Lectures 11 & 12: Organelles Flashcards Preview

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Flashcards in Lectures 11 & 12: Organelles Deck (171):
1

When did prokaryotes arise?

3.5 billion years ago

2

When did eukaryotes arise?

2.5 billion years ago

3

What is the first evidence of life? To how long ago does this bring us (2 types)?

Stromatolites in carbonate sediments 1. Archaea: 3.4-3.5 billion years ago 2. Proterozoic: 2.8-3 billion years ago (in rocks)

4

What are 2 another names for stromatolites?

Cyanobacteria/Blue-green algae

5

What is the theory that explains how eukaryotes arose? What evidence do we have for this?

Archae were the host cells of bacteria (the formed an endosymbiotic relationship) Evidence: 1. Archae contain DNA w/ introns, promoters, histones, and transcriptional machinery similar to eukaryotes, which probably formed the eukaryotic nucleus 2. Archae glycosylate proteins and bacteria do not

6

What are metazoans?

Evolved versions of eukaryotes with cell junctions and connective tissue

7

When did metazoans arise?

850 million years ago

8

What is the homeotic gene family?

Genes which regulate the development of anatomical structures in various organisms

9

When did the homeotic gene family arise?

600 million years ago

10

What are the 3 domains of life?

1. Bacteria 2. Archaea 3. Eukarya

11

What was the first version of life? What are the 2 types?

Prokaryotes: unicellular without organelles 1. Bacteria 2. Archaea

12

Are all eukaryotes multicellular organisms?

NOPE

13

What are the 3 types of eukaryotic multicellular organisms?

1. Animals 2. Plants 3. Fungi

14

What are extremophiles?

Subtype of archaea that thrives in extreme environments

15

What are thrombolites?

Fossils that appear in the early proterozoic and are related to stromatolites

16

What are oncolites?

Fossils that appear in the pre-Cambrian and are related to stromatolites and thrombolites

17

What are algal filament fossils?

Fossils that appear in chert (dark rock in the North Pole and Australia) and are evidence of life 3.5 billion years ago

18

What are spheroidal bacterial structures?

Prokarytic fossil evidence from 3 to 3.1 billion years ago found in South Africa

19

What are the surface mats of stromatolites?

Bicarbonate sediments that contain mainly cyanobacteria and have other eubacteria, archaebacteria and eukaryotes in close proximity

20

What do thrombolites and oncolites look like?

Very uniform rocks

21

What did the bacteria that fused with the archaea become in the eukaryotes? 2 options

1. Mitochondria 2. Chloroplasts

22

How did other organelles (other than mito) develop in eukaryotes?

Infolding of plasma around bunches of proteins and enzymes

23

What are the main roles of integral proteins?

Pores and receptors

24

What is the main role of peripheral proteins?

Accessory proteins for the integral ones

25

What is the glycocalyx?

All of the sugars attached to glycolipids on the exterior of the lipid bilayer

26

What is the E face of the lipid bilayer?

The external face of the internally fractured membrane

27

What is the P face of the lipid bilayer?

The protoplasmic (internal) face of the internally fractured membrane

28

What do prokaryotes have instead of a nucleus?

Nuclear organizing region, but it's not a distinct organelle

29

What are the 4 components of the nuclear membrane?

1. Inner membrane 2. Outer membrane 3. Cisterna (between the 2) 4. Nuclear pore complexes to regulate the mvt of macromolecules

30

What does the outer membrane of the nucleus sometimes contain? What does this mean?

Ribosomes, which means the nucleus is continuous with the RER

31

What kind of permeability does the nuclear envelop have?

Selectively permeable

32

What is the inner membrane of the nucleus associated with?

Nuclear lamina protein meshwork that binds to chromatin in non-dividing cells

33

What kind of filaments are the lamins of the nuclear membrane made of?

Intermediate filaments

34

What do nucleoporins look like?

8-fold symmetry

35

What are the 4 subunits of a nuclear pore? What 2 other parts are attached to it?

What is the whole thing called?

Q image thumb

1. Luminal subunit 2. Ring subunit 3. Column subunit 4. Annular subunit Other parts: - Fibrils toward the cytosol - Nuclear cage toward the nucleus

 

Nucleoporins

A image thumb
36

How do nuclear pores work?

Translocating proteins have nuclear export or import localization sequences that bind specifically to transport proteins that in turn interact w/ proteins in the pore for transfer

37

What are the 2 types of transport proteins?

1. Importins 2. Exportins

38

What kind of molecules through a nuclear pore complex and through what transport mechanism?

1. Small ions and solutes (like H2O): simple diffusion w/o regulation 2. Macromolecules: active transport regulated by the pore

39

What molecules are transported out of the nucleus?

