Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BICD 110 > Midterm 1 > Flashcards

Midterm 1 Flashcards

1
Q

Robert Hooke

A

Discovered using compound microscope (50X):
-plant cells

-saw “honeycomb” “pores” “cells”

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Anthonie van Leeuwenhoek

A

Discovered using single lens microscope (200-300X):
-microorganisms
-red blood cells
-cell theory

-saw “animacules” (tiny animals) from gum swabs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Schleiden

A

-every part of a plant is made up of cells
-cells made from “crystallization process”
(Idea stolen from Dumortier)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Schwann

A

Both plants and animals are composed of cells and their products

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Virchow

A

All cells arise only from preexisting cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Cell theory

A
  1. All living organisms are composed of one or more cells
  2. The cell is the most basic unit of life
  3. All cells arise only from preexisting cells

OBP
One Big Prison

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Brown and Flemming

A

Discovered the nucleus, chromosomes, and different stages of cell division with the help of basic stains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

C. Golgi

A

Identified Golgi apparatus using a “black reaction” (black stain)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Scanning electron microscopy (SEM)

A

-creates an image by detecting reflected electrons
-Surface of sample is metal-shadowed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Cryogenic electron microscopy

A

Hydrated, unfixed, untainted samples are frozen (cells not dead)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Transmission electron microscopy (TEM)

A

-uses transmitted electrons to create an image
-thin samples: stained/ shadowed with heavy metals
-thick samples: fixed, dehydrated, embedded in resin, sectioned, and stained with heavy metals

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Last eukaryote common ancestor

A

-last common ancestor of eukaryotes and archaea
-1.5-2 billion years ago

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Biological scale

A

Individual proteins (20nm)
Macro molecular complexes (0.2 um)
Organelles (2 um)
Cells (20um)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Palade

A

-changed the field of cell biology
-perfected electron microscopy
-picture of cell with clear organelles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Visible spectrum of light

A

VBGYOR
Wavelength increase ->
Frequency decreases —>

Violet: 380-450 nm (70)
Blue: 450-495 (45)
Green: 495-570 (75)
Yellow: 570-590 (20)
Orange: 590-620 (30)
Red: 620-750 (130)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Spectrum of light

A

Lower wavelength = higher energy and higher frequency

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Fluorophores

A

-Fluorescent proteins
-FP genes can be fused to a gene of interest to produce a recombinant fluorescent protein, and expressed in an organism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Strategies for live-cell microscopy

A

Recombinant proteins: plasmid DNA + vector
GFP: allows for identification and localization of proteins in the cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Immunolabeling (antibodies)

A

-helps identify and localize proteins
-uses an antibody to which a probe has been covalently attached
- antibodies can be generated by injecting an animal with the protein of interest (antigen)/ generate antibodies from a cell line (monoclonal antibodies)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Immunolabeling terms

A
  1. Fixation: with formaldehyde or glutaraldehyde; tissue embedded in paraffin for sectioning
  2. Permeabilization: with non-ionic detergent that makes the plasma membrane permeable to reagents (ex antibodies)
  3. Stained: with a marker (fluorescent dyes or gold particles that are covalently attached to specific antibodies
    -heavy metals: stain diff. Bio molecules to gain contrast
    -small fluorescent dyes: bind to membranes, DNA, etc.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Chemistry of life: 4 key concepts

A
  1. Molecular complementarity
  2. Polymerization
  3. Chemical equilibrium
  4. Energy

My Pretty Connie Expects (too much of my life)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Types and energy of different bonds

A

Van der waals < hydrogen bonds < hydrolysis of ATP phosphoanhydride bond< C-C < C=C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Dissociation constant (Kd)

A

Concentration of ligand
Higher concentration= less interaction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Hydrophobic effect

A

Hydrophobic aggregation due to higher entropy of water (molecules released into bulk solution are less ordered)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

How macromolecules are built

A

Proteins: peptide bond; amino acid combined from N to C; H2O taken out; NCrC

Nucleic acids: phosphodiester bond 3’ and 5’ sugar; H2O taken out

Carbohydrates: glycosidic bond; 1’ and 4’ bond; H2O taken out

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

L vs D

A

L-serine natural
D- glucose natural

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Amphipathic molecules

A

Hydrophilic and hydrophobic group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Melting temperature of lipids

A

Tm: temperature at which ~50% of lipids are fluid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Glycerophospholipids

