Biol 112- Cell Structure and Function Flashcards
1
Q
What is a cell?
A
Basic biological component, simplest alive thing ever.
2
Q
describe the basic lore of prokaryotic cells
A
they developed like 3.5 billion years, and are the most abundant type on earth today. eukaryotic cells developed from prokaryotic cells around 2 billion years ago.
collective biomass of prokaryotic cells on the world is 10 x eukaryotes.
they are simple in structure but biochemically diverse + don’t have a membrane-bound nucleus
3
Q
which 2 domains can prokaryotes be divided into, and briefly describe their vibe?
A
bacteria: enormous medical + economic importance
archaea: often live in very extreme environments
4
Q
how big are: prokaryotic cells, viruses + eukaryotic cells on average?
A
prokaryotic cells: 0.1-5.0 micrometers
viruses: 20-200 nanometers
eukaryotic cells: 2-100 micrometers
5
Q
archaea are usually extremophiles, name some habitats they could occupy
A
sea ice, permafrost + polar regions
mud volcanoes
shallow water, hydrothermal vents
hot-springs, fumaroles
hyperacid lakes + volcanoes
deserts + arid environments
deep-sea anoxic lakes + brines
serpentinising environments
deep-sea sediments + trenches
marine + continental subsurface
soda lakes + hypersaline lakes
6
Q
if life is ever found on another planet, which domain would it probably be similar to and why??
A
archaea, extremophiles can colonise extreme environments on earth
7
Q
how, basically, can archaea act as extremophiles like structurally and such
A
Can continue metabolism at higher/ lower temperature, proteins (enzymes) can fold differently, and the lipid membrane can change structure to accommodate them.
They also have diverse energy sources, they don’t just use carbon for energy; they can also use iron, sunlight, etc.
8
Q
name + explain 5 biotechnical applications of extremophiles
A
1) PCR- taq polymerase (e.g. thermus aquaticus)
2) biofuels- making energy from biomass
3) biomining- extracting metals from solid materials
4) carotenoid production- halophiles usually involved in this (antioxidant potential)
5) detergents- usually protease extremophiles
9
Q
name + explain an epic thermophile involved in biotechnical things
A
thermus aquaticus xxxxx
its a thermophilic prokaryote, which is a source of the heat-resistant enzyme Taq DNA polymerase, used in PCR to amplify DNA.
In the thermacae family.
10
Q
do cells from the bacteria, archaea + eukarya domains contain nuclear envelopes?
A
no for bacteria + archaea, yes for eukarya
11
Q
do cells in the bacteria, archaea + eukarya domains contain membrane-enclosed organelles?
A
no for bacteria, archaea, yes for eukarya
12
Q
do cells from bacteria, archaea + eukarya contain peptidoglycan in their cell wall?
A
yes for bacteria, no for the others
13
Q
do cells from bacteria, archaea + eukarya contain membrane lipids?
A
unbranched hydrocarbons in bacteria + eukarya, some branched hydrocarbons for archaea
14
Q
do cells from bacteria, archaea + eukarya contain RNA polymerase?
A
one kind in bacteria, but loads in archaea + eukarya
15
Q
do cells from bacteria, archaea + eukarya contain introns in their genes?
A
very rare in bacteria, some genes have it in archaea, many Gennes have them in eukarya
16
Q
do histones associate with the DNA of bacteria, archaea + eukarya cells?
A
no for bacteria, some species do in archaea, all species will associate with histones in eukarya
17
Q
which of bacteria, archaea + eukarya cells contain circular chromosomes?
A
yes for bacteria + archaea, no for eukarya
18
Q
do bacteria, archaea + eukarya cells grow at temperatures below 100 degrees?
A
bacteria + eukarya won’t, but some archaea will
19
Q
what are the components of prokaryotic cells (7 potential ones)?
A
nuceloid region
plasma membrane
ribosomes
cell wall
some have a flagella
pili
capsule
20
Q
describe the nucleoid region in prokaryotic cells
A
contain genetic info in the form of circular DNA, separate to potential plasmids. No nuclear membrane.
21
Q
describe the plasma membrane of prokaryotic cells
A
basically same as in everything else. Pretty much has ribosomes and nothing much else. Some membranes have infolding with contains specialised enzymes e.g. thylakoid membranes in cyanobacteria which carry all necessary components for photosynthesis.
22
Q
describe the ribosomes in prokaryotic cells
A
pretty much the only thing in prokaryotic cytoplasm.
smaller and distributed throughout cytoplasm instead of held with an ER.
23
Q
describe prokaryotic cell walls (not all of them have one but a lot of them do)
A
helps maintain shape and rigidity (peptidoglycan), helps protect against mechanical and osmotic shock. Gram stains are important to identify whether the bacteria needs to be treated with antibiotics such as penicillin that target peptidoglycan.
24
Q
describe flagella in prokaryotic cells
A
not all of them have one but they’re quite epic- they are made of protein flagellin.
both eukaryotic and prokaryotic cells can have flagella, but with different functions. Energy required to drive the motor of the flagella is from the oxidisation of ATP, means it can rotate and propel. We were able to find this out through electron microscopy- shows protein rings in the cell wall.
25
describe prokaryotic pili
they are composed of the protein Pilin and help bacterial adhesion substrates and each other.
(conjugation- circular plasmids and stuff can exchange genetic information between bacteria which is important for evolution).
26
describe prokaryotic capsules
nothing interesting, made of polysaccharides and were also not fully sure what they do
27
what are the most common shapes of bacteria?
cocci, rod, spiral
28
were gonna compare gram negative + positive prokaryotic cell walls xxxx
peptioglycan layer, structure, teichoic acids or not, lipopolysaccharides or not, gram stain result + antibiotic resistance or not
29
name like 2 bacteria with a gram positive cell wall + which illness they cause
Clostridium botulinum (botulism)
Streptococcus pneumoniae (pneumonia)
30
name 2 bacteria with a gram negative cell wall + which illness they cause
Chlamydia trachomatis- most common cause of infectious blindness ever
Vibrio cholerae- cholera
31
describe some medical applications bacteria can have in biotechnology
1. they can be used to produce large quantities of proteins (E.coli is used of this a lot as its cheap + reliable).
2. they are also used for drug screening tests + diagnostics
32
describe an agricultural application for bacteria in biotechnology
introduction of a new gene in a plant chromosome, giving resistance to various viruses or improve human health e.g. purple tomatoes have high anthocyanin which has antioxidant features
33
describe an environmental application for bacteria in biotechnology
bioremediation- removing pollutants, industrial by-products, oil spills, generating water instead of dangerous chemicals and stuff
34
describe industrial applications of bacteria in biotechnology
1. lactic bacteria develop the flavour + colour of some foods
2. improves storage longevity of wines
35
what are autotrophs?
producers- make their own food- plants, algae, bacteria
36
what are heterotrophs?
consumers- consume produces/ consumers- mammals
37
there can be photoautotrophs, photoheterotrophs, chemoautotrophs + chemoheterotrophs. which are prokaryotes and which applies to eukaryotes?
38
name some types of organisms that are photoautotrophs
can be eukaryotic or prokaryotic
usually photosynthetic prokaryotes (e.g cyanobacteria), plants, or certain protists (e.g. algae)
39
names some types of organisms that are chemoautotrophs
only certain prokaryotes e.g. Sulfolobus
40
name some types of organisms that are photoheterotrophs
only certain aquatic + salt-loving prokaryotes e.g. Rhodobacter
41
name some types of organisms that are chemoheterotrophs
can be prokaryotic (e.g. Clostridium) or eukaryotic (e.g. protists, animals, some plants, fungi)
42
why are viruses considered not alive?
can't self-repair + no energy transduction system
43
which protein units is the viral protein coat made of?
capsomers
44
briefly describe filamentous viruses + give an example of one
the nuclei acid is arranged in a helix, with the protein sub-units surrounding + stabilising it.
TMV is an example
45
briefly describe spheroid viruses + give an example
the nucleic acid is condensed inside a protein envelope which is usually organised into a multisided geometric shape.
adenovirus is an example
46
briefly describe enveloped viruses + give an example
have lipid envelopes
e.g. influenze + coronaviruses
47
briefly describe tailed spheroid viruses + give an example
this is basically a spheroid one with tail
e.g. lambda phage
48
how in history have microscopes been used to image cell culture?
whether cells are alive, how many, etc. For example, SARS-CoV-2 cells- used to show different epithelial cell membranes had a different effect.
49
how is microscopy useful in imaging proteins?
abundance of different proteins, how cells respond to protein expression on the surface.
colocalisation of proteins
also localisation of proteins
50
which cells does SARS-CoV-2 affect?
induces the dedifferentiation of multi ciliated cells + impairs mucociliary clearance
51
describe the historical development of cell biology
1665- Robert Hooke published this epic thing called Micrographica, where he described cells as a "honeycomb of chambers"
1675- Van Leeuwenhoek- improved polishing lenses. his microscopes could resolve to like 1.5 microns. he described protozoa as a host of little animals in rainwater
19th century- max theoretical resolution of the light microscope was like 0.25 microns
1930s- electron microscope was developed, allowing organelles to eb seen. "ultrastructure" was coined to describe the level of detail obtainable with the EM
52
what is magnification?
the ratio of an object's image size to its actual one
53
what is a resolution?
the measure of the minimum distance of 2 distinguishable points
54
what is contrast with microscopes?
visible differences in brightness or colour between parts of the sample
55
describe the general lore of dissecting light microscopes
not the ones we use I'm afraid, Use reflecting light to look mainly at the surface of cells, 70x mag.
56
describe general lore of compound brightfield microscopes
the ones we use, they can look at the in depth features due to higher resolution and magnification (400x to 1000x mag)
57
describe the major advantage of light microscopes, and the disadvantage, also the approx. resolution
+: ability to image living cells
-: limited resolution of about 0.2 microns
58
what is the only way to improve the resolution of a light microscope?
a shorter wavelength of radiation
59
describe brightfield microscopes with unstained specimens
passes light directly through specimen (they are partially transparent); unless cell is naturally pigmented or artificially staines, image has little contrast
60
describe brightfield microscopes with stained specimens
staining with various dyes enhances contrast but most staining procedures require cells to be fixed (preserved), which is annoying
needs to be stained as cells don’t naturally have that much colour
61
describe the 7 steps of light microscope sample preparation
whole mounts: small relatively transparent specimens mounted directly onto slides
tissue sections: most tissues needs to be sectioned before they can be examined
fixation: involves chemical fixatives to prevent cell autolysis and to preserve the tissue structure
dehydration + clearing: removes the water from the tissue in preparation for wax impregnation
embedding: the specimen is infiltrated with molten wax, after transferred to a mould
sectioning: the specimen approx 5 microns thick are cut on a microtome, and collected on a glass slide
staining: the wax is removed + tissue is stained with dye such as Eosin (cytoplasm) + haematoxylin (nuclei)
62
describe the specific specimen preparation for brightfield microscopy
the specimen embedded with paraffin wax/ plastic resin, is like scaled on a rotating metal or glass blade to produce a ribbon of thin sections.
the ribbons are put on a glass slide, stained + mounted under a cover slip
63
how does advanced light microscopy (phase-contrast + differential-interference-contrast) help?
permits observation of transparent living cells.
light phase shifts induced by specimen are used to generate contrast: phase contrast- refracted + unrefracted light. DIC- 2 light beams
64
how are light shifts used to image cells?
Light shifts are converted into phase changes or intensity changes, allowing us to image cells that could, for example, be vibrating over time (just moving).
