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What are the most stably stacked proteins?
Transmembrane proteins
Which of the following is not part of the endomembrane system: peroxisomes, mitochondria, Golgi apparatus, nuclear envelope or plasma membrane?
What's one purpose of glycosylation?
to aid in cell surface recognition through determining protein structure
In a plant cell, which organelle provides the cell with a supply of energy?
In Frye and Edidin's experiment to verify the lateral movement of transmembrane proteins using hybrid cells formed from a mixture of mouse and human cells, why did the cells which were cooled to 0oC show no movement of transmembrane proteins?
it was too cold so movement was inhibited due to membrane solidity
How are peripheral membrane proteins bonded to the cell membrane?
hydrogen and/or ionic bonds
what is the main function of the plasma membrane in an animal cell?
controls movement of substances in and out of the cell, site of cell signalling
the plasma membrane is made up of what components?
proteins, lipids and carbohydrates
What allows for the best resolution in a light microscope?
When the illumination source has a shorter wavelength
in TEM, what is true about the stain that is used on the biological sample?
The stain consists of heavy metals
Who discovered cells and how?
Robert Hooke, looking at cork using a self designed compound microscope
What are the 4 basic concepts of cell theory?
Cells only arise through mitosis of existing cells. They are the functioning unit of life, capable of independent life under certain conditions and contain inherited DNA
Compare eukaryotic and prokaryotic DNA
Eukaryotic DNA is linear and contained within a nucleus, whereas prokaryotic DNA is circular and contained within a nucleus and sometimes plasmids. Eukaryotic DNA is associated with histone proteins whereas prokaryotic DNA is not.
Describe the shape and location of squamous epithelial cells
Flat and very thin, found lining surfaces such as bronchioles
Describe the shape and location of cuboidal epithelial cells
cube shaped, found in tissues responsible for secretion and absorption
Describe the shape and location of columnar epithelial cells
long and thin, found in areas which secrete mucus
location and function of simple squamous epithelial cells
found lining blood/lymphatic vessels and air sacs, for lubrication and diffusion
location and function of simple cuboidal epithelial cells
found in ducts and secretory areas of glands and kidney tubules for secretion and absorption
location and function of simple columnar epithelial cells
makes up ciliated tissue in bronchi, uterus and smooth tissue in digestive tract and bladder to absorb and secrete enzymes and mucus
location and function of pseudostratified columnar epithelial cells
lines trachea and most of upper respiratory tract to secrete and move mucus
location and function of stratified squamous epithelial cells
found in oesophagus, mouth and vagina to protect from abrasion
location and function of stratified cuboidal epithelial cells
protective tissue found in sweat, salivary and mammary glands
location and function of transitional epithelial cells
found in bladder, urethra and ureter lining so urinary organs can expand and stretch
describe the structure of connective tissue and where it's found
made up of many cell types and found throughout the body with either no blood supply or is highly vascularised, made up of ground substance, fibres and cells
Connective tissue function
support, protect, insulate, store fuel and transport
define amphiphatic
contains both hydrophilic and hydrophobic parts
basic functions of the cell membrane
protection from surroundings, create optimum environment for cellular functions, cell signalling, cell adhesion to other cells and the ECM
lateral movement of phospholipids
passive, frequent process which occurs within the layer as the phospholipids aren't bound together (semifluid membrane)
flip flop of lipids
active process requiring ATP where phospholipids flip from one leaflet (layer) to the other
what is the function of cholesterol
regulates fluidity of membrane, making bilayer stronger, more flexible and less permeable to hydrophilic molecules
Where are transmembrane proteins found?
part(s) are physically embedded in the fatty acid portion of the membrane. The transmembrane section is folded into an alpha helix
structure of lipid anchored proteins
amino acid is covalently bonded to a lipid
examples of lipid anchored proteins
G proteins and some kinases
where are peripheral/extrinsic proteins found?
on the membrane surface only
are peripheral proteins a permanent part of the membrane?
