Week 1 Flashcards
(144 cards)
1
Q
How does the structure of cell membranes differ from that of organelle membranes?
A
There are variations in both membrane-associated proteins and phospholipids. And some organelles have membranes with two lipids bilayers.
2
Q
Name two types of phosphoglycerides found in the cell membrane.
A
Phosphatidylcholine and Phosphatidylserine
3
Q
What describes membrane lipids derived from Sphingosine?
A
Sphingolipids
4
Q
There are five major phospholipids distributed asymmetrically within the cell membrane bilayer, some live predominantly in the outer leaflet and some in the inner leaflet. Where do each of these live?
A
Outer leaflet: Phosphatidylcholine, Sphingomyelin
Inner Leaflet: Phosphatidylethanolamine, Phosphatidylserine, and Phosphatidylinositol.
5
Q
What happens when Phosphatidylserine, traditionally an intracellular phospholipid, flips its position to join the outer leaflet?
A
The lipid is recognized by immune cells and is quickly eliminated, marked for destruction. “Danger signal”
6
Q
True/False: Cholesterol is a five-ring structure, in which it is oriented parallel to the phospholipid tails so the hydroxyl group of cholesterol can interact with the phospholipid head groups.
A
False, because Cholesterol is actually a four-ring structure not five.
7
Q
How are Phospholipids amphipathic?
A
Phospholipids contain a hydrophilic polar phosphate head group and two hydrophobic non polar fatty acid tails, making them amphipathic.
8
Q
There two main types of membrane proteins: _____ and _____. Some may be anchored to the membrane via GPI (also define this) or lipid anchors.
A
1) Peripheral 2) Integral proteins
GPI - Glycophosphatidylinositol
9
Q
Peripheral membrane proteins are exactly what they sound, as far staying “outside” of the membrane, what are some of the functions a peripheral membrane protein may have?
A
Function as electron carrier, cytoskeletal elements or intracellular secondary messengers.
10
Q
Integral membrane proteins are _____ within the lipid bilayer. What do they function as?
A
Anchored.
Function as membrane receptors, enzymes, cell adhesion molecules, signal transduction proteins, and transporters.
11
Q
What are peripheral membrane proteins?
A
Peripheral membrane proteins are those that are noncovalently bound to other membrane proteins.
12
Q
Three types of transporters for proteins in the transmembrane.
A
1) Uniporter 2) Symporter 3) Antiporter
13
Q
What are the three factors that influence membrane fluidity?
A
1) Temperature 2) Saturation of phospholipid fatty acid tails 3) Cholesterol
14
Q
Will decreased saturation increase or decrease membrane fluidity?
A
Decreased saturation, meaning increased number of double bonds within fatty acid tails, will INCREASE membrane fluidity.
15
Q
What effect does cholesterol have on membrane fluidity as temperature increases or decreases?
A
Temp Increases: Cholesterol will decrease fluidity
Temp Decreases: Cholesterol will increase fluidity
16
Q
What is cell Polarity?
A
A property in which cell membranes exhibit spatial differences in shape, structure, and function within one cell type.
17
Q
What can Glycocalyx be thought of? Its functions: attachment, antigen-binding, cell-cell recognition, and protection from injury.
A
“Cell coat” - located on the outer surface of the plasma membrane and is the sum of the sugars associated with every proteoglycan on the cell surface.
18
Q
Where would you usually find lipid rafts? What do they help with?
A
You would find them in localized regions with elevated cholesterol and glycosphingolipid content in the cell membrane. More so where fatty acid tails are highly saturated (low fluidity).
Mostly, lipid rafts will help among the chaos, signal transduction.
19
Q
What are the major functions of the cytoskeleton?
A
Cytoskeleton supports cell structure, cell and organelle movement, and cell division.
20
Q
Which of the three types of protein filaments is the smallest?
A
Microfilaments (7nm)
21
Q
In respect to the cell, where would you find microfilaments?
