TBL 1 Cells and Organelles Flashcards
Eukaryotic cell size is limited by a minimum and maximum.
The lower limit is __________; whereas the upper limit is __________.
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.
The cell ________ (organelle) is responsible for the control of cellular organisation and all cellular activities.
nucleus
The nucleus is embedded with specialised pore complexes, _________, allowing for the movement of resources to and from the nucleus.
Nuclear pores
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.
nuclear envelope; rough ER
Endosymbiotic theory: _________ and ________ (organelles in eukaryotes) are believed to be derived from the incorporation of prokaryotic cells.
Both of them have their own _______ DNA.
mitochondria and chloroplast; circular DNA
Conventional light microscopes allow us to see up to ___ (units); whereas electron microscope allows us to see up to ___.
Light - micrometres
Electron - nanometres
________ motion is the spontaneous movement of molecules into and out of the cells, and is what allows molecules to diffuse freely.
Brownian motion
__________ converts angiotensin I to bioactive angiotensin II which helps to (increase/decrease) blood pressure.
Angiotensin Converting Enzyme (ACE)
___________ 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.
Glucose-6-phosphatase
__________ (Clinical condition) is an autosomal recessive disorder resulting from G6PD deficiency. (low levels of glucose-6-phosphatase enzyme –> hypoglycaemia)
Von Glerke’s disease
Enzymes act by _________ that impede chemical reactions from happening.
lowering activation energy
The first law of thermodynamics states that
Energy can neither be created nor destroyed. (only converted)
The second law of thermodynamics states that
Any isolated system tends towards entropy/disorderliness. (i.e. degree of disorder can only increase)
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.
take energy from surrounding environment
=> increased disorder as a whole system
________ is the amount of energy within the molecule that can perform useful work at a constant temperature.
Gibbs free energy
delta(G) =
free energy of products - free energy of reactants
Change in Gibbs free energy is a measure of the change in order within the cell and change in entropy of the system.
-
Reactions are spontaneous if delta(G) <0 (exergonic) or >0 (endogenic)?
delta(G) < 0
i.e. free energy of reactants > free energy of products
Do enzymes change the delta(G) of the reaction?
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.
Anabolic reactions are generally energetically unfavourable (i.e. delta(G) <0), so how do cells overcome this problem?
Couple anabolic reactions to energetically favourable reactions like ATP hydrolysis –> delta(G overall) > 0 and is therefore spontaneous.
In ATP hydrolysis, energy is released through the hydrolysis of __________ bonds.
Phosphoanhydride bonds
__________ is the minimum amount of energy that reactants need to possess before the reaction can proceed.
Activation energy
Catalytic amino acid residues within the enzyme participate in the creation/breaking of bonds of substrates by ______________.
altering electron arrangement (redox reactions)
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.
Contortion; transition state
The _________ hypothesis states that the 3D conformation of the substrate is completely and exactly complementary to that of the enzymatic active site.
lock-and-key
=> only bind to one substrate and catalyse one reaction (Substrate specificity)
The ________ hypothesis suggests that the 3D conformation of the substrate is not completely complementary to that of the enzymatic active site.
induced fit
=> accounts for the ability of enzymes to bind to substrates which are structurally/chemically similar
(group specificity)
_______ is a component of tears and nasal secretions and serves as a first line of defence against bacterial infections.
Lysozyme
Lysozyme functions to catalyse ________.
catalyse the hydrolysis of sugar molecules within the bacterial cell walls (cells are induced to undergo lysis and die).
Substrate of lysozyme:
Alternating polysaccharide co-polymers of N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM) - unit structure of bacterial cell walls.
Lysozyme cleaves at the __________ connecting C_ of NAM to C_ of NAG.
cleaves at the B(1,4) glycosidic linkage connecting C1 of NAM to C4 of NAG
Lysozyme (protein enzyme) secondary structure:
both alpha helical and B pleated sheets
Lysozyme (acidic/basic) catalytic amino acid residues:
Glutamate-35 and Aspartic acid-52
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.
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.
The optimum pH for lysozyme enzyme is ___, when Glu-35 is (unionised/ionised) and Asp-52 is (unionised/ionised).
pH 5.0
Glu-35 is unionised; Asp-52 is ionised
Proteins are a group of organic compounds that is composed of ___% of our human body.
20%
Amino acids with positively-charged R groups are (acidic/basic).
Basic (i.e. can accept H+)
Amino acids with negatively-charged R groups are (acidic/basic).
e.g. Asp and Glu (lysozyme)
Acidic (i.e. can donate H+ to form negative charge)
______ (AA) has a 5-membered ring involving backbone N atom, causing steric hindrance in the backbone –> kinks.
Proline
Amino acids can act as buffers (resist small changes to pH) by forming _________.
zwitterions
______ is the only amino acid that is non-chiral.
Glycine
All natural endogenous amino acids are of the ___-form.
Laevorotary (L)-form: i.e. rotates plane polarised light to the left.
Polypeptide chains are formed from the _______ of amino acids. A covalent peptide bond is formed between __________.
