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Biochem Y1 > cells to organisms > Flashcards

cells to organisms Flashcards

1
Q

What are the differences in pro and eukary genome organisation

A

Nucleus vs nucleoid

Nucleus (top) is a Eukaryotic compartment

Entrance and exit of material is tightly controlled

In prokaryotes nuclear material is arranged in the cytosol

introns spliced out in eukaryotes

Circular / linear

Histones / not

2 copies / 1 copy

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2
Q

binary fission vs mitosis/meiosis

A

Binary fission is simpler & quicker

A form of asexual reproduction.

Produces two identical daughter cells (like mitosis).

Some Eukaryotes do something similar

Meiosis in Euk – enables genetic novelty! Sex!

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3
Q

differences between rna polymerase in Eukary and Prokary

A

Complexity in gene regulation generated by transcription factors in Eukaryotes, rather than different σ factor subunits.

prokaryotic less complex

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4
Q

how did evolution of eukaryotes come about

A

Compartmentalisation
The evolution of separate compartments enables a broader set of biological processes to happen simultaneously

keeping biological processes that need to be sperate, separate

processes could be stopped if they happened in the cytosol

needs to be a concentration of factors in order for a reaction or process to happen

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5
Q

key features of eukaryotic nucleus

A

Entry and exit into the nucleus is tightly controlled via pores
Nuclear Lamina provides important anchor point for chromosomes

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6
Q

how does the nucleus import and export of materials

A

movement of biomolecules through the nuclear pore complex is tightly controlled

Nuclear pore complex contains many proteins

proteins and nucleic acids can only be transported in where and when they are needed to be

proteins require nuclear localisation (or import) sequence in order to be brought into the cell

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7
Q

how is the nuclear lamina arranged

A

chromosomes arent neatly arranged

heterochromatin located at the edge of the lamina whereas euchromatin is located more towards the centre

tethering proteins anchor chromosomes to lamina to maintain nuclear territories

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8
Q

how does mitochontrial fusion and fission work

A

Often touch or fuse other mitochondria & Exchange membrane

transfer genetic information

Can track this with flourescence

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9
Q

key features of endomembrane system

A

has a surface area 10x the size of the etermal surface of the cell

nucleus mitochondria chloroplasts

exchange of materials between parts of the endomembrane system through membrane bound vesicals

most proteins that have entered the system end up being secreted or at the cell membrane

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10
Q

how does the endoplasmic reticulum work

A

proteins are sorted depending on whether they are on free or membrane bound to ribosomes and the presence of signal sequencing

Proteins translated by free ribosomes will tend to require chaperone proteins to translocate them to target compartment

transport to golgi in a vesicle

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11
Q

how does the golgi work

A

The golgi is made up of a series of flattened stacks of membrane bound organelles called cisternae

Crucial for protein and lipid modification

Different cisternae may contain different enzymes or different reaction conditions

Sequential sugar modification is a good example of how the Golgi can work to separate process that need to happen separately

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12
Q

the roles of endosome system

A

store proteins so that they can be reused

can recycle and degrade membrane prtoeins from the cell surface

can be used to take in raw materials or nutrients

selectively transport materials to different places

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13
Q

why do cells need to communicate

A

homoeostasis and maintainance of internal state
buffers against changes in the external
environment
regulate development
cell cycle, cell movement, differenciation and
patterning

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14
Q

what is the flagellar synthesis constraint hypothesis

A

cells with flagella allow cells to be moved
the microtubule required for flagella formation is required to form spindle fibres in cell division
presence of both flagella cells and non flagella containing cells allow both movement and growth

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15
Q

what causes cell lineage

A

the turning on and off of genes as all cells have the same genetic material

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16
Q

what do cells require with multicellularity

A

Maintaining balance requires cell communication
requires the ability torecognise the same cells and different cells
cells need to be able to adhear to one another

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17
Q

types of cell response

A

cells may change gene expression
cells may move
contract
alter metabolism
proteins within may alter activity
concentration of ions may change

