Exam #1 Flashcards
(317 cards)
1
Q
What are the threepoints of the Cell Theory?
A
- All organisms are composed of one or more cells
- The cell is the structural unit of life.
- Cells can arise only from a preexistng cell.
2
Q
What are some properties of cells?
A
- complex, organized
- Use a genetic program
- Reproduce
- Acquire and use energy
- Carry out chemical reactions
- Engage in mechanical activities
- Respond to stimuli
- Self-regulate
- Evolve
3
Q
How do cells acquire and use energy?
A
ATP production through glucose (animals)
or
ATP production through photosynthesis (plants)
4
Q
How are chemical reactions catalyzed in a cell?
A
Enzymes
5
Q
What is the difference betwwen a catabolic and an anabolic metabolism?
A
Catabolic - big molecules —> small. Releases energy.
Anabolic - small molecules —> big. Requires energy.
6
Q
What is metabolism?
A
The summation of the total of all chemical reactions in the organism.
7
Q
How are materials within the cell transported from place to place?
A
microtubules, filaments
8
Q
How are cells able to respond to stimuli?
A
Have receptors on membranes that sense the environment and intiate responses.
9
Q
What are some examples of actions the cell can take in response to stimuli?
A
- Alteration of metabolic activities
- Preparing for cell division
- Moving from one place to another
- cell apoptosis
10
Q
What are some shared features of prokaryotes and eukaryotes?
A
- Plasma membrane
- Genetic info in DNA
- Mechanisms for transcription & translation
- Metabolic pathways
- Similar ATP synthesis
11
Q
What are features that are unique to eukaryotes?
A
- Nucleus
- Complex chromosomes within DNA & associated proteins
- Complex organelles
- Complex cytoskeleton with motor proteins
- Cell division mediated by microtubules
12
Q
What were the three discoveries that supported the hypothesis that DNA was the genetic material?
A
- Griffith: The transformation of bacteria through external DNA
- Avery, MacLeod & McCarty: Transformation agent was DNA
- Hershey and Chase: DNA, not protein, was the hereditary material.
13
Q
What are the two pyrimidines?
A
Thymine and Cytosine.
14
Q
What are the two purines?
A
Adenine and Guanine.
15
Q
What is Chargaff’s rule?
A
%Purines = %Pyrimidines %A = %T %G = %C
16
Q
How many hydrogen bonds do A-T have?
A
2
17
Q
How many hydrogen bonds to G-C have?
A
3
18
Q
What is the DNA backbone comprised of and what is the bond name that connects the backbone together?
A
Composed of alternating sugar and phosphate groups.
Backbone connected through 3’-5’ phosphodiester bonds.
19
Q
What is the Watson-Crick Model of DNA?
A
- 2 strands (duplex)
- Double helix structure
- Strands run antiparallel.
- Sugar-phosphate backbone is outside, nucleic bases are inside.
- Bases are planar and perpendicular to long axis.
- Two strands held together by hydrogen bonds.
- Purines pair with pyrimidines.
- Has major and minor grooves (has protein specificity)
- Two strands have complementary sequences.
- Phosphate gives DNA -charge.
- DNA stabilized by hydrophobic interactions and van der Waals forces.
20
Q
What is the difference between negatively supercoiled and positively supercoiled?
A
Negatively supercoiled: DNA is underwound
Postiviely supercoiled: DNA is overwound
21
Q
How do you fix supercoiling?
A
An enzyme called topoisomerase reduces the strain.
22
Q
What are the two types of topoisomerase and what is the difference between the two?
A
Type 1: create transient break in ONE strand of the duplex
Type 2: Create a transient break in BOTH strands
23
Q
What are the three possible models for replication?
A
- Semi-conservative
- Conservative
- Dispersive
24
Q
What is semi-conservative replication?
A
Each daughter has 1 parental and 1 newly synthesized strand.
25
What is conservative replication?
2 parental strands remain together and the daughter duplex contains only newly synthesized strands.
26
What is dispersive replication?
Parental strands are broken into fragments, and the new strands would be synthesized in short fragments and the old and new pieces will join together to form the duplexes.
27
How was the replication method of DNA determined?
Meselson & Stahl experiment.
- Parental with heavy 15 N, daughter with light 14N.
- DNA grown in 15N-ammonium chloride (only 15N DNA)
- Equilibrium sedimentation in 14N medium
- Hybrids of light and heavy seen and disappearance of heavy. Therefore, must be semi-conservative.
28
What is a major problem with unwinding the DNA duplex?
Supercoils form and DNA become more tightly wound.
29
What does DNA polymerase require to synthesize DNA?
1. A template
2. Needs a single strand portion
3. Needs a primer or a 3'OH terminus to begin on
30
Can DNA polymerase synthesize DNA on a single stranded circular DNA?
NO, because there is no primer or a 3' OH end.
31
If DNA pol can only synthesize 5'-->3', how does it synthesize the other antiparallel strand?
Semi-discontinuous replication:
- Leading strand assembled continuously
- Lagging strand assembled in fragements with primer and then joined.
32
How are the gaps in Okazaki fragments fixed?
DNA ligase removes the primer and seals it.
33
What is the function of DNA helicase?
Unwinds DNA
34
What is the funtion of Single stranded DNA-binding proteins (SSB)?
Keep unwound strands separated
35
What is the function of primase?
Synthesizes RNA primer
36
What is the function of the Beta clamp?
Keeps polymerase associated with DNA template
37
What is the function of the gamma clamp loader?
- Assembles the clamp around the DNA.
| - Loads the next Beta clamp on DNA for the next Okazaki fragment.
38
What is the function of the Tau subunits?
- Holds the core pols in the complex
| - Binds the helicase.
39
DNA polymerase I is a 3-in-1 enzyme. What are the three possible functions?
- 5'--->3' polymerase
- 5' ---> 3' exonuclease
- 3' ---> 5' exonuclease
40
What is the function of 5' --> 3' exonuclease?
Allows for removal of RNA primer of Okazaki fragment.
41
What is the function of 3' ---> 5' exonuclease?
Removes mismatched base pairs.
42
How is high fidelity maintained during replication?
- Accurate selection of nucleotides
- immediate proofreading by engaging 3'--->5' exonuclease activity
- proofreading (mismatched repair)
43
How is replication different in eurkaryotes from prokaryotes?
- replication in small portions at many sites (replicons)
| - Timing of replication related to the state of chromatin: Acetylated histones (early), highly compacted regions (last).
44
What is present at the eukaryotic replication fork?
1. DNA pol (sigma)
2. Sliding clamp (PCNA)
3. Clamp loader (RFC)
4. binding protein (RPA)
45
What are Telomeres?
Repeated sequences at the ends of chromosomes TTAGGG
46
What is the end replication problem?
Removal of 5' RNA primer leaves a gap on lagging strand---> duplexes will get shorter and shorter with each replication.
47
What is the central dogma?
DNA --> RNA ---> Protein
48
what enzyme is responsible for transcription?
