1
Q
What is Synthetic Biology?
A
Engineering biological systems to produce desired products
2
Q
Which event regarding synthetic biology happened in 1996?
A
Cloning of Dolly the sheep
3
Q
In 2012, Charpentier / Doudna invented __, which had the following qualities __
A
CRISPR: Precise, Reliable, Cheap, Easy
4
Q
In 2010, Venter created the first __
A
self-replicating bacterial cell (synthetic cell)
5
Q
The first microscope was invented in 1660 by __, who looked at slivers of __, and named cells after __. A much better microscope was made in the 1670s by __, who saw and recorded __.
A
Hooke, Cork, Little rooms, Van Leuwenhook, “animalcules.”
5
Q
Electron microscopes function by __. Describe the difference between a TEM and SEM.
A
Beaming electrons on or through a specimen, penetrating a specimen to show organelles vs. scanning specimen surface to give a 3D image.
6
Q
What does a Cryo-EM do?
A
Flash-freezes biomolecules without causing damage
7
Q
Describe Fluorescence microscopy
A
Using fluorochromes to visualize biomolecules: Step 1 uses antibodies to detect protein in a dead cell, step 2 fuses GFP to coding sequences of genes to make versions of protein attached to GFP that glow green, can watch protein location in living cell.
8
Q
What were schleiden and schwann responsible for, and when?
A
Cell theory, late 1830s: “all organisms consist of 1+ cells, cells are the basic unit of structure for all organisms
9
Q
Who said “all cells arise by division from pre-existing cells,” and when?
A
Virchow, 1850s
10
Q
Characteristics of prokaryotes?
A
Evolved earlier than eukaryotes, no membane-bound nucleus (only nucleoid), no membrane-bound organelles, circular chromosomal dna, 1-5 µm, contain bacteria and archaea
11
Q
describe archaea and give some examples
A
Archaea live in extreme environments and have unique metabolic strategies, examples include Methanogens (anaerobic, hydrogen), Thermoacidophiles (acidic, hot), Halophiles (salt)
12
Q
Characteristics of eukaryotes?
A
Consist of protists, fungi, plants, animals, dinosaurs, 10-100 µm, Linear chromosomes, Compartmentalized organelles, Uni- or multi-cellular, most do not look alike
13
Q
Which size of cell has a better SA:V ratio?
A
Small
14
Q
What was the first cell and when was it formed?
A
LUCA (protocell), 3.5 bya
15
Q
What are Urey and Miller famous for? When?
A
Abiogenesis experiment, 1950s
16
Q
Who was responsible for the endosymbiont theory and when? Describe it
A
Lynn Margulis, 1960s, primitive eukaryotic cell engulfs prokaryotic cell as food, prokaryotic cell makes ATP
17
Q
Provide a brief timeline of events
A
4.6 bya: Earth formed
3.5 bya: Protocell (LUCA)
3 bya: First prokaryotes
2.4 bya: Cyanobacteria (followed by great oxygenation event)
2 bya: First single celled eukaryotes
1.25 bya: Mitochondria and chloroplasts
1 bya: Multicellularity
0.00002 bya: Humans
17
Q
What are the 4 classes of large biological molecules?
A
Proteins, nucleic acids, carbohydrates, lipids
18
Q
Which macromolecule is not a polymer?
A
Lipids
19
Q
Most molecules form via __ reactions. These are considered __ pathways because __
A
Dehydration (or condensation), anabolic, they require ATP to occur
20
Q
What are lysosomes responsible for?
A
Intracellular digestion, contain hydrolytic enzymes
21
Q
What are amino acids composed of?
A
Central carbon, H atom, carboxy group, R-group, amino group. Identity is determined by R-group.
22
Q
What are the three particularly tiny amino acids?