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18
Q

when is gene expression regulated

A

multipul levels
can be
regulated by RNA
messenger rna before translation
export from the nucleus
proteins can be regulated using post translational modifications

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19
Q

what is a cis-regulatory element

A

regions of DNA involved in gene regulation
provide the information for when when, how and at what levels genes should be expressed

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20
Q

what are trans-acting factors

A

they bind cis-regulatory elements. bind to regulate expression usually proteins. alter the activity

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21
Q

what do transcription factors do

A

transcription fo protein coding genes require the binding of RNA polymerase II
forms a complex that allows the start of transcription
(may bind indrectly to other proteins)
complex formed at the TATA box
diifferent transcription factors hve different specific sequences
unwind the DNA helix

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22
Q

what is the TATA box

A

region of DNA 30 base pairs up from the transcription start site that forms a section fo the promoter. Named due to the sequences of TATA DNA bases

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23
Q

What is different with specific transcription figures

A

They bind to regions of the enhancer or silencer regions
in enhancers activate transcription
in silencers bind repressor proteins that prevents transcription

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24
Q

what does specific transcription factors bind too

A

enhancer silencer
binding motifs (between 6-12)
short to increase probability of binding

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25
how do specific transcription factors work
contain DNA binding domain (this being either an activation or repressor) THis domains allows and encourages for interactions with other proteins
26
How do specific transcription factors influence the promoter
enhancer and silencer sequence are thousands of base pairs long when binded with STF can form a loop bringing it within the proximity of the promoter interact with transcription initiationcomplex by the mediator complex
27
whats the effect ofenhancers and silencers on organisation of cells
as different cells have different specific transcription factors,different cells will activate different genes even though they have the same genome
28
Explain How Wnt works
The Wnt Pathway is critical for development of the embryo, and in tissue regeneration in adult bone marrow, skin and the intestines. Wnt activates the Frizzled receptor on the cell membrane, the message is then carried through a series of steps to stop the degradation of β-catenin.activates Dishevelled. Dishevelled inhibits the β-Catenin Destruction Complex. Leading to the stabilization of β-Catenin which can then activate the transcription factor TCF.
29
Why do we need hypoxia sensing
detects when there's a lack of O2 in tissues as O2 is less accessable this detection allows the stimulation of growth of blood vessels
30
main features of signaling
can diffuse over long distances can create localised signals (only cells connected to cell recieve the signal (achieve by membrane bound singal or associated with extracellulr matrix) transmited by a viety of mediums (peptides, small molecules, metabolic products, lipids) receptors enable cells to react to signal 3D structure of receptor protein must be highly specific for the binding of signaling molecule typically found on the cell surface
30
what to do if you only have rna to applify
cDNA can be formed that is complementary to the mRNA showcasing the sequence free from introns
31
how do differences in hyprophobicity lead to different pathways
hydrophilic molecules wont dissolve in membrane therefore a receptor is likely found to combat this
32
type of signaling
contract/justacrine (direct contact), paracrine and autocrine secreted by extracellular space and endocrine signalling is produced locally and transfered through the organism through blood
33
protein phosphorylation is an example of what?
molecular switch that turns a pathway on or off
34
how are RTKs activated
dimerization and autophosphorylation this increases the activity of the recpetor enables the binding of adaptor proteins which are unable to bind without phosphorylated tyrosine
35
how are GTPases activated
are activated by the exchanging of GDP to GTP. they are off in GDP stage and on in GTP stage. They hydrolyse to terminate the signal
36
what does GDP require to be activated
requires a GEF (Guanine nucleotide exchange factor).
37
what is ras relationship with cancer
50% of human cancers have mutations in Ras. What those mutations do is lock Ras in the active form. What that means is once activated it cannot attenuate that signal and it is no longer transient therefore driving growth.
