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BH4 > Lecture 7/8 > Flashcards

Lecture 7/8 Flashcards

1
Q

Where did the first cells come from

A

Experimental evidence suggests:

  • abiotic (nonliving synthesis) of simple organic compounds
  • abiotic polymerization of these monomers
  • evolution of molecule(s) capable of both information storage and replication
  • enclosure of such molecule(s) within simple membrane(s) to form the first primitive cell
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2
Q

Stanley Miller found what organic compounds in his exp

A

Glycine and alanine

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3
Q

If subbed CO2 and CO instead of CH4 and NH3 in stanley miller exp what compounds form

A

numerous amino acids, formaldehyde, formic acid, hydrogen cyanide, sugars, and adenine

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4
Q

Other possibilities where first cells came from

A

FeS2, deep-sea hydrothermal vents, catalytic surfaces, primitive enzymes

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5
Q

Why are most cells small

A

Cells must have adequate surface area/volume ratio (because of the required exchanges between environment: the surface area represent the amount of cell membrane available for uptake and excretion)

If cell too big ur limited by simple diffusion

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6
Q

Molecules move by diffusion: the rate of diffusion decreases as the size of molecules
_____, so active transport
is necessary (carrier proteins, vesicles, etc.)

A

increases

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7
Q

[reactants and catalysts] ___ through enclosure into organelles = compartmentalization

A

increase

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8
Q

Which of the following have nuclei: bacteria, archaea, eukaryotes

A

eukaryotes

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9
Q

Fxn of membranes in eukaryotes

A

use of internal membranes to segregate function

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10
Q

Fxn of plasma membrane

A

Define cell boundaries and retains contents

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11
Q

Plasma membrane composed of

A

Phospholipids, glycolipids, single lipids

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12
Q

How is plasma membrane organized in

A

Lipid bi-layer

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13
Q

Glycolipids and glycoproteins exposed to the

___ side of the membrane. Fxn?

A
  • External

- make it stickier and easier to organize into structures

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14
Q

Functions of membrane proteins?

A
  • enzymes: catalyze reactions associated with the membrane
  • anchors for structural elements of cytoskeleton
  • receptors (for external signals that trigger response within the cell)
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15
Q

What is the nucleus

A

The cell’s info center

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16
Q

What does the nucleus consist of

A

Histones + DNA

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17
Q

Nuclear envelope consists of what

A

inner and outer membrane

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18
Q

What organelle is continuous with outer membrane of the nuclear envelope

A

Endoplasmic reticulum

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19
Q

The space between 2 nuclear membranes is?

A

Perinuclear space

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20
Q

Proteins are synthesized on ribosomes in the cytoplasm,

so how do they get into the nucleus?

A

Nuclear pores

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21
Q

What are nuclear pores

A

: channels lined up with pore complexes that regulate the movement of macromolecules
(ribosomal proteins, mRNAs, histones, etc.) in and out of the nucleus

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22
Q

What are nucleoli

A

rRNA and ribosomal assembly

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23
Q

What is the fxn endomembrane system

A

Dynamic system: synthesizes proteins that are destined for various organelles, cellular membranes, or secretion

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24
Q

Where are proteins synthesized

A

ribosomes associated w/E.R

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25
Q

Where are proteins packaged and processed

A

Golgi apparatus

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26
Q

How do proteins move out of cell

A

in small membrane-bound vesicles

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27
Q

Where are lysosomes derived from? So part of what system

A

ER, endomembrane system

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28
Q

Are peroxisomes part of endomembrane system

A

no

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29
Q

What is the E.R.

A

Interconnected network (“reticulum”) of tubular membranes and flattened
sacs, or cisternae
(singular: cisterna)

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30
Q

Lumen of E.R. continuous with?