Ribosomal subunits and other RNA-associated proteins

40

What molecules are transported into nucleus?

Molecules for DNA replication and trancription: chromatins, ribosomal proteins, transcription factors, and enzymes

41

What is the nucleolus?

A subsection of the nucleus responsible for making ribosomal RNA (rRNA)

42

What does the nucleolus look like under a microscope? When can you observe it?

Darker region within the nucleus Resting state in interphase

43

What are the 3 parts of the nucleolus and what does each consist of?

1. Pars amorpha: DNA that codes for rRNA 2. Pars fibrosa: rRNA 3. Pars granulosa: maturing ribosomal subunits

44

What is another name for pars amorpha?

Nucleolar organizer region

45

What is the nucleolonema?

Pars fibrosa + pars granulosa

46

How to distinguish the different parts of the nucleolus looking through a microscope?

1. Pars amorpha: lighter circular part 2. Pars fibrosa: slightly darker around the pars amorpha 3. Pars granulosa: slightly darker but not around the pars amorpha

47

What happens to the nucleolus during the cell cycle?

It assembles and disassembles

48

What are the 2 forms of chromatin? Describe each

1. Hetero: heavy staining, highly condensed 2: Eu: light staining and uncoiled

49

What are the 2 components of chromatin?

1. DNA

2. Protein: histones and non-histone chromosal proteins (eg: transcription factors)

50

What is the nucleolus-associated chromatin? What kind of chromatin?

NAC: heterochromatin around the nucleolus

51

Describe each condensation step from the DNA double helix to the metaphase chromosome

1. DNA double helix 2. DNA w/ histones: nucleosomes (beads on a string) 3. Additional folding and packing: 30 nm chromatin fiber 4. Looped domains 5. Condensed chromosome 6. Metaphase chromosome

52

What 2 types of organisms have a larger genome than others?

1. Plants: because they are sedentary and need genes to help them survive (flooding, insects attacking, etc) 2. Amphibians: need more genes to help live in both terrestrial and aquatic environments

53

How many nucleotide pairs in the human genome?

10^9-10^10

54

Which type of chromatin is transcriptionally active?

Euchromatin

55

What are the 2 cell division processes for eukaryotes?

1. Mitosis 2. Meiosis

56

What is the division process for prokaryotes?

Binary fission

57

What is the division process for mitochondria and chloroplasts?

Binary fission

58

What accounts for the large majority of genetic diversity?

Meiosis

59

What can explain why it took so long for eukaryotes to evolve?

Because genetic diversity was only possible through chemical mutagenesis, which is very slow vs meiosis which enables rapid evolution

60

Describe the cell cycle. How long does it last?

- G1: normal function (in this stage most of the time) and accumulation of enzymes and nucleotides - S phase: DNA duplication - G2: preparation for mitosis - M phase: mitosis 24 hours

61

What are the 6 phases of mitosis? How long does each last?

• Interphase: Growth period; cell carries out normal functions

• Prophase (1 hr): Nuclear membrane disappears, chromatin condenses into chromosomes and the centrosomes move to opposite poles of the cell, mitotic spindle forms

• Metaphase: Chromosomes further condense and align at the equatorial plane.

• Anaphase: Sister chromosomes move toward spindle poles.

• Telophase: Sister chromosomes arrive atthe poles.

• Cytokinesis: A cleavage furrow divides the cytoplasm and duplicated chromosomes into two daughter cells.

62

Describe the composition of ribosomes

Small and large subunit

63

What RNA do ribosomes bind?

mRNA

64

What kind of proteins do free ribosomes synthesize?

Intracellular proteins: cytosolic and cytoskeletal proteins and proteins for import to the nucleus, the mitochondra or the peroxisomes

65

What kind of proteins do RER ribosomes synthesize?

Proteins that require further processing

66

Which types of proteins get more PTMs than others?

Those synthesized by the RER vs the free ribosomes

67

On what are ribosomes attached on the RER?

The cisternal membrane

68

What is a polysome or polyribosome?

Single mRNA molecule associated with a number of ribosomes along it 

69

What happens to proteins after they are synthesized by ribosomes on the RER?

Often stored in lysosomes or secreted out

70

Describe the movement of nascent peptides from free ribosomes to RER the lumen

1. Nascent peptide's has a signal peptide that binds a signal-recognition particle which inhibits further elongation

2. SRP-peptide complex binds an SRP receptor on the ER membrane thanks to docking proteins

3. SRP releases the signal peptide for translation to continue

4. Protein translocators bing to the ribosome and form a channel for the peptide to go through the ER membrane: vectorial discharge 

5. The peptide pushes itself and is pulled by chaperones

6. The signal peptide is removed inside the RER lumen

71

What does TEM stand for?