A
Abundant in eukaryotic cells, yes, are found especially at the cell periphery.
22
Q
In what way do actin microfilaments display polarity?
A
In their assembly and disassembly, which occur at the positive (+) end where G actin is bound to ATP.
23
Q
Where would you find intermediate filaments in a cell?
A
Located throughout the cytoplasm.
24
Q
Do Intermediate filaments have polarity?
A
NO, and they do not require ATP for assembly.
25
Desmin, a type of intermediate filament, is found where?
Skeletal, cardiac, and smooth muscle. Framework lining the myofibrils and myofilaments. Desmin = muscle
26
Which type of intermediate filament, is found in glial cells of the brain, providing structural support to these cells in the nervous system?
Glial fibrillary acidic protein (GFAP)
27
Which type of intermediate filament is found in neurons, providing structural support for axons and dendrites, important for signaling?
Neurofilaments
28
If a patient's tumor is GFAP positive, what cell type must this cancer originate from?
Neuroglia, because GFAP is the intermediate filament of neuroglial cells.
29
Is it Microfilaments or Microtubules that form cell appendages like cilia and flagella?
Microtubules do! In fact, they are larger than microfilaments made up of alpha and beta tubular structures.
30
Do microtubules have polarity?
Yes! Each tubulin within binds two GTP molecules, forming the positive end, while the non-GTP binding end forms the negative end.
31
How can you remember whether it's the positive or negative end of microtubules that reaches toward the periphery or toward the nucleus?
Mnemonic: Negative end Near Nucleus
| Positive end Points to Periphery.
32
Microtubules also bind motor proteins necessary for transportation of vesicles. (It's used kind of like a highway) What are the names of the motor proteins? Do they use ATP?
Kinesin and Dynein
| Both use ATP
33
Which direction do these motor proteins move in the cell?
Dynein is retrograde transport (from periphery to nucleus)
| Kinesin is anterograde transport (From nucleus to periphery)
34
Can Cilia be nonmotile?
Yes, it can motile or nonmotile
35
What is the microtubule structure of motile cilia?
Motile cilia have a 9 + 2 microtubule arrangement, with 9 doublets surrounding 2 singlets
36
Oh the ways a cell can get injured! Let's think of one example, what happens there is decreased ATP production?
Without ATP cell swells. Without ATP, the Na+/K+ pumps are unable to function. What usually would maintain fluid homeostasis, does not, and water will follow salt, causing the cell swelling.
37
Another way a cell can be injured/die, what happens when Calcium pumps also fail? What organelles rely on the function of Calcium pumps?
Low Calcium pump function due to low ATP causes the buildup of Calcium in the cytosol, which activates specific mediators of apoptosis, initiating the cell-death process.
Two organelles: ER, Mitochondria
38
An irreversible type of damage that causes inflammation, as well as spilling lytic enzymes into the cytoplasm is due to ______.
Membrane damage, especially here lysosomal membrane damage.
39
One way to injure the cell again, messes with the cell's ability to transcribe and translate information. How it is released is from a damaged mitochondria. What are they?
Reactive Oxygen Species (ROS)
40
True/False: Necrosis is pathologic.
True
41
There are 6 different types of necrosis
Coagulative, liquefactive, gangrenous, caseous, fat, and fibrinoid
42
When apoptosis occurs, is there an inflammatory response?
No inflammatory reaction
43
True/False: Apoptosis is the only one out of the two death pathways that uses Caspase activation.
True.
44
Under what circumstance is apoptosis a physiologic process?
When embryogenesis occurs and certain cells must die to shape a particular anatomic structure such as fingers.
45
What circumstance would apoptosis use a pathologic process?
If they detect fatal DNA damage or irreparable problems of protein mis-folding.
46
In the Intrinsic Pathway, how does the cell undergo apoptosis this way?
What are the important proteins that kickstart this process?
The cell will basically kill itself.