A

PC, PS, PE, PI, PG, CL

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Sphingophospholipid

A

SM

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Glycolipids

A

Cerebroside, LPS

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Sterols

A

Cholesterol

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Homeoviscous adaptation

A

-cells dynamically change their membrane lipid composition to control membrane fluidity
- to decrease transition temperature:
-unsaturated bonds and shorter acyl chains
-to increase transition temperature:
-saturated bonds and longer acyl chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Special fluidity regulator

A

-cholesterol
-lowers membrane permeability (tight acyl chain packing)
- at low temp, it increases fluidity by preventing tight acyl chain packing
-at high temp, it decreases fluidity due to its rigid structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Memorize 20 amino acids

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

Phosphorylation

A

-most abundant post translational protein modification in eukaryotes
-kinases transfer phosphoryl groups to side chain from ATP
-serine, threonine, tyrosine: major eukaryotic phosphorylation
- kinases phosphorylates and phosphatase dephosphorylates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Protein hierarchical structure:

A

Primary: linear sequence of amino acids
Secondary: alpha helixes and beta sheets
Tertiary: 3D shape
Quaternary: multiple peptides
Supramolecular: large scale assembly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Secondary structures

A

Alpha helix: 3.6 amino acids per turn
Beta sheet: anti parallel strands with connecting loops

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Coiled-coil proteins

A

-two alpha helixes wound around each other
-heptad repeat with a hydrophobic residue at positions 1 and 4

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Difference in plant and animal cells

A

-microvilli in animals
-cell wall in plants
-plasmodesmata
-vacuole
-chloroplasts

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Monolayer vs. single bilayer vs. two bilayers

A

Monolayer:
-lipid droplets

Single bilayer:
-ER
-ER- golgi intermediate compartment (ERGIC)
-golgi apparatus
-trans golgi network
-plasma membrane
-lysosomes
-peroxisomes

Two bilayers:
-mitochondria
-chloroplasts
-nucleus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

How did the first membranous organelles form?

A

Engulfing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Inheritance of membranous organelles

A

Every organelle stems from another organelle

44
Q

Total cell membrane

A

ER (50%) and mitochondria (40%)

45
Q

Cell volume

A

Cytosol > mitochondria (20%) > ER

46
Q
  1. Endoplasmic reticulum (ER)
A

Rough ER:
-ribosomes
-protein folding and post-translational modifications (N-glycans, S-S bonds)
-protein quality control

Smooth ER:
-lipid synthesis
-steroid hormone synthesis
-detox center
-calcium ion storage

47
Q
  1. ERGIC
A

-vesicular tubular clusters
-adjacent to ER exit sites
-COP 1 dependent sorting of retrograde cargo
-concentration/sorting of biosynthesis cargo toward the golgi

48
Q
  1. Golgi apparatus
A

-sorting hub
-lipid synthesis and transport
-remodeling of N-glycans
-addition of O-glycans
-lipidation of proteins
-3-8 disc-like cisternae
- cis, medial, trans
-stepwise modification of cargo

49
Q
  1. Trans golgi network (TGN)
A

-sorting hub
-clathrin coated vesicles
-extracellular matrix proteins
-protein complexes
- calcium dependent sorting

50
Q
  1. Plasma membrane
A

-physical barrier
-selective permeability
-transport of solutes and macromolecules
-endocytosis/phagocytosis/exocytosis
-cell signaling
-interactions
-fluid mosaic model

51
Q
  1. Endo-lysosomal system
A
  1. Endocytosis
  2. Phagocytosis
  3. Autophagy: ER engulfs damaged organelles

Lysosomes: ph 4.5-5, containers enzymes that degrade polymers

52
Q
  1. Nucleus
A

-storage of blue prints
-separates transcription from translation
-continuous with the ER
-nuclear pore complexes
-nucleoplasm
-inner mmebrane is reinforced by lamin
-nucleolus: site of rRNA production and assembly of ribosome components

Ribosomes: help with mRNA translation; contained rRNA and protein

53
Q
  1. Mitochondria
A

-production of ATP
-have their own genome
- two bilayers

54
Q
  1. Lipid droplets
A

-energy storage
-neutral lipids and cholesterol esters
-monolayer
-biogenesis within the bilayer of the ER
-size can be dynamically controlled
-membrane homeostasis

