Cell Biology Lecture Exam 3

Front 1

What is a Neutrophil?

Back 1

a type of blood cell (making 50-75% of your blood cells) that is the first type of cell to respond to an outside attack (usually w/in first hour). Pus contains dead neutrophils as well as bacteria, etc. Often have specific oligosaccharides bound to them.

Front 2

Describe the pathway/mechanism by which endothelial cells are stimulated by cytokines to produce membrane lectins.

Back 2

1) Stimulus cytokine reaches receptor

2)signaling pathway activates gene regulatory proteins

3) Activation of specific lectin genes occurs
(followed by mRNA transcription and translocation of mRNA outside the nucleus).

4) Protein synthesis

5) Protein goes to ER/Golgi/Secretory vesicle and becomes lectin/goes to the membrane.

Front 3

What are 3 classes of Gene Regulatory proteins?

Back 3

Proteins with...

1) homeodomain sequence

2) zinc finger motif

3) leucine zipper motif

Front 4

Gene regulatory proteins may either be ________________ or __________________

Back 4

activators or repressors

Front 5

True or False: Expression of genes may require multiple gene regulatory proteins.

Back 5

True

Front 6

Pertaining to Gene Regulatory Proteins, What is a homeodomain?

Back 6

A sequence found in certain Gene/transcriptional regulatory proteins that mediates binding to DNA. A single homeodomain has 3 overlapping alpha Helices, packed together by hydrophobic forces. Helix 2+ Helix 3 make up the DNA binding element (a helix-turn-helix motif) and Helix 1 is the recognition helix.

Front 7

In a homeodomain, what is are the components of the Recognition helix (helix 1 and what do they do)?XXXXXXXXXXXXXXXX

Back 7

Amino acids here make important, sequence-specific contacts with bases in the DNA major groove. 3 Side chains from the recognition helix form H bonds with bases in the DNA. IN ADDITION, an Arginine molecule from a flexible loop of the protein contacts bases in the minor groove. XXXXXXXXXX they make strong connections using H bonds.

Front 8

Pertaining to gene regulatory proteins, What is a zinc finger domain?

Back 8

A motif that has a centrally coordinated zinc atoms as crucial structural elements. Has a beta sheet and alpha helix. The Zn is coordinated by 2 Cysteine residues from the beta sheet as well as 2 histidine residues from the Alpha helix.

Front 9

True or false: a single zinc finger motif is large enough to bind many, many bases of DNA.

Back 9

FALSE: a single zinc finger domain is only large enough to bind a few bases. Hence, zinc fingers are often found in tandem repeats as part of a larger binding region.

Front 10

What are the basic structural components of a zinc finger domain and where are they?

Back 10

Centrally coordinated zinc atom

Alpha helix (rests in the major groove of DNA)

Side chains from Alpha helix project outward and contact DNA bases, whch vary based on the type of side chain.

Beta sheet (on the opposite side of the alpha helix, away from the DNA)

Front 11

What parts of the alpha helix and beta sheet of a zinc finger domain help keep the zinc atom centered?

Back 11

2 cysteines from the beta sheet.

2 histidines from the alpha helix. XXXXXXXXXX

Front 12

Regarding the classes of gene regulatory proteins, what is a Leucine Zipper?

Back 12

A motif consisting of 2 long, intertwined alpha helixes (hydrophobic side chains extend in the space between them, especially a ton of leucines).

Front 13

How does a Leucine Zipper domain work to bind/regulate DNA?

Back 13

extensions of the 2 alpha helices straddle the DNA major groove, and side chains from both helices extend into the groove to hydrogen bond to specific DNA bases.

Front 14

If a protein isn't needed, what happens?

Back 14

Transcription will be turned off and any existing proteins/mRNA for that protein will degrade into amino acids and base pairs.

Front 15

What are lectins?

Back 15

a class of proteins that can bind to cell membranes. They are sugar-binding and offer a way for molecules to stick together without getting the immune system involved, which can influence cell-cell interaction.

Front 16

What are selectins?

Back 16

a type of lectin that binds to glycoproteins (specifically, carbohydrates on a white blood cell's membrane's surface proteins)

Front 17

What are cytokines?

Back 17

Particles released at the site of an infection/wound/inflammation that stimulate entothelial cells to express selectins.