The two pro-apoptotic proteins are (BAX/BAK), they overcome the anti-death proteins (Bcl-2), imitating the apoptosis cascade. Cytochrome C is also a factor, as it also activates the Caspase cascade, leading to cell death.
47
In the Extrinsic Pathway, what are the important receptors and proteins that play here?
First of all, extrinsic is activated by an external stimulus...by Fas/FasL receptor or cytotoxic T cell. Then executioner caspases finish the job.
48
The Eukaryotic postal service consists of what two organelles?
Rough Endoplasmic Reticulum and the Golgi Apparatus
49
What about the Smooth endoplasmic reticulum? Does it also take part in sorting and packaging and shipping of proteins?
No, not really, but it is important for detoxification and steroid hormone production.
50
Where is RER placed in the cell?
It's located throughout the cell, but is most concentrated right around the nucleus and near the Golgi Apparatus.
51
In RER, where there are studded ribosomes, what is the job of the ribosomes?
Involved in protein translation.
52
What is the RER analogous to, when its job is to fold, modify, and package proteins? Where does it send the proteins next?
Analogous to a warehouse.
| Next, it'll send the proteins to the Golgi Apparatus for further processing.
53
Where would there be a lot of RER? In what type of cell?
Cells that make a lot of secretory proteins, such as antibody-secreting plasma cells, are rich in RER, making them appear darker on staining.
54
The Smooth Endoplasmic Reticulum is responsible for:
Synthesizing ______ and ______ hormones. Fatty Acids and _______.
________ drugs and metabolites
Releasing ___ ions for muscle contraction.
Steroids, and steroid hormones, fatty acids, and phospholipids.
Detoxifying drugs and metabolites.
Releasing Calcium ions for muscle contraction.
55
Where would you find a lot of SER?
Ex: Hepatocytes, because one of their main roles is detoxification.
56
Where does the Golgi Apparatus sit in the cell?
Located close to the nucleus and the RER.
57
The Golgi apparatus is supported by cytoplasmic microtubules. What happens clinically if there is a deficiency of these microtubules?
Clinically, it will result in a type of achondrogenesis, a rare skeletal disorder characterized by short trunk, small limbs and narrow chest. (Fun fact, don't really have to know)
58
What is the cell's main processing and distribution center, analogous to the post office?
Golgi Apparatus
59
3 main sections of Golgi:
1) ____ - receiving dock, protein-containing vesicles from RER
2) ____ - main processing area, protein modifications occur
3) ____ - exporting dock, packs proteins into transport vesicles and sends them off.
1) Cis
2) Stack/Medial
3) Trans
60
What is the main function of the Golgi Apparatus?
Golgi apparatus' main function is to modify and package proteins it receives from the RER for transport to their final destination.
61
There is something called a signal peptide on proteins, and they are recognized by a signal recognition particle (SRP). In this analogy of the production line and warehouse, what is the use of the SRP? What does it traffic?
Traffics translating ribosomes and their products from the production line to the warehouse as if it is a forklift that take package.
62
What happens if an SRP is dysfunctional?
Proteins with a signal peptide accumulate in the cytoplasms, and never make their way to the RER and cannot function.
63
What happens to the signal peptide, if the protein is meant to be an RER membrane protein? Is it still needed?
Yes, the signal protein is left on the finished product to anchor it to the RER membrane, as opposed to being removed and releasing the free-floating peptide into the RER lumen.
64
When the Golgi is packaging all these proteins, what happens to those that have a hydrophobic transmembrane region? What happens to those that are free-floating?
Hydrophobic transmembrane region - they become cell surface proteins.
Free-floating - they are secreted into the extracellular space.
65
What happens to proteins that don't have a signal recognition particle?
These proteins complete their translation in the cytosol on free ribosomes. They remain cytosolic or get shipped off to organelles based on their specific localization sequences.
66
What role does the signal recognition particle (SRP) play in protein trafficking?