55
Q
  1. Peroxisomes
A

-generation and scavenging of reactive oxygen species from oxygen
-breakdown of long chain lipids, etc
-biosynthesis of special membrane lipids
-pentose phosphate pathway
-bile acid synthesis

56
Q

SDS polyacrylamide gel electrophoresis (SDS-PAGE)

A
  1. Denature proteins with ionic detergent (SDS)
  2. Acrylamide acts as a sieve; proteins move toward the anode (+)
57
Q

Palade’s famous pulse-chase experiment

A

3 minute pulse: amino acid in rough ER
7 minute chase: in golgi
120 minute chase: secretory granules

58
Q

Gunter Blobel signal sequence hypothesis

A

Proteins contain signal sequences that can direct them to the rER

59
Q

Translation and translocation occur simultaneously

A
60
Q

3 things required to direct proteins to the ER

A
  1. Signal sequence
  2. Signal recognition particle (SRP)
  3. Translocon (sec61) + SRP receptor
61
Q

Cotranslational translocation

A
  1. N terminal ER signal sequence emerges from the ribosome
  2. Signal recognition particle binds to signal sequence, arrests protein synthesis
  3. SRP nascent polypeptide chain ribosome complex binds to the SRP receptor in the ER membrane
  4. Ribosome transfers to the translocon, opens it to admit the growing polypeptide
  5. Elongating polypeptide chain passes through the translocon channel. SS cleaved by signal peptidase
  6. Growing peptide chain translated toward the 3’ end
  7. Translation completes at mRNA stop codon and ribosome is released
  8. Nascent proteins folds into native conformation. Translocon closes
62
Q

Sec61

A

-translocon; preserves integrity of the ER membrane by three gating mechanisms
1. - peptide: channel closed by plug
2. +peptide: ring of isoleucine residues form a gasket
3. Lateral exit: for the signal sequence and for hydrophobic transmembrane domains

63
Q

Type 1 membrane protein

A
  1. Translocation initiation and SS cleavage
  2. Peptide elongates
  3. Elongation continues until a hydrophobic stop transfer anchor sequence enters the translocon
  4. Stop transfer anchor sequence moves laterally through a hydrophobic cleft between translocon subunits and becomes anchored in bilayer; translocon closes
  5. Synthesis continues in cytosol
  6. Synthesis completes at stop codon, releasing ribosome
64
Q

Classes of ER membrane proteins

A

Type 1: cleaved signal sequence; COO- in cytosol, NH3+ in ER lumen
Type 2: NH3+ outside, COO- inside
Type 3: COO- outside, NH3+ Inside
Tail anchored proteins: NH3+ outside and COO- is embedded in the membrane
Type 4: many transmembrane domains
GPI anchored protein: anchor with NH3+ tail inside

65
Q

Type 2 and 3 single spanning membrane proteins

A

Positive inside rule: positively charged residues anchored in the cytosol side

66
Q

Tail anchored proteins

A

-hydrophobic C terminus
1. Sgt2, get4, get 5 sequester nascent protein hydrophobic C terminal tail anchor sequence and transfers it to get3-ATP
2. Get3 ATP nascent protein complex docks onto the ER membrane get1/get2 receptor
3. Get3 ATP hydrolysis, release of tail anchored protein into the get1/get2 receptor, releases it into the ER membrane
4. Get 3 release of ADP and binding of ATP releases it from get1/get2

67
Q

GPI anchored proteins

A

GPI molecule anchor covalently attached protein in membrane

68
Q

N-glycans are added to proteins in the ER lumen

A

-N-glycans are attached to asparagine residues
-Asn-X-Ser/Thr
- N glycan precursor is synthesized at the ER membrane
-promotes protein folding, stability, adhesion, and recognition

69
Q

Synthesis of N-glycan precursor

A
  1. 2 GlcNac and 5 mannose residues added on the ER membrane cytosolic face
  2. Flipped to ER membrane luminal face
  3. Additional sugars added by ER enzymes to complete the n-glycan precursor

=Glc(3)Man(9)GlcNAc(2)

70
Q

Addition of N-glycans to target proteins and initial processing

A
  1. Precursor is transferred to asparagine residues in a Asn-X-ser/thr sequence on a nascent protein while coming out of the translocon
  2. Glucose residue removed
  3. Additional and removal cycles of glucose residue
  4. Removal of one mannose residue