65
how are phase contrast microscopes specifically useful for living, unpigmented cells?
enhances contrast in unstained cells by amplifying variations in density within the specimen
66
how is differential-interference-microscopy useful for imaging living, unpigmented cells?
like phase contrast, it used optical modification to exaggerate differences in density
67
how does fluorescent microscopy show the locations of specific molecules in the cell?
fluorescent substances will absorb short-wavelength, UV radiation + emit longer-wavelength, visible light.
the fluorescing molecules may occur naturally in the specimen but more often are made by tagging the molecules of interest with fluorescent molecules
68
describe basic principles of confocal microscopy + how it works (optical sectioning)?
uses lasers + special optics for optical sectioning.
only those regions within a narrow depth of focus are imaged. regions above + below the selected plane of view appear black rather than blurry.
this microscope is typically used with fluorescently stained specimens.
69
which type of light microscopy is used for 3D objects?
confocal scanning:
generates 3D images of living cells, removes out-of-focus images with optical sectioning + can look inside thick specimens like embryos because of added depth
. You can also do live cell imaging with this (4D) which is cool.
70
which 2 microscopes "break the resolution limit" + how?
1. deconvolution microscopy- algorithms remove out-of-focus light + this sharpens the image and improves resolution
2. super resolution- gathers light from individual fluorescent molecules + records their position. combined info from the molecules breaks the limit
71
describe basic lore of electron microscopes: resolution, penetrating power, + the 2 different types
developed in the 30s in germany
electrons have a very short wavelength so the resolution is 1000s of times better than the light microscopes.
the full potential resolution of the EM has not yet been reached, it is currently around 0.08 nm, its theoretical limit is way less.
electrons have poor penetrating power so the electron microscope must be kept vacuum- electrons can be focussed by magnetic fields.
the arrangement of lenses in a TEM is very similar to a light one, 2 main types are TEM + SEM
72
how big do samples need to be for electron + light microscopes?
Samples need to be around 50-100 nanometres for EM, instead of 5-10 micrometres like in light microscopes.
73
describe basic lore of how TEMs work
electron gun: usually a heated tungsten filament which produces electrons by thermionic emission
electron beam goes through specimen, the image is focussed and magnified by magnetic objective + projective lenses
the electron image is converted into a visible image by a fluorescent screen, which is viewed through a glass window.
kept under a vacuum during this xxxxxxxxx
74
describe sample preparation for TEMs
whole mounts: bacteria + viruses can be examined directly
tissue sections
fixation: usually in Glutaraldehyde (protein cross linking) followed by a second fixation step in Osmium Tetroxide (lipid cross linking)
dehydration
embedding: specimens for TEM are embedded in plastic resins such as Epoxy resins.
sectioning: 50nm thick sections are cut using a ultramicrotome
staining: biological tissue has little contrast under the electron beam, so heavy metal stains such as lead are used to improve contrast
75
describe basic lore of how SEMs work
called that because the electron beam is scanned across the specimen. used for looking at specimen surfaces- gives an image representing the topology of the sample.
top part of microscope is similar to TEM.
electrons are reflected from the specimen surface, collected by a electron detector and converted into an electronic signal which is displayed on a screen.
76
which aspect of the SEM will give the images a 3D appearance?
the depth of focus
77
how does cryoTEM help treat illnesses with different drugs?
CryoTEM gives rise to being able to view atomic structure, showing how proteins fold and stuff.
78
describe SEM sample preparation
biological samples must be fixed + dried before being examined in a SEM under vacuum.
fixation: same fixatives are used as with TEMs
dehydration: the water is replaced with ethanol
critical point drying: this allows all the ethanol to be removed in a way that minimises shrinkage
coating: specimen is coated with a thin layer of gold to protect from electron beam damage
79
what is cell fractionation?
allows the major organelles to be individually separated out so that they can be studied in isolation + their functions can be observed.
separates organelles based on size and density.
80
how does cell fractionation work?
cells are first homogenised to release the organelles, then differential centrifugation isolates cell components on the basis of size + density by using increasing duration and g force
81
what are 3 specific applications of cell fractionation?
1. protein enrichment- enrich target proteins + improve detection of low abundance protein
2. protein characterisation- identify sub cellular localisation of a protein
3. protein translocation- monitor translocation of cell signalling molecules from the cytoplasm of the nucleus
82
how is the genetic material of eukaryotic cells organised?
into chromosomes + enclosed in a nuclear envelope
83
what is plasmodesmata?
just allow diffusion of molecules between different plant cells.
84
label this epic animal cell
85
what do chloroplasts do?
capture light energy + convert it into chemical energy, in the thylakoid stacks (grana).
86
what do vacuoles do?
store various chemicals + play a role in cell growth
87
what does the plant cell wall do?
maintains the cell shape + prevents mechanical damage.
88
what is the plant cell wall composed of?
cellulose fibres embedded in a protein/ polysaccharide matrix consisting mainly of hemicellulose + pectin
89
label this epic plant cell
90
describe the nuclear membrane
it encloses the nucleus, separating it from the cytoplasm.
it is. double membrane + contains nuclear pores about 100 nm in diameter
91
describe the eukaryotic nucleolus
is it where the components of ribosomes are manufactured
92
describe the chromatin in eukaryotic nuclei
within the nucleus, DNA is organised (with histones) into chromatin.
during cell division, the chromatin condenses into chromosomes.
93
how do nuclear pores help the nucleus?
messenger RNA (mRNA) is synthesised inside the nucleus from a DNA template + released into the cytoplasm via the nuclear pores where it controls protein synthesis.
94
what does the plasma membrane in eukaryotic cells do (4)?
defines + contains the cell, separating the cell from its external environment.
controls the entry of nutrients + exit of waste.
maintains electrolyte balance in the cell.
acts as a sensor to external signals.
95
describe the structure of the plasma membrane in eukaryotic cells
plasma membranes are assemblies of lipids + protein molecules held together by mainly non-covalent interactions= fluid-mosaic model.
the lipid bilayer provides the basic structure of the membrane + serves as an impermeable barrier to most water-soluble molecules.
protein molecules are dissolved in the lipid bilayer + carry out most of the specialised functions of the membrane
96
membrane lipids are amphipathic, what does this mean?
they contain both a hydrophobic and hydrophilic region. Membrane proteins e.g. transmembrane ones are also amphipathic.
97
describe the lipid bilayer of the PM
in an aqueous environment, the lipids either form micelles or bilayers.
if damaged, the lipid bilayer is able to repair itself.
lipids constitute about 1/2 of the mass of biological membranes
3 types of lipids in the cell membranes: phospholipid;ipids, cholesterol + glycolipids
98
describe the structure of a single phospholipid, and how they make membranes more fluid
One hydrophobic phospholipid tail is fully saturated, and one has a C=C double bond which results in a kink, which makes it more difficult to pack the phospholipids together making the membrane more fluid and more resistant to, for example, temperature damage.
99
describe the 2 types of movement phospholipids do, + how often
lateral movement which is more frequent (like 10^7 times per second). the lipids also rotate rapidly on their axis.
flip-flopping between the 2 layers, with enzymes called flippase and flopase- once a month
100
how does cholesterol increase + reduce membrane fluidity?
depends on temperature.
at high temperature, it reduces fluidity at moderate temperatures by reducing phospholipid movement,
but at low temperatures it hinders solidification by disrupting the regular packing of phospholipids, increasing the distance between PLs.
101
would an arctic fox or desert fox have a more fluid membrane?
An arctic fox would have a more fluid plasma membrane than a desert fox as the phospholipids would have a kink with the unsaturated bonds.
102
why are transmembrane proteins called that xxx?
the polypeptide chain of membrane proteins often crosses the lipid bilayer several times
103
how are peripheral membrane proteins associated with the membrane?
by non-covalent linkages, they are easily dislodged
104
describe the process of freeze-fracture electron microscopy
used with Cryo Electron Microscopy
1. fixation + preservation with glycerol
2. rapid freezing- liquid nitrogen
3. fracturing- under pressure using a liquid nitrogen cooled microtome
4. replication
5. replica cleaning
105
describe the experiment for evidence of drifting membrane proteins
they put together a mouse cell + human cells, and the proteins mixed after an hour in the hybrid cells
106
describe + explain the 4 types of membrane proteins in plasma membranes like in terms of function
transport proteins: homeostasis of the cell e.g. the Na/K ATPase pump which pumps 3 sodium ions out of the cell + 2 potassium ions into the cell
receptor sites: exterior region of a transmembrane protein may act a a receptor for a chemical messenger such as a hormone or growth factor
structural roles: membrane proteins called integrins allow the cell attach to the extracellular matrix
cell junctions: tight junctions are present between some cell types. they act to separate the apical + basal membranes which have different functions. also cell-cell recognition
also enzymatic activity, signal transduction, intercellular joining + attachment to the cytoskeleton and extracellular matrix
107
describe how cystic fibrosis is caused
it is a autosomal recessive disease
caused by a defective chloride ion channel (transmembrane protein). the failure of the chloride channel in a build-up of viscous mucus within the lungs making the individual prone to infections.
it appears to be an ideal disease to treat with gene therapy, but progress has been much slower than expected.
108
describe membrane carbohydrates
all eukaryotic cells have carbohydrates on their surface in the form of oligosaccharides and polysaccharides bound to membrane proteins + as glycolipids.
they account for up to 10% of membranes mass.
a glycocalyx consisting of a thin layer of carbohydrate is present on the outside of the plasma membrane of most cells. cell surface carbs are known to be important in cell-cell + cell-extracellular matrix recognition
109
what are ABO blood types determined by?
carbohydrates on the surface of red blood cells
110
how does HIV bind to immune cells?
it must bind to the immune cell surface protein CD4 + a co-receptor CCR5 to infect a cell.
HIV can't enter the cells of resistant individuals that lack normal CCR5, as in resistant individuals.
111
what are the 4 types of tissue?
connective tissue, epithelial tissue, muscle tissue, nervous tissue
112
name like 5 organ systems
digestive, circulatory, respiratory, immune, excretory, endocrine, reproductive, nervous, integumentary, skeletal, muscular
113
describe the structure of epithelial tissue
consists of sheets of tightly packed cells, covers the outside of the body e.g. the inner surface of the digestive tract + respiratory tract and the outer surface of the body.
most epithelial cells are fastened together via desmosome junctions + sealed via tight junctions to withstand stresses + strains.
epithelia can be simple (1 layer) or stratified (several layers)
114
what does the epithelium do?
protects against technical injury + also provides a barrier against microbes and fluid loss
they usually have specific functions, e.g. the epithelia which line the digestive tracts (glandular epithelium) which secret mucus. it can also be ciliated as in the respiratory tract.
115
what are the 5 types of epithelial tissue?
usually have a top and bottom of the cell that are involved in different processes, vital for reparation.
116
what's the main role of connective tissue?
It’s the most abundant type of tissue e.g. tendons + ligaments. Contain fibrous proteins e.g. collagen.
mechanical strength binds + support for other tissues it consists of an extracellular matrix through which cells are sparsely scattered.
dense connective or loose connective
Protection, insulation, storage and transport, while loose tissue is more just general holding.
117
describe what dense connective tissue is and what its structure is
cartilage bonds which have great mechanics strength + elasticity. consists of extracellular matrix with few cells e.g. bone tendon, ligaments, sclera.
made of: fibrous proteins (mainly collagen + elastin) + ground substance usually proteoglycans
118
describe what loose connective tissue is
it holds small glands + epithelia together and includes basal lamina of cells. loose tissue is more just general holding
blood + adipose tissue are also considered connective tissue although they don't really fit very well into this category- adipose tissue is cells full of fat but also made to store energy.
119
what is the role of muscle tissue + general structure of muscles?
the role of muscle tissue is to support + movement. muscle consists of long excitable cells, which contain large numbers of actin + myosin filaments.
each fibre is further divided into myofibrils, which contain 2 types of filaments:
1. thin filaments composed of actin
2. thick filaments composed of myosin
the regular arrangements of the filaments creates a banding pattern called a sarcomere
120
what are the 3 vertebrate muscle types?
skeletal muscle (striated)- responsible for voluntary movement
smooth muscle- responsible for involuntary body activities
cardiac muscle- responsible for contraction of the heart
121
what is nervous tissue (talk about glia as well)?
it senses stimuli + transmits signals throughout the animal.
neurons (nerve cells) transmit nerve impulses.
glial cells (glia) help nourish, insulate and replenish neurons.