A

nuclear Membrane

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31
Q

Characteristics of rough ER

A
  • studded with
    ribosomes on the side
    of the membrane that faces the cytosol.
  • Ribosomes synthesize ER membrane or resident proteins: many of these will be secreted via the endomembrane system
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32
Q

Characteristics of rough ER

A
  • studded with
    ribosomes on the side
    of the membrane that faces the cytosol.
  • Ribosomes synthesize ER membrane or resident proteins: many of these will be secreted via the endomembrane system
  • synthesize most secretory and membrane proteins
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33
Q

Characteristics of smooth ER

A
  • no role in protein synthesis (no ribosomes)
  • involved in synthesis of lipids and steroids
  • importantly, smooth ER also inactivates and detoxifies drugs
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34
Q

Free ribosome vs ribosome on E.R

A

Free ribosomes synthesize proteins intended for use within the cytosol or for import into organelles, whereas ribosomes on the rough ER synthesize most of secretory and membrane proteins

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35
Q

What are dark spots near smooth ER?

A

Glycogen storage granules

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36
Q

What is the golgi apparatus

A

A stack of flattened discs (cisternae)

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37
Q

Fxn of golgi apparatus

A

processing and packaging secretory proteins and in synthesizing complex polysaccharides (analogy: central post office, processing station, vesicles fuse in – vesicles fuse out, modified and ready for export )

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38
Q

Most outer membrane and secretory proteins are ____

A

Glycoproteins

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39
Q

What are glycoproteins

A

.

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40
Q

Characteristics of mitochondria

A
  • present in most eukaryotic cells
  • Energy production in cells: sites of aerobic respiration- oxidation of sugars and other cellular fuels to CO2 and generation of ATP
  • inner and outer membranes
  • Mitochondria contain their own ribosomes and circular
    dsDNA (mtDNA), inherited only
    through the mother (useful in tracing genetic linkages)
41
Q

What are cristae

A

infolding of inner membrane of mitochondria

42
Q

of mitochondria within a cell can often be related to ___

A

their role in that cell; e.g., sperm, muscle cells

43
Q

What is the site of photosynthesis

A

chloroplasts

44
Q

What is photosynthesis

A

the light-driven process that uses solar energy and CO2 to synthesize the sugars and other organic compounds

45
Q

Characteristics of chloroplasts

A

Large organelles (~5-10 μm long), large # in the leaves of green plants, double membrane, third membrane system: flattened sacs thylakoids connected by stroma thylakoids and stacked together to form the grana

46
Q

Reactions that depend on solar energy are localized in or on ____

A

thylakoid membrane system

47
Q

Fxn of stroma

A

Rxns involved in conversion of CO2 to sugar molecules

48
Q

How is chloroplasts and mitochondria similar

A

ribosomes and own circular dsDNA in the stroma

49
Q

What is the endosymbiont theory

A

mitochondria and chloroplasts evolved from ancient bacteria that established a symbiotic relationship with primitive nucleated cells 1 to 2 billion years ago

Phagocytosis (“cell eating”)

Anaerobic vs aerobic metabolism

50
Q

Evidence for endosymbiont theory

A
  • inner membranes have bacterial- type lipids, outer membranes have eukaryotic-type lipids
  • mt rRNA sequences match those of aerobic purple bacteria
  • chloroplast rRNAs match photosynthetic cyanobacteria
51
Q

Characteristics of lysosomes

A
  • 0.5-1 μm in diameter
  • Single membrane, pH~5
  • Use by cells as storage containers for hydrolases (enzymes that digest proteins, carbohydrates, or fats) AKA cell’s recycling system
52
Q

Why sequester hydrolases in lysosomes?

A

They will be digesting things away otherwise. You do not want to be eating your intracellular environment

53
Q

Like secretory proteins, lysosomal enzymes are synthesized in ___, transported through the ___, and then packaged into vesicles that can become lysosomes

A
  • ER

- Golgi apparatus

54
Q

The inner face of the lysosomal membrane is highly glycosylated. Why?

A

Want to protect from degradation.

55
Q

Effects of defects in any of ~40 lysosomal enzymes can ?

A

disrupt normal cellular degradation processes & lead to serious human disease

56
Q

Fxn of each hydrolase?

A

Breaking down covalent bonds, hydrolysing diff molecules into their constituent parts

57
Q

What happens when hydrolases fail to fxn? What enzyme would you predict to be defective in this condition

A
  • their target molecules accumulate, producing swollen lysosomes (e.g., α-mannosidosis).
  • A-mannosidosidase
58
Q

What happens when there is a defect in transport of hydrolases to lysosomes?