DNA-dependant RNA polymerase (RNA polymerases)
49
How does Transcription begin?
With help from transcription factors, RNA pol attaches to the promoter.
50
How does Transcription proceed after the RNA pol binds to the promoter?
1. RNA pol moves along DNA 3' ---> 5' (DNA unwound)
2. RNA pol lays down complementary bases (RNA strand extends 5' ---> 3')
2. The helix reforms behind the polymerase
51
How long is the primary transcript (pre-RNA)?
As long as the DNA being transcribed
52
What are some similarities between RNA and DNA pol?
- both add bases according to Watson-Crick properties
- Direction of synthesis 3' ---> 5'
- Uses DNA template
53
What are some differences between RNA and DNA pol?
- RNA adds U instead of T
- DNA doesn't need primer
- Product is different (DNA or RNA)
54
In all mRNA precursors in eukaryotes, what polymerase is it transcribed by?
RNA pol II
55
What is the preinitiation complex (PIC)?
The complex formed when RNA pol II binds to promotor whith help from general transciription factors (GTF).
Occurs during transcriptional initiation.
56
What end of the preinitiation complex is phosphorylated and by what GTF?
The CTD (carboxyl-terminal domain) is phosphorylated on the RNA pol II by TFIIH
57
Once the CTD of the preinitiation complex is phosphorylated, what happens?
Triggers the release of the transcriptional machinery from the GTF and promoter ---> RNA synthesis begins
58
What are some properties of structure of mRNA?
1. sequences---> polypeptide
2. Found in cytoplasm
3. Attaches to ribosome in translation
4. 5' and 3' UTR
5. 5' cap and poly A tail
59
What is the purpose of the poly A tail?
Protection against degradation.
60
What are the functions of the 5' Methyl Guanosine cap?
1. Prevents 5' end from being digested by exonucleases
2. Aids in transport of the mRNA out of the nucleus
3. Important role in translation initiation.
61
5' Capping ocurs very quickly, but how does the 5' MeG cap form?
Capping enzyme recuited to the CTD of RNA pol II---> makes MeG cap
62
How is the 3' Poly A tail formed?
- Endonuclease cleaves the 3' end downstream of the recognition site AAUAAAA.
- Poly (A) Polymerase adds A to 3' end.
63
Where does all the polyadenylatiion, transcription, 5' capping and splicing occur in the cell?
In the nucleus
64
What is the difference between miRNA and siRNA?
miRNA:
- small fragments transcribed in genome
- involved in translation inhibition mRNA degradation.
siRNA:
- small double stranded fragments formed during RNAi
- siRNA is foreign.
65
miRNA regulate 1/3 of protein-coding genes. Through what three mechanisms does it achieve this?
1. Cause rapid mRNA degradation
2. Affect mRNA stability (de-capping)
3. Inhibit translation of mRNA
66
Does miRNA regulate just one loci and does it produce the same effects?
No, they can regulate many loci and produce different effects.
67
Does miRNA's encode protein?
No, they encode RNA only.
68
What is RNA interference (RNAi)?
A cell defense mechanism to degrade foreign RNA molecules, especially double stranded RNA.
69
How does RNAi work?
1, double stranded RNA triggers RNAi
2. Dicer cleaves double stranded RNA---> siRNA
3. siRNA bound by Argonaute (RISC)---> one RNA strand cleaved & discarded
4. The single stranded siRNA bound to RISC directs RISC to the RNA produced by virus.
5. Exact match causes RISC to cleave target RNA---> degradation.
70
What is the function of tRNAs?
- Carries the anticodon of the amino acid attached to an A on the 3' end.
- Bring proper amino acid to the RNA---> produces protein.
71
What is the effect of the unusual bases concentrated in the loops of the tRNA?
- disrupt hydrogen bonding
| - serve as potential recognition sites.
72
What is Crick's wobble hypothesis?
Pairing is only strict for first postions.
| Third position can be variable.
73
According to Crick's wobble hypothesis, U in anticodon, G in anticodon ad I in anticodon can pair with what bases?
U in anticodon---> G or A
G in anticodon---> C or U
I in anticodon---> U, C, or A
74
What is the advantage presented by the wobble hypothesis?
Fewer tRNAs.
75
What is the most complex synthetic activity in a cell?
Translation
76
How does Translation Intiation work?
1. mRNA binds to separate group of eIFs
2. 43S scans for AUG start codon on mRNA
3. 60S subunit joins the complex
5. Hydrolysis of two GTP forms complete 80S
6. Initiator tRNA binds to AUG at P site.
77
How does Translation Elongation work?
1. amino acyl-tRNA brought to A site by Elongation Factors (EF)
2. GTP hydrolysis---> ribosome conformational change
3. Peptide bond formation between amino acids.
4. Hydrolysis of GTP---> Movement of the ribosome one codon
5. tRNA in P exits from E---> new amino acyl-tRNA comes in A.
78
How does Translation Termination work?
1. Ribosome reaches a stop codon---> signals enlongation to stop.
2. eRF1 (release factor) enters at A site and recognizes the stop codon.
3. eRF3 ---> GTP hydrolysis---> cleaves the polypeptide chain from the tRNA at the P site.
4. mRNA dissocaties from ribosome and ribosome disassembles.
79
What are the levels of control of gene expression?
1. Transcription
2. Processing
3. Translational
4. Post-translational
80
What does transcriptional control determine?
Whether a gene will be transcribed and how often.
81
What are the two functional classes of Transcriptional factors (TF) and what function do they serve?
1. General TFs ---- Bind to promotor with RNA pol.
| 2. Sequence specific TFs ---- Bind to various sites of genes, act as activators or repressors of transcription.
82
What is the combinatorial control of transcription?
1. Genes have multiple binding sites and affinities from TFs.
2. Binding of multiple TFs---> transcription
3. Specific combination of TFs bound to regulatory elements determines the level of transcription.
83
How do TFs determine a cell's phenotype? Example?
- can direct cells to express a specific tissue.
| ex. MyoD---> tissue specific TF can direct cells to become muscle.
84
What are the two types of promoters?
1. Proximal Promoter elements
- Close to start site.
2. Distal promoter elements
- Farther from start site
- Alternate promoter pathway (transcription can occur at more than one site upstream)
85
What are the two types of proximal promoters and what is their function?
1. TATA --- Core promoter element; identifies start site where transcription complex assembles
2. CAAT, GC boxes ---- Determine frequency of transcription
86
Expression of genes can also be regulated by Enhancers. What are enhancers?
- Distant DNA elements that can be moved on DNA molecules.
| - Bind to TF's and stimulates transcription.
87
What is one property that distinguishes enhancers from promoters?
Enhancers are movable, can be inverted and will still exert their influence on transcription.
88
What happens if you delete and enhancer?
Your rate of transcription decreases drastically.
89
What are insulators? How does it work?
- DNA sequences that act as "boundary sequences"
- ISOLATE a promoter and its enhancer.