122
where is nervous tissue found?
found in brain, spinal cord
123
describe the structure of nerve cells
it consists of a cell body (soma) + 2 or more nerve processes.
dendrites are processes, which conduct impulses towards the nerve body.
axons transmit impulses away from the nerve body.
specialised cells called Schwann cells wrap around an axon to form a multi-layered membrane sheath to provide electrical insulation.
the signal is transmitted along the nerve cell in the form of ion fluxes across the plasma membrane of the cell.
124
is the endomembrane system unique to prokaryotes, eukaryotes, or both?
eukaryotic cells only
125
which 5 organelles components is the endomembrane system composed of?
nuclear membrane, smooth endoplasmic reticulum, rough endoplasmic reticulum, Golgi apparatus, lysosomes
126
describe the outward structure of the smooth endoplasmic reticulum
Basically the same as rough but without ribosomes.
most cell types have relatively little SER.
127
which 3 things does the smooth ER generally manufacture?
phospholipids, fats + steroids (including sex hormones)
128
what does the smooth ER break down in hepatocytes (liver cells)?
glycogen to release glucose
129
which kind of drugs does the smooth ER detoxify (barbiturates is an example), and how?
detoxifies lipid-soluble drugs such as barbiturates, by adding water-soluble groups such as sulphate or glycuronic acid
130
where is the sarcoplasmic (endoplasmic) reticulum found?
muscle cells
131
describe the structure of a muscle, and where sarcoplasmic reticulum fits in
network of tubular sacs- muscles consist of myofibrils. myofibrils are surrounded by sarcoplasmic reticulum.
myofibrils are composed of a repetitive arrangement of filaments called a sarcomere. a sarcomere is the region where the myosin + actin filaments overlap
132
why does sarcoplasmic reticulum contain a lot of mitochondria?
to provide energy for the submission of electrical impulses through T-tubules.
133
describe the steps of the function of sarcoplasmic reticulum in muscle cells
transmits electrical signals.
muscle cells receive action potentials from the neuromuscular junction through T tubules in the sarcoplasmic reticulum.
the sarcoplasmic reticulum sequesters calcium ions from the cytosol, which bind to troponin causing a conformational change in tropomyosin.
myosin + actin can now interact which results in muscle contraction.
the level of intercellular calcium regulates muscle contraction in muscle cells
134
label this epic drawing of a sarcomere with:, myosin, actin, Z line, H line, A line, I line
myosin= thick purple ones
actin= thin orange ones
135
why is troponin essential to allow muscle contraction to occur?
calcium needs to bind to troponin complexes to allow myosin binding sites to be exposed, allowing muscle to contract
136
describe the hypothesis of how myosin-actin interactions generate the force for muscle contraction, and how ATP is essential for this
at first, the myosin head is of fairly low-energy conformation.
Each myosin head is bound to an ATP molecule; during the conformational change, ATP is dislodged and hydrolysed to give energy for the contraction. This allows the actin to bind to the myosin at the cross-bridge binding site, forming a cross bridge. The myosin + actin will then slide between each other.
The ATP will become reattached when the contraction needs to be stopped, and the myosin head flicks back to its original conformation.
When our muscles become fatigued, it’s because we’re running out of ATP in the cells.
137
just an epic picture showing all of skeletal muscle contraction xxxx
138
epic picture showing what muscle cells look like via haemotoxin + eosin staining. The axons allow the signal to be carried along a long stretch.
139
the rough ER is the site of 4 classes of protein synthesis, what are they xxxx
1. secreted
2. glycosylated
3. lysosomal enzymes
4. membrane bound proteins
140
which proteins does the rough ER produce?
pretty much all proteins apart from cytoplasmic ones.
141
explain the signal mechanism for targeting proteins to the ER (signal peptide + SRP)
only ribosomes synthesising proteins with a specific signal peptide sequence become attached to the RER.
the N-terminus of these proteins contains a signal peptide usually 20-30 amino acids long. a signal recognition particle (SRP) attaches to the signal peptide and stops translation in the cytosol.
the SRP docks to a SRP receptor on the ER membrane (sending the mRNA and ribosome still attached to a translocation thing in the cell) and translation starts again.
the hydrophobic signal peptide passes through the membrane + loops back through the sequence + is cleaved off. the rest of the peptide passes through the membrane + into the ER lumen.
the signal sequence is cleaved off with the enzyme signal peptidase.
142
what is the function of ribosomes on the RER?
cell machinery for joining together amino acids which travel along the length of the mRNA during translation
143
what are polyribosomes + how do they help in translation?
an mRNA molecule is generally translated simultaneously by several ribosomes in clusters called polyribosomes.
Polyribosomes will join polypeptide sequences faster than usual.
144
what is the definition of glycosylation?
addition of sugars or oligosaccharides
145
what happens in glycosylation in the RER?
an oliugosaccharide is added in the RER. it's composed of N-acetylglucosamine, mannose + glucose residues containing a total of 14 sugar residues which is transferred to the proteins in the RER, by the Golgi apparatus cis face.
They are then secreted out through the trans face, then out of the plasma membrane by exocytosis.
146
what does the Golgi apparatus do (2)?
following their synthesis in the RER, most proteins move in small transport vesicles to the Golgi complex. the Golgi apparatus modifies + sorts the proteins which pass through it.
it also mediates the flow of proteins from the RER to various destinations in the endomembrane system.
147
what is the default pathway of proteins synthesis?
synthesised in the RER, then through the Golgi + to plasma membrane for secretion
148
name a protein that deviates from the default pathway of protein synthesis in the endomembrane, and how?
some proteins are tagged in the Golgi for specific destinations in the cell e.g. lysosomal enzymes- mannose residues of lysosomes enzyme proteins are phosphorylated in the cis Golgi.
a mannose 6-phosphate then binds these proteins in the trans-golgi reticulum + directs their transfer to lysosomes. in this pathway, the pH change allows the receptor to dissociate from the protein so it can be used again.
149
explain why glycolsylation is essential to proteins' function, especially in the protein mucin
these are glycoproteins with long oligosaccharide chains which are essential to produce a highly hydrated gel-like material.
Mucus is so viscous due to the glycosylation that happens in the Golgi.
150
what are lysosomes ?
they are vesicular structures, limited by a single smooth membrane containing enzymes active at acid pHs.
151
how many hydrolytic enzymes do lysosomes contain?
about 60 (manufactured in the RER), they will degrade almost all biomolecules
152
where do primary lysosomes originate from?
the trans face of the golgi
153
what do lysosomes do?
they're the recycling platform of the cell. once a lysosome fuses with a target, H+ ions are pumped into this secondary lysosomes to bring down ph + activate the enzymes.
they can carry out autophagy (recycling of worn out organelles), phagocytosis, or apoptosis.
154
what can happen if a particular lysosomal enzyme is defective, and what can it result in?
partially degraded insoluble metabolites can accumulate within lysosomes
the resulting material results in enlarged lysosomes that compromise cell function in over 50 different lysosomal storage diseases e.g. Tay-Sach's disease
155
describe how Tay-Sachs disease comes about (lysosomal storage disease)
Hexosaminidase A enzyme deficiency results in accumulation of the lipid ganglioside.
the clinical symptoms are due to accumulation of ganglioside in nerve cells.
death usually occurs by 2-3 years old
156
what is the difference between endocytosis + exocytosis?
endo: material taken into cell
exo: material released out of cells
157
how does exocytosis remove things from the cell?
exocytosis involves fusion of vesicles from the cell interior with the plasma membrane. the vesicles contents are then expelled into the surrounding medium
158
why is exocytosis important?
it is crucial in the secretion of numerous proteins including hormones, and extracellular structural proteins such as collagen + fluids like mucus
159
describe how endocytosis helps the cell in phagocytosis
uptake of insoluble material.
the plasma membrane forms extensions called pseudopodia which kind of wrap itself around the molecule it wants. In macrophages, a phagolysosome forms, eliminating the bacteria.
160
describe how endocytosis helps the cell in pinocytosis
basically how the cell drinks.
cells pinch their PM to take up extracellular fluid in small vesicles. non-specific.
161
describe how receptor-mediated endocytosis works
binding of macromolecules to specific cell surface receptors which triggers endocytosis.
receptors will recognise specific molecules like ligands. Important in cell recognition. The same pinching happens like in pinocytosis but with aid of a coated pit. The pinching happens with a dynein protein.
162
describe how receptor-mediated endocytosis works specifically with clathrin
the macromolecules (such as transferring which transports iron from the blood into cells) become concentrated in endocytic pits.
the endocytic pits are coated with a bristle-like protein called Clathrin. Clathrin polymerises around the vesicle forming a cage-like structure
163
name a very not good and known diseases that enters cells via receptor-mediated endocytosis
SARS-CoV-2
164
describe evidence mitochondria endosymbiotic theory
all mitochondria derive from a common ancestral organelle that originated from the integration of an alphaproteobacterium (oxygen-using non photosynthetic prokaryote) into a host cell related to Archaea.
The transition from endosymbiotic bacterium to permanent organelle involved loads of evolutionary changes including origins of new genes and a protein import system, insertion of membrane transporters, integration of reproduction, so on. These changes occurred incrementally as the endosymbiont and the host became integrated.
evidence: double membrane, retain their own genome, replicate independently within the host cell, similar size to prokaryotic cell
165
do prokaryotic or eukaryotic cells have mitochondria, or both?
only eukaryotic- nearly all of them do, as a few of them get ATP from glycolysis.
most cells contain several hundred mitochondria, liver cells have like 2500
166
describe mitochondrial structure (2 compartments)
all mitochondria have an inner + outer membrane, with the inner folded into Cristal.
there are 2 compartments: the matrix inside the inner membrane + the inter-membrane space between the inner and outer membranes
167
how do mitochondria move in the cell?
the microtubules of the cytoskeleton
168
where are mitochondria usually found?
regions of high ATP consumption, foe example in the myofibrils of muscle cells
here, the mitochondria stained red sit on the cytoskeleton + are motile, move about quite a bit to areas of high, intense activity as and when needed.
169
what is the major protein component in mitochondrial membrane?
porin- large aqueous channels that allow access between the cytosol + mitochondria, communication through exchange of molecules, etc. Under normal healthy conditions, things aren’t moving through there.
170
what are the 3 major types of membrane complexes in the mitochondria inner membrane?
1. electron transport chain
2. ATP synthase
3. specific transporters of metabolites which vary according to cell/ tissue type
Liver mitochondria have the greatest variety of transporters since they are involved in the initial reactions of several anabolic pathways.
171
what do mitochondrial Cristae do (3)?
increase membrane surface area.
energy-transducding membrane
impermeable to most small ions
172
which 3 things does the mitochondrial matrix contain?
1. enzymes which catalyse Krebs cycle + fatty acid oxidation
2. ribosomes
3. mitochondrial DNA
173
what is ATP?
A nucleotide derivative, composed of adenine bound to ribose sugar, with 3 phosphates.
the energy currency of the cell. The exergonic process of ATP hydrolysis is used to drive an endergonic process.
174
how does ATP help the cell directly + indirectly, and give examples of both?
ATP hydrolysis causes changes in the shapes and binding affinities of proteins. This can occur either directly, by phosphorylation, for example for a membrane protein carrying out active transport of a solute, or indirectly, via noncovalent binding of ATP and its hydrolytic products, as is the case for motor proteins that move vesicles (a type of organelle) along cytoskeletal “tracks” in the cell.