Front 18

In response to a wound, how do lymphocytes/white blood cells travel to the wound?

Back 18

1) Inflammation/wound/infection site releases particles called cytokines that stimulate endothelial cells (the cells that line nearby blood vessels) to express surface proteins called selectins.

1a) specifically, cytokines bind to surface proteins--> gene regulatory proteins turn on lectin genes --> mRNA produced, translocated out of cell --> lectin synthesized --> gets modified in the ER, packaged in Golgi, sent out of cell onto its surface via secretory vesicle=lectin is now expressed.

2) Selectins then bind to carbohydrates in the white blood cell's membrane's surface proteins.

3) This attachment allows white blood cells to "adhere" to the entothelial cells and "roll along" here until they find an access point they can squeeze themselves through without disrupting the vessel's integrity.

Front 19

True or False: the pathway through which lectin gets produced and white blood cells travel to an infection site happens on the endothelial cells of all types of blood vessels.

Back 19

FALSE: This process doesn't happen in arteries, since they're too thick and high pressure to penetrate.

Front 20

What is a transcription factor?

Back 20

(Excluding RNA polymerase) Proteins that attach to a specific segment of DNA and affect/regulate transcription.

Front 21

What is a Master Control Gene? Give an example.

Back 21

A gene that controls many other genes. It turns on genes and turns off genes that aren't needed.
Example: The "Ey" gene controls the production of eyes by coding for a gene regulatory protein.

Front 22

What is the Oct-4 gene?

Back 22

The "Master Control Gene" for PLURIPOTENCY. When activated, produces the gene regulatory protein Oct-4, which seems to be responsible for keeping cells in an undifferentiated, pluripotent state; it can also turn differentiated cells into stem cells. It is expressed in embryonic stem cells.

Front 23

What is the "ey" gene? What does it do? Where is it found?

Back 23

A master control gene that codes for a regulatory protein which in turn codes for the production of eyes by turning on multiple other genes that code for various, specific eye structures. Normally found in a group of undifferentiated cells.

Front 24

What happens if you switch on the "ey" master control GENE in cells where it would not normally be activated?

Back 24

You can end up with ectopic eyes--eyes produced ANYWHERE.

Front 25

True or false: one regulatory protein may control different genes in a coordinated expression of different proteins?

Back 25

TRUE. Ex: Oct4 gene, a master control gene for pluripotency.

Front 26

What accounts for the formation of the eye and the production of eye proteins?

Back 26

Gene regulation

Front 27

Many genes are silent unless there are _____________________ bound to the regulatory region.

Back 27

Gene Regulatory Proteins.

Front 28

Genes homologous to the eyeless gene in Drosophila are found across many phyla. What is the gene called in

a) mice?

b) humans?

Back 28

a) Pax-6

b) Aniridia

In both species, they involve 3 spliced introns.

Front 29

What would happen if you put a Pax-6 mouse eyeless gene into a fruit fly?

Back 29

The fly would end up growing an extra FLY eye (NOT mouse eye), since you're essentially introducing a master control gene which would turn on eye formation genes PRESENT (in this case, fly eye genes).

Front 30

What 2 things make up a Genetic Switch?

Back 30

1) Gene Regulatory sequence (found upstream of target DNA)

2) Gene Regulatory Proteins (bound to the sequence).

When Gene Regulatory Proteins are bound to a Gene Regulatory Sequence, the genetic switch is "ON".

Front 31

Once a master control gene is activated, the master control transcription factor protein
(ex: for eye production) may work by 3 mechanisms (sometimes all 3 at once). What are they?

Back 31

1) Can turn "ON" eye tissue genes so THEY can produce structural proteins by binding to their regulatory sequences OR turn "OFF" incorrect structural genes (ex: Gonad genes)

2) Can turn on genes that produce ADDITIONAL transcription factors (NOT structural proteins) (ex: if TF1 is produced by master control gene activating another gene will profuce TF2)

3) Eye transcription factors TF1 and TF2, together or individually, regulate other eye genes.

Front 32

Note: Some gene regulatory sequences will also bind ____________, which can turn the coding region of a gene OFF.

Back 32

Inhibitory binding proteins

Front 33

Homologs of the eyeless gene of Drosophila (ex: Pax-6 in mice and Aniridia gene in humans) are very similar. What 3 things do they all have in common?