No, they can attach and remove themselves from the membrane eg hormones
What is the first law of thermodynamics?
energy can be neither created or destroyed, only changed from one form to another. Therefore the total energy content of the universe remains the same
What is the second law of thermodynamics?
the universe tends towards disorder/entropy tends to a maximum
what increases entropy?
increasing temperature and increasing the number of particles in a system
Are cells at higher or lower entropy than their compartments?
the cell is at lower entropy but higher energy level than all its compartments
how do cells gain energy?
by oxidising compounds such as glucose and releasing heat and CO2 to the surroundings, increasing entropy
what is the transition state
has higher free energy than either reactants or products, so is the least stable species in the pathway.
What is the free energy between the substrate and transition state?
activation energy
how do enzymes lower activation energy?
by providing a different route for the reaction to occur, acting as a catalyst
define catalysis
specific stabilisation of the transition state of a reaction
what is metabolism?
conversion of different chemicals in the body by catabolism (break down) or anabolism (build).
What metabolic pathways are most efficient?
Cyclic or spiral metabolic pathways
What are the 4 different structures of metabolic pathway?
linear, branched, cyclic or spiral
How are metabolic pathways regulated?
switching genes which code for enzymes/regulate enzymes on or off, negative and positive feedback
allosteric regulation
molecule binds to one enzyme site to affect another site and either activate or inhibit an enzyme. Binding of activators stabilises the active form whereas inhibitors binding stabilises the inactive form
How do allosterically regulated enzymes differ in structure from other enzymes?
quaternary structure
define cooperativity
Allosteric regulation that increases enzyme activity. A substrate binds making the enzyme more able to bind other substrates at other sites
What is neurospora crassa and what is it used for?
common pink mould often used in genetic research as it can reproduce asexually, creating haploid spores meaning recessive mutations aren't masked
what is minimal medium
contains basic essential nutrients: sugar, nitrogen source, mineral ions and vitamins. Neurospora is able to make all other compounds it needs
what is complete medium?
minimal medium + all amino acids
What did Beedle and Tatum do?
Grew Neurospora on minimal medium and exposed it to xray to induce mutations then cultured each spore in complete medium for a next gen. They took subcultures of the next generation to see if they'd grow in minimal medium. Some couldn't therefore were lacking enzymes to make certain amino acids
depurination of bases
purine base completely detaches from the sugar. This can be caused by heat and could lead to insertion of the wrong bases during replication
What happens in base excision repair?
A damaged base is removed by DNA glycosylase and the sugar phosphate removed by AP endonuclease. New nucleotides are added by DNA polymerase then joined by DNA ligase
harmless genetic differences usually found outside of coding regions
What causes cystic fibrosis?
mutation in the CFTR gene leading to non functional protein so chloride ions aren't pumped out of lung cells, water remains in the cells and lungs aren't kept moist. Mucus also is very thick leading to infections and other damage
how do some diseases evade natural selection?
Many diseases only show after childbearing age and Sometimes having one copy of a recessive allele is advantageous (sickle cell anaemia)
Sickle cell anaemia
Single amino acid mutation in Hb beta globulin chain creating HbS rather than HbA In low oxygen, HbS forms crystals which distorts RBC shape
What are mitochondria?
Energy-converting organelles found in eukaryotic cells. They produce 2.5% of their own proteins as they contain circular DNA and 70S ribosomes.
describe oxidative phosphorylation
Reduced NAD is oxidised releasing electrons that are transferred to NADH dehydrogenase (complex I). Electrons are transferred to coenzyme Q then complex III. Reduced FAD is also oxidised and electrons transferred to complex II then coenzyme Q. The energy is used to pump H+ across the inner membrane. H+ then moves down its electrochemical gradient via ATP synthase, driving ATP synthesis. The electrons and H+ are transferred to oxygen, which acts as the final electron acceptor, forming water.
how does cyanide affect mitochondria?
Inhibits complex IV, preventing electrons being transported from cytochrome C to oxygen, disrupting the electron transport chain so aerobic production of ATP ceases
what is alkaptonuria?