175
what is ATP's most important function, and how does it help mechanically + chemically ?
Most important function is phosphorylation. It can phosphorylate ion channels, which can close/open it, allowing many things to move through. It can help mechanically e.g. motor proteins, changing its conformation by altering amino acid sequence so that it can move/stop. It can also work chemically e.g. enzyme reactions.
176
which process is needed to generate energy to synthesis ATP?
oxidation of organic molecules.
this releases energy to the surroundings because the electrons lose potential energy when they end up being shared unequally, spending more time near electronegative atoms such as oxygen
177
what is the most important thing that happens at the mitochondria?
cellular respiration
178
describe what happens in cellular respiration
During glycolysis, each glucose molecule is broken down into two molecules pyruvate. In eukaryotic cells, as shown here, the pyruvate enters the mitochondrion.
There it is oxidized to acetyl CoA, which is further oxidized to CO2 in the citric acid cycle. NADH and a similar electron carrier, FADH2, transfer electrons derived from glucose to electron transport chains, which are built into the inner mitochondrial membrane.
(In prokaryotes, the electron transport chains are located in the plasma membrane.)
During oxidative phosphorylation, electron transport chains convert the chemical energy to a form used for ATP synthesis in the process called chemiosmosis.
179
what do electron carriers like NAD+ do?
accept high-energy electrons from organic molecules + donate them to the electron transport chain. they can't be transported into/out of the mitochondria directly so much be regenerated
180
describe the structure of the electron carrier NAD+
The full name for NAD+ , nicotinamide adenine dinucleotide, describes its structure—the molecule consists of two nucleotides joined together at their phosphate groups (shown in yellow). Nicotinamide is a nitrogenous base, although not one that is present in DNA or RNA
181
how is NAD+ reduced to NADH?
The enzymatic transfer of 2 electrons and 1 proton (H+ ) from an organic molecule in food to NAD+ reduces the NAD+ to NADH: Most of the electrons removed from food are transferred initially to NAD+ , forming NADH.
the enzyme is called a dehydrogenase
182
describe the epic 2 steps of the electron transport chain
1. uncontrolled not good reaction: the one-step exergonic reaction of hydrogen with oxygen to form water releases a large amount of energy in the form of heat and light: an explosion.
2. epic cellular respiration: the same reaction occurs in stages. An electron transport chain breaks the “fall” of electrons in this reaction into a series of smaller steps and stores some of the released energy in a form that can be used to make ATP. (The rest of the energy is released as heat.)
183
where does glycolysis happen in respiration, and how does it produce energy?
it takes place in the cytosol, and only releases a small amount go the energy stored in glucose (through substrate level phosphorylation)
most of the energy remains in the 2 pyruvate molecules
184
where does the Krebs cycle take place in the mitochondria?
matrix
185
where is the electron transport chain located in respiration + how do electrons end up here after the krebs cycle?
the inner membrane of the mitochondria.
electron carriers NAD + FAD collect electrons from Krebs cycle and transfer them to the ETC
186
glycolysis uses substrate level phosphorylation to generate ATP, what does this mean?
substrate with "high energy" phosphate bond.
ATP is produced directly from the substrate binding to ADP.
187
how many steps does glycolysis actually involve?
like 10, with a lot of intermediates
188
by which process does pyruvate enter the mitochondrion after glycolysis, and why?
Pyruvate is a charged molecule, so in eukaryotic cells it must enter the mitochondrion via active transport, with the help of a transport protein.
189
if this is the structure of pyruvate, what is the structure of acetyl CoA (produced in link reaction)?
after pyruvate enters the cell, the pyruvate dehydrogenase complex will catalyse the entrance of the acetyl group of acetyl CoA into the citric acid cycle. the co2 will diffuse out the cell.
190
the Krebs cycle also uses substrate level phosphorylation to generate ATP, describe what goes on here briefly x
high energy electrons from the acetyl group (2c) are passed onto electron carriers NAD+ and FAD.
FAD accepts electrons of slightly lower energy than NAD+.
only a small amount of ATP is produced. (all I need to know)
In the chemical structures, red type traces the two carbon atoms that enter the cycle via acetyl CoA (step 1), and blue type indicates the two carbons that exit the cycle as CO2 in steps 3 and 4.
Notice that the carbon atoms that enter the cycle from acetyl CoA do not leave the cycle together. They remain, occupying a different location in the molecules on their next turn, after another acetyl is added. Therefore, the oxaloacetate regenerated at step 8 is made up of different carbon atoms each time around.
In eukaryotic cells, all the citric acid cycle enzymes are located in the mitochondrial matrix except for the enzyme that catalyzes step 6, which resides in the inner mitochondrial membrane.
191
by which type of reactions does the electron transport chain generate energy, and how do they occur?
redox, which occurs when there is a transfer of one or more electrons from one reactant to another.
the reactant which loses an electron is oxidised, while the one receiving the electrons is reduced. this is associated with energy release.
192
what does the electron transport chain mostly consist of?
loads of multi protein complexes embedded in the mitochondria inner membrane.
most components of the chain are proteins to which are attached prosthetic groups, these are non protein components essential for the catalytic functions.
193
how does the electron transport chain work, like what happens as the electrons pass from one component to another?
each member of the chain becomes reduced when it accepts an electron, it then passes it to its downhill neighbour (which always has a slightly higher affinity for the electron), and so returns to an oxidised state
194
describe the specific molecules that electrons will pass between in the electron transport chain
first one will be a flavoprotein (prosthetic group= flavin mononucleotide).
then will be an iron-sulphur proteins, then to ubiquinone and then to a series of electron carriers termed cytochromes. the prosthetic groups of cytochromes have 4 organic rings surrounding an iron atom (like haemoglobin), except the iron of cytochromes transports electrons not oxygen.
the last cytochrome in the chain gives the electrons to oxygen, which picks up a pair of H+ to form water. FADH2 also transfers electrons into the ETC but adds its electrons at a lower energy than that of NADH. FADH adds its electrons direct to ubiquinone.
the bottom of the chain is oxygen (very electronegative). the fall in energy is broken up though.
195
how much ATP is formed from the electron transport chain?
none
196
what is ATP synthase?
a large multi protein complex which can be seen under an electron microscope in the inner membrane of the mitochondria.
has a mushroom kind of build.
197
what is the ion gradient that drives ATP synthesis in chemiosmosis, and how is it generated?
an H+ gradient, generated + maintained by the electron transport chain.
198
describe how the H+ gradient in chemiosmosis of respiration is maintained by the electron transport chain
the ETC uses the energy from the exergonic flow of electrons to pump H+ from the mitochondrial matrix into the inter membrane space.
H+ then pass back through the ATP synthase and this exothermic process is used to attach inorganic phosphate to ADP, producing ATP.
199
describe the process of chemiosmosis with the cytochromes and everything
yellow arrow= electron transport, which are finally passed to oxygen, the terminal acceptor, forming water.
most of the electron carries of the chain are grouped into 4 complexes (I-IV). Two mobile carriers, ubiquinone and cytochrome c, move rapidly, ferrying electrons between large complexes. As the complexes shuttle electrons, they pump protons from the matrix into the intermembrane space.
FADH2 deposits its electrons via complex II—at a lower energy level than complex I, where NADH deposits its electrons— and so results in fewer protons being pumped into the intermembrane space than occurs with NADH.
Chemical energy that was originally harvested from food is transformed into a proton-motive force, a gradient of H+ across the membrane. During chemiosmosis, the protons flow back down their gradient via ATP synthase, which is built into the membrane nearby. The ATP synthase harnesses the proton-motive force to phosphorylate ADP, forming ATP.
Together, electron transport and chemiosmosis make up oxidative phosphorylation.
200
describe the structure of ATP synthase with the Fo + F1 things
The ATP synthase protein complex functions as a mill, powered by the flow of hydrogen ions.
Fo= a H+ channel.
the H+ causes rotation of the rotor and central stalk, which the stator keeps F1 stationary. this also provides energy for ATP synthesis.
F1= site of ATP synthesis
201
describe how cyanide acts as a mitochondrial poison
it prevents passage of electrons from one of the cytochromes thereby blocking the ETC.
probs the fastest poison known.
202
describe how 2,4-dinitrophenol (DNP) acts as a mitochondrial poison
it makes the inner membrane leaky to H+ so that a gradient can't be established. ETC still works but energy is released as heat.
basically cooks you from the inside oh no
203
what is brown fat, and what is the function of mitochondria in it?
brown fat is basically like a specialised adipose tissue found in newborn babies. mitochondria produces heat in brown fat.
ATP synthase is sort of deactivated. thermogenin is a H+ channel in inner membrane in brown fat mitochondria. H+ leak back without passing through ATP synthase= no ATP made. energy produced in ETC released as heat
204
describe myoclonic epilepsy and ragged-red fibre disease (MERRF), a mitochondrial genetic disease
caused by a mutation in the mitochondrial encoded tRNA Lys gene.
affects translation of mitochondrial encoded proteins= abnormal mitochondrial morphology.
epilepsy and muscle weakness, no cure
205
are mitochondrial diseases inherited from the mother or father, but how are we trying to get around it?
mother, however. a new IVF technique has been developed which avoids passing on defective mtiochondria= the embryo has 3 genetic parents
206
in aquatic environments, which kind of organisms are photoautotrophs?
unicellular and multicellular algae, such as this kelp; some non-algal unicellular eukaryotes, such as Euglena; cyanobacteria; and other photosynthetic prokaryotes, such as the purple sulfur bacteria, which produce sulfur
207
describe the structure of chloroplasts
they are surrounded by an outer + inner membrane which together are termed the envelope.
the envelope encloses an aqueous compartment called the storm in which starch granules are usually found.
the inner most compartment is the thylakoid space which is enclosed by the thylakoid membrane, which contains chlorophyll + is where photosynthesis happens. in some chloroplasts, they form grant.
the storm is where the Calvin cycle happens
208
how are the light reactions and Calvin cycle linked?
The light reactions use solar energy to make ATP and NADPH, which supply chemical energy and reducing power, respectively, to the Calvin cycle.
The Calvin cycle incorporates CO2 into organic molecules, which are converted to sugar.
209
label this epic diagram
210
describe and explain how light reactions + chemiosmosis happen at the thylakoid membranes
yellow arrows= electron flow.
light energy is absorbed by chlorophyll for this
1. water is split by PS2 on the side of the membrane facing the thylakoid space
2. as plastoquinone (Pq) transfers electrons to the cytochrome complex, 4 protons are translocated across the membrane into the thylakoid space
3. a H+ is removed from the storm when it's taken up by NADP+.
4. The diffusion of H+ from the thylakoid space back to the stroma (along the H+ concentration gradient) powers the ATP synthase.
oxygen= waste product
These light-driven reactions store chemical energy in NADPH and ATP, which shuttle the energy to the carbohydrate-producing Calvin cycle.
211
what does the light reaction in photosynthesis convert solar energy into?
chemical energy
212
how is light energy absorbed by chlorophyll for the light reaction, name specific pigments and such xxx
when pigments absorb light energy as photons, an electron in the pigment is elevated to an orbital of higher energy.
there are loads of pigments in the thylakoid membrane like chlorophyll a + b, and carotenoids. only chlorophyll a can be in light reactions but the other ones absorb light at different wavelengths and transfer it to chlorophyll a.
213
what is a photosystem?
when pigments absorb light, the electrons quickly drop to their go energy losing excess energy as heat. a primary electron acceptor traps a high-energy electron that has absorbed the photon before it can drop.
only 1 localised pair of chlorophyll a molecules can donate their excited electrons to the primary acceptor electron= called the reaction centre. the reaction centre + primary electron acceptor= a photosystem.
214
which kind of light on the EM radiation spectrum drives photosynthesis?
visible light
215
why are leaves observed as green?