The SRP recognizes signal sequences on peptides early in the translation and transports the ribosome to the RER membrane to continue translation of the peptide into the RER lumen.
67
When is the term nucleoside used? Instead of nucleotide?
When there is no phosphate group attached to the nitrogenous base and the pentose sugar in the structure of DNA.
68
What type of bond is between the sugar and the nitrogenous base?
A Glycosidic bond
69
What type of bond links the nucleotides together connecting the 5' carbon of one and the 3' carbon of the other?
Phosphodiester bond
70
Nucleotides pair with each other via ______ bonds.
Hydrogen
71
Name the purines and pyrimidines that make up DNA. How do they pair with each other?
Adenine (purine) pairs with Thymine (pyrimidine); guanine (purine) pairs with cytosine (pyrimidine)
72
How many hydrogen between A-T? G-C?
```
A-T = 2 H bonds
G-C = 3 H bonds
```
73
Why does DNA associate with Histones?
Histones contain an abundance of positively charged amino acids (i.e lysine and arginine) that bind tightly to the negatively charged phosphate groups within DNA helices.
74
When DNA is wrapped around the Histone, what is this new unit called?
A nucleosome
75
When DNA is methylated, what happens?
| When Histones are methylated what happens?
DNA: Added methyl groups recruit proteins that repress gene expression.
Histone: 1 Methyl group, increases gene expression, 2 or more methyl groups, decreases gene expression
76
Recall: When there is a CpG site on DNA, that is an indication that there are lot of what?
Lot of Guanine and Cytosine residues, where epigenetic can occur.
77
What regulates the degree of chromatin condensation?
Methylation facilitates tighter coiling of DNA, condensing chromatin; acetylation loosens coiling.
78
Are Homologous chromosomes identical?
No, because they can contain different versions of a gene called alleles.
79
What protein keeps newly synthesized chromosomes organized and remain attached to each other before undergoing cell division?
Cohesins
80
What constitutes a metaphase chromosome?
Metaphase chromosomes are highly condensed DNA structures that result from supercoiling chromatin.
81
What is the use of a Telomere? Also describe what it is.
Every chromosome has at each end a Telomere, TTAGGG, and it prevents the degradation of portions of chromosomes that contain coding sequences (genes). Each time a cell divides, the telomeres of each chromosome shorten.
82
How can a cell maintain the length of a Telomere?
Stem cells contain the enzyme telomerase, which regenerates telomeres by adding more repetitions.
83
What is the name of the enzyme that dissociates the hydrogen bonds within base pairs to separate the strands of a helix?
Helicase
84
Which regions do you think Helicase tends to favor?
Regions rich in A-T base pairs, easier to pull apart.
85
How is DNA synthesis initiated?
Initiator proteins facilitate duplex opening at origins of replication and recruit helicase; this establishes a replication bubble where replicative enzymes can associate with each parent strand.
86
What proteins keep the newly separated DNA parent strands from re-bonding to each other?
Single-stranded binding proteins (SSBs) bind with newly separated parent strands, providing a physical barrier.
87
To alleviate the strain introduced by helicase, the enzyme _____, acts to unwind the helix ahead of replication fork.
Topoisomerase
88
In Polymerization, the enzyme class, ____ ______, create new phosphodiester bonds between free nucleotide and the growing polynucleotide. They add free nucleotides according to the sequence of the parent strand.
DNA Polymerases
89
What's the purpose of RNA primers?
DNA Polymerase can only elongate an existing polynucleotide. Once associated, DNA Polymerase always elongate the 3' end
90
In the lagging strand, where there is continuous use of RNA primers, what is the result called?
Okazaki fragments
| DNA polymerase is unable to follow steadily behind the helicase in the synthesis of a new daughter strand.
91
In which direction do DNA polymerases construct new DNA strands?
DNA polymerases synthesizes new strands in a 5' --> 3' direction by moving along the template strand in a 3' --> 5' direction.