Back 33

1) Include similar extensive sequence identity

2) Contain the same 3 intron splice sites

3) Have similar expression during development.

Front 34

True or False: Combinations of just a few regulatory proteins may produce many different cell types during the differentiation stage of development.

Back 34

TRUE

Front 35

True or false: you can get DNA from the nuclei of red blood cells.

Back 35

FALSE: Red blood cells don't have nuclei, so you best get them from white blood cells.

Front 36

What's the difference between an antigen and an antibody?

Back 36

Antigen=any foreign particle that ellicits an immune response.

Antibodies=attack antigens

Front 37

What is the difference between Blood types A, B, AB and O?

Back 37

A possesses anti-B antibodies, which makes it incompatible with B antigens but allows A antigens to exist. Vice-versa with type B.

Type AB contains no antibodies, allowing the presence of A and B antigens.

O contains BOTH anti-A and anti-B antibodies, making it intolerant to having either antigen present.

Front 38

What is the Amelogenin gene? What is its significance?

Back 38

gene involved in tooth enamel development, with different-looking copies being found on both X and Y chromosomes (the X-copy is shorter). It can therefore be used to tell males and females apart.

Front 39

True or False: DNA can be used directly for identifying a suspect, etc.

Back 39

FALSE: it must be amplified first.

Front 40

What are the 2 methods of amplifying DNA so it can be worked with?

Back 40

1) Cloning genes in bacterial plasmid DNA.

2) Polymerase Chain Reaction (PCR)

Front 41

If you were looking at a DNA gel run after PCR, etc., why might some bands look brighter than others?

Back 41

Brighter bands would mean that there are more copies of the DNA fragment.

Front 42

How can DNA hybridization be used to identify how closely 2 species are related?

Back 42

After the DNA of 2 birds are split, they're recombined as a hybrid strand. The more heat it takes to split this hybrid, the more closely related the birds are.

Front 43

What are the 3 main techniques for DNA hybridization?

Back 43

1) Genome comparisons (ex: melting temp comparisons)

2) Microarray (using the Gene Chip to identify gene sequences)

3) In Situ hybridization (to detect RNA or DNA in cells and tissues)

Front 44

What does the microarray/Microchip DNA hybridization technique entail?
(XXWhen looking at DnA, you're usually looking at mutations; when looking at mRNA, you're usually looking at gene expression).

Back 44

1) Making the microchip: A synthetic, custom-made, KNOWN DNA sequence is put on a microchip (typically, a short sequence that can act as a probe for a specific gene).

2) Take a DNA sample, make into a single strand and cut into small pieces.

3) Label the DNA pieces and spread over chip-- any sequence in the sample that matches a sequence in the chip will hybridize to it, and the probe will make it visible.

Front 45

What is a Probe in the context of DNA hybridization?

Back 45

A piece of DNA or RNA used to detect complementary strands by annealing to them to form a double-stranded hybrid. Often labeled (by making it radioactive, fluorescent, etc), therefore rendering any sequences it binds to labeled.

Front 46

What are some applications of DNA Microchip/Microarray hybridization?

Back 46

1) detecting genes of disease-causing bacteria

2) looking for genes that might predispose individuals for diseases (cancer, alcoholism, etc).

3) see how active a set of genes is in a particular cell/tissue type.

4) look for mutations in a gene.

5) compare the gene expression profiles of different samples (ex: tumors compared to normal tissues)

Front 47

The Microarray Assay technique has 2 different approaches:

1) The Gene Chip (which identifies gene sequenceS) and

2) Microarray Analysis of gene EXPRESSION (mRNA).

Describe the process of the second approach.

Back 47

1) mRNA purified

2) Reverse transcriptase PCR added

3) double-stranded cDNA produced FROM mRNA

4) hybridization occurs

Front 48

What is In Situ hybridization (ISH)?

Back 48

A THIRD hybridization technique, which uses a labeled complementary strand of DNA or RNA (ex: a probe) to localize/find a specific DNA/RNA sequence in a portion/section of tissue and visualize it on the actual organism

(hence, "in situ"="in its original place").

Front 49

What is FISH and what is it good for?

Back 49

FISH=Fluorescence in Situ Hybridization. Uses a fluorescent probe to detect and vividly paint genes on chromosomes in cells and tissues. Can be used in humans for gene mapping or to detect mutations.
Unlike other techniques that look at chromosomes, FISH can be performed on nondividing cells.

