Biochemistry and cell biology Flashcards
What do atoms consist of, and where are they situated
Protons, neutrons and electrons
Protons and neutrons are tightly packed in the nucleus, whereas electrons orbit the nucleus and
What is the atomic number
Number of protons
what is an elements mass number
Number of protons + number of neutrons
What are isotopes
When the same element contains different numbers of neutrons which changes the atomic mass but not the chemical characteristics
What makes an isotope unstable
It doesn’t want to retain its number of protons/neutrons in its nucleus and can discharge them. This, changes the atomic weight and/or the proton number
What is radiocarbon dating
Carbon 14 decays slowly but is replenished in living organisms. Hence on death 14C decays exponentially and can be used to make determinations of age
What are the three major classes of molecules
Carbohydrates, lipids, proteins
What are carbohydrates
Are molecules containing only carbon, hydrogen and oxygen (often denoted CHO)
What are saccharides
The simplest form of carbohydrate
How are carbohydrates classified, and what are the class
Number of saccharides present
- Monosaccharide = 1 CHO, e.g. glucose
- Disaccharide = 2, e.g. Glucose and fructose
- Oligosaccharide = 3-10, e.g. maltose
- Polysaccharide = greater than 10. E.g. Glycogen
What are monosaccharides function and an example
Has functions in cellular energy production and the building of nucleic acid.
Glucose, fructose, galactose
What are disaccharides and examples
When two monosaccharides combine via a CONDENSATION REACTION
Sucrose, Maltose, Lactose
What are lipids and functions
A group of compounds that are mostly insoluble in water. These are often found in a liquid like oil. They are an essential nutrient for biological function in: Protection, insulation, absorption of fat soluble vitamins, hormone production, form cell membranes
What is the simplest form of lipids
Fatty acids, an organic chain with a carboxyl functional group
What are the three groups of lipids
Triglycerides - Make up the main part of body fat
Phospholipids - Have a phosphate group replacing a fatty acid. Are arranges in bilayers and help transport fats.
Sterols - Cyclic compounds found in grains, nuts and seeds. Sub group of steroids
What is the basic Structure of an amino acid
- An amine group
- Carboxyl group
- An organic side chain
What is a condensation reaction
A reaction that releases hydrogen and oxygen to make water
What is the primary structure
Is the amino acid sequence from N to C terminus
What is the secondary structure
Is the local structural features including alpha helix and beta sheets. These interactions are stabilised by hydrogen bonds.
How is an alpha helix formed
By polar bond interactions between + and – ends of dipoles, which causes the AA chain to begin twisting into a helical structure
How are beta sheets formed
From the angular conformation of the peptide chain causing a zigzag shape
What is the tertiary structure
Is the way the AA chain folds around itself. They consist of many Alpha helixes and beta sheets twisted around each other
What is the quaternary structure
Is the arrangement of subunits and how they interact with one another
What are the two laws of thermodynamics
The total amount of energy within a system and its surroundings is constant, can only be interconverted between forms.
The total entropy (the level of disorder) of a system and its surroundings always increases
What is entropy and Enthalpy
Entropy - The level of disorder of a system
Enthalpy - Is the heat storage capacity of a system
What is the Enthalpy calculation
Enthalpy = internal pressure + (Pressure x Volume)
or
H (J/mol) = E(J) + (P(PA) x V(m3)
Define an endothermic and exothermic reaction
Endo - absorbs heat (energy)
Exo - Emits heat (energy)
What is gibbs free energy and its equation
Gibbs Free Energy is ‘the amount of available energy to do work’ It tells us if a biochemical reaction will occur spontaneously or not.
ΔG = ΔH – (T x ΔS)
ΔG = a change in gibbs free energy (KJ/Mol)
ΔH = A change in enthalpy
T = Temperature (in kelvin, 0 degrees C = -273 kelvin)
ΔS = change in entropy
What can we tell from gibbs free energy calculations
If ΔG is less than 0, it is a spontaneous process
If ΔG is greater than 0, it is not a spontaneous process
What are coupled reactions
They are when an exergonic (catabolic) reaction takes place alongside an endergonic (anabolic) reaction.