The chlorophyll molecules of chloroplasts absorb violet blue and red light (the colors most effective in driving photosynthesis) and reflect or transmit green light.
216
what is an absorption spectrum with photosynthetic pigments, and how do they help?
An absorption spectrum shows how well a particular pigment absorbs different wavelengths of visible light. Absorption spectra of various chloroplast pigments help scientists decipher the role of each pigment in a plant.
217
how would you go about getting an absorption spectrum of photosynthetic pigments perchance (2 ways)?
Technique A: spectrophotometer measures the relative amounts of light of different wavelengths absorbed and transmitted by a pigment solution. One by one, different colors of white light are passed through the pigment. Green light and blue light are shown here.
The transmitted light hits a photoelectric tube, converting the light energy to electricity. The current is measured by a galvanometer. The meter indicates the fraction of light transmitted through the sample, from which we can determine the amount of light absorbed.
218
analyse this graph of absorption spectra for algae exposed to different light wavelengths, and determine which wavelengths work most efficiently for photosynthesis
The three curves show the wavelengths of light best absorbed by three types of chloroplast pigments. Doesn't match the action spectrum fully, partly due to the absorption of light by accessory pigments such as chlorophyll b and carotenoids.
Aerobic bacteria was used, which concentrate near an oxygen source, to determine which segments of the alga were releasing the most O2 and photosynthesizing most. Bacteria congregated in greatest numbers around the parts of the alga illuminated with violet-blue or red light.
Conclusion: Light in the violet-blue and red portions of the spectrum is most effective for photosynthesis.
219
what is the head of chlorophyll a + b called (the part that absorbs light)?
porphyrin ring
Chlorophylls a + b sit in the thylakoid membrane, with the porphyrin rings kind of coming out at the top.
220
how do chlorophyll a + b differ?
only in the functional groups bonded to the porphyrin ring
221
how is transfer of energy between photosynthetic pigments aided by the fact that porphyrin rings and chlorophyll are sat quite close together?
This forms a chain of electron transfer, as when the electrons are excited and they start falling to the ground state, the energy isn’t released as heat or something but is transferred between pigments.
There is a general loss of electrons happening at the central pair of molecules that excites the electrons to the primary electron acceptor.
222
how does excitation of chlorophyll happen by light?
the absorption of a photon by chlorophyll causes a transition of the molecule from its ground state to its excited state, as energy derived from light elevates the electrons to a state it has more potential energy.
If the illuminated molecule exists in isolation (no other pigment near), its excited electron immediately drops back down to the ground-state orbital, and its excess energy is given off as heat and fluorescence (light).
223
how do photosystems absorb photons + how does this lead to electrons elevation?
they have antennae pigment molecules which absorb them.
energy transferred between pigments to the central pair of chlorophyll. electrons elevated to higher energy state + taken by primary electron acceptor.
224
just a lovely pic of a photosystem showing electron transfer to the primary acceptor
225
why is the reaction centre of PS1 called P700, and why is the reaction centre of PS2 called P680?
PS1 absorbs light energy best at 700nm, and PS2 absorbs light energy best at 680nm
226
in what process do PS1 + 2 co-operate?
they work together to produce non-cyclic electron flow to generate NAPDH, ATP + split water.
227
describe non-cyclic electron flow
1. PS2 spilts water, electrons replace those lost at P680. this generates oxygen + H+.
2. favourable movement of electrons down ETC with platoquinone + plastocyanin, to get to the oxidised P700 at PS1. energy gained pumps H+ into thylakoid space, generating H+ gradient to produce ATP with ATP synthase.
3. no water split by PS1. electrons originally from water replace those lost act P700. linear flow of electron with ferrodoxin.
4. the other ETC reduces the energy of the electrons, forming NADPH, which is electron carrier required for Calvin cycle.
228
is ATP produced during non-cyclic electron flow?
yep
229
does cyclic electron flow use both PS1 + 2, or not?
PS1 only- it can operate alone to produce ATP + doesn't make NADPH or oxygen.
230
describe the epic events of cyclic electron flow using only PS1
the whole point is to recycle electrons as PS1 can't regenerate them I fear.
1. photoexcited electrons from PS1 are occasionally shunted back from Fd to chlorophyll via the cytochrome + Pc. this supplements the supply of ATP (via chemiosmosis) but makes no NADPH.
2. this replaces the electrons lost in P700
This goes on at the same time as the non-cyclic one.
231
how does the Calvin cycle use ATP + NADPH?
it requires ATP as an energy source + consumes NADPH as a source of high energy electrons
232
name 5 types of organic molecules generated in the Calvin cycle in photosynthesis
hexose phosphates for starch (storage), cellulose (cell walls), sucrose (translocation), lipids (cell membranes), amino acids (protein synthesis)
233
describe what happens in the Calvin cycle
The G3P molecule is the start of producing anything important.
1: CARBON FIXATION- CO2 + Rubisco= G3P. For every three molecules of CO2 that enter the cycle, the net output is one molecule of glyceraldehyde 3-phosphate (G3P), a three-carbon sugar.
2. REDUCTION- output of 1 G3P molecule (forms glucose and other organic things).
3. REGENERATION OF RuBP- the other 5 G3P go on to form RuBP.
234
can the Calvin cycle function in the dark?
yeah, its only fuelled by ATP/NADPH generated by light reactions
235
what are the similarities in chemiosmosis in chloroplasts/ mitochondria?
1. ETC in the membrane pumps H+ ions across the membrane. energy for this is generated by passing electrons through a series of progressively more electronegative carriers.
2. membrane contains ATP synthase which uses H+ ion gradients to phosphorylate ADP to produce ATP
3. some similar quinones + cytochromes
also similar endosymbiotic origin
236
differences in the ETCs of chloroplasts + mitochondria?
1. in mitochondria, the ETC pumps H+ out the matrix. in chloroplasts, they're pumped into the thylakoid compartment
2. in mitochondria, the high energy electrons fed into the ETC come form oxidation of food molecules. in chloroplasts, they're generated in photosystems by absorption of photons
237
what are the main basic functions of the cytoskeleton (5)?
cell mobility, cell division cell shape, organelle movement + chromosomes
238
why do many drugs target the cytoskeleton?
it has wide effect, e.g. abnormalities result in diseases affecting every tissue in the body
239
what are the 3 main fibres in the cytoskeleton?
1. microfilaments
2. microtubules
3. intermediate filaments
240
what is the basic structure of a microfilament in the cytoskeleton + what is its basic function?
2 actin chains twisted around each other (composed of G-actin + F-actin which is formed when polymerised with ATP hydrolysis).
about 7-8 nm long
shape + cell movement
241
what is the basic structure of a cytoskeletal microtubule + what is its basic function?
straight hollow dimers 25 nm wide, up to 20 um long, composed of alpha + beta tubulins
basically largest things in cytoskeleton
mechanical strength
242
what is the basic structure of a cytoskeletal intermediate filament + what does it do vaguely?
about 8-12 nm wide. made of lots of proteins. usually permanent fixtures, important in maintaining the cell shape + organelle positions (intracellular movement)
243
how is the f-actin (filamentous actin) in microfilaments in the cytoskeleton formed?
from g-actin being polymerised by ATP hydrolysis. each g-actin monomer has an ATP binding cleft for this.
G-actin assembles into long, helical F-actin polymers with a +ve + -ve end.
244
what links the 2 lobes of the actin monomer in a cytoskeletal microfilament?
ATP.
245
which end of an f-actin molecule will be where a g-actin molecule binds to it in a microfilament?
the positive end
246
white blood cell transmigration is a process driven by actin polymerisation in the cytoskeleton, what happens here vaguely?
With white blood cell transmigration, leucocytes will roll, and epithelial cells will also have to change their shape to accommodate the cell when it breaks through the chain- driven by actin polymerisation.
247
describe how cellular extensions like pseudopodia are driven by actin polymerisation, for example in echinoderm sperm's acrosome
when activated, polymerised actin filaments will extend, linked by fascin cross-links
248
name a structure in epithelial cells that are supported by microfilaments + how does it help function?
Microvilli are supported by microfilaments, which generates a brush border, allowing movement of cells e.g. cilia in the respiratory tract to move mucus away.
249
describe the essential role actin + myosin II (actin-based motor protein) have in cytokinesis
they will be present in the cleavage furrow that forms, splitting the cells
250
how do microfilaments in the cytoskeleton aid plant cells?
cytoplasmic streaming using parallel actin filaments
251
describe how microfilaments can aid in muscle contraction
Motor proteins (myosin for actin) will bind to the polarised microfilaments end, allowing muscle contraction, for example, which is only type-2 myosin.
252
name processes that involves exit and entry into a cell, that widely uses microfilaments in the cytoskeleton
endo + exocytosis, as they also connect tight + adherence junctions at the plasma membrane.
253
how does myosin act as actin's motor protein + what kind of roles do they accomplish?
myosin uses energy derived from ATP hydrolysis to "walk" along actin filaments, used in contraction/ transporting/ membrane association (endocytosis)
254
how do toxins such as phallodin aid as fluorescent tags for the cytoskeleton?
they bind to f-actin preventing disassembly, so we can use it to image the cytoskeleton, and see what transport within the cell looks like, and trap cellular extensions that occur.
255
how do microtubules in the cytoskeleton exhibit dynamic instability, how does it help?
the GTP molecule, for example, in beta-tubulin can just kind of be hydrolysed, meaning the microtubule can alternate between cycles of growth + shrinkage
this allows the cell to reorganise the cytoskeleton when needed
GTP is kind of like its ATP, its the same but with guanine
256
why does microtubule dynamic instability occur in beta tubulin more than alpha?
Depolarisation at the GTP end is way faster than if it were with GDP.
257
how does the cancer drug taxol for ovarian cancer used microtubule drugs?
it binds + stabilises microtubules, preventing microtubule disassembly and therefore cell division in cancerous cells
258
describe the 9+2 arrangement of microtubules in the cytoskeleton
microtubules consist of a core of axonemal microtubules ensheathed in an extension of plasma membrane.
9 doublets of MTs are arranged in a ring + connected to 2 central ones by radial spokes
259
microtubules are the main component in cilia + flagella, with the 9 + 2 arrangement, how does dynein help the structure?
each doublet is connected to its neighbour by sidearms composed of dyne, which contracts at the expense of ATP forcing the doublets to move relative to each other.
260
what prevents doublets in the microtubules in cilia + flagella from sliding past each other, enabling them to bend?
nexin cross links
The protein nexin + ATP causes the tubules to bend, causing the wave-like motion we see in cilia + eukaryotic flagella.
force generated by dyne movement causes cilium to bend.
261
what are the 2 basic differences between cilia and flagella?
cilia: shorter (2-20 um), and more of them
flagella: longer (10-200 um), fewer
262
do both prokaryotic + eukaryotic flagella show the 9 + 2 microtubule arrangement, and describe how this affects their movement?
just eukaryotic, hence why they be twirling like a propeller + prokaryotic ones whip
263
how do microtubules aid in metaphase of a mammalian cell?
kinetochore microtubules are the ones that join onto the centromere of a chromosomes and center them
264
how are the microtubules involved in metaphase different to normal cytoskeletal ones?
In a metaphase mammalian cell, there is a 9+3 arrangement, where mitotic spindles connect to the chromosome via a microtubule called a kinetochore, aided by astral microtubules, which pulls chromosomes apart in cell division.
265
what is the basic function of kinesis + dynein motor proteins, but how do they differ slightly in their function?
they transport membrane-bound vesicles, proteins + organelles along beta-microtubules with ATP (each walking step requires hydrolysis from 1 molecule of ATP).
kinesins move cargo towards the +ve (anterograde) MT end, while most dyneins transport cargo towards the -ve end (retrograde)
266
axonemal microtubules are the type found in cilia and flagella and stuff, what is the other type of microtubule called + what does it do?
cytoplasmic- more dynamic + loosely organised in the cytoplasm
used for maintaining cell shape, movement and chromosome separation
267
how does the structure of an intermediate filament help with its function?