Front 50

What are the steps to producing a transgenic animal via Direct Injection method?

Back 50

1) breed mice to produce zygotes
2) in the pronuclear stage (before mom and dad's DNA have fused), introduce via pipet many copies of the Trans gene into the (usually male) pronucleus that will add in random locations to the DNA.
3) Once blastocysts form, implant these into a female (now "pseudopregnant") to lead to a full grown, transgenic baby!
Not all pups necessarily have the gene; run gel electrophoresis to check for hybrids and breed them to establish a line or trans mice.

Front 51

What are the steps to producing a chimeric animal (and eventually, trans mice) via the Gene Targeting (2nd) technique?

Back 51

1) A mutant trans gene is created with flanking sequences that are identical to the DNA surrounding the normal target gene.

2) 2 mice are mated and AFTER the pronuclei fuse, the blastocyst is removed from the mother to *culture ES cells in a dish. *

3) Transgenic DNA is inserted into the ES cells.

4) brief electical pulse moves trans DNA into the ES cell nuclei and the trans gene replaces the normal DNA. Homologous recomb occurs.

5) The trans gene contains a marker which is used to only select those ES cells that have integrated it.

6) Selected ES cells cultured to form their own colonies

7) ES cells injected into blastocyst of a new mice, which is then put in a foster mom and allowed to develop.

8) resulting mice born are Chimeras--contain tissues with DNA from different genotypes (original blastocyst + ES cells you put in).

9) To establish a line of trans mice, chimeras with the trans DNA in their GERMLINE cells must be bred.

Front 52

What is the advantage of homologous recombination-made knock-in/knock-out mouse over making a transgenic mouse made from the direct injection method?

What is the disadvantage?

Back 52

Only one copy of the target trans gene is inserted, and it's inserted into a controlled location.

Disadvantage=homologous recombination doesn't happen often in mammals.

Front 53

What are the 3 main methods of creating transgenic animals?

Back 53

1) Direct Injection (into pronuclei)

2) Gene Targeting/REplacement

3) CRISPR

Front 54

What does CRISPR stand for and how does it work?

Back 54

Clustered Regularly Interspaced Short Palindromic Repeats. Used by a natural protection method used by bacteria to protect themselves from viruses:

1) When a bacterium detects DNA, it produces 2 types of short RNA, one of which (the guiding RNA) contains a sequence complementary to that of the invader. In this technique, you can engineer the guide RNA.

2) These 2 RNAs form a complex with Cas-9, a type of nuclease (cuts DNA).

3) when the guide RNA finds its matching target w/in the genome, Cas-9 cuts the target DNA.

3) the cut DNA will naturally try to repair itself, but it's often rife with mutations. You can either take advantage of this to study mutations or also insert proper DNA for gene therapy.

Front 55

What are 2 applications of the CRISPR method?

Back 55

1) Studying mutations in specific genes

2) Gene therapy--inserting healthy genes where the DNA was cut.

Front 56

What are some advantages of the CRISPR method over other Gene targeting methods?

Back 56

1) you can target many genes at once with as many types of guiding RNA as you can make.

2) It can be performed both in a culture AND in living cells.

Front 57

What is GFP and what is it used for?

Back 57

Green Fluorescent Protein isolated from jellyfish that can be used to mark other proteins by inserting its gene NEXT to the protein gene you're interested in. XXXXXSince we know the sequence of GFP, we put it right next to the gene of interest. when synthesizing protein from this, the resulting protein will CONTAIN the GFP, marking the protein you're looking for. WE DON'T INJECT GFP.

Front 58

What was one discovery from GFP application?

Back 58

It was used to mark/track the HIV virus. Showed that direct cell-to-cell transfer of HIV happened, therefore revealing that HIV might not be exposed to the intercellular fluid (and hence might be able to avoid detection by the immune system).

Front 59

What does the structure of a Glycerol molecule look like?

Back 59

3 central carbons, each with 1 attached OH group (so 3 total OH groups) and bonds to hydrogen for the rest.

Front 60

What does the basic structure of a fatty acid look like?

Back 60

A long carbon chain with an H at one terminal and a COOH at the other terminal.

Remember, in the COOH end, the terminal C is double-bonded to an O and single-bonded to another O which is in turn bonded to an H.