Transmission Electron Microscopy

72

What are the 5 functions of the ER?

RER:

1. Cleavage of signal-peptide

2. Protein folding

3. Glycosylation

SER:

1. Breakdown of glycogen

2. Detoxification of drugs

3. Regulation of muscle contraction

4. Synthesizes phospholipids, fats, and steroids

73

What happens to the protein in the ER if it's not folding properly?

Ubiquitylated to be sent to the proteasome

74

What is Golgi apparatus ?

Stack of membranes that modifies, sorts, and packages proteins from th ER

75

What are the 2 faces of the Golgi?

1. Cis: forming: close to ER 2. Trans: secreting: where proteins are released near the plasma membrane

76

What are the 3 parts of the Golgi? What does each do?

1. cis Golgi network: phosphorylation of oligosaccharides on lysosomal proteins 2. Golgi stack (other slide) 3. trans Golgi network: addition of NANA and sorting (!!)

77

What are the 3 parts of the Golgi stack? What does each do?

1. Cis cisterna: removal of Man 2. Medial cisterna: removal of Man and addition of GlcNAc 3. Trans cisterna: addition of Gal

78

What is NANA?

N-acetylneuraminic acid

79

What is GlcNAc?

N-acetylglucosamine

80

What about the environment changes as a protein moves through the Golgi?

pH: decreases from cis to trans

81

How do proteins from the RER get to the Golgi?

Vesicules

82

What regulates the movement from the RER to the Golgi?

Coat protein-II (COP-II)

83

What happens to proteins in the Golgi that are misfolded?

Recognized by KDEL receptor proteins and sent back to the RER by COP-I for refolding or degradation

84

What happens to the proteins once they are secreted by the Golgi?

1. Directed to fuse with an late endosome to become a lysosome 2. Directed for secretion

85

What is the pH in lysosomes? How did scientists figure this out?

5 Using certain fluorescent dyes that change spectrum with pH

86

What is the cytoslic pH?

7.2

87

What type of enzyme are in the lysosomes? List some of these

Acid hydrolases: 1. Nucleases 2. Proteases 3. Glycosidases 4. Lipases 5. Phosphatases 6. Sulfatases 7. Phospholipases

88

How do lysosomes create that acid pH?

Proton pumps using ATP

89

What is necessary when primary lysosomes form secondary lysosomes?

Need to fuse with membrane bound organelles to maintain pH

90

What are the 4 types of secondary lysosomes and what do they correspond to?

1. Lysosome + phagocytosis vesicle = digestive vacuole 2/3. Lysosome + endocytosis vesicle = multivesicular body or generalized secondary lysosome 4. Lysosome + mitochondrion = autophagic vacuole

91

What is an endocytosis vesicle?

A vesicle that has taken in material from the cell surface

92

What is special about peroxisomes?

They are very primitive in date, appearance, and function

93

What is another name for peroxisomes?

Microbodies

94

Describe the composition of a peroxisome

Vesicular organelle composed of small packets of oxidative enzymes surrounded by a single membrane

95

How do peroxisomes grow?

Uptake of peroxisomal proteins from cytoplasm by specific proteins that catalyze the import

96

How do peroxisomes divide?

Cytoplasmic fission (no DNA involved)

97

What are the 3 functions of peroxisomes?

1. Oxidation of harmful substances via generation of H2O2 2. Detoxification of alcohol and other harmful chemicals 3. Beta-oxidation of long-chain fatty acids (first step of their breakdown)

98

What is the major function of peroxisome?

Oxidation of harmful substances via generation of H2O2

99

What is the rxn that happens in peroxisomes?

RH2 + O2 --> R + H2O2

100

Where are mitochondria found? Why?

On the cytoskeleton to be able to move

101

Describe the 6 parts of the mitochondria

1. Inner membrane 2. Outer membrane 3. Intermembrane space 4. Cristae: folds in inner membrane to increase surface area 5. Elementary particles on inside of inner membrane: proton pumps to facilitate ATP generation 6. Matrix: inside the inner membrane

102

What is another name for elementary particles?

F1 particles

103

What gave rise to mitochondria? What are the 4 pieces of evidence

Endosymbiosis of aerobic bacteria: 1. Mito has its own circular chromosome of DNA, ribosomes, mRNA, tRNA (just like bacteria) 2. Undergo fission (like prokaryotes) 3. Double membrane: outer from ancestral host and inner from symbiotic prokaryote 4. Closest genotypic relatives of mitos are rickettsia bacteria: intracellular parasites of eukaryotic cells

104

Explain mitochondrial inheritance

Maternal because very few paternal mitos can survive the fertilization process

105

What is the mitochondrial eve? How long ago did it exist?

