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Cell Biology Midterm 1 > Cell Biology Mid 1 prep > Flashcards

Cell Biology Mid 1 prep Flashcards

1
Q

What are the macromolecules?

A

Proteins, nucleic acids and polysaccharides

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2
Q

What is a cell?

A

It contains a plasma membrane that separates non-living worlds. Inside, the cell has order and structure while the outside is dynamic.

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3
Q

What’s the reaction that joins sugar together and, in the process, removes H2O?

A

Nucleoside Triphosphate Hydrolysis

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4
Q

Is nucleoside triphosphate hydrolysis reaction energetically favourable?

A

No, it is energetically unfavourable because it requires energy.

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5
Q

What are polysaccharides?

A

They are energy storage, structural functions and involved in cell signalling

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6
Q

What interaction stabilizes DNA?

A

non-covalent interactions such as HYDROGEN BONDING, ionic interactions, hydrophobic interactions, van der Waals interactions

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7
Q

Whats responsible for folding in a protein?

A

NON-COVALENT interactions within the polypeptide chain are responsible for folding.
-Electrostatic forces (ionic interactions) bond with charged amino acid groups
-Hydrogen bonds bond with polar amino acid residues
-Van Der Waals attractions bond with many amino acid residues

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8
Q

What is the primary structure for building amino acids

A

A linear order of amino acids in the polypeptide

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9
Q

What is the secondary structure?

A

FOLDING of alpha helices and beta sheets

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10
Q

What is the tertiary structure?

A

GLOBAL 3-dimensional FOLD of the entire polypeptide

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11
Q

What is the quaternary structure

A

Positions of all polypeptide chains needed to make a functional protein

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12
Q

What is the bond holding the Helix in place?

A

HYDROGEN BONDS between nearby peptide bonds

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13
Q

What is the bond holding the beta sheets?

A

HYDROGEN BONDS BETWEEN peptide bonds adjacent to each other.

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14
Q

What is a ligand?

A

Interacting molecules that bind to proteins via NON-COVALENT BONDS. A ligand binds to a specific proteins depending on the number of covalent bonds.

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15
Q

What happens if the proteins structure is altered?

A

It can lead to a disease or be non-functional. Example, a prion disease is caused by the change of conformation of a specific protein. The proteins were misfolded to a flat square (Prp). Its original conformation was circular. This altered protein can concert normal Prp into its abnormal conformation. This leads to an increase in abnormal Prp protein. This is called MAD COW disease.

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16
Q

What are the regulating proteins reactions?

A

Protein phosphorylation and binding to GTP or GDP

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17
Q

What happens to the protein when it is turned off or on?

A

Change of conformations, enzymatic activity, and protein-ligand interactions.

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18
Q

Describe the process of protein phosphorylation

A

The enzyme Kinase adds a covalent addition of a phosphate group to bind to a specific amino acid in a specific sequence. This addition of phosphate is called PHOSPHORYLATION.

The enzyme phosphatase removes the phosphate group. This process is called DE-PHOSPHORYLATION.

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19
Q

What amino acid sequences does the phosphate bind to during protein phosphorylation?

A

Serine, threonine or tyrosine amino aicds.(OH GROUPS)

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20
Q

What is GTPases?

A

It is a specialized molecular switch that binds and controls other proteins and its ability to hydrolyze GTP.

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21
Q

What is the process of GTPases.

A

The GEF (guanyl exchange factor) loads GTP onto GTPase. This turns it ON. This changes the shape and FUNCTION.
The GAP (GTPase activating protein) causes GTP hydrolysis to GDP. This turns it OFF.

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22
Q

How can a covalent attachment of a phosphate group change the function of a protein?

A

The attachment to a specific area of the protein adds NEGATIVE CHARGES to that area. These negative charges REPEL the other negative charges in the area and now attract positive ones. That is why the protein conformation changes and the secondary, tertiary and quaternary structure changes.

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23
Q

What happens when the GTPase is ON?

A

It has a GTP binding pocket called the switch helix. This pocket allows GTPase to bind and control other proteins.

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24
Q

What happens when the GTPase is turned OFF?

A

The switch helix is blocked due to the hydrolysis of the GTP to GDP. Thus blocking interaction with other proteins.

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25
Q

What happens if a molecular switch such as Akt has a mutation?

A

If it is left on, the cell will undergo abnormal metabolism, cells divide uncontrollably, and cells survive when not supposed to. This can lead to cancer.

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26
Q

Name the non-membrane bound organelles. (4)

A

Ribosomes: are enzymes that are responsible for TRANSLATIONNN

Nucleolus: Inside the nucleus that is responsible for RNA SPLICING

Centrioles: forms MICROTUBLUS

Cytoskeleton: PROTEIN FILAMENTS that give shape, strength and movement to cells.