Front 61

What are triglycerides and what are they made of?

Back 61

Triglycerides are the main building blocks of natural fats and oils.

Triglyceride= 1 glycerol + 3 fatty acids

Front 62

What kind of bond joins glycerol and 3 fatty acids together to make a triglyceride and what's the process by which this bond is formed?

Back 62

Ester bonds; formed by dehydration synthesis.

Front 63

since fats and cholesterol don't dissolve in blood well (due to being hydrophobic), how do they get transported?

Back 63

Via lipoproteins.

Front 64

What is the difference between low-density lipoproteins (LDLs) and high-density lipoproteins (HDLs)?

Back 64

LDLs transport cholesterol and lipids INTO the blood and tissue cells. Too much, and they get deposited in arteries.

HDLs transport cholesterols and lipids OUT of tissues to the liver for elimination from the body.

Front 65

Why was hydrogenation developed for oils and how does it work?

Back 65

Developed to engineer a solid, spreadable oil and prevent rancidity/chemical breakdown.

Produced by heating oil to a high temp w/ hydrogen using a metal catalyst to break double bonds and replace them with 2 H atoms.

Front 66

How did food chemists solve the issue that fully hydrogenated oils were too hard to be used like butter?

Back 66

Partial hydrogenation, which unlike fully hydrogenated oil, can produce the variants cis and trans fats because of the presence of double bonds.

Front 67

True or False: the classification of "Lipids" includes fats, oils, waxes, phospholipids, steroid (cholesterol, steroid hormones), etc.

Back 67

TRUE

Front 68

True or false: lipids account for much of the structural properties of membranes.

Back 68

TRUE

Front 69

What makes phospholipids (the lipids that make up membranes) different than regular triglycerides?

Back 69

They consist of a Serine molecule joined to a phosphate molecule joined to a glycerol, with 2 fatty acids (hydrophobic hydrocarbon tails) attached to the glycerol.

Front 70

What is "Amphipathic"?

Back 70

a molecule possessing both hydrophilic and hydrophobic parts (ex: proteins, phospholipids).

Front 71

When placed in water, lipids naturally form vesicles. What are these called?

Back 71

liposomes

Front 72

What is a phospholipid?

Back 72

A nonpolar lipid molecule that is made amphipathic by the addition of a phosphate and polar head group.

Front 73

The fact that the core of most globular proteins is composed of non-polar residues is because of the Hydrophobic Effect. What is that?

Back 73

The observed tendency of nonpolar substances to aggregate in aqueous solution and exclude water molecules (so they clump), because water molecules want to maximize the hydrogen bonds between them, so they are more attracted/prefer other water molecules over nonpolar, non-H-bond-forming lipids.

Front 74

Once the lipid bilayer formed, the lipids become more cohesive because of ____________ interactions.

Back 74

noncovalent

Front 75

The properties of a lipid bilayer are determined by the structures of its lipid molecules. Predict the properties that would result if the hydrocarbon chains were SHORTER than usual.

Back 75

Fluidity would be HIGHER; stability= lower; because the shorter hydrocarbon tail lengths would mean less interaction among tails, reducing the forces promoting the bilayer.

Front 76

What would happen if phospholipids only had 1 hydrocarbon tail instead of 2?

Back 76

No bilayer would form; instead, a micelle (a round ball of phospholipids with tails all pointing interior like a group of buffalo protecting their offspring.)

Front 77

What does cholesterol in the hydrocarbon tails do the properties of the tail?

Back 77

1) straightens and decreases mobility of tails, leading to a thicker membrane with less fluidity.

2) Lowers the freezing temp of the tails b/c it prevents close packing/gelling/crystalization at lower temps.

Front 78

The inner mitochondrial membrane lacks cholesterol; however, it includes many phospholipids whose fatty acids have 1/more double bonds. What is the effect of this?

Back 78

Decreases the temp at which the membrane would crystallize/freeze.

Front 79

Regarding membranes, STRUCTURE is provided mostly by ________________

most FUNCTION is carried out by _____________

Back 79

lipids, proteins.

Front 80

What do detergents do?

Back 80

release transmembrane proteins (kind of surround everything in a fatty layer to separate everything)

Front 81

Who came up with the Fluid Mosaic Model? What does it say?