The matrilineal most recent common ancestor of all humans, which lived about 200 K years ago

106

Descrive mito DNA

37 genes = 16,000 base pairs

107

How do the mito proton pumps generate ATP?

Flow of H+ down their electrical gradient creates mechanical rotational energy (of specific proteins) which is then converted into chemical energy to bind ADP and Pi = oxidative phosphorylation = chemiosmotic mechanism

108

When does mitos synthesize ATP the most?

During aerobic respiration

109

What does the matrix of the mito contain? 2 types

1. Metabolic enzymes for the TCA 2. Materials necessary for protein synthesis: DNA, mRNA, tRNA, ribosomes, and dense granules of precipitated salts

110

How does the mito get H+ inside its inner membrane?

Pumps because the membrane is impermeable to them

111

Is there a lot of genetic diversity in mDNA?

NOPE because of binary fission (instead of meiosis)

112

Are all of the proteins needed by the mito coded for in the mDNA?

NOPE

113

List the 3 types of cytoplasmic inclusions

1. Pigment granules 2. Glycogen 3. Lipid

114

Are glycogen and lipids membrane bound in the cytoplasm?

Nope but they are round to minimize surface tension

115

What are the 2 types of pigment granules?

1. Melanosomes: contain melanin 2. Lipofuscin: contain residues of lysosomal digestion

116

Are pigment granules membrane enclosed?

Yes!

117

What are 2 other names for lipofuscin?

1. Residual body 2. Tertiary lysosome

118

What is glycogenolysis?

Degradation of glycogen to produce glucose

119

What are the 3 parts of the cytoskeleton (from smallest to largest)?

1. Microfilaments 2. Microtubules 3. Intermediate filaments

120

Where are melanosomes found?

Epidermis and inner pigmented layer of the non-neural retina

121

What organelle fills up almost the entire interior of the cell?

Lipid droplets

122

What are microfilaments?

Helical chains of actin

123

What are the 2 types of actin?

1. Filamentous actin = F actin 2. Globular/monomeric actin = G actin

124

Describe the composition of actin fibers. When do they assemble?

Globular monomers that assemble in the presence of K+ and Mg2+ into double-stranded helices of filamentous actin

125

How is F actin elongated/shortened? How fast does this happen?

- Elongated: monomers are added at the + end - Shortened: monomers are removed from - end Rapid!

126

What are 4 functions of actin?

1. Intracellular mvt 2. Muscle contraction 3. Membrane structures 4. Locomotion

127

What are the 2 models of intracellular movement? Explain each

1. Cortical Flow Model: cell mvts controlled by the flow of actin filaments into the cell cortex governed by gradients of tension in the cortex generated by myosin (from low tension to high tension) 2. Leading Edge Model: actin at the leading edge of the migrating cell undergoes rapid remodeling

128

What does the Cortical Flow Model of intracellular movement account for?

Cytokinesis: cells divide due to high tension in the equatorial midline of the cell creating a cleavage furrow

129

How does actin contribute to cell motility and contractibility (shape) of the cell?

Actin attaches and forms stress fibers

130

How does actin contribute to cell structure? 2 ways

1. The filaments form the terminal web attached to zonula adherens under the apical cytoplasm 2. Filaments in microvilli and stereocilia (different from cilia) anchor into the terminal web

131

How does actin contribute to cell locomotion?

Actin filled filopodia (look like fingers) on cells to move them around, sense their surroundings, and interact with other cells

132

Describe the composition of microtubules

Heterodimer of alpha and beta subunits (tubulin) form a hollow slight spiral organization and polarity

133

What are the 3 types of microtubules?

1. Individual fibers: mitosis spindles or axons of neurons 2. Doublets w/ other proteins = axoneme: cilia core (flagella) and sperm tail 3. Triplets: centrioles

134

How are microtubules elongated/shortened? How fast does this happen?

- Elongated: free tubulin dimers are added (fast)

- Shortened: dimers are removed (slow)

135

What is a centrosome?

Two orthogonal centrioles (triplets of microtubules) which are the nucleating sites for polymerization of microtubules

136

What is another name for a centrosome in a mitotic cell?

Microtubule organizing center (MTOC)

137

What is a basal body?

A centriole (doublet of microtubules) that nucleates the axoneme of cilia

138

What are the 2 types of cilia?

1. Motile: axoneme with a central doublet of microtubles 2. Primary: axoneme lacking a central doublet of microtubules which are non-motile but have a sensory function

139

How many primary cilia do most cells have?