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27
Q

Name the membrane-bound organelles (9)

A

Plasma Membrane: Separates the outside world from the inside and is responsible for forming a SEMI-PERMEABLE MEMBRANE around the cell.

Nucleus: Has a double lipid bilayer that encloses and protects DNA.

EDR: BIOSYNTHESIS of proteins and lipids.

Golgi Apparatus: PROCESSING of proteins and lipids. SORTING to different parts of the cell.

Peroxisomes: REDOX REACTIONS. Synthesis or breakdown of some lipids.

Endosomes: They do endocytosis of material from the plasma membrane and sort material, and transport it to an organelle. AKA DELIVERY DRIVER

Lysosomes: DEGRADATION of membranes and proteins.

Mitochondria: Oxidation of ENERGY MOLECULES to make ATP

Chloroplasts: use sunlight to make ORGANIC MOLECULES from CO2 and water.

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28
Q

Whats a prokaryotic cell (BACTERIA)

A

It lacks a nucleus duuh.
Lacks other membrane-bound organelles.
The PLASMA MEMBRANE is the ONLY membrane structure.

29
Q

What is a Eukaryotic cell

A

DNA is enclosed in the nucleus (DOUBLE MEMBRANE)
Has a lot of MEMBRANE BOUND organelles with a distinct function.
They have a cytoskeleton
They have MITOCHONDRIA and CHLOROPLASTS that have their own GENOMES!!!!!

30
Q

What did the LUCA organism cell have?

A

It had ENZYMES that could SYNTHEZISE LIPIDS to make membranes! (so it had lipid bilayer….)
It had many metabolic enzymes and pathways. IT also had TRANSLATION (ribosomes… AKA RNA WAS THE FIRST BEFORE DNA)

31
Q

What protected the primordial pre-eukaryotic cell DNA during phagocytosis?

A

NUCLEAR ENCLOSURE protected DNA from entanglement and breakage.

32
Q

Why are mitochondria and chloroplasts unique?

A

They have their own genome, own ribosomes and tRNAS to make proteins. They have a DOUBLE MEMBRANE.
ONCE LIVED INDEPENDENTLY. (not anymore and depend on host for survival)

33
Q

Origin of Mitochondria

A

A primordial cell relied on predation of OXIDIZING BACTERIA.
After “eating” the bacterium, the cell did not digest it, and the cell and bacterium became SYMBIOTIC. The cell provided protection and food, and bacteria OXIDIZES food to release ATP.

34
Q

Origin of Chloroplasts

A

The primordial cell relied on predation of PHOTOSYNTHETIC BACTERIA. Became symbiotic, and cyanobacteria convert sunlight to food and the cell with mitochondria OXIDIZE food to make CHEMICAL ENERGY.

35
Q

What did the earliest eukaryotic cell have?

A

It HAD A NUCLEUS
IT HAD A MITOCHONDRIA
IT HAD CHLOROPLASTS

36
Q

Are cells non-spontaneous or spontaneous?

A

NON-SPONTANEOUS
because enthalpy (+H) is INCREASED (heat/energy in bonds)
and a reduction in entropy (-S) (disorder) aka the cell has order!

37
Q

What is ATP?

A

It’s an energy currency that drives energetically UNFAVORABLE reactions

38
Q

How can you test a gene that helps cancer cells divide?

A

First, get the cell with a functional gene. Then have the same cell with the non-functional gene. If the non-functional gene does NOT divide any more cancer cells, then it means that gene was the cause of the cell division. If there are cells that continue to divide cancer cells, then that gene was not the cause of the cell division.

39
Q

What do gene slicing do to a gene?

A

An interfering RNA is added to its complementary nucleotide sequence to target mRNA. A RISC protein is recruited and the mRNA is destroyed (sliced)

40
Q

What does a knockout do to a gene.

A

Involved a specific mutation of the DNA sequence for a specific gene. This mutation makes the gene loss function which then leads to deletion.

41
Q

How do pharmacological drugs inhibit a gene?

A

It involves adding molecules that alter the function of the protein. It blocks the binding site of the proteins to prevent ligand bonding.

42
Q

What is a condenser?

A

It focuses light onto the specimen

43
Q

What is the resolution limit?

A

No more than >0.2nm apart. NOT LESS THAN <0.2nm because they will appear as one particle, and the images will look blurry because light passes around the EDGE of objects. This is due to OPTICAL DIFFRACTION.

44
Q

What is Resolution?

A

Visual SEPERATION of individual components of an object. (opposite of the resolution limit)

45
Q

What is Optical Diffraction?

A

Light waves interfering with one another (crashing into one another)

46
Q

What does the RESOLUTION depend on?

A

WAVELENGTHS AND NUMERICAL APERTURE of the objective lenses

The smaller the wavelength, the smaller the resolution limit

The lower the resolution limit, the better RESOLUTION!