Back 81

Singer and Nicolson (1972). Describes the structure of cell membranes: a flexible layer made of lipid molecules is interspersed with large protein molecules that act as channels through which other molecules enter and leave the cell. Also, proteins may either move freely in the membrane OR be restricted. Evidence: FRAP

Front 82

What is FRAP (Fluorescence Recovery/Redistribution After Photobleaching)?

Back 82

A technique used to glean quantitative info about the dynamic beh of molecules in the cell.

1) A high-intensity laser beam irreversibly bleaches fluorescent molecules in one region of the cell.

2) Redistribution of both bleached and remaining fluorescent molecules is monitored over time in regions of interest.

3) Fluorescence recovery in bleached area indicates proteins can diffuse in the membrane, whereas no fluorescence recovery in the area means that proteins cannot diffuse in the membrane.

Front 83

What is a membrane domain?

Back 83

A restricted area of activity for membrane proteins. There are a few types:

1) membrane domains that allow binding to internal molecules (ex: cytoskeleton).

2) M. domains that permit binding to external molecules (ex: the ECM)

3) M. domains that permit binding proteins to those of other cells.

4) Tight junctions: really tight connections between cells that are formed when proteins are restricted in one particular place on the membrane and are prevented from diffusing into the cell (ex: desmosomes, which link this way via intermediate filaments)

Front 84

What are the 4 classes of molecules that can be transported through the cell membrane? List them in order from most permeant to least permeant:

Back 84

1) Small, hydrophobic molecules (O2, CO2, N2, benzene) can cross easily with diffusion

2) Small, uncharged POLAR molecules (H20, glycerol, ethanol) can cross easily with diffusion.

3) Larger, uncharged polar molecules (amino acids, glucose, nucleotides)

4) ions (H+, Na+, HCo2-, K+, Mg2+) (travel via channel-mediated transport)

Front 85

What are the 2 forms of facilitated diffusion and what's the difference between them?

Back 85

Both passive transport methods. However,

Channel-mediate transport only requires that a channel be open for a molecule to pass through. Ions travel this way. Selectivity based on size and charge.

Carrier-mediated transport=where there's a protein that changes its conformation to let a molecule through, once that molecule fits in a specific solute-binding site of the carrier protein.

Front 86

What are the 2 criteria of specificity for channel-mediated transport?

Back 86

1) size

2) charge

Front 87

What is the similarity between Carrier-mediated transport and active transport?

What is the difference?

Back 87

Similarity=both involve the mediation of a carrier protein to let stuff through.

Difference=Active transport requires ATP b/c it goes against the concentration gradient.

Front 88

True or False: The plasma membrane is highly impermeable to all charge molecules.

Back 88

FALSE: Clarification: the LIPID bilayer is impermeable to charged molecules; however, they can still pass through the plasma membrane via certain ion channels and carriers (and your life depends on it).

Front 89

What would increasing the number of double bonds in some phospholipids in the cell membrane do?

Back 89

Make the membrane MORE fluid.

Front 90

Which component of a cell membrane--lipids, proteins, carbohydrates or cholesterol--is likely to function as a receptor in cell to cell signaling?

Back 90

Proteins

Front 91

If the rate of transport of a substance into a cell is reduced when the formation of ATP is blocked, you can conclude that the transport system must be a form of ____________

Back 91

Active transport.

Front 92

The ability of a cell membrane to allow hydrophillic molecules to pass into a cell is determined by _________________

Back 92

Integral membrane proteins (membrane proteins that are PERMANENTLY attached to the cell membrane). ex: transmembrane proteins

Front 93

What are transmembrane proteins?

Back 93

A class of integral membrane proteins that can cross the membrane and can act as channels.

Front 94

How can you distinguish crossing the membrane via simple diffusion VS facilitated diffusion?

Back 94

Simple diffusion is NOT saturable; facilitated diffusion rates, however, are limited by the number of functional membrane proteins and CAN be saturated.

Front 95

Why does the integrity of the shape of the phospholipid bilayer remain even after a tear/rupture?

Back 95

Phospholipids are cylindrical in shape and will automatically form a bilayer to remain energetically stable (a micelle/hemimicelle is not energetically favorable).

Front 96

Is it more likely to see a membrane and associated (trans?) protein with the carbohydrate (visually, looks like a pitchfork) on the outside or the inside of the membrane?