Lack of homogentisic acid oxidase -> dark brown urine. Tyrosine and phenylalanine aren’t broken down homogentisic acid builds up
What is phenylketonuria?
Lack of phenylalanine hydroxylase so phenylalanine accumulates in blood leading to mental retardation.
which amino acids have aromatic R groups?
phenylalanine, tryptophan, tyrosine, histodine
amino acids with non polar R groups
proline, phenylalanine, tryptophan, leucine, methionine, isoleucine, glycine, alanine, valine
polar R groups
tyrosine, histidine, lysine, arginine, serine, threonine, cysteine, asparagine, glutamine, aspartate, glutamate
positively charged R groups
histidine, lysine, arginine
negatively charged R groups
aspartate, glutamate
essential amino acids
histidine, lysine, threonine, phenylalanine, tryptophan, leucine, methionine, isoleucine, valine
amino acids containing OH
tyrosine, serine, threonine
amino acids containing S
methionine and cysteine
What is pyruvate dehydrogenase complex (PDC)?
multienzyme, supramolecular machine found in both prokaryotes and eukaryotes, involved in converting pyruvate into acetyl CoA, in which pyruvate is oxidatively carboxylated
How is pyruvate's acetate unit activated?
linking it to Coenzyme A, so that it can then undergo further reactions
what happens during mitochondrial oxidative decarboxylation of pyruvate?
carbon atoms of carbohydrates and amino acids committed to oxidation via the TCA cycle or to the synthesis of fatty acids
when does mitochondrial oxidative decarboxylation of pyruvate occur?
only occurs if ATP is needed or two-carbon fragments are required for fatty acid biosynthesis
how is oxidative decarboxylation of pyruvate controlled?
allosterically and by phosphorylation
What are the three reactions of the pyruvate dehydrogenase multienzyme complex?
1) decarboxylation of pyruvate to a 2C alcohol. 2) oxidation of the alcohol to acetic acid with reduction of NAD+ to NADH. 3) esterification to coenzyme A
What are the three subunits of PDC?
pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and dihydrolipoamide dehydrogenase (E3)
advantages of a multienzyme complex
direct transfer from one enzyme to another avoids metabolite dilution in the aqueous environment and increases rate of reaction so diffusion of the substrate isn't rate-limiting.
what are the six major components of human PDC?
pyruvate dehydrogenase (E1), dihydrolipoyl acetyltransferase (E2), dihydrolipoyl,dehydrogenase (E3), E3-binding protein (E3BP), pyruvate dehydrogenase kinase (PDK) , pyruvate dehydrogenase phosphatase (PDP)
how does E2 act as a scaffold to organise and connect the different components?
Two lipoyl domains (L1, L2) are connected by alanine-proline rich linkers. Outer linker regions allow a ‘‘swinging arm’’ active site coupling mechanism between the E1, E2 and E3 components. The lipoic acid prosthetic group, which is covalently bound to the lipoyl domains via a lysine residue, can extend into the active-site channels and perform the substrate channelling. C-terminal part is the inner catalytic domain (IC).
What species have one lipoyl domain per E2?
yeast, chloroplast, or Bacillus stearothermophilus
What species have two lipoyl domain per E2?
mammalian, plant mitochondria, and Streptococcus faecalis
What species have three lipoyl domain per E2?
Escherichia coli or Azotobacter vinelandii
Define cell communication
The process by which cells detect, interpret and respond to signals in their environment
What does cell communication allow?
This allows cells to respond to environmental changes and allows cell-to-cell communication
Why is cell communication important? Use yeast as an example.
Yeast cells have receptors which glucose binds to. Cell responds by increasing expression of glucose transporter proteins and enzymes allowing cell to hydrolyse/use/store glucose
Why is cell communication important? Use plant shoots as an example.
Cells in the growing shoot tip sense light and send a signal (auxin) to cells on the shaded side of the shoot. Cells located below the growing tip receive this signal and elongate, causing the shoot to bend so the tip grows towards light.