1

140

What's the relationship between intermediate filaments and tumors?

Keratins have 30+ isoforms and can be used to grade a tumor (gage degree of transformation)

141

What are the 4 types of intermediate filaments?

1. Nuclear lamins 2. Vimentinlike proteins 3. Keratins 4. Nuclear intermediate filaments

142

What are the component polypeptides of nuclear lamins? Where are nuclear lamins found?

Lamins A, B, and C Nuclear lamina

143

What are the 4 possible components of vimentinlike proteins and where is each found?

1. Vimentin: many cells of mesenchymal origin 2. Desmin: muscle 3. Glial fibrillary acidic protein: glial cells 4. Peripherin: neurons

144

What are the 2 types of keratins and where are they found?

1. Type 1: acidic 2. Type 2: Neutral/basic Epithelial cells and their derivatives

145

What is the role of keratins for terrestrial vertebrates?

They accumulate to provide a barrier to reduce dehydration and protect from pathogens

146

What is the role of keratins?

Attach to the desmosomes in the cytoplasm to form a framework

147

What are the 4 types of cell junctions?

1. Zonula occludens (tight junctions) 2. Zonula adherens (intermediate junctions) 3. Macula adherens (desmosomes) 4. Communicating (gap) junctions

148

What is the basolateral portion of the cell?

The one toward the ECM = interstitial space

149

What is the apical portion of the cell?

The one toward the lumen

150

Describe zonula occludens (tight junctions). What do they maintain? With what proteins do they do this?

Band encircling the apical end of a cell to prevent mvt of molecules between the lumen and the interstitial space (therefore solutes need to go through cells) This maintains cell polarity and forms a seal between neighboring cell membranes due to interactions between transmembrane proteins: claudin and occludin

151

Describe zonula adherens (intermediate junctions)

Anchor cells to each other:

Encircle epithelial cells right below the zonula occludens by using cadherins bound to catenin bound to actin like filaments (form the terminal web that help anchor actin filaments originating from microvilli at the apical end of cells)

152

Describe the 2 types of macula adherens (desmosomes)

1. Full one: spot welds around the cell perimeter (lateral sides) to attach cells together 2. Hemi: anchors the basal lamina of the basement membrane

153

What are the 2 parts of the basement membrane?

basal lamina + lamina reticularis

154

What is a desmosome composed of?

Transmembrane proteins of the cadherin family: (desmoglein and desmocollin) insert into a dense attachment plaque made of anchoring proteins inside the cell (plakoglobin and desmoplakin) which attach to keratin inside the cells

155

What's the difference between the protein composition of desmosomes and hemidesmosomes?

Integrins replace cadherins in hemidesmosomes

156

What is the role of communicating/gap junctions

Mediate rapid communication between cells by letting small molecules pass through channels(<1.5 nm) (ions, sugars, amino acids) 

157

What are the small molecules that can go through gap junctions?

Ions, sugars, AAs (hydrophilic molecules)

158

What is a type of coordinated function allowed by gap junctions?

Rhythmic contractions

159

What proteins are gap junctions made of?

6 connexins = 1 connexon 2 connexons = channel with a hydrophilic core

160

What is a nucleosome?

DNA + histones = beads on a string

161

What is sialic acid?

N-acetylneuraminic acid!!!! NANA

162

163

What is the transitional ER?

A specialized region of the ER which is free of ribosomes and contains vesicles to take the proteins away

164

What is the cisternal maturation model?

New cis cisternae continually form and migrate to the trans face in the Golgi 

165

What are condensing vacuoles?

Vacuoles in the trans Golgi network to become transport vesicles

166

What is the enzyme catalase used in? For?

Used in peroxisomes to use H2O2 to oxidize various substances

167

168

What is dynein?

Protein associated with individual microtubules in an axoneme that allow for ciliary movement by hydrolyzing ATP to generate a sliding force between 2 microtubule doublets 

169

What is myosin? What are the 2 types?

Family of proteins that interact with actin to produce tension 

1. Type 1: present in non-muscle cells and responsible for mvt of organelles along actin filaments

2. Type 2: present in muscle and non-muscle cells and contains a globular head that can bind actin and a fibrous tail that can form polymers

170

What is the cell cortex?

Layer of actin right beneath the plasma membrane of many cells and gives mechanical strength to the cell surface and enables it to change shape and to move 

171

What are the 4 molecules that mediate cell adhesion?

1. Integrins 

2. Ig (embryogenesis, healing, and inflammatory response)

4. Selectins (bind to carbs)

4. Cadherins (Ca2+ dependent)