38
what are the three main domains of ras
p loop and switch 1 and switch 2
39
key mutations in ras
G12V, Q61N and S17N
40
what does S17N do
Unable to bind GTP Still can bind GDP
41
what does Q61N do
Low rate of GTP Hydrolysis Intrinsic GDP/GTP exchange ability
42
what a does G12V do
Low rate of GTP Hydrolysis GAPs no longer increase GTPase Activity
43
what do FGFs do
Regulation of cell growth and survival, ii) regulation of cell differentiation, iii) regulation of embryonic development.
44
how does FGF respond
its an RTK so can phosphorylate proteins within the cell FGF ligands form a complex with extracellular proteoglycans these allow them to bind to receptors multipul layers of kinases allows for signal amplification can activate MEK MEK can phosphorylate MAP Kinase molecules MAP-kinase (Erk) translocates to the nucleus where it binds to and phosphorylates to modulate the activity of multiple transcription factors.
45
how to proteins get to the correct location
specific petide motif or a single motif
46
what is a stem cell
a cell that has the ability to self renew and differenciate
47
how do the river anolgy and epigenetic landscape analogies differ
potency in river cells are limited to particular tissues whereas in th eother cells make progressive choices about how to differenciate developmental history stem cell specification relies of differencial history but cells are able to respond to cues
48
what are the types of potency
totipotent - all embryonic and extraembrionic tissues pluripotent - can contribute to all germ layers can poften produce all embryonic tissues but not extraembrionic tissue multipotent- tissue or germ layer restricted can generate multipul specialised cell types
49
what type of stem cell are most embrionic cells
totipotent until morula stage
50
what happens during the cleavage stage
rapid division, synchronous (all division occurs at the same time all in the same stage of the cell cycle), reduction division
51
what happens in the blastula stage
division becomes asynchronus, fluid filled cavity forms (blastocoel), some specialisation forms
52
what are the stages of development
cleavage stage, blastula, gastrulation,neurolation, tailbud
53
what happens in gastrulation
the three germ layers separate endoderm, mesoderm and ectoderm. the blastula envaginates
54
what happens in neurolation
ectoderms folds in on its self and merge together enclosing the neural plane.
55
what is tailbud
phylotypic stage development of nortichord
56
what did old models suggest about development
during the cleavage stage nuclear 'determinants' segregate to different cells. the uneven segregation leads to development of different cell fates. mosaic development results from autonomus specification of cells fate
57
what suggested the old models of development were wrong
Half an embryo wasnt created in an experimental setting it was able to regulate and develop a full embryo with no missing parts. This suggested it was controlled via regulations
58
what happened in the Spemann's organiser experiment
dorsal lip of blastopore was transplanted into a host embryo on the opposite side. This new embryo was double headed with 2 connected complete embryo made entirely of the host cells not the donar cell. This suggested cell to cell signaling is important for regulating cell fate
59
what is gene constancy
development does not involve a loss of genetic information rather the cells become different from one another during development through differential expression responding to cell signalling
60
what proof is there of gene constancy
in cloned animals none of the gentetic material is lost the nucleus from a fully differenciated cell is used to generate clones. This then reprogrammes to be able to produece all types of cells
61
how can signals be used as morphogens
diffusion from a source establishes a concentration gradient of secreted signal, cells sense the concentration and respond depending upon the signal therefore morphogen as ellicits different responces from cells depending on concentration
62
what is the french flag model
signal source at one end of a bunch of cells diffusion of signals establish gradient of morphogen, the morphogen gradient allows cells to aquire information depending on their position to the source cells respond appropriately as a result of this
63
what do the germ layers form
ectoderm - eperdermis and central nervous system, mesoderm - notochord, dermis, skeleton, muscle, kidney heart and blood endoderm - gut liver pancreas and lung
64
whats the difference in formation at the equatorial region between early blastular phase and later
early only forms epidermis whereas later it only forms mesoderm cell. This occurs as the vegetal pole emits mesoderm inducing signal factors. This shows the mesoderm is derived from the animal pole