A
Glycine (r-group is just H, can be either polar or non-polar), Cysteine (forms covalent bond with other cysteine called disulfide bond, very strong), Proline (forms disruptive kink in polypeptide)
22
Break down the 3 types of R-groups
Non-polar (hydrophobic), associate with each other via VDW forces and hydrophobic interactions, polar (hydrophilic) uncharged, side chains have partial charge at cellular pH, will form H bonds with other molecules, incl. water. Polar (hydrophilic, charged), side chains have full charge at cellular oH, form ionic bonds with other charged species
23
Describe the four levels of protein folding
Primary: amino acid sequence, Secondary: 3D shape in localized area (alpha-helix, beta-pleated sheet), Tertiary: Overall 3D shape (interactions between side chains), Quaternary: Multiple proteins associate to work together as one
23
In which organelle are primary protein structures formed, and via which reaction?
Ribosomes, condensation
24
What is a prosthetic group?
Large, non-protein molecule embedded in protein, allows protein to do extra functions
25
What is a molecular machine and how common is it?
Very rare, multiple proteins come together to make multi-protein complex
26
What did Anfinson work on in the 1950s?
Protein folding (specifically that is completely defined by primary sequence)
27
All information needed for correct folding is in the __
Amino acid sequence
28
Which groups stabilize alpha helices?
Carboxy and Amino
29
What prevents inappropriate actions in protein folding?
Heat shock proteins, AKA molecular chaperones: e.g. chaperonin
30
If a protein is exposed to a hydrolytic enzyme, what would happen to the protein and why?
Protein would get shorter as amino acid monomers are removed from the growing chain
31
__ are the monomers for nucleic acids
Nucleotides
32
What are the three parts of a nucleotide?
Phosphate group, sugar, nitrogenous base
33
Bonds between a phosphate of one nucleotide and sugar of another are called __
Phosphodiester bonds
34
__ molecules are single strands, while __ molecules are made of a two-stranded double helix
RNA, DNA
35
Carbohydrates have a molecular ratio of __, nomenclature often ends in __ or contain __
1C 2H 1 O, ose, glycol
36
__ are monomers for carbs
monosaccharides
37
Oligosaccharides contain __ units, and are exclusively found
3-10, on the exoplasmic leaflet
38
__ contain hundreds to thousands of monosaccharides. Examples include __
polysaccharides, starch, glycogen, cellulose, chitin
39
Glucose, fructose, and galactose are __ while lactose, maltose, and sucrose are __
monosaccharides, disaccharides
40
Examples of lipids include __
Triacylglycerides, phospholipids, steroids
41
Lipids are generally __ because they include __
hydrophobic, non-polar hydrocarbon chains
42
Fatty acids have a __ group on an end, whether they are saturated or unsaturated depends on __
carboxy, whether they include a double bond (unsaturated = double bond)
43
The main function of triacylglycerides is to __. They contain __ and are synthesized in the __.
store energy and insulate, 1 glycerol and 3 fatty acids, smooth ER membrane between two leaflets, in the area with the tails
44
Seipins help __
bud triacylglycerides into a lipid droplet
45
Lipid droplets have a __ leaflet because __
single, they require a hydrophobic interior
46
Saturated triacylglycerols are __ at room temp, and usually called __, while unsaturated triacylglycerols are __ at room temp and are usually called __.
solid, fats, liquid, oils
47
Difference between cis and trans __ fatty acids?
unsaturated, cis forms a bend while trans has no bend and is shaped like a saturated FA
48
Stinky dead whale bones contain lots of __
oil in the bones: unsaturated triacylglycerides
49
The two types of phospholipids are __ and __
phosphoglycerides and sphingolipids
50
Phosphoglycerides are __ molecules, have a __ head group containing __, a __ backbone, and __ fatty acid chains which are __
amphipathic, polar, choline and phosphate, glycerol, 2, non-polar
51
Bacteria living in hot springs: Membranes are likely enriched in phosphoglycerides with fatty acid tails that are __ and __
saturated, very long
52
Steroids are all derived from a __-ringed __ skeleton. For example:
4-ringed, hydrocarbon, cholesterol
53
membranes are __ nm thick. Functions include:
5-10, boundary / permeability barriers, specific protein locations, cell adhesion
54
The phospholipid bilayer will form __ in water
spontaneously
55
Phosphoglycerieds can be differentiated based on their __
head groups
56
Different membranes can have dramatically different __ distributions, even variation from one __ in membrane to another. This is an example of __.
phosphoglyceride, leaflet, asymmetric distribution
57
Sphingolipids have a __ backbone instead of __. They have __ fatty acid chain(s)
sphingosine, glycerol, one
58
Who came up with the phospholipid bilayer hypothesis and when?