- Binds to the nuclear matrix ----> sequences between insulators loop out.
90
How is a transcriptional activator bound to an enhancer able to stimulate initiation at the core promoter?
Through co-activators.
91
What do the two types of co-factors do?
1. Interact with components of basal transcription machinery
| 2. Modify the chromatin to make it more accessible to transcription machinery.
92
What are examples of the first classification of co-activators (interact with basal transcription at core promoter)?
- TAFs = TBP associated factors
| - Mediator: interacts with RNA pol II
93
How does the modification of chromatin strucutre regulate transcription?
The more tightly wound the chromatin is, the less accessible it is to DNA machinery. (decrease in transcription)
94
Histone Modifications allow a way for DNA to be more accessible to transcriptional machinery. How do Histone modifciations work? What is an example?
Covalent modifications to the N-terminal tails of histones affect chromatin structure & function.
ex. H3K9--> methylation leads to compaction and transcriptional silencing
95
What is DNA methylation, how does it work and what is its function?
- DNA methylation is the methylation of Cytosine (CG-rich islands on the promoter)
- Causes gene repression.
- Catalyzed by DNA methyltransferases (DNMT)
96
What are the two types of processing level-control?
1. Alternative splicing of mRNAs
| 2. RNA editing.
97
Through what mechanisms does alternative splicing of mRNAs alter gene expression at the processing level?
1. Sequences in RNA (splicing enhancers) can lead to the use of "weak" splice sites---> exon can be included or excised.
2. Can generate several polypeptides from a single gene---> different protein produced.
3. Exon skipping---> could skip over faulty sections, end up with normal phenotype.
98
How does RNA editing alter gene expression at the processing level?
- Specific nucleotides converted to other nucleotides
| - Creation of new splice sites, stop codons and amino acid substitutions.
99
What is the translational level control of gene expression?
Involves the regulatory mechanisms affecting the tranlation of mRNAs.
100
Wht are some examples of translational level control of gene expression?
1. Cytoplasmic localization of the mRNAs
2. Translational activation
3. Stability of the mRNA
4. miRNA mediated silencing.
101
How does iron concentration affect gene expression at the translational level?
- Ferritin mRNA regulated by repressor Iron Regulatory Protein (IRP)
- in low [Fe], IRP binds to the iron-response element (IRE) at the 5' UTR---> prevents binding of ribosome---> prevents transcription
- in high [Fe], IRP changes conformation---> released from IRE---> translation can start.
This determines whether protein is produced ----> affects gene expression.
102
How is mRNA localized and how does cytoplasmic mRNA localization affect gene expression at the translational level?
- 3' UTR determines localization
- microtobules and motor proteins transport mRNA
- depending on the localizaion, a certain part is developed
103
How does mRNA stability affect gene expression at the translational level?
- The longer an mRNA is present in the cell ---> longer it serves as template .
104
What happens when there is only 30A residues left in the poly A tail?
1. Poly A tail removed at 3' end---> mRNA decapped by decapping enzyme ---> 5' to 3' exonuclease degrades message. (Occurs in P-bodies: cytoplasmic granules)
OR
2. Removal of Poly A tail ---> Digestion of mRNA from 3' end by 3' to 5' exonucleases (exosome)
105
What is miRNA mediated gene silencing and how does it affect gene expression at the translational level?
1. miRNA pairs with 3'UTR sequence: perfect match ---> degradation, sort of match---> inhibition of translation
2. suppresses gene expression:
- promotes mRNA deadenylation & degradation
- inhibits initiation and elongation (translation)
- degradation of nascent polypeptide
106
What is the post-translational level of control in gene expression?
Protein stability
107
What is an example of a post-translatioinal level of control?
Protein ubiquitylation
108
What is protein ubiquitylation? How does it work?
It's a mechanism for tagging proteins for proteosomal degradation:
1. Ubiquitin monomers are attached to lysine residues of proteins.
2. Cap proteins on proteosome recognize polyUbq-protein, removes Ubq and unfolds target protein.
3. Protesome digests the protein into small peptides
4. Peptides released to cytosol and degraded to amino acids.
109
What is the function of the nuclear envelope?
A barrier that separates the genetic material in the nucleus from the cytoplasm
110
What are the functions of the Nuclear Lamina?
- Gives shape and mechanical stability
| - Directly interacts with chromatin.
111
What types of molecules move across the nuclear envelope?
- RNA
- Replication, transcription machinery
- Histone proteins
- viral DNA
112
What is the function of the FG nuceloporins in the NPC?
Line up in the channel and forms a mesh to block the free dffusion of larger macromolecules.
113
How does the cell know what to pass through to the nucleus?
If the cell contains a Nuclear Localization Signal (NLS), the proteins is able to pass through the nuclear pores and enter the nucleus.
114
What are the steps of transport through the NPC?
1. Cargo protein with NLS binds to importin α/β in cytoplasm---> receptor-cargo complex.
2. receptor-cargo complex docks with the cytoplasmic filaments that extend from the NPC cytoplasm ring
3. receptor-cargo complex moves throug the nuclear pore by ingaging with FG domains of the FG-containing nucleoporins.
4. In the nuclear compartment, complex interacts with Ran-GTP---> disassembly and release of cargo.
5. Importin β is bound by Ran-GTP and shuttled back to the cytoplasm. Ran-GTP is hydrolyzed into GDP and transported back to the nucelus to be made into Ran-GTP again.
6. Importin α is bound to exportin and sent back to the cytoplasm.
115
What are the two types of transport receptors and how are they different?
Importins move macromolecules from cytoplasm---> nucleus
Exportins move macromolecules from nucleus---> cytoplasm
116
What is the respective level of concentration of Ran-GTP in the cytoplasm and nucleus?
Cytoplasm: low
Nucleus: high
117
What is the function of GEF?
Promotes conversion of Ran-GDP---> Ran-GTP in the nucleus.
118
What is the function of GAP?
Promotes hydrolysis of Ran-GTP ---> Ran-GDP in the cytoplasm.
119
What is the function of the Nuclear Matrix.
1. Maintain shape of nucleus and organize chromatin
2. Anchor machinery for replication, transcription and RNA processing
3. Provides the means to which segments of chromatin can acquire or mainain oepn conformation for transcription.
120
What is the function of the nucleolus?
Site of RNA synthesis.
121
How is DNA packaged into chromatin?
1. DNA wraps around histones---> nucleosomes
2. Nucleosomes organize--->30 nm fiber
3. In interphase the 30 nm fiber form chromatin loops maintained by cohesin.
4. As cells prepare for mitosis, loops become further compacted into mitotic chromosomes
122
What is the difference between euchromatin and heterochromatin?
Euchromatin returns to a DISPERSED state after mitosis
Heterochromatin remains COMPACTED during interphase.
123
What are the two types of heterchromatin?
1. Constiuitive = remains compacted at all times. (DNA permanently silenced)
2. Falcultative = specifically inactivated at certain times in certain cells.
124
How do you know that the nucleus is an organized structure?
