guanine and Adenine; 2-ringed structure

Question 74

Pyrimidines include ______, ______ and _____. They have a __-ringed structure.

Answer 74

Cytosine, Uracil and Thymine; 1-ringed structure

Question 75

Nucleosides are nucleotides without _______.

Answer 75

Without phosphate groups | i.e. sugar + base

Question 76

Up to ___ phosphate groups can be linked to the __' carbon of the sugar via ________ bonds to form nucleotides.

Answer 76

Up to 3 phosphate groups; linked to C5 of sugar via phosphoester bonds.

Question 77

DNA and RNA sequences are read from the __' to __' direction

Answer 77

5' to 3'

Question 78

DNA is a (right/left-) handed double helical structure with antiparallel strands running in opposite directions.

Answer 78

right-handed helical structure

Question 79

2 DNA strands (to form a single double helix) are held by 2 types of forces:

Answer 79

1. Hydrogen bonds between the bases | 2. Hydrophobic interactions between adjacent base-pairs (stacking)

Question 80

__ hydrogen bonds between Adenine and _____. __ hydrogen bonds between Cytosine and ________.

Answer 80

2 H bonds: A and T/U 3 H bonds: C and G

Question 81

To denature DNA, use high temperature or _________.

Answer 81

low salt concentration

Question 82

To reanneal DNA, use low temperature or __________.

Answer 82

high salt concentration

Question 83

During interphase, DNA exists as chromatin which has 2 forms: ________ (loosely condensed) ___________ (highly condensed)

Answer 83

Euchromatin (loosely condensed --> Transcriptionally active) Heterochromatin (highly condensed ---> Transcriptionally inactive)