65
whats different between dorsal and ventral cell in blastular phase
different types of cells are produced in different orientations. dorsal produces notochord and a little skeletal muscle cells whereas the vental side produces blood and smooth muscle
66
What is the 3 signal model?
a model conveying the different patterning present within embryos. conveys there are 3 signals that induce differenciation.
67
How is TGF beta cells present in development
they act as morphogens for formation, activin and nodal are present specifically
68
what is the evidence that activin signals are required for mesoderm induction
a mutant receptor was formed without intracellular kinase domain when expressed in cells the activin receptor dimerises withnormal activin receptors and no signal can be transmitted no mesoderm is formed
69
what are somites?
in vertebrates, all skeletal muscle is derived from somites. They are segmented blocks of mesoderm new somites form from the anterior end of the presegmental plate mesoderm
70
what are the derivatives of somites
scleratome forms in the ventral medial part of somite and differenciate as chondrocytes forming ribs and vertebrae dermamyotone forms in the dorsal part and form the dorsal skin and deep muscle
71
what are microorganisms
living organisms of microscopic size
72
what are common features of pathogenic microbes that help them be good
Ability to enter the host and locate a suitable niche Evade host immune responses both the innate and adaptive Replicate within the host Transmitted from infected to uninfected host
73
common structural features of bacteria
pilus, capsule (can be there or not promotes sticking to surfaces and antiphagocytosis properties), cell wall, cytoplasm, plasma membrane, nucleoid, ribosomes and flagellum
74
classifications of bacteria
based on shape coccus: spherical Coccobacillus: between coccus and bactillus Bacillus: rod shape cylindrical Vibrio: slightly curved long Spirillum: wavy Spirochetes: tighter coil spiral
75
what are the differences between gram positive and gram negative bacteria
gram negative has an outer membrane whereras gram positive doesnt gram positive has a thick peptidoglycan levelwhereas this is only thin in gram -
76
key features of bacterial invasion
feature virulent genes which can be transfered to a host cell virtical gene transfer : plasmids replicate and create two identical daughter cells horezontal gene transfer: bacteria also produce adhesins, form biofilms and some inject effector proteins into host cells composed of alpha and beta subunits with b subunit binding to specific receptor of host cell
77
how does vibrio cholerae toxin work
b subunit bind to ganglioside receptor on the surface of epithelial integine cell. enter in endosome and are transfered to the golgi and endoplasmic reticullum. activate the adenylate cyclase. this creates cAMP from ATP move cl- out of the cell
78
key features of viruses
Obligate intracellular parasite, rely on host cell. Unlike bacteria and eukaryotic parasites, viruses cannot replicate or survive on their own. They lack the ability to produce the proteins encoded by their DNA or RNA genomes. Virion when outside the host cell.
79
how do viruses invade cells
bind to cell surface receptors and enter host cell by either membrane fission or endocytosis. they replicate and form viral DNA which is coded into mRNA to assemble more viruses whih are them released. drug resistant they are host specific recognise specific receptors of specific cells
80
key features of protozoan
Protozoans are a diverse group of unicellular eukaryotes. Some require more than one host to carry out their life cycle
81
key features of protozoan invasion (in trypanosoma cruzi)
attach to host cell surface receptors Ca2- singel encourages lysosome fusion of lysosome with plasma membrane invade the cell T. cruzi must escape from the parasitophorous vacuole to gain access to the host cell cytoplasm, where it can replicate and establish infection secration of pore forming proteins lysis of surrounding membrane with release of pathogen into cytosol The parasite secretes pore-forming protein that disrupts the lysosome membrane, thus allowing it to escape into the host-cell cytosol and proliferate
82
What is Hematopoiesis?
the process of hematopoietic stem cells differenciate into mature blood cell types
83
what are the types of mature blood cells
red blood cells , granulocytes, macrophages, dentritic cells, lymphocytes
84
Where does hematopoiesis occur?
it first occurs in the yolk sac during fetal development. This then occurs in the dorsal aortal and produce multipotent hematopoietic progenitors mature into adult HSCs in the aortal or in fetal liver After birth this occurs in the bone marrow most HSCs are quiescent (dont devide) in the absence of infections
85
Whats different about t cells
t cells mature in the thymus
86
what are the primary lymphoid organs