What are activated carrier molecules used for
Can stored energy lost as heat, and transfer it as electrons to be used in an endergonic reaction
How is energy obtained in cells
Through the oxidation of organic molecules
What is oxidation and reduction
Oxidation - The loss of an electron
Reduction - The gain of an electron
What are enzymes
Are biological catalysts, that speed up metabolic reactions that occur in the reaction without themselves being altered. They are regenerated at the end of each reaction. They LOWER THE ACTIVATION ENERGY OF A REACTION
How can mutations in enzyme activity disrupt homeostasis
DNA mutation - Disease
AA substitutio
Cell cycle mutations
Phenylketonuria PKU
What environment does enzymatic binding occur in
Polar (no water) to allow for the most effective way of binding
What are the two theories of enzyme/substrate interaction
Lock and Key
Induced fit
What are enzyme cofactors
When some enzymes need another molecule to fully function. E.g:
- Cofactors
- Coenzymes
-Prosthetic groups
How do enzymes lower the activation energy of a reaction
They reduce the energy needed for reactants to come together and react due to them being spatially complimentary via induced fit, and chemically complimentary via the specific amino acid R groups.
What are the 4 catalytic mechanisms
By Approximation
Metal ion
Covalent
Acid Base
What is the enzyme volecity
The initial rate of reaction, that can be used to calculate enzyme activity
What is Vmax and Km
Vmax - Is the rate of the reaction at which the enzyme shows the highest turnover
Km - is a measure of the affinity of the substrate to the enzyme and vice versa.
How does increases in temperature affect the rate of enzyme catalysed reactions
Small Increases - Overcome activation energy and Increase rate in reaction
Increases beyond the optimal Temp - causes rapid decrease in reaction rate as
- Breaks multiple weak bonds
- Alters the active site
- Denatures the protein structure
How does pH affect enzyme activity
Small deviations in pH results in reduced activity. This can cause the ionisation of groups on the active site
Large deviations can cause denaturation
What are the regulatory mechanisms of enzymes
Controlling how many molecules of each enzyme it makes by regulating gene expression
Subcellular compartmentation
Covalent modification to control activity
Change the rate of protein destruction
Binding of small molecules
What is enzymatic regulation
When end products inhibit earlier pathway steps to prevent the build-up of unnecessary metabolites and minimise energy use.
What are the differences between reversible and irreversible inhibition and the different types of inhibition
Reversable inhibitors bind to the enzyme via weak non-covalent interactions like Hydrophobic/ionic
Irreversable ones bind chemically
What are the three types of irreversable inhibitors of enzymes, and how do they affect Km and Vmax
Competitive - Km increase
Non Competitive - Vmax decrease
Uncompetitive - not freeing the enzyme
- Both Vmax and Km decrease
What are catabolic reactions and anabolic reactions
Catabolic, breakdown (oxidation)
anabolic, build up (synthesis)
What are the 4 stages of getting energy from glycogen
Glycolysis
Pyruvate dehydrogenase reaction
TCA
Electron transport chain (oxidative phosphorylation)
What happens in glycolysis
Glucose into pyruvate.
Energy investment - Glucose into 2x G-3-Posphate
Energy payoff - G-3-Phosphate is oxidaised into pyruvate
What are the inputs and output from glycolysis
Input
2 x NAD+
1 glucose molecule
2 ATP
Output
2 pyruvate
2 ATP
2 NADH
What happens in the Bridge (PDH) reaction
The carboxyl group is removed from pyruvate which releases CO2
2C acetyl group is attached to coenzyme A to form Acetyl-CoA
What is the TCA
Is a sequence of biochemical reactions
The Acetyl group from Acetyl CoA is attached to oxaloacetate to form a 6C Citrate molecule. This citrate is then oxidised in a series of steps.
What do we get from the TCA from each acetyl CoA
1 ATP
3 NADH
1 FADH2
What is oxidative phosphorylation
Where the NADH and FADH2 molecules we gained from Glycolysis and the TCA are being converted into ATP, usable energy.