92
In Eukaryotic DNA Polymerases, what are the types labeled? (3)
1) Alpha, 2) Delta 3) Epsilon
93
How are some species of DNA polymerase able to proofread?
Certain species of DNA polymerase possess 3' to 5' exonuclease activity, which allows them to remove any nucleotides that incorrectly incorporated and continue synthesis with the correct nucleotide.
94
One of the subunits of DNA pol alpha has __ _____ activity; allowing initiation of polymerization on the leading strand and for each Okazaki fragment.
RNA primase
95
True/False: DNA pol Alpha has low processivity.
| How is polymerization continued otherwise?
True
DNA pol delta and epsilon are recruited to complete synthesis of the leading strand and Okazaki fragment of lagging strand.
96
True/False: DNA pol delta and epsilon also have 3' to 5' exonuclease activity for proofreading purposes.
True
97
How are primers laid down in eukaryotes?
One of the subunits of DNA pol alpha has RNA primase activity, allowing it to initiate polymerization.
98
True/False: Prokaryotic chromosomes can have multiple origins of replication.
False, only eukaryotic chromosomes can have multiples.
99
Name two examples of eukaryotic promoter elements: 1) ____ and 2) ____
CAAT and TATA boxes
100
How far upstream do CAAT box and TATA box occur on a coding strand?
CAAT: 70-80 nucleotides upstream
TATA: 25-30 nucleotides upstream of gene's start site.
101
Enhancer sequences are good for?
Efficient initiation and elongation. The sequences recruit activating transcription factors that promote the recruitment of RNA polymerase II, up regulating expression of the target gene and therefore the resultant protein.
102
Silencer sequences do what?
Recruit represser factors that inhibit transcription, down regulating expression of the gene and resultant protein.
103
The template strand is sometimes referred to as: _____
| The coding strand is sometimes referred to as: _____
Template = Antisense
Coding = Sense
"Coding strand makes sense"
104
When RNA Polymerase II dissociates from DNA helix and RNA transcript is released, is the RNA transcript immediately ready to be translated into a protein?
In eukaryotes, no it's not.
The immediate product of transcription is heterogeneous nuclear RNA (hnRNA) or "pre-mRNA", and it requires modification before it's ready to be translated.
105
How is gene expression initiated and regulated?
Promoter sequence upstream from a gene recruit transcription factors, which then recruit RNA polymerase II. Distal regulatory sequences - i.e enhancers, and silencers - regulate expression.
106
Not only does the 5' cap protect mRNA from degradation by 5' exonuclease, but it also can serve as _____ factor for translation.
Initiating factor
107
Each intron has a 5' donor site (___) and a 3' acceptor site (__).
5'-GU site
| AG-3' site
108
What purpose do introns and exons serve?
Organisms make use of a process called alternative splicing to produce a range of unique but structurally related proteins.
109
What modifications occur to transform pre-mRNA into mRNA?
Splicing, and the addition of a 5' 7-methylguanosine cap, and 3'-poly(A) tail.
110
Two more types of RNA is used in the process of translation. What are they?
Ribosomal RNA and Transfer RNA
111
Which end of mRNA do ribosomes begin their translation?
5' end, with the assistance of helper proteins and initiation factors.
112
At which site of the ribosome, do charged tRNAs enter?
The A site
113
Which site of the ribosome holds onto the growing peptide chain?
P site
114
What is the name of the enzyme that catalyzes the charging process of tRNA using ATP?
Aminoacyl-tRNA synthetase
115
Two important functional sites in every tRNA: 1) ____ and 2) ____.
1) T-arm 2) D-arm
116
What does the T-arm help tRNA with?
Help tRNA enter the ribosome.
117
What is the D-arm used for?
Used by the aminoacyl-tRNA synthetase to ensure that the correct amino acid is charged to each tRNA.
118
What happens if a tRNA is charged with an incorrect amino acid?
They will still enter the ribosome and still pair with the codon, but will incorporate the incorrect amino acid into the elongating polypeptide.