(Glc)3(Man)9(GlcNAc)2 —>(Man)8(GlcNAc)2
-glucose
- 1 mannose

71
Q

Calnexin/ calreticulin cycle

A

-bind N-linked oligosaccharides and 1 glucose added
-retain protein in the ER until properly folded
-if proteins misproperly folded, mannose trimming
-OS-9 binds to Man5-6(GlcNAc)2= dislocation of the misfolded protein out of the ER, degrades

=Glc(3)Man(9)GlcNAc(2) —-> Man(9)GlcNAc(2)

72
Q

Formation of covalent disulfide bonds

A

Reduced substrate protein + oxidized PDI protein disulfide isomerase —> reduced PDI + oxidized substrate protein

Reduced PDI gives electrons to oxidized Ero1 —> oxidized PDI

73
Q

Rearrangement of disulfide bonds

A

Reduced PDI (SH-SH) forms transient disulfide bonds to break improper disulfide and protein is correctly folded

74
Q

BiP chaperone

A

-membrane protein folding
-binds to exposed hydrophobic regions of the nascent chain and stabilizes them until the protein is folded correctly

75
Q

Unfolded protein response

A

Ire 1: transmembrane ER protein, its luminal domain binds excess BiP, its cytosolic domain is a specific RNA endonuclease

  1. Unfolded proteins bind available BiPs, BiPS released from Ire1= activation of endonuclease activity
  2. Endonuclease cuts unsliced mRNA
  3. Two cut mRNA joins together
  4. Translation of functional mRNA moves into the nucleus and activated transcription of gene encoding more BiPs
76
Q

ER golgi interface

A

-30% of all proteins encoded in the genome
-50% of ER volume exported every 40 mins
- 150 COP2 vesicles per second
-90% of membrane leaving the ER is recycled

77
Q

Temperature sensitive (Ts) mutant genes

A

Permissive temperature (24C): protein folds
Restrictive temperature (37C): protein does not fold

Several classes of mutants were identified

78
Q

Rothman’s simplest hypothesis

A

Specificity dictates anatomy

79
Q

Vesicle trafficking

A

Requirements:
1. Machinery to attract coat
2. Coat proteins
3. Uncoating of carrier
4. Machinery for fusion

80
Q

GTPase

A

-molecular switches

GTPase (GDP) off — GTPase (GTP) on— effector

GEF= GTP binding
GAP= GTP hydrolysis

81
Q

Bidirectional transport at the ER-Golgi interface

A

COP2 carriers: anterograde transport (away from ER)
COP1: retrograde transport (return to ER)

82
Q

Assembly and disassembly of COP2 coats

A
  1. sar1-GDP interacts with the ER membrane protein Sec12, sec12 GEF activity, sar1 integrates its hydrophobic N terminus into the ER membrane
  2. Sar1-GTP recruits the Sec23/Sec24 coat protein complex; sec13/sec31 coat complex assembles into coat
  3. Sec23 GAP activity stimulates Sar1 GTP hydrolysis
  4. Release of Sar1-GDP from the vesicle membrane causes disassembly of the coat

COP2 carriers form at ER exit sites

83
Q

The inner layer of the COP2 coat recognizes cytoplasmic signals on membrane cargo proteins

A

Di-acidic signals: DXE, EXE, DXD
DI-hydrophobic signals: FF, YY, FY

84
Q

Luminal cargo is clustered into COP2 carriers via the pectin ERGIC-53

A

Lectin: a carbohydrate binding protein
ERGIC 53: type 1 transmembrane protein, dihydrophobic motif in cytoplasmic tail; binds high mannose N-glycans on cargo proteins made in the ER

PH neutral= glycans bound= ON
PH acidic= cargo released at ERGIC= OFF

85
Q

Uncoating prepares the COP2 carrier for the target membrane (ERGIC)

A
  1. Vesicle budding from donor membrane; vesicle-snares captured in budding vesicle membrane
  2. Vesicle fusion with target membrane: interaction of specific V-snare with specific target membrane T-snares
86
Q

Docking and fusion of transport vesicles with their target membrane

A
  1. Rab1 GTPase on COP2 vesicles interacts with Rab effectors in golgi to melt through the cocoon
  2. 1 V snare proteins forms stable coiled coil interaction with 3 t-Snares
    NSF unwinds this coiled coil
87
Q