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
Proteins will assume a conformation where the folding is of ________ energy, by maximising _______ and _________ bonds.
lowest energy; maximising hydrogen and covalent bonds
_______ bind to partially folded polypeptide chains to ensure that folding continues along the most energetically feasible pathway.
Chaperones
Why are C=O and N-H bonds of each peptide always on the same plane?
Because the C=O bonds on amino acids restrict free rotation
Proteins can be denatured using _____ to break the H bonds in the secondary, tertiary and quaternary structures.
urea
Proteins can be denatured using 2-mercaptoethanol, which breaks _______ bonds.
disulphide bonds
a-helices have hydrogen bonds formed between amino acid residues ___ positions apart. One turn spans ___ amino acid residues, with side chains projecting outwards.
bind to amino acid residues 4 positions away
each span 3.6 AA residues
Amino acids a-helices are ____-handed.
right-handed a-helices (due to L-form AA)
Proline residues terminate the a-helix due to:
large 5-membered ring structure that restricts the C-N bond rotation and prevents hydrogen bond formation —> kink is inserted and helix is terminated.
Disulfide bonds are formed from the _______ of ______ side chains.
oxidation of 2 cysteine amino acid side chains
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.
N-terminal glutamate residues to be modified by vitamin K-dependent carboxylase to form y-carboxyglutamate
For vitamin K to be functional (for vitamin K-dependent carboxylase to work and produce suitable blood clotting factors), it must be reduced by __________.
vitamin K epoxide reductase
_______ is an anti-coagulant drug which prevents blood from clotting.
Warfarin
What is the main mechanism of action of Warfarin?
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.
Phospholipids are ______ (contain both hydrophilic and hydrophobic groups).
amphiphilic
All phospholipids contain __________.
1 glycerol connected to 2 fatty acid chains and 1 phosphate group
Saturated fatty acid chains are (less/more) densely packed.
more densely packed (membrane less fluid)
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.
lecithin
_________ is a membrane constituent which regulates membrane fluidity and permeability depending on the temperature and nature of the membrane.
Cholesterol
The short hydrophobic tail of cholesterol functions to __________.
anchor the cholesterol to the lipid bilayer
The planar steroid ring of cholesterol causes __________.
stiffening of the cell membrane
The polar head of cholesterol functions to ________.
anchor cholesterol to the lipid bilayer via hydrogen bonds with the phospholipid heads.
At low temperatures, cholesterol will (increase/decrease) membrane fluidity by _________.
Increase membrane fluidity by preventing the phospholipids from packing too closely by intercalating between them.
At high temperatures, cholesterol (increases/decreases) membrane fluidity by ___________.
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
Cholesterol (reduces/increases) membrane permeability.
Reduces membrane permeability.
It plugs transient pores between phospholipids.
Membranes are asymmetrical in nature.
- Glycolipids are on the extracellular side of membrane.
- Negative charges are inside the cell.
________ of phospholipids is when lipids diffuse within the monolayer (i.e. swap places).
Lateral diffusion (frequent)
_______ is the process of lipids switching sides in the bilayer.
Flip-flop (rare)
The fluid mosaic model suggests that:
the presence of integral proteins (unilateral/transmembrane) or peripheral proteins which will increase membrane fluidity as it breaks the orderly fashion of the membrane
Fence & Picket model:
Membrane proteins were found to be constrained in their movement.
Proteins were constrained by fences (__________).
Membrane cytoskeleton
=> Actin filaments on cytosolic side of membrane form spaces where proteins can move freely.
DNA is (more/less) stable then RNA due to the ________.
DNA is more stable than RNA due to the lack of -OH group on C2. (less reactive, and allows for closer packing of molecule)
Purines include ______ and ______. They have a __-ringed structure.
Guanine and Adenine; 2-ringed structure
Pyrimidines include ______, ______ and _____. They have a __-ringed structure.
Cytosine, Uracil and Thymine; 1-ringed structure
Nucleosides are nucleotides without _______.
Without phosphate groups
i.e. sugar + base
Up to ___ phosphate groups can be linked to the __’ carbon of the sugar via ________ bonds to form nucleotides.
Up to 3 phosphate groups; linked to C5 of sugar via phosphoester bonds.
DNA and RNA sequences are read from the __’ to __’ direction
5’ to 3’
DNA is a (right/left-) handed double helical structure with antiparallel strands running in opposite directions.
right-handed helical structure
2 DNA strands (to form a single double helix) are held by 2 types of forces:
- Hydrogen bonds between the bases
2. Hydrophobic interactions between adjacent base-pairs (stacking)
__ hydrogen bonds between Adenine and _____.
__ hydrogen bonds between Cytosine and ________.
2 H bonds: A and T/U
3 H bonds:
C and G
To denature DNA, use high temperature or _________.
low salt concentration
To reanneal DNA, use low temperature or __________.
high salt concentration
During interphase, DNA exists as chromatin which has 2 forms:
________ (loosely condensed)
___________ (highly condensed)
Euchromatin (loosely condensed –> Transcriptionally active)
Heterochromatin (highly condensed —> Transcriptionally inactive)