What happens in direct intercellular signalling and where is this type of signalling important?
molecules pass through gap junctions from the cytoplasm of one cell to adjacent cells. Important in heart as synchronised contraction of cardiomyocytes essential
What happens in contact dependent signalling and where is this type of signalling important?
Membrane-bound signalling molecules bind to receptors on adjacent target cells, inducing a response. Important in synapses in the brain to allow neurones to know connection has been made with others
What is autocrine signalling?
Cells release signals that affect themselves and nearby target cells. Used to sense cell density in the tissue for control of cell growth
What is paracrine signalling?
Cells release signals that affect nearby target cells. Important in blood vessel dilation
What is endocrine signalling?
Cells in one part of the body release hormones that travel long distances in the bloodstream to affect target cells in another part
What are the three stages of cell communication?
receptor activation, signal transduction and cellular response
What does receptor activation involve?
The binding of a signalling molecule causes a conformational change in a receptor that activates its function.
What does signal transduction involve?
The activated receptor stimulates a series of proteins, forming a signal transduction pathway.
What does the cellular response involve?
The signal transduction pathway affects the functions and/or amounts of cellular proteins, producing a cellular response.
If the intracellular target is an enzyme, what is the cellular response?
Altered metabolism or other cell functions
If the intracellular targets are structural proteins, what is the cellular response?
Altered cell shape or movement
If the intracellular target is a transcription factor, what is the cellular response?
Altered gene expression, which changes the types and the amounts of proteins in the cell
Why are most receptors found on the cell surface?
Most signalling molecules are hydrophilic (polar) so can't cross the cell membrane. Cell surface receptors are usually enzyme linked, G-protein coupled or ligand gated ion channels
What do protein kinases do?
transfer a phosphate group from ATP to a protein substrate in a process called phosphorylation
How do G protein coupled receptors work?
A signalling molecule binds to a GPCR, causing it to bind to a G protein. The G protein exchanges GDP for GTP. The G protein then dissociates from the receptor and separates into an active α subunit and a β/gamma dimer. The activated subunits promote cellular responses.
When are intracellular receptors needed/important?
Some signalling molecules eg hormones are hydrophobic so can cross the plasma membrane to activate intracellular responses. They are often involved in regulating transcription.
Describe oestrogen receptor signalling
Oestrogen diffuses across the plasma membrane, enters the nucleus, and binds to the oestrogen receptors. The receptors undergo a conformational change and form a dimer, binding to promoter regions of specific genes to activate transcription.
What is a signal transduction pathway?
Stimulated by the conformational change that occurs when a signalling molecule binds to a receptor. May involve a cascade of intracellular kinases or generation of intracellular signals called second messengers
What is epidermal growth factor?
signalling molecule that binds to the EGF receptor to stimulate cell growth and division
Describe the EGF signal transduction pathway.
Two EGF molecules bind to EGF receptor subunits, causing them to dimerize and phosphorylate each other on tyrosines. Grb binds to the receptor then Sos which stimulates Ras to release GDP and bind GTP. Ras activates Raf, which starts a protein kinase cascade where Raf phosphorylates Mek, then Mek phosphorylates Erk. Erk enters the nucleus and phosphorylates transcription factors Myc and Fos.
give 4 examples of second messengers
cAMP, calcium ions, diacylglycerol, inositol triphosphate
signal transduction via cAMP
Activation of GPCR stimulates GTP binding by G alpha subunit, releasing it from G beta gamma. Alpha subunit binds to adenylate cyclase, stimulating cAMP synthesis
How does cAMP activate protein kinase A?
Binding of cAMP to protein kinase A (PKA) activates it. PKA phosphorylates specific proteins, including enzymes, structural proteins and transcription factors
How is signal amplification an advantage of second messengers?