- Each chromosome occupies a distinct territoy in the interphase nucleus.
- location within nucleus related to activity (chr 18 and 19 stains)
125
What determines the ability of charged and uncharged solutes to move across membranes?
charged: concentraction and electrical gradient (electrochemical gradient)
ucharged: concentration gradeitn and ability of the molecule.
126
What types of solutes are highly permeable?
1. Less polar molecules
| 2. Small inorganic molecules (O2, CO2, H2O, NO
127
What are the 4 different ways to move substances across membranes?
1. Simple diffusion
2. Diffusion through channels
3. Facilitated diffusion
4. Active transport
128
What is diffusion?
Spontaneous process by which a substance moves from high to low concentration.
129
What is simple diffusion?
Movement of small uncharged molecules from high to low concentration.
130
What is osmosis?
Movement of water from a region of low solute concentration to a region of higher solute concentration.
131
What is conductance?
The movement of ions across the membrane through ion channels
132
What kind of solutes emlploy diffusion through channels and how?
Ions.
They use ion channels---> conductance to get across.
133
Ion channels respond to certain stimuli to open. What are the three types?
1. Voltage-gated: difference in ionic charge
2. Ligand-gated: binding of specific molecule
3. Mechano-gated: mechanical forces
134
How does the K+ ion channel operate?
- K+ gate responds to LOW pH
- gating accomplished by conformational changes
- selects K+ over Na+, oxygen atoms of the carbonyl groups in the channel interact with K+ only.
- 2 carbonyl occupied at a time, no energy input needed
135
What is the difference between the two types of transporters?
1. Facilitative: catalyze transmembrane movement of solute from one side to the other.
2. Active: transports specific solute against concentration gradient using ATP
136
How does faciliated diffusion differ from simple diffusion?
- Diffusion rate increased
- Specific and passive (high---> low)
- can mediated solute movement in BOTH directions
137
What are steps the Na+/K+ pump undergoes?
** Each ATP hydrolyzed: 3Na+ out, 2K+ in
1. Pump in E1 (binding sites open) on cytoplasmic side. 3NA+ and ATP bound
2. occluded E1 (Na+ cannot flow back into cytosol)
3. Hydrolysis of ATP. E1---> E2
4. Binding sites open to extracellular, E2 releases 3Na+
5. Protein binds 2K+
6. Becomes occluded E2
7. Dephosporylation
8. ATP binds--> E1, 2K+ released
* ** Note, ATP is not used to release K+. ATP just causes the conformational change. It is only used in releases Na+
138
What is the difference between a channel and a transporter?
1. Channel: translocation of ions with littel energetic interaction between channel protein and ion
2. Transporters: involve selective recognition of ion, conformational changes in proteins due to binding of ion, coupling conformational changes to movement of ions.
139
What is cotransport?
Established concentration gradients have potential energy that can be used to transport other solutes (secondary transport). Couples the movement of TWO solutes.
140
What is secondary transport?
Couples transport with the enegy of an electrochemical gradient.
141
What is symport and antiport?
Symport: solutes moved in same direction
Antiport: opposite direction
142
What are exchangers?
porteins that act as antiports
143
What are the functions of the plasma membrane (PM)?
1. compartmentalization
2. scaffold for biochemical activities
3. selectively permeable barrier
4. transorting solutes
5. responding to external signals
5. intercellular interaction
144
How does the PM perform compartmentalization?
Encloses the contents of the cell.
145
How does the PM act as a scaffold for biochemical activities?
- Provides framework for biochem interactions.
| - Orders components for more effective interactions
146
How does the PM act as a selectively permeable barrier?
- Prevents unrestricted exchange of materials
| - means of communication between compartments
147
How does the PM transport solutes?
Contains machinery to transport solutes (amino acids, sugars, ions) across the membrane
148
How does the PM respond to external stimuli?
Have receptors that respond to different types of stimuli.
149
How does the PM act in intercellular interactions?
Allows cells to recognize and signal one another to exchange materials via cell-cell junctions.
150
What is the fluid mosaic model?
1. A lipid bilayer with hydrophillic OUT, hydrophobic IN.
2. Membrane proteins are a mosaic of discontinuous particles that penetrate the sheet.
3. lipids and proteins mobile and can interact with other membrane molecules.
151
The membrane lipids are said to be _____ because they have both hydrophilic and hydrophobic regions, usually a polar head and a non-polar tail.
Amphipathic
152
What are the three types of membrane lipids?
1. phosphoglycerides
2. sphingolipids
3. cholesterol
153
What are phosphoglycerides?
- Diglyceride with 3rd OH attached to phosphate.
| - Built on glycerol backbone
154
What are the additional groups that can be attached on the phosphate (polar head group) in phosphoglycerides?
phosphatidyl-
1. PC - choline
2. PS - serine
3. PE - ethanolamine
4. PI - insitol
155
What are sphingolipids?
- sphingosine (amino alcohol on carbon chain) + fatty acid
-
156
Why is the terminal alcohol of sphingolipids interesting?
Different sphingolipids have additional groups esterified on OH.
157
What are glycolipids?
Sphingolipids that have a carbohydrates (sugars) esterified to the terminal OH.
158
What role do glycolipids play?
Important in the nervous system.
159
What is cholesterol?
- flat, rigid hydrophobic molecule
| - has a single OH group that is embedded in the lipid bilayer
160
What is the function of cholesterol?
Affects membrane fluidity by restricting movement of fatty acyl chains.
161
How is the plasma membrane asymmetrical?
PC and glycolipids are found in the outer leaflet
| PS ad PE are found in the inner leaflet
162
Why are glycolipids found exclusively in the outer leaflet of the PM?
probably serve as receptors for extracellular ligands.
163
Why is PS found in the inner leaflet?
produces a net negative charge as physiological pH---> good for binding positively charged residues.
164
What happens when PS appears in the outer leaflet of aging lymphocytes in the PM?
Signals for destruction by macrophages
165
What is the function of carbohydrates?
Assist in identification and specificity of interactions.
166
What is glycosylation?
The addition of a carbohydrate.
167
Where does glycosylation mainly occur?
In the lumen of the ER or the Golgi body.
168
What are the three types of membrane proteins?
1. integral
2. peripheral
3. lipid-anchored.
169
What are integral membrane proteins?
They are transmembrane proteins that contain either alpha-helices or beta sheets.
170
What are transmembrane proteins?
Proteins that pass entirely through the lipid bilayer and have domains that protrude from both the extracellular and cytoplasmic sides of the membrane.
171
Why are the transmembrane domains very hydrophobic?
Can interact with hydrophlic fatty acyl interior of bilayer---> preserve premeability barrier.
172
When are the integral membrane proteins glycosylated and form disulfide bonds?
When they are exposed to extracellular space
173
What are peripheral membrane proteins?
- located entirely on inner or outer surface of membrane.
| - via interactions with lipid head groups.
174
Are peripheral membrane proteins permanent?
No, they are transient.
175
What are the functions of peripheral membrane proteins?