Gorter and Grendel, 1920s
59
Membrane lipids are arranged in bilayers because they are __
amphipathic
60
The cytoplasmic leaflet touches the __, while the exoplasmic leaflet __
cytoplasm, does not
61
Liposomes are __, formed when __. They contain __
hollow vesicles, phospholipids are exposed to water. Hydrophilic head, aqueous solution, hydrophobic tail.
62
mRNA is both __ and __
fragile and charged
63
__ in water may have formed liposomes trapping some __ in the process
Primordial lipids, nucleic acids
64
Some lipids could form a __ instead of a __. These lipids are __-shaped.
micelle, bilayer / liposome, wedge
65
Different types of lipid movement include:
Transverse diffusion (flip flop), rotation, lateral diffusion
66
What does FRAP stand for and what is it?
Fluorescence Recovery After Photobleaching, technique to study lipid mobility, can also study protein mobility
67
__ is critical to membrane function. High temps lead to __, while low temps lead to __
Fluidity, increased fluidity, lower fluidity
68
Homeoviscous adaptation is __. This includes adjusting __ and __
Ability for cell to change lipid content to adapt to temperature, amount of saturation, length of fatty acids
69
Longer hydrocarbon chains lead to __
lower fluidity, sorter hydrocarbon chains lead to increased fluidity
70
__ affects membrane fluidity and tends to be evenly distributed between leaflets, can also buffer lipid movement by making membrane more rigid
Cholesterol
71
Who came up with the fluid mosaic model and when?
Singer and Nicolson, 1970s
72
The three types of membrane proteins are: __ and are categorized based on __
Integral, Peripheral, Lipid-anchored, how they associate with lipid bilayer
73
Integral proteins __, examples include __
Penetrate into hydrophobic region of bilayer, are asymmetric / amphipathic, any type of channel, cell adhesion proteins, some receptors involved in signal transuction
74
Transmembrane proteins are often rich in __
alpha-helcies
75
Peripheral proteins are located __. They have _ bonds, __ distribution, and are __.
On the membrane surface, electrostatic, asymmetric, dynamic
76
Lipid-anchored proteins are located __, but are __
On membrane surface, covalently linked to lipids.
77
Lipid-anchored proteins are attached to __ in exoplasmic leaflet, and __ in cytoplasmic leaflet
GPI, fatty acid
78
What are lipid rafts?
Localized areas with unique liquid composition that sequester signaling proteins, tightly packed, many sphingolipids, cholesterol, and fatty acids
79
Membrane carbohydrates are always located __. Their functions include __
On the exoplasmic leaflet (facing away from cytoplasm). Important in cell-cell interactions, sorting proteins, always attached to something
80
__ can benefit a virus as they may aid in host entry or act as shield
Glycoproteins
81
Fusion of mouse and human cells was done by __ in __, proved __.
Frye / Edidin, 1970, membrane proteins can move
81
Lactose and amylopectin would be digested by an enzyme that cleaves __ bonds.
Glycosidic
81
When cells have an "up and down," they have __ polarity. These cells are __
apical-basal, polarized
81
A/B Blood antigens are actually __
glycolipids in RBC membranes
82
If a protein has a low % of hydrophobic amino acids, it is likely a __ protein
lipid-anchored
83
Who is considered the "father of microbiology?"