Back 96

OUTSIDE

Front 97

Would it be likely to see a membrane-associated protein in between/completely embedded within the phospholipid tails?

Back 97

NO, not likely; though alpha helices can be found in the membrane, entire proteins are NOT found buried (paritally or fully) in the membrane.

Front 98

For the following ions, say whether they are more abundant inside or outside of a typical mammalian cell:
Na+,

K+,

Mg2+,

Ca2+,

Cl-,

A- (occurs in molecules with phosphate groups as ATP)

Back 98

(Na+) outside

(K+) INSIDE

(Mg2+) outside

(Ca2+) outside

(Cl-) outside

(A-) INSIDE

Front 99

What are the 3 reasons why the resting membrane potential of most cells negative (-70)?

Back 99

1) More anions (A-) inside the cell.

2) More (K+) ions inside the cell; however...

3) (K+) tends to leave through channels (sodium potassium pump), leaving the inside more negative.

Front 100

When depolarizing a cell, what happens?

Back 100

Electrical signaling leads to sodium (Na+) ion channels opening temporarily. Positive SODIUM ions rush inside, making the interior comparatively more positive.

Front 101

What does the Nernst equation say/predict?

Back 101

It predicts the membrane potential for ions, so long as the cell is freely permeable to that ion (AKA the channels are open).

Front 102

In accordance with the Nernst equation, what 2 forces act on ion flow?

Back 102

1) concentration gradient: ions flow DOWN a concentration gradient.

2) electrical forces (ions move in response to an electrical field): for example, if the inside of the cell is negative, positive ions will be attracted and move in.

Front 103

The cell membrane potential is altered during an action potential due to ____________

Back 103

the opening of sodium channels.

Front 104

True or false: the voltage-gated Na+ (sodium) channels inactivate automatically after the membrane depolarizes, returning the membrane potential to its original level.

Back 104

TRUE

Front 105

What are the 3 components of a phospholipid?

Back 105

1) 1 glycerol molecule

2) 1 polar head group

3) 2 fatty acid chains

Front 106

When mixed in an aqeous solution, phospholipids form ___________

Back 106

Liposomes

Front 107

inducing the expression of genes for fatty acid desaturase enzymes would have what effect on the membrane?

Back 107

it would make the membrane more fluid.

Front 108

The ability of a cell membrane to transport glucose into the cell is determined by what?

Back 108

integral membrane proteins.

Front 109

Given the usual resting concentration of ions inside/outside the mammalian cell, which direction would the net flow of K+ ions be if additional potassium ion channels were opened?

Back 109

OUT of the cell.

Front 110

Which component of a cell membrane is likely to function as a receptor for the neurotransmitter dopamine (which acts in the signaling in cells of the nervous system+other tissues)?

Back 110

Proteins

Front 111

A carrier protein transports solutes across membranes. True or False: these proteins bind a solute and undergo a confirmation change that transfers the bound molecule across the membrane.

Back 111

TRUE

Front 112

The major driving force for the formation of a lipid bilayer is _________; once formed, the membrane is further stabilized by _______.

Back 112

hydrophobic forces on the phospholipid fatty acid carbon chains;

H-bonds, electrostatic attractions and van der Waals contacts.

Front 113

Each ion has its own Equlibrium potential. What is an equilibrium potential?

Back 113

The membrane potential where the net flow through any open channels is 0.

Front 114

True or false: Voltage gated K+ channels are present in some--but not all--neurons. Why or why not?

Back 114

TRUE; Inactivation of the Na+ (SODIUM) channels are what bring the membrane potential back to the resting potential; K+ channels/flow of K+ ions NOT NEEDED to bring the resting potential back down after an action potential.

Front 115

Why are there extra voltage-gated K+ channels in certain neurons?

Back 115

Presence of slower opening/slower inactivating K channels may can help to produce an action potential with the classical hyperpolarizing overshoot.

Front 116

What is the active toxin in pufferfish tissues and how does it work?

Back 116

Tetrodotoxin (TXX)=a neurotoxin that mimics a hydrated soidum and specifically blocks the voltage-gated sodium ion channels. Therefore, the flow of Na+ is blocked and there can be no rising phase to an action potential.

Front 117

Why would you experience numbness after eating pufferfish poison?

Back 117

Sensory neurons stop firing, preventing communication with the brain, resulting in numbness.