Provide support, coat proteins or enzymes.
176
What are lipid-anchored proteins?
- Proteins that are located outside the lipid bilayer, on either side
- covalently linked to a lipid moleculate that is situated within the bilayer.
177
What functions can lipid anchored membrane proteins serve?
Various receptors, enzymes, cell adhesion, and signalling proteins.
178
The PM has various membrane domains. What does that mean?
Different regions in the PM carry out different functions.
179
What is the transition temperature?
The temperature at which the membrane changes from a fluid state to a frozen gel-like state.
180
What affects membrane fluidity? How?
1. Temperature ( lower temp = less fluidity)
2. Number of chains (shorter chains = lower TS)
3. Saturation (More unsaturation = lower TS)
3. Cholesterol (abolishes transitions and promotes fluidity)
181
Why is membrane fluidity so important?
- maintains function
- provides a compromise between rigid ordered structure and completely non-viscous liquid
- allows for interactions to take place in the membrane
- key role in membrane assembly
- needed in many basic processess (ex. endocytosis, secretion, division etc.)
182
What are the 6 ways integral membrane proteins can move?
1. diffuse randomly throughout the membrane
2. fixed by interaction with "membrane skeleton"---> composed by peripheral proteins which form a mesh
3. moves in a certain direction because of interaction with motor proteins on cytoplasmic side
4. restricted by other integral membrane proteins
5. restricted by "fences" formed by the membrane skeleton
6. restricted by extracellular materials
183
How do you determine the movement of membrane proteins?
Through FRAP
184
In what ways can phospholipids move?
1. diffuse laterally
| 2. transverse diffusion (flip flop)
185
Some phospholipids can move across the membrane rapidly. What kind of phospholipids can do this?
Lipids lacking polar groups (ex. cholesterol)
186
What is the endomembrane system?
The membrane system within the cell, the individual components function together as a coordinated unit.
187
How are material transported between organelles in a cell?
By transport vesicles.
188
How do transport vesicles work?
Transport vesicles carry the cargo and bud from the donor membrane compartment, move through the cytoplasm pulled by motor proteins which fuse into the membrane of the acceptor membrane , releasing the cargo.
189
What are the two pathways through the cytoplasm?
1. biosynthetic/secretory pathway
| 2. endocytic pathway
190
What are the two types of secretion of the biosynthetic/secretory pathway (exocytosis)?
1. Constitutive
| 2. Regulated
191
What is the difference between constitutive and regulated secretion?
Constitutive: materials discharged into extracellular space by vesicles which contribute to the formation of the extracellular matrix and the PM and other organelles.
Regulated: materials stored in membrane bound packages and only released after stimulus.
192
What is the difference between the biosynethetic and the endocytic pathway?
Biosynthetic: materials move OUT of cell. ER--> Golgi---> other destinations (PM, lysosome)
Endocytic: materials move INto the the cell. Outside ---> cell---> endosomes and lysosomes.
193
Why are endosomes and lysosomes good at processing endcytosed materials?
The low pH and degradative enzymes are good at processing endocytosed material.
194
What are the two types of endoplasmic reticulum (ER) and how do they differ in composition?
1. Rough ER (RER) : contiuous with nuclear envelope with ribosomes, composed of a network of cisternae
2. Smooth ER (SER) : Tubular strucutres that forms a network of pipelines through the cell which are able to bend.
195
What are the functions of the SER?
- steroid hormone synthesis in the gonads or adrenal cortex
- detoxification of ethanol and organic compounds in the liver
- sequestration of calcium ions in muscle cells--> forms sarcoplasmic reticulum. Regulated release of calcium triggers contraction
196
What are the functions of the RER?
- protein synthesis
197
What are the two ways that proteins can be synthesized?
1. Membrane bound: in the ER
| 2. Free ribosomes: in the cytoplasm.
198
What kind of proteins are synthesized in the RER?
- integral membrane proteins
- soluble proteins to be secreted
- soluble proteins that will reside within organelles
199
What kind of proteins are synthesized in the cytoplasm?
- Enzymes
- cytoskeletal proteins
- peripheral proteins of inner PM
- proteins destined for the nucleus
- proteins to be incorporated into the mitochondria and peroxisomes.
200
What is the signal hypothesis?
Proteins have built in address codes that direct them to the cytoplasm or the RER.
201
How does a cell know where the protein should be synthesized?
Secretory proteins have a sequence of amino acids on the N terminus that directs the emerging polypeptide and ribsome to the ER membrane.
202
What happens when the protein's DNA sequence don't contain a code that translated to a signal sequence?
It will be synthesized in the cytoplasm.
203
How are proteins synthesized in the RER?
1) Synthesis begins on free ribosomes---> produces nascent polypeptide--> signal sequence emerges---> SRP binds--> translation arrested.
2) SRP-ribosome binds to an SRP receptor on ER membrane.
3) Ribosome binds to translocon on ER---> SRP released---> signal protein binds to interior of translocon
4) contact between nascent polypeptide inside translocon--> plug displaced---> channel open --> Polypeptide enters ER lumen ---> signal peptide is cleaved ---> protein is folded
204
How are the new proteins processed in the ER (as soon as it enters the RER cisterna)?
1. signal peptide is removed by signal peptidase.
2. Addition of carbohydrate (important to protein function and aids in proper folding)
3. Molecular chapertones in ER Lumen assist in proper folding
4. Protein processing enzymes in ER reduces cysteine residues on proteins entering lumen and join residues into disulfide bonds of proteins leaving ER.
205
Where are the newly synthesized proteins and lipids inserted?
Existing membranes in ER.
206
Where are lipids made? Any exceptions?
In the ER
Exceptions:
- sphingomyelin and glycolipids (synthesis begins in ER, completed in Golgi)
- unique mitochondrial lipds (synthesized by enzymes on mitochondrial membrane)
207
Where are phospholipid synthesis enzymes located?
ER. They are ER integral membrane proteins.
208
What is the order in which membrane components move from the ER to other compartments?
ER ---> Golgi---> transport vesicles ----> PM
209
How is membrane asymmetry maintained in the ER?
- As each protein is made it is instered into the lipid bilayer in a particular orientation (carb on luminal side).
- orientation is maintained as it travels through endomembrane system
- Carbohydrate modifications in ER always stay on the LUMINAL side of ER which become the extracellular side of the PM after the fusion of the vesicles.
210
Nearly all proteins produced on membrane bound ribosomes become what kind of protein?
glycoproteins
211
How are glycoproteins synthesized? (N-linked Glycosylation in the ER)
1) Lipid carriers (dolichol phosphate, DP) accept sugar molecules by glycosyltransferases
2) pre-assembled block of sugars is transferred from DP to certain asparagine residues on the nascent polypeptide. ---> modifications---> glycoprotein
212
What does the quality control in the ER screen?
Whether or not the glycoprotein is fit enough to move on to the next compartment of the biosynethetic pathway. Ensures misfolded proteins do not proceed forward.