Van Leuwenhooke
84
Adherens junctions __
Link cells into tissues, prominent in epithelial cells (lining intestine), mediated by cadherin proteins attached by catenins to actin filaments
85
__ from two cells interlock with each other to zip the cells together.
Cadherins
86
Focal adhesions __
are attachment sites between cell and substrate, are how cells attach to culture dishes, bind actin, attachment and linker proteins are integrins and talins
87
Cells "crawl" using __
Focal adhesions
88
Integrens form __ links between __ and __
mechanical, actin cytoskeleton, substrate
89
Desmosomes and Hemidesmosomes are points of __. Desmosomes are __ while hemidesmosomes are __
strong adhesion, cell to cell attachment, cell to substrate attachment
90
Gap junctions __
permit flow of stuff from cell to cell, six transmembrane proteins (connexins) form one connexon, two connexons form one gap junction
91
Tight junctions __
prevent cell movement by sealing space between cells, are found in intestinal epithelia, urinary bladder, endothelial cells lining blood vessels of brain (creating blood/brain barrier)
92
Tight junctions establish __ by acting like __ against __, and are composed of
apical-basal polarity, fences, transmembrane diffusion, claudins
92
Desmosomes are found in __ and contain __
tissues subjugated to mechanical stress (cardiac muscle, cervix), keratins, linker proteins, cadherins
93
__ are cytosolic channels in plant cells
Plasmodesmata
94
ECM provides __
structural support and scaffolding for cells
95
Osteocytes and fibroblasts are embedded in the __
ECM
95
__ ECM is much more flexible than bone ECM
Cartilage
96
The basal lamina is __
the ECM of epithelial cells
97
Structural proteins like __ provide __
Collagens and elastins, strength elasticity and flexibility
98
Cross-linking proteins like __ attach __
Fibronectins and Laminins, ECM to cell
99
Fibronectin attaches __ to __
Collagen, Integrin
100
Laminins cross-link __ to __
Epithelial cells, Basal lamina
100
Cell walls allow plant cells to withstand __ pressure exerted by __. The cell wall is made of __
Turgor, water uptake, cellulose
100
Proteoglycans are __ complexes, often huge polysaccharides called __, fill space and protect against __ forces
Protein-Carbohydrate, GAGs, compression
101
An anabolic pathway __, making it __gonic. A catabolic pathway, __, making it __gonic.
requires energy, ender, releases energy, exer
101
ECM carbs are __ charged, __ huge amount of water
negatively, absorb
101
Cellulose associates __ to make __, several twist together to make a __
laterally, microfibril, macrofibril
102
Metabolism is the __
Total of all chemical reactions in a cell
103
In the absence of oxygen, the cel can extract energy from glycose via __
Glycolysis
103
Positive ∆G = __gonic
ender
104
Adenosine triphosphate contains 3 things: __
Adenine, ribose, triphosphate
104
Complete oxidation of Glucose:
Sugar + 6O2 -> 6CO2 + Energy
105
ATP Hydrolysis reaction:
ATP + H2O -> ADP + Phosphate
106
Glycolysis: Occurs in __, starts with __, finishes with __, total of _ ATP made ( __ invested at the beginning), ATP made via __, __ NADH are made by __ NAD+ (which is a __, carries __), other sugars can be converted into intermediates like __, net products of glycolysis: __
cytoplasm, glucose,
two 3C pyruvate,
4, 2,
substrate level phosphorylation,
2, reducing,
non protein co-enzyme, 2 electrons and 1 H,
fructose, galactose, sucrose, 2 Pyruvate + 2 ATP + 2 NADH
106
We only get ATP from glycolysis if there is __ available
NAD+
107
Two possible routes to making ATP?
Fermentation and Aerobic Respiration
108
In aerobic respiration: __ enters the __, synthesizing large amount of ATP via __
pyruvate, mitochondria, oxidative phosphorylation
109
Fermentation regenerates __
NAD+
110
Two types of fermentation: __
Lactate (delicious examples), Alcoholic
111
__ cells perform glycolyis at a rate __ times faster, they undergo __ even in presence of oxygen
Cancer, 10, lactate fermentation
112
Mitochondria are found where __
ATP needs are greatest: sperm cells, muscle cells
112
Aerobic respiration takes place in the __
Mitochondria
113
Which organelle plays a role in mitochondrial fission? What forms the helix around mitochondrion and what does it hydrolyze?
Endoplasmic reticulum (both smooth and rough), Drp1, GTP
114
Why are mitochondria not little jelly beans?
They are likely interconnected networks
115
Inner mitochondrial membrane has a lot of __, and is well __.
protein, insulated
115
Mitochondria contain these four main parts: __
Cristae, Outer membrane, Inner membrane, Cristae junction
116
__ is an unusual lipid in inner membrane of mitochondria, it's a double __ that __ the membrane
Cardiolipin, phospholipid, insulates
116
Porins are __, located __
Channels permitting moderately sized molecules to move freely in cytosol into intermembrane space made up of mostly beta sheets, outer mitochondrial membrane
117
Inner mitochondrial membrane has a protein:lipid ratio of __
3:1
118
How many membranes do chloroplasts have?
3
119
The central compartment of the mitochondria with a high __ concentration is called the __. It is the site of the __, also contains __ DNA
protein, matrix, citric acid cycle, circular
120
Chloroplasts are examples of __ (double-membraned organelles in plants, algae, etc.)
Plastids
121
In the Citric Acid cycle, the __ group leaves and the __ group attaches to __ to make __. __ CO2 molecules are removed.
CoA, Acetyl, Ocaloacetate, Citrate, 2
122
Pyruvate oxidation is catalyzed by __
Pyruvate dehydrogenase
123
Gritty fluid inside chloroplasts is called the __
Stroma
123
Chloroplasts have __ DNA, and their ribosomes resemble __ ribosomes
circular, bacterial
124
__ FADH2 are produced. These carry _ electrons and _ hydrogens, and the electrons have __ energy compared to the NADH ones
one, 2, 2, less
125
One pyruvate nets us __
One CO2, One Acetyl CoA, one NADH
126
For each acetyl CoA that enters the citric acid cycle, _ NADH are produced.
3
127
The net products of one acetyl CoA from the citric acid cycle are __
2 CO2, 3 NADH, 1 FADH2, 1 GTP, 1 oxaloacetate
127
The final reaction of the citric acid cycle is __
regeneration of oxaloacetate
127
GTP is like an __, containing __
ATP, Guanine, Ribose, Triphosphate
128
Oxidative Phosphorylation consists of the __ and __
ETC and chemiosmosis
129
We call it Oxidative phosphorylation as opposed to substrate level phosphorylation because __
Movement of electrons through ETC depends on presence of oxygen
130
At the ETC we cash in the __ NADH and __ FADH2, containing __% of the glucose energy in those 12 molecules
10, 2, 90
131
Carriers that carry NADH and FADH2 electrons include: __
Flavoproteins, Iron-sulfur proteins, Cytochromes, Coenzyme Q
132
Proteins are organized into __ mega complexes in the __. The complexes are arranged in order of __. The more positive the number is, the better it is at __ electrons. Energy is __ every time an electron is passed to the next complex, __ has the highest reduction potential of them all.
four, inner mitochondrial membrane, increasing reduction potential, accepting, released, oxygen
133
CoQ is also called __, it is a __, __ in lipid bilayer, can be both __ and __
ubiquinone, lipid, soluble, reduced, oxidized
134
__ is a mobile protein component of the ETC. It is not a part of the larger complex, it acts like a __ to __ electrons
Cytochrome C, shuttle, move
135
What is the function of the enzyme known as complex II?
Catalyzes reaction that produces one FADH2 (succinate dehydrogenase)
136
The __ is a target for many poisons
ETC
137
The ETC's end result is pumping __ across the membrane
H
138
The __ provides the energy to phosphorylate ADP, synthesizing __
H+ gradient, ATP
139
The H+ gradient has a difference in both __, and results in __ force
concentration (pH) and charge (voltage), proton motive
140
H+ flows back into the matrix through __, AKA the __ complex
ATP synthase, FoF1
141
The Fo part contains __ while the F1 part contains __
ab2c10 and carousel, banana on top and a3b3ydeltae and clementine
142
O confirmation: __, L confirmation: _, T confirmation: _
open ADP + Pi float in, loose holds ADP and Pi in place, tight squeezes ADP and Pi into ATP
142
FoF1 complex works via the __. __ subunit in F1 is attached to ten __ subunits in Fo, so as __ rotates, __ will rotate too
Binding change mechanism, gamma, c, c subunits, gamma
143
Ionophores: _
Allow protons to leak across membrane bypassing ATP synthase and are uncouplers
BIOL 2020
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