How is oxidative phosphorylation done
via the electron transport chain, where the high energy electrons from NADH and FADH2 are passed from one protein complex in the membrane to another through a series of redox reactions. The energy that is released from these are used to move protons (Hydrogen ions) from one side of the membrane to another, to create a proton gradient used to spin the ATP synthase
What happens to electrons when they get to the other side of the compelx
They meet the final electron acceptor (oxygen) which combines with the electrons and hydrogen ions to form water
How many ions crossing does it take for the ATP synthase to make 1 ATP
4
How many ions cross the Electron transport chain from one glucose molecule
112
How much ATP do we get from one glucose molecule
32
What is produced in anaerobic respiration
Lactate, produced by the reduction of pyruvate in the absence of oxygen
What is lactate used for (2)
- Be taken up by some tissues (e.g. heart) converted to pyruvate and used for energy
- Be transported to the liver – and converted to glucose
What is process of oxidation of fats and lipids
Lipolysis - Breakdown of triglycerides
Activation
Beta oxidation - Oxidation of fatty acyl CoA
What must happen to fatty acyl CoA so it can be oxidised
Must enter the Mitochondria
It uses carnitine as a co-factor and allows its transport in a shuttle like system
What are the 4 steps of beta oxidation
1- Oxidation by FAD
2- Hydration
3- Oxidation by NAD+
4- Thiolysis by CoA
What does each beta oxidation cycle produce
Acyl CoA, NADH and FADH2
What is ketogenesis
The production of ketone bodies by breaking down fatty acids.
If glucose levels are low, oxaloacetate is used in gluconeogenesis, so acetyl CoA builds up.
2 of them snap together to form ketones.
What are ketones used for
Many tissues use ketones in preference to glucose (heart and Kidney) and even the brain does during starvation. They can also be converted back to acetyl CoA to enter the TCA cycle.
How are Amino acids oxidised
Transamination
Deamination
Urea Cycle
What does Transamination and hence urea cycle produce
Transamination - Apspartic acid which is used in the urea cycle
Urea - makes urea that goes to the blood and Fumerate which enters the TCA or is used to regenerate glucose
How is glycolysis regulated
By phosphofructokinase
The binding of regulatory molecules to the allosteric site can increase or decrease the affinity of PFK for fructose 6-Phosphate.
How is the TCA regulated
The rate of the TCA cycle is matched to the cells energy needs. To do this, two enzymes can be allosterically regulated:
* ISOCITRATE DEHYDROGENASE
Is stimulated by – ADP, NAD+, Isocitrate
Is Inhibited by – ATP, NADH
- ALPHA-KETOGLUTERATE DEHYDROGENASE
IS stimulated by ADP
IS inhibited by Succinyl CoA, ATP, NADH
What is gluconeogenesis
Is the formation of glucose from non-carbohydrate precursors, it is essentially the reverse of glycolysis.
What is fatty acid synthesis
Is the elongation of the fatty acid chains by the sequential addition of 2Carbon units derived from Acyl CoA.
What regulates fatty acid synthesis
AMPK
Which are activated protein kinases that can sense the energy levels of cells
When levels are low it phosphorylates acyl CoA Carboxylase and inactivates it
How is Acyl CoA transfered from the mitochondira to the cytosol
Acetyl CoA is converted to citrate via the TCA, which is then transported to the cytosol where citrate lyase converts it to oxaloacetate, which regenerates Acetyl CoA
What is the pentose phosphate pathway (PPP)
Is a process that branches off from the upper part of glycolysis and is used to create sugars in DNA and RNA
What are the two pathways of the PPP and what do they generate
Oxidative = Glucose-6-P becomes Ribulose-5-P, which generates 2x NADH
Non-oxidative = Ribose-5-P to 2x Fructose-6-P and 1x Glyceride 3-Phosphate which are glycolysis intermediates
How is the PPP regulated
Its regulation is coordinated with Glycolysis
The PPP is also regulated by the cells requirement for ATP and ribose 5-Phosphate.