bone marrow and thymus
87
secondary lymphoid organs
lymph node, spleen, tonsils and peyers patches in the small intestine
88
what is the first responce to infection
myeloid cells neutrophils, basophils and eosinophils are released. N's released into blood from bone marrow and engulf pathogens like bacteria in phagocytosis. B's contain large granules filled with proteins like histamine. B and E's are the immune response to parasitic worms Mast cells Cytoplasmic granules contain histamine &do not mature in the bone marrow but in peripheral tissues such as the skin, connective tissues of various organs monocytes migrate to tissue in response to infection and differentiate into macrophages
89
what types of response cells are adaptive response
b cells, t cells
90
How does pathogens activate innate immune cell?
innate immune cells have pattern recognition receptors (PRRs)recognises pathogen-derived molecules known as pathogen-associated molecular patterns (PAMPS). A host cell doesn't produce PAMPS therefore immune cells can recognise whether the cell is its own or not. These inamecells activate adaptive immune cells
91
what do dentritic cells do
professional antigen presenting cell
92
what are the basic componants of the neurone
dendrites, nucleus, cytoskeleton, axon and growth cone
93
how does neurulation work
neuroectodermal cells differenciate and thicken into neural plate and the neural plate boarder separates it from the ectoderm. This bends dorsally and the two ends join forming the neural crest. Neural tube closes and disconnects the neural crest from the epidermis. notochord degenerates and forms the nucleus pulposus of invertebrate disks
94
where does CNS and PNS come from
CNS from neural tube PNS from neural crest
95
How is the spacial expression of transcription factors regulated?
signal gradients of sonic hedgehog and BPM in the neural tube with both proteins moving down the concentration gradient in opposite directions
96
how do Neural crest-derived stem cells give rise to the peripheral nervous system
The Neural Crest (NC) is a transient embryonic structure which appears between the Neural Chord and the future ectoderm during development of the vertebrate embryo. NC is a stem cell niche NC cells migrate out of their niche after neurulation and give rise to various cell populations
97
what are the developmental stages of a neuron
initiation/ polarisation , pathfinding, target recognition, branching, synapse formation
98
development of Retinal ganglion cells
establishment of retinal layers directional axonal growth progression into optic nerve, decision to cross of turn (depending on whether it controls the left or right side of the eye) honing in on target region arrival at target establishment of topographic map
99
what is the chemoaffinity hypothesis
cells and fibres of the brain must carry some type of identifying tag, chemochemical in nature, so they are distinguished from one another
100
principles of axon guidence
axons are guided by certain processes tht control signl movement Adhesive substrate cues convey when singals should go and stop
101
How does ephrin control limb patterning
The transcription factor LSL induces expression of EphB receptor in the LMCm Neurons that grow towards the developing limb are repelled the ligand ephrin-B2 and therefore grow towards the ventral side (away from ephrin-B2) If any of those factors is lost (TF, receptor or ligand), axons are no longer repelled and therefore grow towards the dorsal side
102
how do growth cones grow in their shape
Lamellipodia (dynamic membrane sheet) expand in all directions from the centre of the growth cone and are is supported by a network of short, branched actin fibres Filopodia are formed by tight parallel bundles of F-actin that polymerise at the leading edge, that push the membrane forward in response to an external cue Parallel bundles of microtubules guide the extension of axonal microtubule bundles
103
What is the extracellular matrix and how is it formed
In tissues, a substantial volume is extracellular space, which is filled with a network of secreted macromolecules: the EXTRACELLULAR MATRIX (ECM) Each tissue will have specialised ECM, adapted for its function. eg. -connective tissue = elastic matrix -bone, teeth = calcified matrix -cornea = transparent matrix -tendons = ropelike, high tensile strength
104
Key components of the ECM
proteoglycans, fibronectin, collagen, elastins and laminin
105
how does filopodia grow through the clutch model
there's no adhesion in the growth stage actin polymerases continuously no force to push the membrane because actin cant generate a force intergrin recepter binds to laminin form focal adhesion between growth substrate and growth cone activation of integrin signaling this links polymerasing actin to focal adhesion

Biochem Y1 (11 decks)

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