213
What are the steps in Quality Control in the ER?
1) 2 of 3 glucose residues removed from protein
2) Bound by chaperone calnexin or calreticulin
3) Glucosidase removes final glucose to release from chaperone
4) motitoring enzyme UGGT recognizes misfolded proteins, adds back a glucose
5) protein re-enters cycle
6) If correct, protein exits cycle
7) If after many tries it is still not, it is destroyed.
214
How does the monitoring enzyme UGGT work?
Misfolded proteins have hydrophobic residues that UGGT recognizes.
215
How are the misfolded proteins dealt with?
They are not destroyed in the ER, but are dislocated to the cytosol where they are ubiquitinated and degraded by the proteosome. (ER associated degradation, ERAD)
216
What is the unfolded protein response (UPR)?
A plan of action triggered after the accumulaion of misfolded proteins.
217
How does the UPR work?
1) ER has sensor proteins kept inactive by BiP
2) High levels of misfolded proteins---> pulls BiP from sensors---> activation of UPR
3) dimerization of sensor (PERK) --> becomes acivated protein kinase ---> phosphorylates eIF2
4) phosphorylated EIF2 is inactive ---> inhibition of protein synthesis.
218
What is the alternate mechanism of UPR?
1) ER has sensor proteins kept inactive by BiP
2)High levels of misfolded proteins---> pulls BiP from
sensors---> activation of UPR
3) Release of BiP allows sensor (ATF6) to go to Golgi complex ---> cytosolic domain of protein cleaved away
4) Cytosolic portion of sensor diffuses through cytosol---> nucleus
5) Stimulates the expression of genes to alleviate ER stress
219
What are the three functionally distinct regions of the Golgi complex?
Cis-Golgi Network (CGN)
Cis, medial and trans cisternae
Trans-Golgi Network (TGN)
220
What is the function of the CGN?
Acts as a sorting station that determines which proteins need to go back to the ER and which need to be processed by the next Golgi station
221
What is the function of TGN?
Sorting station where proteins are sorted into various vesicles intended for either the PM or various intracellular destinations
222
How do proteins proceed through the Golgi and what happens along the way?
Proteins pass through one cisternae to the other until they reach TGN. Modifications happen along the way.
223
How does glycosylation work in the Golgi?
- Similar to RER, spatial location of transferases determines how sugars are added
- N-linked glycoslylaion begins in the ER, but is modified in Golgi
- Unlike ER, Golgi glycoslyation is varied ---> diversity
- O-linked glycoslyation happens entirely in the Golgi
224
What are the two different ways to move through the Golgi?
1) Vesicular transport model
| 2) cisternal maturation model
225
What is the vesicular transport model through the Golgi?
- Cargo move cis to trans in vesicles that bud from one membrane---> fuse with a neighbouring compartment farther along the stack.
- Anterograde (forward) movement
226
What is the cisternal maturation model of the Golgi?
- Cisternae move cis to trans---> disperse at the TGN.
- Vesicles move cargo proteins in a retrograde (backgwards) direction.
- Enzymes that characterize each cisternae are sent back to lower cisternae ---> large cargo carried along with moving cisternae up.
227
What is the difference between the vesicular transport model and the cisternal maturation model?
The cisternae in Vesicular stay stable, but in Cisternal they move.
Vesicular is anterograde direction (forward) and Cisternal is retorgrade direction (backgward)
228
In what are materials in the biosynthetic/secretory pathway transported in?
Protein coated vesicles.
229
What purpose does the protein coat on the vesicles serve?
1) mechanical device that curves membrane to form a budding vesicle
2) mechanism for selecting components to be carried by vesicles.
230
What are the three classes of coated vesicles?
1) COPII
2) COPI
3) Clathrin-coated vesicles
231
What is the difference between COPII, CPI and Clathrin-coated?
COPII moves material forward from ER ---> ERGIC (ER-Golgi intermediate compartment) ---> Golgi complex
COPI moves material retrograde from Golgi ---> ERGIC ---> ER
Clathrin-coated moves material from TGN onwards or PM ---> cytoplasmic compartment via endocytic pathway.
232
What function do the antibodies to the COPII coat proteins serve?
Block budding from ER, but no effect on movement of cargo elsewhere.
233
What proteins do COPII vesicles select?
- Enzymes that act later in pathway
- Membrane proteins for docking/fusion to target membrane
- Membrane proteins that can bind soluble cargo (ex. cargo receptors that bind secretory proteins)
234
How is the COPII coat assembled?
1) Sar 1 recruited to ER membrane by GEF (catalyzes GDP---> GTP)
2) Conformational change in Sar 1-GTP causes it to insert into cytosolic leaflet ---> induces curvature in membrane
3) Dimer of 2 COPII proteins (Sec 23 & Sec 24) are recruited by Sar 1-GTP ---> induces more curving.
4) Sec 24 interacts with ER export signals in cytosolic tails of cargo receptor proteins ---> bind cargo on luminal side
5) Sec 13 and Sec 31 bind to form the outer cage of the protein coat.
235
How is the COPII coat disassembled?
1) Hydrolysis of bound GTP ---> Sar 1-GDP ---> decreased affinity for the vesicle membrane
2) Dissociation of Sar 1-GDP is followed by the release of COPII proteins.
236
Why is it critical for the COPII coat to be disassembled first before fusion to acceptor membrane?
If the coat remains, it will not fuse to the acceptor membrane.
237
What material does the COPI coated vesicles move from the Golgi ---> ER?
- Golgi resident enzymes in a trans --> cis direction
| - ER resident enzymes from the ERGIC and the Golgi back to the ER
238
How is the COPI coat assembled?
Arf 1 plays similar role as Sar 1 in COPII vesicles
| Arf 1-GTP also needs to be hydrolyzed to GDP for disassembly of COPI coat.
239
if vesicles continuously bud from membrane compartments, how does each compartment retain its unique composition?
- Retention of resident molecules (based on physical properties)
- Retrieval of escaped molecules
240
How are escaped ER proteins retrieve by COPI vesicles?
1) Solule ER proteins (ex. BiP) bear an ER retrieval sequence on c terminus (KDEL)
2) escapted proteins are recognized by KDEL receptors in the Golgi---> recruit COPI proteins---> return to ER
241
How is the clathrin-coated vesicle assembled?
1) Like COPI, Arf 1 is involved in coat assembly
| 2) Coats are shed after budding and uncoated protein proceeds to destination
242
Where are Clathrin-coated vesicles present?
At the start of the endosomal pathway (TGN and PM)
243
Clathrin-coated vesicles that bud from TGN contain a GGA adaptor protein. What is its function?
GGA adaptor protein has several binding domains:
1) binds to cytosolic tails of membrane proteins (ex. manose-6-phosphate receptors) important for lysosomal transport
2) Binds to Arf 1-GTP
3) Clathrin molecules
244
How do lysosomal proteins leave the Golgi complex?