What is the mitochondrial genome
Is a single circular chromosome in the mitochondrial matrix. It has 37 genes in total: 2 rRNA, 22 tRNA and 13 that are protein encoding
How do MtDNA copies increase and decrease
Fussion - When two mitochondria merge their inner and outer compartments to make a single compartment
Fission - When the mitochondria split into smaller organelles or fragments
What are mitochondrial ribosomes formed from
A 12S rRNA and a 16S rRNA form together to make mitochondrial 55S ribosomes
What does the S stand for in mitochondrial ribosomes sub units
Stands for svedberg units, which is how long it takes for a substance to fall to the bottom of the tube when centrifuged.
How did mitochondria originate
Via enosymbiosis - where it was englufed by an aerobic bacterium.
What allows entry into the mitochondria through its two membranes
TOM - allows certain proteins into the intermembrane space
TIM = llows those molecules into the matric and controls passage through the inner mitochondrial membrane.
How do TOM and TIM transport
They both recognise signal sequences on specific proteins and allow entry by pulling the chain through the complex.
Which mitochondrial intermediates need to be entered into the mitochondira
Pyruvate, NADH, Fatty acids
Functions of membranes (5)
Physical and chemical barrier
Communication
Recognition
Energy conservation
Platform for cellular processes
What are the 4 ways phospholipids can moev
Lateral diffusion
Flexion
Rotation
Flip Flop
How is membrane fluidity regulated
- If the hydrocarbon chain is saturated or unsaturated
- If cholesterol is present
What are protein rafts
They form when Proteins often congretgate to lipid raft regions in preperation for vesicular budding and transport. They acts as an organizing centers for assembly of signaling molecules.
What are the ways proteins can interact with the membrane (9)
1- Alphe helix’s
2- Single Pass
3- MultiPass
4- Beta sheets
5- Covalently bonded to a lipid
6- Embedded in the membrane
7- Non-covalent attached to integral membrane proteins.
8- Integral/Transmembrane
9- Peripheral
How do the following molecules react with the membrane:
Non polar
Small uncharged
Large uncharged
Ions
Non polar - Easily diffuse
Small uncharged - Ok but slowly
Large uncharged - Need a transporter of some sort
Ions - Need specialized mechanisms
What are the two types of transport proteins
Carrier proteins – These bind a solute and undergo a conformational change
Channel proteins – These interact only weakly with the solute, and form aqueous pore solutes
What is at the top of membrane channels
a selective filter, choosing by size and charge
What dictates the direction of flow through a channel protein
Concentration gradient, but if it is an ion then it is a combination of charge and conc gradient
Where do active transport carriers get their energy from
Light energy (in bacteria)
Energy released from the transfer of electrons
ATP hydrolysis
What are the two types of Active transport mechanisms in eukaryotes?
Coupled carriers - Symport and antiport simultaneously
ATP driven pumps - Uses free energy released by ATP hydrolysis to power transport
What are the functions of the cytoskeleton
Celluler shape, strength and movement
What are the three types of filaments in the cytoskeleton
Actin filaments
Intermediate filaments
Microtubules
What do actin filaments do
Allow cell movement and aid the shape of the cells surface.
What do intermediate filaments do
Provide mechanical strength, have very diverse characteristics
What do microtubules do
Allow the movement of cargo and organelles within the cell and form the mitotic spindle.
How is actin formed
By the polymerization of globular actin molecules. Non covalent bonds form between the adjacent molecules to form a protofilament. 2 of them twist to form an alpha helix
How does actin filaments and microtubules extend
Via polymerisation and depolymerisation by treadmilling
Units at the plus end are added faster whilst units at the minus end dissociate faster.
The overall length of the actin remains constant
What is the centrosome
A region of the cell contiaining, a pair of centrioles surrounded by a matrix of proteins called pericentriolar material.
It contains the MTOC, which organises microtubules and cell division
What are the three families of macromolecules that make up the extracellular matrix
Glycosaminoglycans (GAG’s)
Fibrous proteins
Glycoproteins
What are the three types of cell junctions
Anchoring
Occluding
Communication
What do anchoring junctions do, and what are the two types of proteins
Anchor the cytoskeleton between cells or between cells and the ECM
Cadherins = cell to cell attachment
Integrins = cell to matrix attachments
What do occluding cell junctions do
Prevent the passage of ions and small molecules between adjoining epithelial cells, by creating a tight seal
What do communicating junctions do
Provide direct connections between the cytoplasm of two cells, typically gap junctions
What are important features of all cell junctions
Actin filaments to enable microvilli formation
Actin connects the the junctions as a physical barrier
Intermediate filaments anchor across the cell providing structure and strength - called desmosomes
What does the nucleus contain
Histones
Nucleosomes
Chromatin
Chromosomes
Sister chormatids
What are histones
Proteins that bind to DNA to form eukaryotic chromosomes.