Front 118

Why would you experience paralysis after eating pufferfish poison?

Back 118

TXX causes motor neurons to stop firing, preventing communication with the muscles (resulting in paralysis)

Front 119

True or false: the sodium-potassium pump requires ATP for the first step (binding 3 sodium ions in the cell interior), but no ATP in the second step (binding 2 Potassium ions in the ECM and moving them into the cell).

Back 119

TRUE

Front 120

What happens when an action potential runs through the axon/nerve terminal of the presynaptic neuron?

Back 120

voltage-gated Ca2+ channels are open, allowing Ca2+ to flow into the terminal, stimulating fusion of synaptic vesicles containing neurotransmitters w/ the cell membrane to dump the contents into the synapse.

Front 121

What are the 4 parts of a synapse?

Back 121

1) a presynaptic ending that contains neurtransmitters in vesicle.

2) Voltage-gated Ca2+ channels in the presynaptic cell.

3) the space between the presynaptic and postsynaptic endings (AKA synaptic cleft).

4) a postsynaptic ending that contains neurotransmitter receptors.

Front 122

Which toxin blocks transmission by acting at the synapse?
A) Batrachatoxin

B) Tetrodotoxin

C) Botulinum toxin

D) Saxitoxin

Back 122

C) Botulinum toxin

Front 123

Clostridium botulinum contains what enzyme that destroys peptide bonds?

Back 123

Endopeptidase (cleaves v-snare, blocking vesicle fusion)

Front 124

Each step of an action potential leading up to neurotransmitter release involves a type of ion channel. Name the 3 steps and the channels they involve.

Back 124

1) Initiation: Ligand-gated Na+ channels.

2) Propogation: Voltage-gated Na+ channels.

3) Neurotransmitter release: Voltage-gated Ca2+ channels.

Front 125

What 4 ions would be best to drive the coupled transport of a solute across the membrane?

Why?

Which is the only one that would move out?

Back 125

(Na+), (K+), (Ca2+) and (Cl-) are all good candidates for driving co-transport, since they have large concentration gradients.

K+ is the only one that would move OUT.

Front 126

What is coupled transport?

Back 126

an energy-requiring method of transporting molecules across the cell membrane that couples the movement of one ion with that of either another ion or a solute.
Unlike active transport, though, there is no direct coupling of ATP; instead, it relies on an electrochemical gradient. If the two substances are moving in the same direction (both into the cell or both out of the cell) it is called symport. If the two substances are moving in opposite directions (one moves into the cell while the other moves out) it is called antiport.

Front 127

What are the 3 key players in the uptake of glucose in the intestine?

Back 127

1) Na/glucose symporter on the apical membrane usine energy stored in the Na gradient to bring in glucose.

2) Glucose uniporter on the basolateral membrane.

3) tight junctions to restrict transport proteins to membrane domains.

Front 128

What are the ionic equlibrium potentials for Na+ and K+?

Back 128

find this out.

Front 129

What are stretch activated channels?

Back 129

Stretch-activated or stretch-gated ion channels are ion channels which open their pores in response to mechanical deformation of a neuron's plasma membrane. In mammalian hair cells, they can detect any combination of the following: detect vibration, pressure, stretch, touch, sounds, heat, volume, basically, movement. This detection changes the membrane potential.

Front 130

What's the difference between monounsaturated and polyunsaturated fat?

Back 130

monounsaturated contains 1 double bond; polyunsaturated contains 2/more.

Front 131

What is a 2-dimensional fluid (compared to a 3-dimensional fluid)?

Back 131

In a two dimensional fluid, molecules can only move in one plane. (Compared to molecule in a normal fluid that can move in three directions).

Front 132

dif between GRPs and TFs?

Back 132

they both bind DNA and they both affect transcription. BUT they affect it in different ways.

For TFs: Promoter regions (TATA box) upstream of the coding region bind general transcription factors. TFIID (a TF) bends the DNA molecule; it;s the only one that does this. TFs allows RNA polymerase to work.

Gene regulatory sequences bind gene regulatory proteins (which are specific kinds of transcriptin factors) ; together, they make a "genetic switch", which REGULATES DNA beyond simply allowing it. Genetic switches must ALWAYS come first before general transcription factors can even allow transcriptions; however, the gene regulatory sequences don't necessarily have to be upstream of the promoter region.