Insoluble components form a rope-like structure which is twisted for mechanical strength e.g. in cell junctions
268
intermediate filaments are found just about everywhere I fear, name like 2 or 3 places its found
269
intermediate filaments interact with desmosomes (specialised adhesive proteins), what happens with this combo?
connect cells to other cells + help the cell attach to its substrate (extracellular matrix). Particularly found in cardiac tissue.
270
what structure do neurofilaments form to strengthen cardiac muscles?
Neurofilaments form a mesh to strengthen cardiac muscles.
271
how does ALS (amyotrophic lateral sclerosis) result in loss of muscle control?
ALS affects the nerve cells of the brain and spinal cords
272
how is ALS (amyotrophic lateral sclerosis) linked to intermediate filaments?
when they aggregate, it causes als
273
how is EBS (epidermolysis bulls simplex) caused by intermediate filaments?
most cases are due to dysfunction of intermediate filaments in basal keratinocytes of epidermis, and are usually caused by defects in a keratin 14 gene.
274
how could you know if EBS (epidermolysis bulls simplex) has reached the brain with a biopsy?
Cells infected with epidermolysis bullosa simplex will break off and might reach the brain. If you take a biopsy of the brain and find keratin, it means the disease has reached the brain.
275
what are the general top, middle + bottom of a cell called?
apical, lateral, basal
276
how do all cellular junctions connect?
via the cytoskeleton
277
briefly describe the 3 types of cell junctions
impermeable junctions- prevent passage of molecules between cells (tight)
adhesive junctions- mechanically hold cell together (adherens junctions + adhesive desmosomes)
communicating junctions- passage of small molecules between cells (gap junctions/ chemical synapses)
278
where on a cell are the tight, adhesive + communicating cellular junctions located roughly?
tight- apical junction complex (top of cell)
adhesive- apical junction complex
communicating- lower down
279
how does the function of tight junctions allow for cellular polarity (fence function)?
keeps the apical plasma membrane from the basal ones, allowing them to have different compositions
280
how does the barrier/ gate function of tight junctions aid the cell?
prevents molecules leaking between adjacent cells (paracellular movement of water, ions, etc), regulating selective permeability. this is done by forming a continuous seal around the cell
e.g. blood-brain barrier
281
the apical surface of the cell has proton + Cl- ions which form HCl, in the gut, how do tight junctions stop the acid from being pumped into the blood?
the tight junctions keep the apical membrane components separate from the basal membrane components
282
how many different tight junction proteins are there?
over 100
283
tight junctions can come in the forms of transmembrane proteins + cytosolic proteins, how do their functions in the separate places differ (6)?
transmembrane: physical barrier, adhesion, permeability e.g. Claudins like JAM (junction adhesion molecule).
cytosolic proteins: scaffolding, signalling, polarity, more in the cytoskeleton (occludins)
284
how can tight junction proteins be affected directly + indirectly by infection, and give examples of pathogens that will affect them?
they can be disrupted directly by pathogens or indirectly
Tight junction proteins are a target for infectious microbes, e.g. Helicobacter pylori disrupt the barrier to transmigrate with paracellular pathways and infect the body. Also, with Clostridium difficile, which can lead to diarrhoea, and sepsis if in the blood, as they affect the TJ protein claudins
285
what is the protein adhesive junctions are mainly made of?
They’re made of mainly cadherins, with both transmembrane + cytosolic proteins.
286
what do adherens junctions specifically (part of anchoring junctions) do?
connect cells to actin filaments- intracellular signalling regulator
287
what do desmosomes specifically (part of anchoring junctions) do?
connect cells to intermediate filaments
288
what is the general function of adherens junctions?
Adherens junction proteins reduce stress + abrasion with cells, keeps them in the place they should be.
289
some anchoring junctions are made from integrin proteins instead of cadherins, what are the 2 types of these kinds?
focal adhesions (connect extracellular matrix to actin filaments) + hemi-desmosomes (connect ECM to intermediate filaments)
290
describe the cadherin/ catenin complex in an adherent junction
E-cadherin will bind to its cytosolic partner (B-catenin), which is the major adheren junction complex. They anchor to the cytoskeleton via actin filaments.
291
what does loss of E-cadherin in adherens junctions induce?
The loss of E-cadherin will cause the cell to change morphology, which is important in allowing cells to change shape to form over a gap to cover a wound.
292
how do anchoring junctions provide structural integrity to tissue?
provide structural integrity by withstanding mechanical stress, by expressing the force throughout the whole tissue sheet instead of just one part receiving it.
spot desmosomes (not belt) spot-weld cells together, attached on the inside of the cell to keratin filaments in the cytoskeleton, spreading stresses from the spot desmosome through the cell
293
which element are anchoring junctions dependent on?
calcium
294
what do hemi-desosomes do?
attach the cell base to the basal lamina (basement membrane)
295
which is the most common cell junction?
gap junctions (communicating) , present in all tissues
296
what are gap junctions structurally (6x2 arrangement)?
tiny pores composed of proteins called connexins; 6 connexins on one cell form a connexon, and there's 2 cells- 6x2 arrangement
this is how cells are connected
297
which 2 factors does the gap junction depend on?
intercellular pH + intracellular calcium levels
298
how does connexin in gap junctions connect cells?
forms cylindrical channels in gap junctions
299
how does the thing about gap junctions allowing connection between cells help in 2 specific cases?
Allows signals to transmigrate across epithelial cells, heart beating for example.
Allows cells to signal to each other when there’s a problem, and important in smooth muscle + neurons.
hence why its abundant in cardiac + muscle tissue.
300
name 3 putative (kind of accepted but were not really sure tho) roles of gap junctions medically
inflammatory bowel diseases (IBD)
gastrointestinal infections
autism spectrum disorder (ASD)
301
give 3 reasons why cells need to divide
1. new organisms- unicellular ones e.g. bacteria
2. growth- multicellular organisms grow by just adding more cells
3. cell replacement- wear + tear (skin exfoliation and stuff), and apoptosis
302
the purpose of cell division is to produce 2 genetically-identical daughter cells. to do this, which 3 things must happen?
1.dna duplication
2. chromosomes segregation
3. daughter cells need to physically divide from each other
303
describe binary fission process
1. chromosome replication- A specific point of origin is copied bidirectionally and each replicate origin moves to opposite cell poles
2. plasma membrane grows inward, new cell wall formed
3. 2 daughter cells produced
very simple + much less complicated than eukaryotic stuff
304
why is prokaryotic cell division way more simple than eukaryotic?
prokaryotic only has like 1 or 2 chromosomes to copy, whereas eukaryotic ones will have more.
305
describe the phases of the cell cycle: G1, S, G2, mitotic
G1: cell grows = prepares to replicate DNA. cells are assessing whether the environment is suitable or not to replicate in
S: "synthesis"- cell grows + DNA replicates. takes around 8 hours.
G2: cell grows + prepares for mitosis. makes sure S phase has been completed.
M: chromosomal segregation (mitosis) + cytokinesis.
306
apart from M, which cell cycle stage (G1, S, G2) is involved in mitosis, describe it in detail?
G2 of interphase: there's an intact nuclear envelope, the centrosome + chromosomes are replicated (not condensed tho so indistinct), and microtubules extend forming asters.
307
how does G2 of interphase look under a microscope?
fluorescent microscope images can show centrosomes with tubulin (protein that forms spindle fibres) are kept away from the nucleus and cytoplasm.
308
describe prophase in mitosis (4)
1. chromatin condenses, forming discrete complex chromosomes
2. nucleoli disappear
3. centrosomes move away from each other
4. mitotic spindle (microtubule extensions) begins to form + elongate from the centrosomes when they start to move away.
309
describe pro metaphase in mitosis (4)
1. breakdown of nuclear envelope (needed for the microtubule extensions to interact with the chromosomes)
2. some microtubules attach to chromosomes at their kinetochores
3. other microtubules interact with those from opposite poles
4. random migration of chromosomes before they align on the metaphase plate.
310
describe metaphase in mitosis (3)
1. centrosomes at opposite poles yayy
2. chromosomes align on the metaphase plate
3. sister kinetochores attached to microtubules coming from opposite poles- allows proper separation.
311
describe anaphase in mitosis (4)
1. begins with centrosome separation
2. sister chromatids move towards opposite poles of the cell
3. each chromatid becomes a new chromosome
4. poles move further apart, so cell kinda becomes oval, which helps with partitioning and septation
312
how do the processes in anaphase allow cytokinesis to occur?
generating space between the sister chromatids (now daughter chromosomes)
313
describe telophase in mitosis (4)
1. elongation of cell by polar microtubules
2. daughter nucleoli begin to form at poles
3. nuclear envelope forms (microtubules can’t interact with chromosomes anymore)
4. chromatin begins to decondense, so transcription can happen
314
what are the 3 main components of the mitotic spindle?
tubules (astral, kinetochore, non-kinetochore/polar), centrosomes, chromatid pairs.
315
what is the function of the mitotic spindle?
to organise chromatids along the metaphase plate + pull sister chromatids apart
316
draw a lil diagram of the mitotic spindle and label where the astral, kinetochore and polar microtubules are
317
which protein are astral motor microtubules in the mitotic spindle made of?
dynein
318
what are the 3 functions of astral motors (dynein)?
1. pulls astral microtubules towards poles during prophase with ATP hydrolysis for dynein
2. microtubules de-polymerise + shorten
3. hold astral microtubules in place during metaphase + later
319
what are the 3 functions/processes of kinetochore motors (dynein)?
1. attach chromosomes to microtubules by kinda walking with ATP hydrolysis from dynein
2. pull on microtubules during anaphase, so chromosomes move towards centrosomes
3. microtubules de-polymerise + get shorter
320
what are the 4 functions/processes of polar motors (kinesin)?
1. motors are attached to a microtubule from either side where the polar microtubules overlap
2. motors push the microtubules away in opposite directions during metaphase + anaphase
3. microtubules polymerised + get longer
4. cell elongates
the kinesin uses ATP to insert tubulin proteins to elongate the Mts, required for cytokinesis
321
what do astral microtubules do + where are they in the mitotic spindle?
Astral microtubules present between centrosome and cell membrane at each cell pole, they contact the cell membrane and anchor the centrosome.
322
what do kinetochore microtubules do + where are they found in the mitotic spindle?
Kinetochore microtubules attach to the middle bit of chromosomes (the kinetochore) + pull the chromosomes to opposite sides of the cell, allowing cytokinesis to occur.
323
what do polar microtubules do + where are they found in the mitotic spindle?
they extend from the centrosomes and overlap with microtubules at the opposite end- involved in elongation of the cell.
324
what is the overall overarching function of motor proteins in mitosis?
to separate sister chromatids during anaphase
325
what occurs in anaphase a?
kinetochore microtubules shorten + chromosomes move to poles.
forces generated are mainly at kinetochores
326
what occurs in anaphase b?
sliding force generated between inter polar molecules microtubules from opposite poles to push the poles apart (from kinesin).
the inter polar microtubules also elongate. More polymerisation= more elongation.
pulling force acts directly on the poles to move them apart.