A

A well known example is I-cell disease (life expectancy 7 years, no treatment):
undigested macromolecules accumulate in lysosomes, leading to engorged lysosomes, forming inclusions, coarse facial features,
enlarged liver and spleen, psychomotor retardation, etc.

59
Q

Characteristics of peroxisomes

A
  • Resemble lysosomes in size
    and structure: single membrane, but unlike lysosomes, not derived from the ER
  • Found in plants, animals, fungi, protozoa, and algae. In animals, especially prominent in liver and kidney cells
60
Q

Fxn of peroxisomes

A

: generate and degrade H2O2 (a byproduct of several normal metabolic reactions, highly toxic to cells: catalase is involved), oxidative breakdown of fatty acids >12C long, detoxification of other harmful compounds (e.g., methanol, ethanol, formaldehyde), catabolism (break down) of unusual substances (e.g., D-amino acids). Peroxisomes may regulate O2 levels within cells and play a role in aging

61
Q

What is the cytoskeleton

A

3D array of interconnected proteinaceous structures: an internal framework that
gives a cell its distinct shape and internal organization

62
Q

Fxn of cytoskeleton

A

Structured yet dynamic, plays
an important role in cell movement and cell division

-a framework for positioning and moving organelles and macromolecules within the cytosol (~80% of the cell proteins are associated with cytoskeleton)

63
Q

3 major structural elements of cytoskeleton

A

Microtubules, microfilaments (actin), and intermediate filaments

64
Q

cytoskeleton prominent where

A

cilia, flagella, muscle fibrils

65
Q

Diff between Microtubules, microfilaments (actin), and intermediate filaments

A

Microtubles tend to be more parallel, micro and intermediate filaments tend to be dispersed

66
Q

What are extracellular structures composed of

A

Materials transported out of cell across plasma membrane

67
Q

In animals, ECM primarily composed of what

A

Collagen and proteoglycans

68
Q

Is ECM stiff or elastic

A

Elastic

69
Q

Plant and fungal cell walls are composed of

A

Cellulose

70
Q

Bacteria ECM composed of

A

GlcNAc-MurNAc

71
Q

ECM in animals varies in composition based on

A

cell type

72
Q

Fxns of ECM in animals

A

Support, regulation of cell motility and migration, cell division, recognition and adhesion, cell differentiation during development

73
Q

Characteristics of viruses

A
  • Intracellularly life style only

- DNA or RNA, segments, ss or dd, protein coat and maybe membrane (enveloped viruses, recall Zitka)

74
Q

Characteristics of viroids

A

Small circles of ssRNA, no protein coat, don’t encode proteins, enter nucleus of infected plant and interfere w transcription of DNA

75
Q

What are prions

A

infectious protein molecules

76
Q

What is Alzheimers disease

A

Disease characterized by degradation of brain cells due to excessive aggregation of proteins outside (amyloid plaques) and inside brain cells

77
Q

What are amyloid plaques

A

Insoluble fibrils of amyloid-beta peptide (AB), produced in plasma membrane on amyloid precursor protein (APP_

78
Q

How do normal vs. alzheimer’s patients differ in their apoE

A

Most patients have defective apolipoprotein E (apoE): normal function of apoE is cholesterol transport, but defective apoE stimulate amyloid plaque formation

79
Q

Unlike bacterial and yeast cells, most animal cells will grow only when attached to ____

A

solid surface

80
Q

What to cell cultures (in vitro) need to grow

A
  • cell culture flask or scaffold material (i.e., chemically modified plastic or coated with ECM proteins)
  • suspension culture/nutrients (aka culture media)
  • environment mimicking in vivo conditions (CO2, temperature 37oC, humidity, oxygen tension maintained at atmospheric, but can be varied depending on cell type)
  • sterility (aseptic technique, antibiotics, and antifungals) – GMP, QC/QA
81
Q