Lysosomal enzymes are made in ER and carried to Golgi
1) In Golgi, mannose residues on lysosomal enzymes are phosphorylated
2) mannose 6-phosphate acts as a sorting signal recognized by MPRs on the TGN membrane which are then incorporated into clathrin vesicle.
3) mannose 6-phosphates interact with lysosomal enzyme on luminal side and the adaptors on the cytosolic side
4) Clathrin coat disassembles and the MPRs dissociate with their ligands
5) MPRs return to TGN
6) lysosomal proteins proceed to endosomes and then lysosomes
7) MPRs on PM capture lysosomal enzymes in the extracellular space and set them on the right path to the lysosome.
245
What are the three methods in which proteins are sorted at the TGN?
1) Regulated secretion
2) Constitutive secretion
3) lysosomal proteins undero phosphorylation and are recognized/captured by MPRs
246
What is regulated secretion?
Proteins mature from the TGN and form dense vesicles that stay in the cytoplasm until a stimulus triggers them to fuse with the plasma membrane, resulting in release of vesicle contents.
247
What is constitutive secretion?
The delivery of integral proteins to the PM is based on sorting signals in htheir cytopasmic domains. In different polarized cells, different sorting signals direct proteins to different domains (apical, basal, lateral)
248
What is the main difference between regulated and constitutive secretion?
Regulated needs a stimulus
| Constitutive needs a signal.
249
What is exocytosis?
Fusion of secretory vesicle with PM leading to discharge of its contents.
250
How does membrane fusion work?
GTP-Rab proteins on vesicle and target membrane recruit tethering proteins
1) Vesicle docks via interactions between v-SNARE (vesicular) and t-SNARE (target)
2) possible transition state
3) Fusion complete, SNAREs reside on same membranes
4) Fusion pore opens allowing dischage of material
251
What determines the specificity of the interaction between a particular vesicle and target membrane?
Specific combination of interacting protein: tethering proteins, Rabs, and SNARES
252
What are lysosomes?
Digestive organelles that contain enzyes capable of breaking down biological macromolecules to its individual components.
253
Why do lysosomal enzymes have an optimal pH of 4.6?
Because it's interior is acidified by H+ATPase (proton pump in the membrane of the lysosome)
254
What is the function of lysosomes?
1) break down materials brought into the cell from extracellular environment
2) Autophagy
255
What is autophagy?
The turnover of organelles where organelles are degraded and replaced
256
How does autophagy work?
1) organelle is surrounded by double membrane (phagophore)
2) outer membrane of phagophore fuses with lysosome---> becomes autolysosomes---> leads to degradation
3) After digestion, becomes a residual body
4) residual body exocytosed or resides in cytoplasm as a pigment granule
257
After exocytosis, which side of the cytoplasmic vesicle becomes the outer surface of the PM upon exocytosis?
Luminal side of the cytoplasmic vesicle.
258
What is endocytosis?
The opposite of exocytosis: mechanism for the utake of fluid and solutes INTO a cell.
259
What are the two types of endocytosis and what are they?
1) Bulk phase endocytosis: constitutive, non-specific uptake of extracellular material and recycling of the plasma membrane
2) receptor-mediated endocytosis: extracellular macromolecules bind to receptors on external surface of PM and are taken into the cell.
260
How does receptor-mediated endocytosis work?
1) Proteins that are to be imported into cell become concentrated on the extracelular surface of an indented region of PM, which forms the coated pit.
2) Coated pit sinks inward to create a coated bud.
3) Dynamine assembles into a helical collar around the neck of an invaginated coated pit
4) GTP hydrolysis causes twisting of the dynamin helix---> separation from the PM---> coated bud pinches off as a vesicle.
261
What kind of moleules does receptor-mediated endocytosis selectively take up?
macromolecules that may be present in low amounts in the extracellular fluid.
262
What is a coated pit?
Specialized domains in the PM that is coated with clathrin (cytosolic surface of PM). Coated pits eventually turn into coated buds in receptor-mediated endocytosis.
263
What is dynamin?
A large G-protein rquired for the release of clathrin-coated vesicles from the PM.
264
What are the two types of receptors invoved in endocytosis?
1. Housekeeping
| 2. signalling
265
What are housekeeping receptors?
Receptors that bind to materials such as transferrin and LDLs. The recepotrs are normally recycled back to the cell surface.
266
What are signalling receptors?
Receptors that bind extracellular ligands (hormone and growth factors) that change the activity of the cell.
267
How are signaling receptors destroyed?
Endocytosed and tagged for destruction by ubiquitination of its cytoplasmic tail.
268
What is the consequences of the destruction of signalling receptors?
Reduces the sensitivity to further stimulation
269
After the vesicle enters the cell throughe endocytosis, what happens next?
It enters the endocytic pathway and moves towards endosomes for sorting.
270
What is the difference between early and late endosomes?
Early endosomes are near the cell periphery and late endosomes are closer to the nucleus.
271
Can early endosomes mature to late endosomes?
Yes, they can mature to late endosomes which is characterized by a decrease in pH, changes in proteins and morphology.
272
Lumen of endosomes are acidified. How?
by H+-ATPase in the membrane.
273
What is phagocytosis?
The engulfing of large particles such as invading micro-organisms by ells such as neutrophils and macrophages.
274
Once a cell, such as a neutrophil and a macrophage, take up a large particle, what is it called?
phagosome.
275
What is a phagolysosome and what does it do?
It is a product of the fusion between a lysosome and a phagosome. It functions to degrade material.
276
Which cell organelles import proteins through outer boundary membranes?
Peroxisomes, mitochondria, nucleus and chloroplasts.
277
How does the uptake of proteins into peroxisomes work?
- Peroxisomal proteins have a peroxisomal targeting signal: PTS for peroxisomal matrix protein or mPTS for peroxisomal membrane protein.
- PTS receptors bind to peroxisome-destined proteins in the cytosol and shuttle them back to the surface of the organelle and pulls through through the membrane.
278
Mitochondria and chloroplasts require imported proteins to assume an unfolded state. What about peroxisomes?
They can import proteins in their folded conformation.
279
Why is mitochondria so important?
1. It is the powerhouse of the cell
(generates the ATP used to run energy-requiring activities in the cell)
2. Important in cell death
3. You can trace ancestry with mtDNA
(maternally inherited, no recombination, high rate of mutation)
4. Can have mitochondrial disease and / or disfunction.
280
How is the structure of mitochondria variable?
1. Can be different sizes and shapes
2. Numbers depend on cell type.
3. Fusion and fission (splitting) and the balance of the actions determine number and length.
281
Describe the struction of mitochondria.
The outer boundry of mitochondria has two membranes:
1. outer mitochondrial membrane (OMM)
2. Inner mitochondrial membrane (IMM)
(divides into inner boundry membrane and cristae)
Mitochondria also has aqueous compartments that consist of an intermembrane space and the matrix.
282
What is the function of the outer mitochondrial membrane?
Act as a barrier to the outside world
283
What is the outer mitochondrial membrane strucually composed of?