327
chromosomal separation is achieved by a combination of pushing + pulling, what does this mean and what proteins are involved?
pulling = dynein. kinetochore motors pull chromosomes towards the pole. astral motors pull centrosomes toward inner face of plasma membrane. both shorten + depolymerise MTs.
pushing = kinesin. polar Mts add subunits (polymerise) microtubules to drive the poles of the spindle apart. this elongates the cell to help telo+ cyto
328
describe anaphase in terms of the specific microtubules and proteins (4)
1. proteins holding sister chromatids together are inactivated so chromatids separate
2. kinetochore MTs have motor proteins (dynein) which walk a chromsomes to nearest pole
3. MTs shorten by depolymerisation at their kinetochore ends
4. polar MTS elongate whole cell- motor proteins (kinesin) attaches to Mts and lengthen them by addition of subunits
329
describe cytokinesis in ANIMAL CELL mitosis (3)
1. microfilaments form a ring at the cleavage furrow
2. ring contracts- because of actin + myosin interaction
3. furrow deepens until the cell is pinched in 2
330
describe cytokinesis in PLANT CELL mitosis (2)
1. cell plate forms at equatorial plane of the cell
2. cell wall forms from plate contents
331
identify the stages of cell division from this pic xxx
A= metaphase, B= prophase, C= prometaphase, D= telophase, E= interphase (DNA is decondensed + present in whole nucleus), F= anaphase
332
what are the 3 reasons that cell division needs to be regulated? explain all
1. development- body parts and stuff need to be the right size
2. injury- cells need to divide after injury but stop when its fine. either breakdown of systems or release of growth factors
3. adaptive responses- e.g. cells in bone marrow respond to low O2, produce more red blood cells, need to stop when oxygen is normal. people who do high-altitude sports need to do altitude training, to naturally boost p(O2).
e.g. lymphocytes divide when antigen triggers response, needs to be controlled.
333
what is the main big consequence of deregulated cell division?
cancer
334
the 2 main ways to regulate cell division are external + internal signals. explain them + give examples of both.
external signals- diffusable chemical signal produced by other cells which kinda tell the cell how to behave e.g. GROWTH FACTORS (mitogens)
internal signals- chemical signals produced internally by the cell itself in order to regulate its own division- in cell cytoplasms e.g. Cdks.
335
external signals regulate cell cycle progression. do they promote or inhibit cell division?
both
336
The only way cells can divide is if there is a long, sustained stimulation of mitogen cells (external signals). what happens if there is an absence of them?
S phase cyclins (i.e. those cyclins which drive cells into S phase) aren't made, and cells won't progress through the G1 checkpoint.
they will enter G0 instead- quiet phase or quiescence. 95% of cells are quiescent- non-dividing, waiting for signals.
337
what do mitogens (growth factors)bind to to promote cell growth?
receptors in plasma membrane
338
platelet-derived growth factors are examples of external growth factors. how do they repair damaged tissue?
Platelet-derived growth factors are specialised cells in blood.
they're released in injury, it binds to its respective receptor meaning blood vessels begin to divide and repair the damaged tissue. important for blood clotting + wound healing.
339
how are internal cell signals stimulated?
These are stimulated by extracellular factors, such as mitogens, through activation of transcriptional factors.
340
internal signals were first identified by fusing cells from different cell cycle stages. what was the result from the M + G2 phase fusion thing?
G2 nucleus will break down, and the DNA condenses to give mitotic chromosomes. Scientists said there must be M-phase cells in the G2 cell to promote mitosis. G1 cell chromosomes were unique because they only had 1-arm chromosomes (just like a chromatid).
341
internal signals were first identified by fusing cells from different cell cycle stages. what was the result with S + G1 cells? also describe how radioactively-labelled nuclei could be used to show it.
when s-phase is entered, radioactivity would increase. When fused with a G1 cell, they left G-phase and incorporated the S-phase into both. The opposite happened with G2, as there’s already a copy of the genome, so it wouldn’t copy again.
342
how do cell cycle checkpoints regulate cell division so it doesn't develop into cancer (2)?
they enable cells to stop dividing if the correct signals aren't present.
they also allow cells to review current circumstances + prevent untimely exit from each cell cycle phase. if they do exit at the wrong time= genetic instability= cancer.
343
what is the function of the G1 checkpoint, and what are the 2 checks?
commits cell to DNA replication + cell division.
checks if cell is a suitable size, and is there a sustained appropriate mitogenic signal.
if not, cell enters G0. if yes, cell goes to S.
344
what is the function of the G2 checkpoint, and what are the 3 checks?
cell makes decision whether or not to go into mitosis.
checks if cell is a suitable size, is DNA replicated + if the environment is favourable.
if not, cell doesn't proceed. if yes, cell goes to M phase.
345
what is the function of the M checkpoint, and what is the check?
occurs in metaphase.
checks that the chromosomes are attached to the spindles + they’re all lined along the midpoint of the cell before anaphase.
if not, the cell doesn't proceed. if yes, cell goes into anaphase.
346
cyclins were discovered by Tim hunt in 1982. what happened + describe how their up + down growth?
Cyclins isolated with sea urchin cells- go through the cell cycle at the exact same time (synchronous).
he found a group of proteins of which their levels increased + decreased between interphase and mitotic phase = cyclins!!!!
For house-keeping genes, they do just kind of grow linearly on that graph. But cyclins have a constant accumulation and degradation.
347
describe the basic mechanism of action of Cdk + cyclin proteins (with phosphorylation as well), and like what they look like
combination of the 2 proteins known as a 'promoting factor'- control progression of the cell into the next cell cycle phase.
phosphorylation may either activate or deactivate it- they regulate by transferring phosphate from ATP to the target protein
348
2 cyclin-idk complexes are the SPF (S phase promoting factor) and the MPF (maturation promoting factor). which checkpoints do they control?
The SPF controls G1, and MPF controls G2.
349
The regulating of cell-cycle phases is controlled by the expression of the cyclin. Why is this the case?
Kinase always exists in the cell, but cyclin is produced and degraded.
Cdk levels are maintained at more or less same concentration throughout the cell cycle, but are only activated when bound to cyclin A or B.
350
what does the Cdk-cyclin complex for SPF look like?
drives cells into S phase
351
what does the Cdk-cyclin complex for MPF look like?
drives cells into M phase
352
describe how the levels of MPF activity correlate with cyclin levels + stages of mitosis (M phase)
peaks of mPF activity correlate with peaks of cyclin cycle- Cyclin B begins to accumulate, and cells move towards the G2 checkpoint.
cyclin expression increases loads at various cell cycle stages (particularly G2) + decreases sharply during M.
the max is during early m.
353
describe the steps of MPF activation in G2 phase (7)
1. cyclin B accumulates
2. cyclin B and Cdk1 bind to form MPF
3. MPF triggers mitosis
4. MPF activates cyclin-degrading enzyme which degrades cyclin
5. loss of cyclin inactivates enzyme after mitosis
6. Cdk1 is recycled
354
the MPF complex stimulates other kinases indirectly by doing what?
causing the nuclear envelope to fragment
355
the internal regulator of the M phase checkpoint isn't Cdk, but a complex of proteins called what?
anaphase promoting complex (APC)
356
epic thing describing how the metaphase checkpoint works
Initially, kinetochore microtubules from one spindle pole binds to the kinetochore in a sister chromatid pair. Additional microtubules can then bind to the chromosome in various ways.
A microtubule from the same spindle pole can attach to the other sister kinetochore, or microtubules from both spindle poles can attach to one kinetochore. These incorrect attachments are unstable, however, so that one of the two microtubules tends to dissociate. When a second microtubule from the opposite pole binds to the second kinetochore, the sister kinetochores are thought to sense tension across their microtubule-binding sites, which triggers an increase in microtubule binding affinity. This correct attachment is thereby locked in place.
357
how does cohesin help in the metaphase checkpoint?
Chromosomes are covered in a protein called cohesin, which keeps the sister chromatids together until they don’t need to be. Basically like an elastic band. Anaphase is initiated when APC ubiquitinates the cohesin.
358
currently, how many people in their lifetime will develop cancer?
1 in 2.
Likelihood to develop a mutation/ tumour increases with age, so the average age of having cancer is slowly increasing- becoming a bit more common. There isn’t a single cause= isn’t a single cure, but treatments have improved since the 70s.
359
cancer has recently overtaken heart disease as the leading cause of death in the UK, why? (2)
1. disease of the aging population
2. better treatment for heart disease, lower mortality.
360
which cancers are the 2nd biggest killer for women and men?
prostate for men
breast for women
361
what is the most common form of cancer for women + men, and is it driven mostly by genetics or environmental factors?
lung cancer- although genetics go into it, lung cancer is almost entirely driven by environmental factors. Reasonably good treatments for it, and most common one to get for all people.
362
why are there so many types of cancers (hence no single cure)?
there are as many forms of cancer as there are types of cell in the body- cell cycle regulation can go wrong in all cells proliferation.
so, a little less than 200 different cancers.
363
cancer classification- carcinoma?
cancers arising from epithelial cells (surface cells e.g. lining of gut, skin, cells lining airways of the lungs).
they constitute 80-90% of all cancers, as these cells are exposed to the environment e.g. carcinogens.
364
cancer classification- sarcoma?
cancers of connective + supportive tissues e.g. bone cancer, muscle, rare 1%
365
cancer classification- myeloma?
one of 3 different tumour types, cancers of the plasma cells of the bone marrow- antibody producing cells- secondary infections (pneumonia + pyelonephritis (UTI).
366
cancer classification- lymphoma?
solid tumours of the lymphatic system- lymph glands, lymph nodes or in organs- tonsils, spleen, thymus- formed from maturing WBCs.
367
cancer classification- leukaemia?
'blood' cancers- more specifically precursor blood cells in bone marrow- circulating white or red blood cells. excess of immature cells- cells aren't differentiated + don't function + nucleus takes up a whole cytoplasm- anaemia- suppressed immunity.
368
cancer classification- mixed classifications?
e.g. teratocarcinoma.
cancers originating in germ cells + stem cells- therefore encompasses a range of cancers (usually associated with reproductive organs)- testicular, ovarian, even placental.
369
how do the growth characteristics of a cancerous cell differ from those of a normal cell in an agar plate? (2)
1. anchorage dependent growth- normal cells grow in a single layer on a basement membrane; no attachment no growth. cancer cells don’t need to be just on the bottom layer, usually kind of clump and aggregate.
2. density dependent growth- normal cells stop growing when confluent + cover the bottom of the plate (signals from other cells). If the bottom is scratched, they will move and grow to cover the gap. Cancer cells can stack up and form multi-layered clumps (foci).
370
a factor of the abnormal proliferation of cancerous cells is immortality- explain this.
normal diploid cells have a limit of cell doubling cycles they can do e.g. fibroblasts have 50-60 doublings then decreases (Hayflick limit).
cancerous cells don't have this limit.
normal cells life expectancy is related to shortening of chromosomal telomeres. cancerous cells can maintain telomere length (telomerase) by expressing an enzyme, so it doesn’t get shorter with each division.
e.g. HeLa cells cultured from cervical carcinoma can do a little less than 20,000 divisions.
371
a factor of the abnormal proliferation of cancerous cells is reduced reliance on growth factors produced by other cells- explain this.
there are external growth factors required for progression through G1 checkpoint.
e.g. 3T3 fibroblasts- normal cells only grow in culture media containing certain growth factors. transform these into cancer cells by viral infection, which will happily grow on a basal media lacking the same growth factors.
372
a factor of the abnormal proliferation of cancerous cells is increased production of growth factors- explain this.
in addition to being less reliant on growth factors produced by other cells, cancerous cells can over-produce growth factors in order to promote growth, by increased expression of growth factors or increased 'shedding' of them.
Some cancer cells can change their environment by secreting growth factors, increasing the number of divisions of cancer cells around them.
373
a factor of the abnormal proliferation of cancerous cells is changes in cell membrane structure + function- explain this.
cell surface/ plasma membrane is as strong determinant of cellular 'social' behaviour e.g. communication, cell movement, adherence, access to nutrients, recognition by the immune system.
they can express markers on the cell so that things that should kill the cell can’t find them.
glycolipids, glycoproteins, proteoglycans, muffins.
