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B1omed - Molecules to cells > Module 1 - Cells and their components > Flashcards

Module 1 - Cells and their components Flashcards

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Organic Chemistry 101 flashcards
1
Q

Cell theory

A
  • Cells are the fundamental units of life
  • All organisms are composed of cells
  • All cells come from pre-existing cells
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2
Q

Unicellular organisms and carrying out the functions of life

A

A single cell carries out all the functions of life

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3
Q

Multicellular organisms and carrying out the functions of life

A

Made of many cells that are specialized for different functions – tissues and organs

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4
Q

Internal structure of prokaryotes

A
  • No nucleus: their DNA floats freely in the cell
  • No (or rudimentary) internal membranes
  • Very basic cytoskeleton
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5
Q

Internal structure of eukaryotes

A
  • Have a nucleus containing DNA
  • A complex internal membrane system
  • Extensive cytoskeleton
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6
Q

Internal membranes within cells

A
  • One or more membranes made up of lipid bilayers that form a physical barrier from the cytosol/other organelles
  • Allows different protein contents and chemical environments to be maintained
  • Allows each organelle to have a specialised function
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7
Q

Characteristics of ER

A
  • Network of interconnected spaces enclosed by a single membrane that is continuous with the nuclear envelope
  • The entry point to the secretory pathway
  • Makes: secretory and membrane proteins, and also lipids
  • Very dynamic
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8
Q

Two types of endoplasmic reticulum

A

Smooth ER: abundant in human cells active in lipid metabolism and in the liver for detoxification of lipid-soluble compounds

Sarcoplasmic reticulum: ER-derived calcium store in muscle cells (important role during muscle contraction)

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9
Q

Characteristics of the Golgi apparatus

A
  • Receives proteins and lipids as cargo from ER
  • Cargo transits Golgi to the plasma membrane
  • Modification of cargo e.g. glycosylation
  • Sorting of cargo to the correct location
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10
Q

Cytosol: what is it, how large is it, what occurs here, what is located here, and what is it not to be confused with?

A
  • The soluble and aqueous portion of the cell
  • Typically largest single compartment in the cell
  • Site of many fundamental cellular processes: protein synthesis and degradation, intermediary metabolism
  • Location of the cytoskeleton
  • Not to be confused with the cytoplasm (everything except the nucleus)
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11
Q

How ATP/GTP is formed

A

ADP/GDP forms a phosphoanhydride bond with an inorganic phosphate along with a proton using energy gathered from either the sunlight or consumed food, forming ATP/GTP and water

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12
Q

How ATP/GTP is used - energy usage

A

ATP/GTP reacts with water, breaking the phosphoanhydride bond, and releasing the energy kept in the bond which is then used for intracellular work

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13
Q

The uses of ATP/GTP - affecting proteins

A

Nucleotide binding is used to change protein shape, activity, and function

Phosphorylation by adding phosphate to serine, tyrosine and threonine

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14
Q

What can phosphorylation do?

A

Affect:
Cell growth
Cell cycle
Cell division
Cell survival
Gene expression
Metabolism

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15
Q

Light microscopes: how high can the magnification and resolution go, what are the prerequisites for the specimen, what do they show, and what cells can be used?

A
  • Magnifies cells up to 1000 times and resolves details to a resolution of 0.2 µm.
  • The specimen must be prepared in a way that allows light to pass through it.
  • Shows the shape of structures, but doesn’t give molecular information.
  • Suitable for live cells.
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16
Q

Fluorescent dyes in fluorescent light microscopy: what do they do and how can they work?

A

Absorb light at one wavelength and release it at a longer wavelength

Some may bind organelles, may be coupled with antibodies that recognize a protein in a chemically fixed cell

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17
Q

Advanced fluorescent light microscopy: what does it allow?

A

Allows for 3D imaging because of “super resolution”

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18
Q

GFP

A

Green fluorescent protein can be attached to a protein as a tag to allow for fluorescent microscopy

? Molecular biology to add GFP coding sequence – produces a fusion protein
? GFP is intrinsically fluorescent, so is visible in living cells
? Potential problems: GFP is 238 amino acids = 25 kD protein. Does is alter function? Misfolding?

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19
Q

Electron microscopes: what are the prerequisites for the specimen, what do they show, and what cells can be used?

A
  • Thin slices of material (sections) stained with heavy metals for contrast
  • Detailed subcellular structure
  • Dead cells
20
Q

Cell fractionation

A
  • Centrifuge to ‘pellet’ particles from suspension
  • Heavier particles sediment at lower centrifugal force
  • Collect supernatant (cytosol) and centrifuge again at a higher speed
  • Tissue -> pellet 1 (nuclear fragments) -> pellet 2 (mitochondrial fraction) -> pellet 3 (rER and Golgi apparatus)
21
Q

SDS: what is it and what does it do?

A

Sodium dodecyl sulphate

An ionic (negative charge) detergent that binds to proteins

Denatures proteins (useful for electrophoresis)

22
Q

Polyacrylamide

A

Mesh-like gel that charged proteins move through, separating based on size

23
Q

Protein targetting

A

When there is no targetting mechanism, the protein remains in the cytosol

When the protein is instructed to go to a certain place (outside the cell), the protein’s receptor interacts with it, the protein then unfolds/loosely folds to cross the membrane, and translocation machinery is used to move the protein through membranes

The whole process uses ATP/GTP

24
Q

Signal sequences: what are they and when are they removed?