What are nucleosomes
Protein DNA complex containing 8 histone proteins that are the most basic level of chromosome packaging.
What occurs in the nucleus
RNA synthesis and Transcription
What is the nucleolus
An area of the nucleus that function is to produce and assemble the cells chromosomes
What is the nuclear envelope
Is on the edge of the nucleus
Is a double membrane that seperates the nucleus from the cytoplasm.
It is continous with the RER and SER
How are macromolecules imported and exported from the nucleus
Via nuclear pore complexes
Describe the structure of nuclear pore complexes
They are a large quaternary protein structure, that contains an aqueous channel that connects the nucleoplasm to the cytosol.
They have a cage like structure on the nucleus side and long cytosolic fibrils that reach into the cytosol. They can transfer in both directions simultaneously
What are the functions of the SER and RER
SER - is involved in lipid synthesis
(also steroid hormone synthesis and detoxification)
RER - Is the site of protein synthesis and processing of transmembrane proteins.
What are the two types of ribosome in protein sorting
Membrane bound - synthesis of proteins that are being concurrently translocated into the ER
Free - Synthesis all other proteins
What are the steps of protein synthesis in the ER
1- Translation occurs in the cytosol
2- mRNA is synthesised by multiple ribosomes
3- Ribosomal sub-unit binds with mRNA and the protein is synthesized from the RNA code
4- It emerges from the ribosome with a specific signal sequence to indicate where it needs to go in the cell.
What is co-translational translocation
When in mammalian cells, most proteins are transported to the ER during protein synthesis
What do chaperone proteins do
Bind and escort other proteins to prevent damage
What are the two Post Translational Modifications that can occur
Folding into its 3D conformation
Glycosylation
What is protein Glycosylation
The addition of a sugar to a protein
is very specific to proteins that enter the Er due to Quality control, recognition and protection
What is glycosylation useful for
Quality control
The free glucose at the end of Oligosaccharides are used to identify proteins that are folded correctly or incorrectly.
What happens when calnexin binds to a misfolded protein
Calnexin binds to misfolded to give another chance to fold correctly.
IF it then folds correctly, it exits the ER, if it doesn’t, the cycle happens again, and adds a glucose residue.
If this time It doesn’t fold correctly it’ll be sent for degradation.
What is the UNFOLDED PROTEIN RESPONSE
Is triggered when misfolded proteins accumulate in the cell it causes ER stress.
It:
- Inhibits protein synthesis
- Degrades the misfolded protein
- Increases the transcription of chaperones
If the protein persists apoptosis is induced
What are the 3 types of vesicles that aid the transport of proteins
COP I coated vesicles=Transport from the golgi
COP II coated vesicles=Transport from the ER
Clattherin coated vesivles=transport from the plasma membrane and between golgis and endosomes
What is RAB GTP -
Is a GTP binding protein and GTPase found on the cytosolic surface of vesicles. They cycle between active and inactive form and bind to rab effector proteins on the target membrane, which tethers the vesicle to the membrane.
How does the membrane fuse to allow cargo to reach its target organelle
Via snare proteins.
V-Snares (vesicle) and T-snares (target) are specific to one another which provides a layer of specificity. They wrap around each other to form a stable trans-snare complex
What is the golgi apperatus and its purpose
Is a stack of flattened membrane enclosed compartments termed cisternae
To further process oligosaccharides chains by promoting the formation of protein.
What are lysosomes
Are degradative organelles meaning they digest unwanted material. They contain a lot of enzymes to breakdown the macromolecules.
How do lysosomes degrade and recycle ingested material
Degredation - It moves towards the centre of the cell and the membranes composition alters. Degredation begins
Recycled - Vesicles containing material for recycling to the plasma membrane bud off and fuse with a recycling endosome.