374
cancer is a multistage disease driven by mutation. it requires multiple mutations to overcome normal cell programming. what are the stages of cancer disease progression? (7)
1. initiation
2. clonal expansion
3. primary tumour
4. secondary mutations
5. malignancy
6. invasion
7. metastasis
375
the 1st stage of cancer progression is initiation. explain it.
a single cell will have a mutation that gives growth advantage e.g. inactivation of tumour suppressor/ activation of oncogene. the growth advantage will cause it to lose some of its growth control.
Leads to displacement of normal cells by the cancer ones.
376
the 2nd stage of cancer progression is clonal expansion, explain it.
proliferation begins- mutated cell divides quicker than surrounding cells to form a cluster of 'clones'- disease is monoclonal.
cancer cells basically take over a little bit of the basement membrane tissue.
377
the 3rd stage of cancer progression is primary tumour, explain It xxxx
the cancer remains in situ (i.e. not moved yet from where it was originally mutated). tumour begins- not invading surrounding tissue- surgery still possible, but highly likely that other mutations will arise from the first.
378
the 4th stage of cancer progression is secondary mutation, explain xxxx
secondary mutations provide a new phenotype with a selective advantage.
379
the 5th stage of cancer progression is malignant cancer, explain.
following secondary mutations, the cells lose contact with their neighbours + become invasive- secrete proteases to breakdown the extracellular matrix holding cells in place- risk of metastasis.
They are more difficult to treat as they begin to invade local tissue. They will go through the basement membrane.
380
in metastasis, why do cells migrate to the blood, and why does this movement make the tumour way harder to treat?
cells migrate towards blood vessel because there’s a lot of oxygen there.
the circulation in the blood helps the cell to invade around the body, so stuff like radiotherapy won’t help as much as it’s localised.
381
the 6th stage of cancer progression is invasion of lymph and/or blood vessels, explain.
first stages of metastasis- cancer cells have low adherence- easy to break off main tumour + enter vessels.
382
the 7th stage of cancer progression is metastatic tumour, explain it.
cells from original tumour in lung has now entered a vessel + emerged at the other end to form a new tumour in another organ.
very hard to treat. can form a series of metastatic tumours in the same location.
383
name at least 3 characteristics of malignant tumour cells (6 total tho)
1. excessive proliferation
2. unusual number of chromosomes (aneuploidy) e.g. HeLa (cervical carcinoma) cells have 82 chromosomes instead of 46.
3. deranged metabolism- e.g. increased demands for nutrients + use aerobic glycolysis for ATP generation.
4. reduced attachments to neighbouring cells- enables spread to other tissues.
5. invasive phenotype- they secrete proteases that remodel the environment round cells. detaches from original tumour + enter blood stream and lymph system.
6. proliferate in other parts of the body (metastasis).
384
(very broad question im sorry) is cancer genetic?
yes but, in most cases, not in the inherited way.
there are carcinogens e.g. cigarettes (mutagenic chemicals); sunlight (UV radiation; viruses like HPV that can cause cervical cancer(insert DNA into genomes).
but you can also develop tumours from inherited stuff e.g. retinoblastoma (eye cancer).
but then also DNA mutations, which encode proteins to regulate cell division. PROTO-ONCOGENE OR TUMOUR SUPPRESSOR.
385
proto-oncogenes become oncogenes in 4 different ways, one is translocation, what does that mean?
1. translocation or transposition so gene just moves to new locus- new promoter means gene transcribed more efficiently= more protein.
386
proto-oncogenes become oncogenes in 4 different ways, one is gene amplification, what does that mean?
the gene is replicated, meaning there is more total protein.
387
proto-oncogenes become oncogenes in 4 different ways, one is point mutation within a control element, what does that mean?
point mutation within a control element e.g. mutation in existing promoter- more efficient transcription.
388
proto-oncogenes become oncogenes in 4 different ways, one is point mutation within a gene, what does that mean?
hyperactive or degradation- resistant protein.
changes the protein itself- more growth promoting?
389
describe the experiment in identifying oncogenes
extract DNA from human tumour cells (which will contain mutated oncogene).
tumour DNA introduced into mouse cells (3T3). cells which have taken up the oncogene proliferate + form foci.
(cells in the foci may have other bits of DNA as well as oncogene)
DNA from foci reintroduced into fresh 3T3 cells to dilute out human DNA other than oncogene.
extract mouse genomic DNA from cells which now contains human oncogene.
fragment DNA + introduce to bacterial virus- phage library
add phages to bacteria plate, which will kill them, leaving empty spot.
'blot' plate onto filter paper. human DNA contains Alu sequences (mouse doesn't)- detect human oncogene DNA using a probe against Alu.
390
what is Ras?
small G protein (binds to guanine nucleotides).
first oncogene that was discovered. It has a function where it only stimulates growth of the cell if it binds to GTP + activated. When mutated, it happens at only one site (glycine 12), In this way, it differs from oncogenes as there is only 1 amino acid it will mutate at.
391
describe the steps of how oncogenes were found to code for components of signalling pathways (Ras). (5)
1. growth factor binds to a receptor at the cell surface.
2. receptor is also a protein kinase which autophosphorylates itself when bound to growth factor.
3. change in receptor phosphorlyation detected by Ras, which binds to GTP which then activates Ras
4. activated Ras signals to mitogen-activated protein kinases (MAPK) operating in a cascade (one phosphorylates + activates another).
5. cascade ends when final kinase phosphorylates a transcription factor in the nucleus, which regulates gene expression.
in cancers case, the TFs enhance expression of genes controlling cell cycle e.g. cyclins.
392
how was the Ras oncogene discovered?
when DNA from a bladder tumour was used to transform mouse 3T3 cells
393
why does the oncogene Ras explain why cancer cells don't require external growth factors?
Ras differs from the proto-gene by a single nucleotide- different amino acid in protein G12V- causes Ras to remain permanently bound to GTP- permanently active.
stimulatory signal to nucleus never switched off- excessive production of cyclins- uncontrollable growth.
394
are the mutations that activate proteins (e.g. Ras) to turn proto-oncogenes into oncogenes dominant or recessive?
dominant
Ras permanently activated which stimulates signalling cascade.
395
are the mutations that inactivate proteins to inactivate tumour suppressor genes dominant or recessive?
recessive- need to be mutated in the maternal + paternal copies for cancer to develop.
one good (functional) copy of the gene is enough to inhibit cell division- so both copies must be mutated for cancer to happen.
396
what do tumour suppressor genes do, and how (mutations)?
normally inhibit cell division.
mutations in tumour suppressor genes reduce the inhibition of cell division- thereby stimulating cell proliferation.
tumour suppressors are inhibitors, so when mutated, cell division is promoted.
397
retinoblastoma protein was the first tumour suppressor gene identified- describe the 2 forms of the disease?
1. familial (10%)- occurs in young children, retinal tumours in both eyes.
2. sporadic (90%)- occurs later in life, affects just one eyes in 2/3s cases.
398
what is retinoblastoma?
A tumour that grows out of the retina in the back of the eye, pushing into the socket and sometimes the optic nerve which is obviously not good.
399
is retinoblastoma dominant or recessive?
recessive- both copies need to be inactivated by mutation for cancer to arise.
400
is the pattern of inheritance for retinoblastoma dominant or recessive?
however, the pattern of inheritance for retinoblastoma carriers is actually dominant, so there is 50% chance of developing this from family, as when there is a mutation in one of the chromosomes arms, it’s likely the other one will be mutated as well. The likelihood of contracting this is also just way higher if it’s from family.
401
is retinoblastoma caused by inheritance or somatic mutation?
a mix xxx, BUT frequency of retinoblastoma inheritance is too high for a rare carcinogen-mediated mutation, so bit of a weird one.
402
retinoblastoma is caused by mitotic recombination, describe the process
starts with a normal cell, with 1 good gene which is enough to inhibit cell division.
then, normal DNA duplication; results in duplication of normal + mutant chromatids.
then, rare complication; simple exchange of genetic material between normal + mutant chromatids. patterns of DNA, which are the same, are used to pass something from one chromosome to the other.
finally, subsequent mitotic segregation of chromatids + cytokinesis- one cell homozygous (normal), and one cell homozygous (mutant).
In chromosome segregation, different combinations can occur where the daughter cells may have different mutations and stuff of the TS gene.
403
the retinoblastoma protein inhibits the G1-S transition, how does it result in high cell proliferation?
when retinoblastoma is functional, cells are allowed to enter S-phase, allowing cells to replicate + divide. In the presence of high levels of inhibitory mitogenic signals, the G1 checkpoint is passed too easily + removed as cell division doesn't require mitogen stimulation, so cells are more likely to proliferate in an uncontrolled manner.
404
what does the tumour suppressor p53 do?
it is a transcriptional regulator of multiple proteins that halt the cell cycle while genetic damage is repaired. protects the genome from change, and the cell from damaged DNA.
does this by arresting the cell cycle, enforcing checkpoints which gives DNA repair machinery more time to fix DNA before mitosis (e.g. wrong bases inserted, break in the double helix, metabolic stress, etc) + passing on the damaged DNA to daughter cells.
In its absence, cancers can introduce mutation at much higher frequency.
405
if cell damage is too severe, what does p53 program?
permanent non-replicative state (senescence) or apoptosis.
406
the 1st of the 3 overall functions of p53 is production of Cdk inhibitor protein p21 when p53 is activated, what does it do?
p21 expression is up regulated by p53. p21 is an inhibitor of cyclin E-Cdk2, which prevents G1 exit causing cell cycle arrest.
prevents duplication of damaged DNA + passing on of DNA to daughter cells.
407
the 2nd of the 3 overall functions of p53 is regulating expression of DNA repair proteins, what do they do?
allow the cell to repair DNA during cell cycle arrest.
Most of the time, genes and cells are repaired sufficiently and the cells can re-enter the cell cycle. If not, they have an irreversible cell-cycle exit called senescence, or apoptosis. This retains the genetic integrity of our body.
these pathways are regulated by p53.
408
the 3rd of the 3 overall functions of p53 is apoptosis, describe the process
1. normal cell 'realises' that its DNA is beyond repair so p53 activates apoptosis.
2. cell begins to shrink + invaginations form at the cell surface (begins to like fold back on itself).
3. organelles (lysosomes, Golgi, etc) become enclosed in vesicles. DNA in nucleus is dissolved by enzymes, cellular material is engulfed + degraded by phagocytes.
Then the cell is stimulated to make a copy of itself to replace the old one.
409
what are the 2 kinds of apoptosis, + why are they different and similar?
intrinsic- induced by factors within the cell
extrinsic- induced by specialised cells by activation of the FAS death receptor.
both regulated by activation of proteins called caspases, the expression of these is promoted by p53.
409
why is apoptosis different + better than necrosis?
none of the harmful material inside the cell is released which is good, unlike necrosis which happens in wounds or bacterial infection.
410
explain how intrinsic apoptosis is regulated by p53.
P53 is involved with the production of a protein called Bid, in a time of genetic stress/ damage. When Bid associates with Bax, a pore is formed in the mitochondrial membrane. The release of cytochrome C activates proteases + nucleases (caspases) that degrade the cell in apoptosis.
411
explain how extrinsic apoptosis is regulated by p53.
P53 induces expression of a death receptors (Fas) in response to genetic damage.
death receptors are activated by cells expressing Fas ligand e.g. lymphocytes.
Fas ligand binding activates the Fas death receptor + recruits the Fas-associated death domain (FADD).
When a killer lymphocyte binds to a Fas death receptor, caspases are recruited forming the death-inducing signalling complex (DISC).
the DISC activates caspases that regulate apoptosis.
412
just a thing about colon cancer- where cells are no longer allowed to undergo apoptosis xxxx
Likely to have a rapid accumulation of mutations before it becomes malignant, as cells are no longer allowed to undergo apoptosis. The basement membrane will be digested away, and the tumour will invade tissue.