119
What are the three types of RNA used during translation, and what function do they serve?
mRNA: RNA is the gene transcript to be translated.
rRNA: forms the ribosome that conducts translation.
tRNA: carry amino acids into the ribosomes, to ensure the growth of peptide chain.
120
In translation, how is the 5' end identified to begin it?
The 40s subunit recognizes the 5' cap or an internal ribosomal entry site to attach to the mRNA.
121
When do ATP and GTP provide energy during translation?
ATP: tRNA Activation (charging)
GTP: tRNA Gripping and Going (translocation)
122
When the ribosome encounters a stop codon, what enters the A site instead?
A release factor, to facilitate hydrolysis between the final amino acid and its tRNA in the P site. Disassembly.
123
Does the release factor (at termination of translation) require energy? From what?
Yes, from one GTP.
124
Does it matter where in the cytoplasm translation occurs?
In eukaryotes, yes. Depending on where a protein is intended to ultimately function, translation occurs via ribosomes either freely floating around or via ribosomes associated with rough endoplasmic reticulum.
125
Freely circulating ribosomes translate proteins meant for where?
Cytosol, nucleus, mitochondria, or peroxisomes.
126
Ribosomes bound to the RER translate proteins meant for where?
Proteins that are destined for secretion, retained in the RER or Golgi, trafficked by the lysosome, or bound by the plasma membrane.
127
What differentiates one amino acid from another?
The R group differentiates one amino acid from another.
128
How to remember the hydrophobic amino acids?
| Mnemonic: _______ stay insides so they don't get wet.
GLAMorous VIPs stay inside.
| Glycine, Leucine, Alanine, Methionine, Valine, Isoleucine, and Proline
129
How to remember the polar amino acids? Mnemonic.
Polar G CATS
| Glutamine, Cysteine, Asparagine, Threonine, and Serine
130
How to remember the basic amino acids:
Mnemonic:
More likely to retain or donate hydrogen ions at body pH?
His Arguments are Basic Lies: HAL
Histidine, Arginine, and Lysine
More likely to retain hydrogen ions at body pH.
131
How to remember the acidic amino acids:
Mnemonic:
More likely to retain or donate hydrogen ions at body pH?
Acidic Glue:
Aspartate, Glutamate
More likely to donate hydrogen ions at body pH.
132
What makes up the primary structure of proteins?
The sequence of amino acids in the polypeptide makes up the primary structure of proteins.
133
The secondary structure are a result of what kind of bonding?
Hydrogen bonds
134
The tertiary structure is formed because of interactions between the ____?
R groups of amino acids
135
The disulfide bond is a bond between what?
| What can it do?
A covalent bond between two cysteine amino acids, that can stabilize tertiary structure.
136
What level of protein structure do hydrophobic bonds have?
Hydrophobic bonds have tertiary structure.
137
What forces constitute the alpha-helices?
Hydrogen bonds between backbone elements constitute the alpha-helices.
138
When are Beta-strands parallel?
When the N terminus to C terminus direction is the same in two Beta-strands in a sheet.
139
To avoid steric hindrance in proteins folding, what two amino acids are found in these particular locations?
Glycine and Proline
140
Proteins fold to maximize bonding between what part of the amino acids?
Proteins are folded to maximize their hydrogen-binding potential.
141
What is a triple helix of three collagen alpha chain called?
Procollagen is a triple helix of three collagen alpha chains.
142
Necrotic cell death of tissues releases _____ in the blood. This is often used as a general marker of necrotic cell death.
Lactate Dehydrogenase (LDH) enzyme that converts lactate to pyruvate.
143
How can you detect Apoptosis in the lab?
You will see DNA fragmentation (Gel electrophoresis, by TUNEL, or Annexin 5 binding on phosphatidylserine)
144
Can Enhancers be located upstream AND downstream of a gene to be expressed?
Yes it can.