Cell morphologies vary depending on ___

A

cell type
- (fibroblasts, cells of the connective tissue, typically divide/grow the fastest and will become the predominant cell type, unless removed)

82
Q

What was Basal Eagle Media developed for

A

HeLa cells

83
Q

Use of Basal Eagle Media

A
  • Maintain pH and osmolarity

- Provide nutrients and nrg source

84
Q

Components of Basil Eagle Media

A

Inorganic Salts

  • Maintain osmolarity
  • Regulate membrane potential (Na+, K+, Ca2+)
  • Ions for cell attachment and enzyme cofactors

pH Indicator – Phenol Red
- Optimum cell growth approx. pH 7.4

Buffers (Bicarbonate and HEPES)

  • Bicarbonate buffered media requires CO2 atmosphere
  • HEPES chemical buffer range pH 7.2 – 7.6 (is better at maintaining physiological pH in cell culture, when compared to bicarbonate buffers despite the changes in [CO2])

Glucose
- Energy Source
Vitamins, trace elements, supplements: antibiotics, antifungals, etc.

FBS provides growth factors and hormones, aids in cell attachment

85
Q

Practically speaking, how do we culture cells in the laboratory?

A
  1. Revive frozen cell population (see ATCC), OR isolate cells from tissue
  2. Maintain in culture (passing/sub-culture under aseptic technique when confluent)
  3. Count cells (see slide 11)
86
Q

If dont have antifreezing what happens to cultured cells

A

Your ice will expand and ur cell will lyse

87
Q

What is a cell strain

A

A lineage of cells originating from one initial primary culture

88
Q

What is senescence

A

Most of the primary cells will divide a finite number of times and then cease growing

89
Q

Exception to finite life span?

A

embryonic stem cell (ES), derived from an embryo. These cells will divide and give rise to all tissues during development: ESs can be cultured indefinitely under the appropriate conditions

90
Q

What are transformed cells

A

Rare cells in a population of primary cells may undergo spontaneous oncogenic mutations. These transformed cells can grow indefinitely in culture

91
Q

What is a cell line

A

A culture of cells with indefinite life span is considered immortal (recall HeLa cells)

92
Q

What does FACS stand for

A

fluorescence-activated cell sorter

93
Q

Fxn of FACS

A

both analyze the cells and select the few fluorescent cells from thousands of others and sort them into separate dishes

94
Q

Common use of FACS and example

A

FACS is commonly used to purify the different types of white blood cells (WBCs), each of which bears on its surface one or more distinctive proteins and so will bind monoclonal antibodies specific for its proteins

Example: only T cells of the immune system have both CD3 and Thy1.2 proteins on their surfaces, and may
be separated from other types of blood cells because on these “molecular markers”
11

95
Q

What are antibodies

A

proteins secreted by B cells that bind with high affinity to their antigens

96
Q

What is monoclonal

A

Each normal antibody-producing B-cell forms a clone of cells in the spleen, or lymph notes, with each cell producing the identical antibody

97
Q

What is polyclonal antibodies

A

Because most natural antigens contain multiple epitopes, however, exposure of an animal to an antigen usually stimulates the formation of multiple B-cell clones, each producing a different antibody (so, there is a mixture of antibodies
circulating in the blood

98
Q

How to produce and purify monoclonal antibodies

A

hybrid cells called hybridomas are made. Individual B-cells are fused with immortal cells called myelomas and the surviving hybridomas are selected/tested for the production of the desired (monoclonal) antibody

99
Q

What should you do if cell fractions obtained by differential and equilibrium density-gradient centrifugation still contains more than one type of organelle

A

Monoclonal antibodies for various organelle- specific membrane proteins are a powerful tool for further purifying such fractions

Example: purification of vesicles whose outer surface is covered with the protein clathrin; these coated vesicles are derived from coated pits at the plasma membrane during
receptor-mediated endocytosis (more on this later in the course)

An antibody to clathrin, bound to a bacterial carrier/magnetic beads, can selectively bind these vesicles in a crude preparation of membranes, and the antibody complex can then be isolated by low-speed centrifugation/attachment to magnets on the side of tubes

BH4 (9 decks)

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