Assembly and disassembly of COP1 coats

A
  1. Arf1-GDP interacts with the p23/p24 membrane proteins in ERGIC/cis golgi; GBF1 GEF activity, Arf1 N terminal integrated into membrane
  2. Arf1 GTP recruits the heptameric coatomer coat protein complex; coatomer binds specific short sequences in membrane cargo protein cystosolic domains
  3. Arf GAP activity stimulates Arf 1 GTP hydrolysis
  4. Release of Arf1-GTP from the vesicle membrane= disassembly of coat
88
Q

COP1 coat recognizes cytoplasmic signals on membrane cargo proteins

A

Basic signals: KKXX, K/HDEL, RR, RXR, RRR

89
Q

Retrieval of ER-resident luminal proteins via the KDEL receptor

A

-prevents depletion of ER luminal proteins needed for proper folding (ex BiP)

90
Q

Golgi

A

-cis, medial, trans
-ribbon, mini stacks
-flat centers: where enzymes are; fenestrated rims: transport machinery and cargo

91
Q

Intra-golgi transport models

A

Maturation model: cisternae are dynamic compartments, mature from cis to trans, COP1 vesicles move enzymes to former cisternae to convert into new cisternae, cargo stays put

Vesicular transport model: cisternae are static compartments, each cisternae has a specific set of resident enzymes which stay put, cargo is transported via tubular or vesicular carriers from one cisternae to the next

92
Q

Processing of N-glycans in the golgi

A
  1. Cis golgi: Man8(GlcNAc)2 —> Man5(GlcNAc)2
  2. Medial: 1 GlcNAc added
  3. Medial: -2 mannose
    1. Medial: 2 GlcNAc added, 1 fucose added
  5. Trans: 3 galactose added
  6. Trans: 3 NANA residues added
93
Q

What are N-glycans used for?

A

-promotes specific interactions (with proteins and lectins)
-a shield/barrier (resistance to proteases)
-to monitor protein folding
-N glycan remodeling can be used to measure protein transport (N glycan in the ER is D-resistant, in the cis golgi it’s D-sensitive)

94
Q

N glycan remodeling can be used to measure protein transport (N glycan in the ER is D-resistant, in the cis golgi it’s D-sensitive)

A

Temperature sensitive VSV G protein:
-permissive temp: 32C = protein folds and moves through secretory pathway
-restrictive temp: 40C = misfolded protein retained in the ER

95
Q

O-glycosylation

A
  • in ser/thr in the cis golgi
    -no consensus sequence
    -linear
96
Q

N glycan and O glycan similarities

A

-can be convalently attached
-linked to nitrogen and oxygen atoms of amino acid residues
-often capped with negatively charged skaldic acid

97
Q

Different liquid composition from cis to trans golgi

A

-plasma membrane is more fluid in the cis; neutral charge
-plasma membrane is more tightly packed in the trans; negative charge
-cholesterol and spingolipids are enriched towards the PM

98
Q

OSBP

A

Feeds cholesterol from the ER into the trans-golgi

99
Q

Covalent attachment of a lipid to proteins: S-palmitoylation

A

S-palmitoylated cargo in golgi —> concentration at cisternal rim —> anterograde transport

100
Q

Trans golgi network: 5 destinations

A
  1. Retrograde back to trans golgi
  2. Lysosomes
  3. Late endosomes
  4. Constitutive secretory vesicles
  5. Regulated secretory vesicles
101
Q

Clathrin coated vesicles

A

-bud from trans golgi and PM
-need AP complexes
-tryskelion (3 heavy chains, 3 light chains)

102
Q

Arf1 recruits AP complexes

A

-hydrophobic and acidic motif
-AP complexes recruit clathrin = curvature bends membrane
-dynamin pinches off the bud
-uncoating of CCVs by Hsc70 and auxilin

103
Q

M6P signal sorts lysosomal enzymes from the TGN to the lysosome

A

-recognizes QSHEY sequences in newly synthesized lysosomal enzymes
-M6P signal + M6P receptor
- receptor lets go of enzyme at late endosome bc low pH

104
Q

Proteolytic processing or pro proteins at the TGN

A

Constitutive secretory pathway: fur in endoprotease
Regulated secretory pathway: PC2 and PC3 endoprotease

105
Q

Ca2+ dependent sorting at the TGN

A
106
Q

Cycling of synaptic vesicles in axon termini

A

Synaptotagmin: prevents membrane fusion and release of NT

BICD 110 (3 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions