93 terms

BIOL 350: Cell Biology Midterm

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T/F: Different cellular functions and activities are based on presence of different genes within an organism.
False; all genes are the same, but not all are expressed
What is the difference between prokaryotes and eukaryotes?
Prokaryotes:
- binary fission
- unicellular
- circular
- cell wall

Eukaryotes:
- membrane bound organelles
- enclosed genetic material
- nucleus
- bigger than prokaryotes
- unicellular and multicellular
- transcription and translation enclosed
- linear
What are the building blocks of a eukaryotic cell?
- amino acids
- sugars
- fatty acids
- nucleotides
Cell theory states:
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 pre-existing cells.
Prokaryotes
a microscopic single-celled organism that has neither a distinct nucleus with a membrane nor other specialized organelles. Prokaryotes include the bacteria and cyanobacteria.
Eukaryotes
an organism consisting of a cell or cells in which the genetic material is DNA in the form of chromosomes contained within a distinct nucleus. Eukaryotes include all living organisms other than the eubacteria and archaebacteria.
Non-covalent interactions
A non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule.
Hydrophobic
tending to repel or fail to mix with water
Hydrophillic
having a tendency to mix with, dissolve in, or be wet by water.
Amphiphilic
a chemical compound possessing both hydrophilic (water-loving, polar) and lipophilic (fat-loving) properties. Such a compound is called amphiphilic or amphipathic.
Phospholipids
a lipid containing a phosphate group in its molecule; the lipid bilayer consists of phospholipids
Liposomes
a minute spherical sac of phospholipid molecules enclosing a water droplet, especially as formed artificially to carry drugs or other substances into the tissues.
Cholesterol
a compound of the sterol type found in most body tissues, including the blood and the nerves. Cholesterol and its derivatives are important constituents of cell membranes and precursors of other steroid compounds, but high concentrations in the blood (mainly derived from animal fats in the diet) are thought to promote atherosclerosis.
The cell membrane is made up of a ____.
Phospholipid bilayer
What is the difference between in vitro and in vivo?
In vitro:
- takes place in test tube
- outside of a living organism

In vivo:
- in a living organism
Which of the following is correct regarding the composition of various biological membranes?
Bacterial plasma membranes are often composed of one main type of phospholipid and lack cholesterol.
What are three types of transmember proteins?
1. Single pass
2. Multi pass
3. Barrel
A protein complex connected by disulfide bonds (found in lumen/outside cytosol/extracellular will be found ___.
Attached via GPI anchor
List these molecules from most permeable to least permeable in the lipid bilayer:

Glucose
DNA
CO2
Estrogen
H2O
Mg2+
CO2, estrogen, H2O, glucose, Mg2+, DNA

size and charge matters (the following is the rank of permeability)
1. Hydrophobic molecules
2. Small uncharged polar molecules
3. Large uncharged polar molecules
4. Ions
T/F: O2 is bigger than Mg2+ and thus will diffuse more slowly across a lipid bilayer.
False, a charged ion is impermeable to the lipid bilayer.
What are the immediate outcomes of the cell with an inactive Na+/K+ (P class) pump?
The concentration of Na+ would continue to increase, and eventually Secondary Active Transport would stop.
What are three types of transmember proteins?
- single pass
- multipass
- barrel
A protein complex connected by disulfide bonds (found in the lumen/outside cytosol/extracellular) will be found ___.
attached via GPA anchor
GFP
The green fluorescent protein (GFP) is a protein composed of 238 amino acid residues (26.9 kDa) that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range.
FRAP
Fluorescence recovery after photobleaching (FRAP) is a method for determining the kinetics of diffusion through tissue or cells. ... This technique is very useful in biological studies of cell membrane diffusion and protein binding.
FLIP
Fluorescence Loss in Photobleaching (FLIP) is a fluorescence microscopy technique used to examine movement of molecules inside cells and membranes.
Transporters
A membrane protein that binds a solute and undergoes a conformational change to allow the movement of the solute across a membrane.
Channels
A channel protein is a protein that allows the transport of specific substances across a cell membrane.
Electrochemical gradient
a gradient of electrochemical potential, usually for an ion that can move across a membrane. The gradient consists of two parts, the chemical gradient, or difference in solute concentration across a membrane, and the electrical gradient, or difference in charge across a membrane.
List the following from most permeable to least permeable in the lipid bilayer:

- H2O
- CO2
- DNA
- Mg2+
- estrogen
- glucose
1. CO2
2. estrogen
3. H2O
4. glucose
5. Mg2+
6. DNA

This is because size and charge matters. DNA is charged and a large molecule, therefore it is least permeable. The following is a rank of what molecules can pass:

1. hydrophobic molecules
2. small UNCHARGED molecules
3. large UNCHARGED POLAR molecules
4. ions
ATP driven pumps
brings ions into/out of the cell against the concentration gradient
T/F: O2 is bigger than Mg2+ and thus will diffuse more slowly across a lipid bilayer.
False; a charged ion is IMPERMEABLE to the lipid bilayer
What are the immediate outcomes of the cell with an inactive Na+/K+ (P-class) pump?
- There would be no membrane potential. The electrochemical gradient and concentration gradient is loss from no Na+ pumping out.
The major ATP-powered pump responsible for maintaining ion gradients across the plasma membrane of mammalian cells is the ___.
plasma-membrane Na+/K+ ATPase
The resting membrane potential in animal cells depends largely on nongated ___ channels.
K+
What determines the function of each organelle?
proteins and enzymes
nuclear pore complex
Nuclear pores are large protein complexes that cross the nuclear envelope, which is the double membrane surrounding the eukaryotic cell nucleus.
nuclear export sequence
A nuclear export signal (NES) is a short amino acid sequence of 4 hydrophobic residues in a protein that targets it for export from the cell nucleus to the cytoplasm through the nuclear pore complex using nuclear transport.
nuclear localization sequence
an amino acid sequence that 'tags' a protein for import into the cell nucleus by nuclear transport.
importins
a type of karyopherin that transports protein molecules into the nucleus by binding to specific recognition sequences, called nuclear localization sequences (NLS).
RAN
...
membrane proteins
Membrane proteins are proteins that interact with, or are part of, biological membranes.

They include integral membrane proteins (permanently anchored or are part of the membrane) and peripheral membrane proteins (temporarily attached to the lipid bilayer or to other integral proteins)
detergents
Detergents are a class of molecules whose unique properties enable manipulation (disruption or formation) of hydrophobic-hydrophilic interactions among molecules in biological samples.
Fluid Mosaic Model
The Fluid Mosaic Model explains various observations regarding the structure of functional cell membranes. The model, which was devised by SJ Singer and GL Nicolson in 1972, describes the cell membrane as a two-dimensional liquid that restricts the lateral diffusion of membrane components.
membrane transport
the collection of mechanisms that regulate the passage of solutes such as ions and small molecules through biological membranes, which are lipid bilayers that contain proteins embedded in them.
How could a scientist experimentally test for a NLS (nuclear localization sequence)?
1. get antibody to mutate a protein that does not normally go to the nucleus by attaching NLS
2. now that NLS is added, the protein will go to the nucleus to show if it's necessary
Consider a transcription regulatory protein that has both a nuclear localization and a nuclear export signal and is normally found both in the nucleus and the cytosol at comparable concentrations. This protein has a high affinity binding partner in the nucleus. Upon activation of a certain signaling pathway, the binding protein is ubiquitylated and degraded. As a result of this...
Since there is no cell signaling in the nucleus, the transcription regulatory protein accumulates in the cytosol. Once the binding protein is destroyed in the nucleus, it would go back to the cytosol.
cotranslation
Any process involving the maturation or delivery of a protein that occurs during the process of translation.
Describe what would happen to the precursor of a mitochondrial matrix protein in the following types of mitochondrial mutants:
- mutation in TOM signal receptor
- mutation in TIM 23 complex
- mutation in matrix signal peptidase
- A mutation in TOM signal receptor would cause the protein to not get imported to the outer membrane of the mitochondria.
- A mutation in TIM 23 complex would cause the protein to be stuck in TOM and will be stuck in the matrix of the mitochondria.
- A mutation in the matrix signal peptidase would cause the proteins to not get cleaved off and stay folded.
Which of the following proteins or protein complexes is directly required for the targeting of mitochondrial inner membrane multipass proteins, such as metabolite transporters, whose signal sequence is normally not cleaved off after import?
TIM 22
TIM 22 complex
binds to TOM, shuttles to matrix
TIM 23 complex
helps fold proteins into inner membrane space or cleave off in the inner membrane
What protein is from bacterial derivatives?
SAM (only for barrel) and OXA
How can one examine the mechanism of cotranslation?
cell fractionation
Imagine a protein that has been engineered to contain a nuclear localization signal, a nuclear export signal, a C-terminal peroxisomal targeting sequence, and a canonical ER signal sequence. With all of these signals, where would you expect to find the protein after synthesis?
It would be found in the ER. This is because the ER is the starting place for ALL proteins (the secretory pathway). All proteins MUST enter the ER before other places.

ER = cotranslational
other places in the cell = post-translational
ionic bonds
the complete transfer of valence electron(s) between atoms
hydrogen bonds
a weak bond between two molecules resulting from an electrostatic attraction between a proton in one molecule and an electronegative atom in the other; a good example of hydrogen bonding would be water
Van der Waals interactions
the residual attractive or repulsive forces between molecules or atomic groups that do not arise from a covalent bond, or ionic bonds
hydrophobic effect
the observed tendency of nonpolar substances to aggregate in aqueous solution and exclude water molecules
hydrocarbons
a compound of hydrogen and carbon, such as any of those that are the chief components of petroleum and natural gas.
glycerides
a fatty acid ester of glycerol
amphipathic nature
molecule containing both polar (water-soluble) and nonpolar (not water-soluble) portions in its structure.
alpha helix
a common motif in the secondary structure of proteins and is a righthand-coiled or spiral conformation (helix) in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid located three or four residues earlier along the protein sequence.
beta sheet
Beta sheets consist of beta strands (also β-strand) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation.
phosphatidylethanolamine
A phospholipid and are a major component of biological membranes. Can mainly be found in the inner (cytoplasmic) leaflet of the lipid bilayer.
phosphatidylserine
A phospholipid and a component of the cell membrane. It plays a key role in cell cycle signaling, specifically in relationship to apoptosis.
phosphatidylcholine
A phospholipid that incorporates choline as a headgroup. They are a major component of biological membranes. Although they are found in all plant and animal cells, they are absent in the membranes of most bacteria.
micelles
an aggregate of molecules in a colloidal solution, such as those formed by detergents.
liposome
a minute spherical sac of phospholipid molecules enclosing a water droplet, especially as formed artificially to carry drugs or other substances into the tissues.
GPI anchors
glycosylphosphatidylinositol; a glycolipid that can be attached to the C-terminus of a protein during posttranslational modification.
uniporters
A uniporter is an integral membrane protein that is involved in facilitated diffusion. They can be either ion channels or carrier proteins. Uniporter carrier proteins work by binding to one molecule of substrate at a time and transporting it with its concentration gradient.
symporters
A symporter is an integral membrane protein that is involved in the transport of many differing types of molecules across the cell membrane. The symporter works in the plasma membrane and molecules are transported across the cell membrane at the same time, and is, therefore, a type of cotransporter.
antiporters
An antiporter (also called exchanger or counter-transporter) is a cotransporter and integral membrane protein involved in secondary active transport of two or more different molecules or ions across a phospholipid membrane such as the plasma membrane in opposite directions.
OXA complex
multisubunit protein located in the inner mitochondrial membrane; responsible for insertion of proteins systhesized in the mitochondrial matrix into the inner membrane of the mitochondrion and assisting TIM complexes in inserting some types of protein into the inner mitochondrial membrane.
What is the role of cytosolic HSP70?
Hsp70 molecular chaperones and their co-chaperones work together in various cellular compartments to guide the folding of proteins and to aid the translocation of proteins across membranes. Hsp70s stimulate protein folding by binding exposed hydrophobic sequences thereby preventing irreversible aggregation.
matrix targeting sequence
What is the role of BiP?
binds newly-synthesized proteins as they are translocated into the ER and maintains them in a state competent for subsequent folding and oligomerization. BiP is also an essential component of the translocation machinery, as well as playing a role in retrograde transport across the ER membrane of aberrant proteins destined for degradation by the proteasome.
What is the role of Calnexin/Calreticulum?
trimming of glucose residues off the core oligosaccharide added during N-linked glycosylation is a part of protein processing.
proteasome
a protein complex in cells containing proteases; it breaks down proteins that have been tagged by ubiquitin.
E3 ubiquitin ligase
A ubiquitin ligase (also called an E3 ubiquitin ligase) is a protein that recruits an E2 ubiquitin-conjugating enzyme that has been loaded with ubiquitin, recognizes a protein substrate, and assists or directly catalyzes the transfer of ubiquitin from the E2 to the protein substrate.
AAA ATPase
AAA or AAA+ is an abbreviation for ATPases Associated with diverse cellular Activities. ... AAA proteins couple chemical energy provided by ATP hydrolysis to conformational changes which are transduced into mechanical force exerted on a macromolecular substrate.
SRP protein
Signal recognition particle (SRP) receptor, also called docking protein, is a dimer composed of 2 different subunits that are associated exclusively with the rough ER in mammalian cells. Its main function is to identify the SRP units.
SRP receptor
Signal recognition particle (SRP) receptor, also called docking protein, is a dimer composed of 2 different subunits that are associated exclusively with the rough ER in mammalian cells. Its main function is to identify the SRP units.
What are the types of ion channels?
- voltage gated
- non-gated
- ligand gated
What determines a specific function of an organelle?
The specific function of a given organelle is determined by the specific proteins present in that organelle.
What is the structure of a lipid molecule?
A lipid molecule:
- is cylindrical in shape
- has 2 hydrocarbon tails
What is the structure of a detergent molecule?
A detergent molecule:
- is conical or wedged-shape
- has only 1 hydrocarbon tail
- has a shorter hydrocarbon tail than a lipid molecule
How would you make a lipid molecule into a detergent?
To make a lipid molecule into a detergent, you would have to make its hydrophillic head larger and/or remove one of its tails so it can form a micelle.
What are the factors of the permeability of a cell?
charge and size
List the following from most permeable to least permeable in the lipid bilayer:

- H2O
- O2
- RNA
- Ca2+
- cholesterol
- glucose
1. O2
2. cholesterol
3. H2O
4. glucose
5. Ca2+
6. RNA
Why do molecules like O2 and cholesterol get to pass through the lipid bilayer freely?
O2 and cholesterol get to pass through the lipid bilayer freely because the molecules are small and have no net charge. All others will require a channel or transporter to get through.
active transport
transport that requires energy; molecules move from a lower concentration to a higher concentration (against concentration gradient); most likely would use a pump
passive transport
transport that requires energy; molecules move from a higher concentration to a lower concentration; transports via diffusion