Binding of the signal to one receptor can cause the synthesis of many cAMP molecules that activate PKA, and each PKA can phosphorylate many proteins
How is speed an advantage of second messengers?
large amounts of cAMP can be produced very rapidly following ligand binding to receptor, and can diffuse rapidly through the cell
How can activated G proteins activate signal transduction pathways via IP3 and DAG
Alpha subunit activates phospholipase C which cleaves PIP2, producing diacylglycerol (DAG) and inositol triphosphate (IP3). IP3 opens calcium ion channels in the ER, increasing levels of calcium ions. DAG activates protein kinase C (PKC)
effects of adrenaline in humans
dilates pupils, inhibits saliva production, relaxes airways, increases heart rate, stimulates sweating, stimulates glycogenolysis in skeletal muscle, constricts blood vessels in skin
function of phosphodiesterases
convert cAMP back to AMP
How can HbS be advantageous?
Having HbA and HbS alleles produces 20 to 45% HbS and protects against severe malaria, perhaps as rupturing RBCs disrupts parasite life cycle
Why is it important to diagnose phenylketonuria young?
Important to diagnose in young babies so diet changes to reduce Phe intake can be made and mental retardation prevented
What 5 cofactors does PDC require?
Thiamine pyrophosphate TPP Lipoamide Coenzyme A FAD (prosthetic group of E3; riboflavin or vitamin B2) NAD+ (this is a co-substrate)
What is thiamine pyrophosphate?
prosthetic group of E1, accepts hydroxyethyl group and is derived from vitamin B1
What is lipoamide?
prosthetic group of E2, accepts acetyl group after oxidation of the hydroxyethyl, forming acetyl lipoamide, vitamin N
What is FAD?
prosthetic group of E3: riboflavin or vitamin B2
What is G0?
Also known as quiescence, G0 is when cells can no longer divide but are metabolically and functionally active
What's the longest phase of cell division?
G1 of interphase, average length 11 hours
What's the shortest phase of cell division?
Centrosome function
centres of microtubule organisation which duplicate during interphase
What part of the centromere binds to the mitotic spindle fibres?
kinetochore proteins
Function of each type of spindle microtubule
Astral microtubules bind the centrosome to the membrane. Polar microtubules lengthen to pull
When are each of the human cyclins active?
D is active throughout the cell cycle but mainly in S phase, E is most active at the end of G1, A is most active during G2 and B most active in mitosis
What controls CDKs?
Inhibitors such as p21, which is regulated by p53
define senescence
when mitotically competent cells cannot replicate indefinitely
what is the Hayflick limit
In 1961, Hayflick and his colleagues observed that human primary fibroblast cells in culture could divide 50 times and that after this point, the cells remained functional but could no longer divide
telomere structure
repeated DNA sequence (TTAGGG) found at each end of chromosomes which shorten with each cell division due to antiparallel DNA structure
telomere function
Organise our 46 chromosomes in the nucleolus and allow the chromosome to be replicated properly as they prevent sister chromatids from fusing and damage (loss of genetic info). Senescence is induced when all telomeric DNA is lost
How does telomerase overcome telomere shortening and the end replication problem?
by adding telomeric repeat DNA directly to 3' overhang
define aging
slow process which leads to a decline of the biological functions and the ability to adapt to metabolic stress of cells, tissues and organs
difference between embryonic and adult stem cells
embryonic stem cells are pluripotent whereas adult stem cells are multipotent
How does telomerase work?
it uses its own RNA as a template to add telomeric repeats. Telomerase activity is highest in early embryonic cells and stem cells
Why can PET scans be used to detect cancer?
Cancer cells have very high glucose usage to produce ATP so radioactively labelled glucose can be used to show areas of high glucose consumption (tumours)
Describe carcinoma
cancer begins in the skin or in tissues that line or cover internal organs eg adenocarcinoma
describe sarcoma
begins in the connective or supportive tissues such as bone, cartilage, fat, muscle or blood vessels. These cancer types are more rare
describe leukaemia
cancer of the white blood cells. It starts in the tissues that make blood cells such as the bone marrow.
describe lymphoma and myeloma
these cancers begin in the cells of the immune system