A

Stretches of polypeptide sequences made up of specific types of amino acids

May be removed after the protein reaches its target location

25
Q

The nuclear envelope: what is it made of and what does each part do?

A
  • The inner nuclear membrane contains proteins that bind to the lamina and chromosomes
  • The perinuclear space between both membranes
  • The outer nuclear membrane is continuous with ER composition
26
Q

Crossing the nuclear envelope

A

30+ different proteins act as a gateway to the nucleus, allowing small, soluble molecules to diffuse through

Larger components must be actively transported in and out of the nucleus across the nuclear pore complex

27
Q

Nuclear targetting signals

A

The nuclear localisation signal (NLS) targets proteins to the nucleus

Usually made of <12 amino acids, usually positively charged (Lysine/Arginine)

May be located anywhere in the nucleus and are not removed even after arriving

28
Q

Protein import

A

A receptor binds to proteins containing NLS in the cytosol

Fibrils direct the receptor to the nuclear pore

Cargo protein is pulled into the nucleus through the large pore (allowing folded proteins to move through)

29
Q

Ran: what is it and what does it do?

A

GTP/GDP-bound proteins which control nuclear import by binding to the receptor, releasing the cargo protein from it. This complex then passes through the nuclear pore and dissociates in the cytosol by converting the GTP to a GDP

In order to ensure the cycle occurs in the right direction, there are two conformations of the Ran protein (Ran-GTP in the nucleus and Ran-GDP in the cytosol)

30
Q

The endoplasmic reticulum: what is it, what are the two types and what do they do?

A

The most extensive membrane system in eukaryotic cells made of connected sacs and tubules

Smooth ER: lipid synthesis
Rough ER: connected ribosomes - protein synthesis

31
Q

Types of proteins produced at the rER

A

Secretory proteins - Water soluble enzymes/hormones

Membrane proteins - Embedded in the lipid bilayer

32
Q

ER signalling sequence

A

Common feature: 8+ hydrophobic amino acids (leucine/isoleucine/valine) usually near the N-terminus

Targetting to the ER begins while the protein is still being synthesised (translocation occurs during translation)

33
Q

Signal recognition particle

A

SRP binds to the ER sequence as it emerges from the ribosome. SRP binds to an SRP receptor in the ER membrane

Once the protein has been fully directed to the ER, SRP dissociates for reuse

34
Q

ER translocation: what is the process behind it?

A

The ER signal sequence moves through the Sec61 translocator and then loops back around and attaches to the Sec61 translocator as the polypeptide still moves through the ER membrane while translation is still occurring.

Once the protein is fully through the ER membrane, a signal peptidase will snip off the ER signal sequence and the protein is then moved around the ER lumen.

35
Q

Stop-transfer sequence

A

If the protein is to be membrane-bound, then a hydrophobic stop-transfer sequence will stop translocation and the Sec61 translocator will dissociate from the polypeptide chain and the protein will be membrane-bound with the stop-transfer sequence as a transmembrane domain

36
Q

How can multiple transmembrane domains be established?

A

By having the stop-transfer sequence later in the chain

37
Q

How do mitochondria make energy?

A

Oxidative phosphorylation to produce ATP which is synthesised by the energy made from the movement of protons through ATP synthase

The proton gradient is established by movement across the electron transport chain after high-energy electrons are obtained from the citric acid (Krebs) cycle

38
Q

DNP: what is it, what can it do, and is it dangerous?

A

2,4-dinitrophenol is an organic compound that is (illegally) sold in slimming aid pills

It uncouples oxidative phosphorylation, reducing ATP production

CAN BE LETHAL

39
Q

Thermogenin: what is it, what can it do, and is it dangerous?

A

A protein that drains the proton gradient, heating up the organism

This can be dangerous as less ATP is produced as the gradient is reduced

40
Q

Where are mitochondrial proteins produced and what are the effects of the mutations?

A

99% in the nucleus but 1% in the mitochondria DNA

If a mitochondrial mutation occurs, it’ll only be passed on the mother’s side

41
Q

IVF to remove defective mitochondria in eggs

A

Method 1: The nucleus of the fertilised egg is removed and the nucleus of the donor egg (father also fertilises) is removed and replaced with the fertilised DNA, essentially replacing the mitochondria

Method 2: fertilisation occurs after the nucleus has been replaced

42
Q

Mitochondrial targeting sequences: what is the primary sequence and what is the secondary sequence?

A

Located at the N-terminus of the polypeptide chain, usually between 20-80 amino acids long and rich with Arginine, threonine, and serine

Usually has an α-helix with positively charged (red) residues on one and non-polar (green) residues on the other face giving it unique amphipathic properties

The MTS is cleaved off after entering the mitochondria

43
Q

The process of protein importation into the mitochondria(?)

A

A receptor in the outer membrane of the mitochondria binds to the MTS and then the MTS binds to another receptor in the inner membrane, entering the matrix.

44
Q

How is protein structure regained when in the matrix?

A

Chaperone proteins (Hsp70s) pull proteins through both membranes by ATP hydrolysis and then refolds them in the matrix

45
Q

How are proteins imported into chloroplasts

A

N-terminal chloroplast targeting sequence (CTS) made of Threonine, Serine, and other small hydrophobic amino acids which is cleaved off after entering the chloroplast

The same general process as ER

46
Q

How are targetting sequences discovered?

A

By removing certain parts of the DNA, we can discover which parts are needed for proteins to go to the right place

B1omed - Molecules to cells (8 decks)

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