50% lipid by weight
| Contains porins.
284
What are porins?
- Integrate proteins with a large channel that can open and close
- When open, the channels are premeable to ATP, NAD, coenzyme A
285
What is the function of the inner mitochondrial membrane?
1. inner boundary: rich in proteins responsible for the import of mitochondrial proteins
2. critstae: increas ethe suface area for aerobic respiration and ATP formation machinery
286
What are some characteristics, structurally of the inner mitochondrial membrane?
- High protein/lipid ratio
(1 protein: 15 phospholipids; no cholesterol)
- highly permeable
(need transporters for entrance)
287
What is the role of the miochondrial intermembrane space?
Contains the proteins that play a role in apoptosis
288
What is the function the mitochondrial matrix?
Contains ribosomes and DNA and contains all the enzymes of the Krebs (TCA) cycle
289
What enzyme of the Krebs cycle does the mitochondrial matrix not contains and where is it located instead?
succinate dehydrogenanse, bound to IMM
290
What are the key reactions of glycolysis?
1. Gulocose (6-C) sugar is phosphorylated and rearranged to form 6-C biphosphate.
2. 6-C biphosphate is split into 2 3-C monophasphates
3. 3-C monophosphates are oxidized and the electrons lost reduce NAD+ to NADH (contains hiE electrons)
4. The phophate groups on carbon is transferred to ADP ---> ATP
5. Produces ATPs per gluocose oxidized and 2 pyruvate molecules.
291
What happens to the pyruvates produced in glycolysis?
In the presence of O2:
1) moves to the mitochondrial matrix via membrane transporter
2) Reacts with Coenzyme A ---> acetyl CoA + CO2 + NADH through an irreversible exergonic, oxidative decarboxylation reaction.
3) Acetyl CoA enters TCA cycle.
292
What is the central role of Acetyal CoA?
- intermediate in numerous biosynthetic reactions (ex. transfer of an aetyl group to lysine residues in histone proteins)
- biosynthetic precursor of cholesterol and other steriods
- Fed into TCA cycle to produce NADH and FADH2
293
Where does glycolysis occur?
Cytosol
294
Where doe the TCA cycle occur?
mitochondrial matrix
295
What are the key features of the TCA cycle?
1) 2-C acetyl group from acetyl CoA condenses with 4-C oxaloacetate ---> 6-C citrate
2) In subsequent reactions, citrate converted back into oxaloacetate, loses 2CO2 molecules in the process.
3) In subsequent reactions, succinyl CoA is produced
4) succinyl CoA is coupled to synthesis of one GTP by substrate level phosphorylation
5) In each turn of the cyle 4 pair os electrons are removed from C atomes ---> forms 3 NADH and 1 FADH2
296
What hapens to the NADH and FADH2 produced in the TCA cycle?
Enters to the electron transport chain to become ATP.
297
Where is the electron transport chain located?
IMM
298
What is the final acceptor of the electron transport chain?
O2
| It is reduced to H2O
299
Through which complex does NADH and FADH2 pass through in the ETC?
NADH: complex 1
FADH2: complex 2
300
What causes the movement of protons into the inter-membrane space during ETC?
Conformational changes that occur do the energy released by electrons being passed from one complex to the next.
301
How is NADH and FADH2 converted to ATP in the ETC?
1) Electrons from NADH and FADH2 enter the ETC.
2) Electrons move to complexes---> releases energy--> translocates proteins to the intermembrane space
3) Proton gradient is established in the inner membrane
4) proton gradient drives the ATP synthase
5) ATP is formed
302
What is ATP synthase?
A large multiprotein complex that drives the synthesis of ATP with the energy formed from the proton gradient it creates.
Has an F1 head that projects into the matrix and has catalytic sites
and an F0 base that is embedded in the lipid layer and forms the channels for proton movement form the intermembrane space to the matrix.
303
What is the difference between oxidative metabolism and oxidative phosphorylation?
Oxidative metabolism consists of Glycolysis and TCA cyle
| and Oxidaive phosphorlyation is the synthesis of ATP at the ETC.
304
What would happen if the proton gradient was established to a high concentration in the mitochondrial matrix and lowered in the intermembrane space at the ETC?
Consumption, not synthesis, of ATP would occur.
305
What is the concept of respiratory control in mitochondria?
- If intact, isolated mitochondria are provided with NADH or FADH2, oxygen and Pi, but no ADP. Oxidation of NADH and reduction of oxygen stops to to the depletion of ADP from ATP.
- If ADP is added, oxidation is restored.
306
Why is respiratory conrol so important in the mitochondria?
Without it, the proton-motive force used to synthesize ATP cannot be dissipated which will result is such a high proton gradient and electrical potential that it will take too much energy to pump protons across which will block further oxidation of substrates.
307
What causes loss of respiratoy control?
- certain poisons (uncouplers), cause IMM to be permeable to protons
- 2,4 - dinitrophenol can reversibly bind and release protons and shuttle them across IMM to the matrix.
Both mechanisms abolish proton-motive force, abolishes ATP synthesis and overcomes respiratory control.
308
When is uncoupling need?
In human infants and hibernating animals becomes continud NADH oxidation produces heat.
309
What are peroxisomes?
Simple, membrane bound vesicles that contain oxidative enzymes. It is the principal organelle for oxidation fo fatty acids.
310
What are similarities between mitochondria and peroxisomes?
- both form by fission of pre-exisisting organelles
- both import proteins from the cytosol
- both are involved in oxidative metabolsim
311
What are some differences between mitochondria and peroxisomes?
- peroxisomal oxidation si not linked to ATP formation, released energy is converted to heat
- peroxisomes don't have ETC
- electrons from FADH2 produced in fatty acid oxidation in peroxisomes are immediately transferred to O2 which produceds FAD and H2O2
- NADH is exported and reoxidized in the cytosol
- Peroxisomes lack the TCA cycle ---> acetyl CoA is not oxidized further ---> instead it's transported to the cytosol for cholesterol synthesis
312
What does the 43 ribosomal subunit, which initiates translation, contain?
- 40s ribosomal subunit
- initiation factors [eIFs]
- initiator tRNA
313
How are integral proteins synthesized?
* SRP & SRP receptor interactions happen as before
1) Nascent polypeptide enters translocon ---> hydrophobic segment blocks translocation through
2) If charges align, Lateral gate opens---> transmembrane segment moves into the membrane
3) protein forms with N terminus in lumen of ER
(positive end in cytosol)
OR
2a) If charges don't align, translocon re-orients the transmembrane segment according to charges
3a) translocon opens ---> segments move into membrane
4a) protein with C-terminus in lumen of ER (positive end in cytosol)
314
What is the function of the nuclear matrix?
Provides a means by which segments of chromatin can open conformation necessary for transcription.
315
How does histone methylation and acetylation affect transcription?
methylation: silencing
acetylation: decrease transcription
316
What is an example of facilitated diffusion?
Glucose transporter
317
What can result due to transport going awry?
CF