NA is the number of DIFFRACTIVE light rays COLLECTED by an OBJECTIVE.

47
Q

Phase-contract microscope

A

Light passes through the sample and falls out of phase. This produces CONSTRUCTIVE and DESTRUCTIVE interference producing CONTRAST.

48
Q

Dark-field microscopy

A

Light enters at 90˙. The light that DOES NOT get interacted with the specimen passes through and appears dark. When the light DOES interact, it changes direction towards the objective (some)

49
Q

What are sample labelling methods used for?

A

Such as dyes indicate the PRESENCE and AMOUNT of molecule

50
Q

What is the process of tissue sampling?

A

FIXATIVE- Covalent cross-linking locks the protein into place.

EMBEDDED IN PARAFFIN- Wax that penetrates and solidifies to HARDEN AND STABILIZE tissue.

SECTIONED- Tissue is thinly SLICED.

51
Q

What are fluorescent compounds?

A

Emit a longer wavelength after excitation with a SHORT WAVELENGTH

52
Q

Fluorescence microscope setup

A

First Barrier Filter: ONLY BLUE LIGHT gets through with a WAVELENGTH between 450-490nm.

Beam-splitting mirror: Reflects blue light because it has a wavelength below 510nm. This light is directed to the specimen. Which gets EXCITED and emits GREEN LIGHT. (bc wavelength is longer when emitted from a shorter one).

Second Barrier Filter: Eliminates any light but the EMISSION LIGHT (green)

53
Q

Confocal Microscope

A

EMITTED fluorescent light focused at the pinhole and reaches the detector

54
Q

What is a B-cell

A

A cell that makes antibodies to DETECT foreign PATHOGENS.

55
Q

How are antibodies developed?

A

The B-Cells undergo a process called VDJ recombination that makes each B-CELL make ONE type of ANTIBODY that reckon that specific PROTEIN.

56
Q

How do we make antibodies in the lab that recognize a specific protein?

A

Immunize the subject with a purified protein you want an anti-body from. One or more B-cells start making Antibodies that reckon the protein you immunized. The B-cell population will expand. Then we can draw blood from the subject and fuse it with a tumour cell. This fused cell is now called a HYBRIDOMA.

57
Q

What is INDIRECT IMMUNOCYTOCHEMISTRY?

A
  1. an antigen A is immobilized on the protein.
  2. A primary antibody binds to antigen A
  3. Then, a secondary antibody is marked with fluorescents which bind to the primary antibody.
58
Q

What does a Green Fluorescent protein do? (GFP)

A

It pinpoints when, where and how much of a protein exists in the cell.

59
Q

How do you find the proteins location using GFP proteins?

A

Bind onto a DNA segment that codes for the protein you want to study.

60
Q

How do you study gene expression using GFP proteins?

A

The GFP gene is fused to any promoter sequence, This indicates where, when and HOW MUCH PROTEIN IS MADEEEE.

61
Q

Name three types of fluorescent dyes.

A
  1. FM4-64 detects where lipid bilayers are
  2. Fura2 intensity increases with INCREASING (Ca ions)
  3. Fluorescein intensity decreases with LOWER pH.
62
Q

How does Single-Molecule Localization microscopy work?

A

Illuminate one or a few fluorophores at a time

63
Q

How do Scanning Electron microscopes work? (SEM)

A
  1. Samples are fixed, dried and coated with a THIN layer of HEAVY METAL.
  2. Electron beam shoots and scans the sample.
  3. SCATTERED ELECTRONS are detected to form an image.
64
Q

How does Transmission Electron Microscope work? (TEM)

A
  1. FIXATION: with glutaraldehyde to CROSS-LINK proteins in place.
  2. Treatment with OSMIUM TETROXIDE to stain lipid membranes with a HEAVY METAL.
  3. DEHYDRATION AND EMBEDDING in resin
  4. SLICED into 50-100nm thick SLICES.
65
Q

What is Immunogold Electron Microscopy?

A

It has gold particle label sections with antigen localization that binds onto a specific protein. Gold particles are ELECTRON DENSE.

66
Q

What is metal shadowing

A

Deep etched samples are SPRAYED with a THIC coat of a HEAVY METAL.
CREATES 3D-DIMENSION.

67
Q

What is Deep Etching?

A

Samples are flash-frozen.

Fractured for access to INTERNAL STRUCTURES.

Ice is evaporated in a vacuum by freeze-drying.

68
Q

What is a NEGATIVE STAIN electron microscope?

A
  1. Macromolecules on a thin film of CARBON
  2. Coated with a heavy metal salt (uranium acetate) and dried.
  3. Salt covers the carbon film except where the macromolecules are present.
  4. This creates a negative image.

Cell Biology Midterm 1 (3 decks)

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