Semester 1: Midterm 2 Flashcards
1
Q
What is he basic unit of a lipid?
A
A fatty acid: carboxylic acid with hydrocarbon chains ranging from C4-C24
2
Q
What is a saturated fatty acid?
A
A fatty acid with no double bonds
3
Q
The double bond of unsaturated fatty acids is usually in … confirmation
A
cis (trans can be found in bacteria)
4
Q
What determines the boiling point of a fatty acid?
A
The more double bonds -> more soluble -> higher surface area -> higher boiling point
5
Q
What are the essential fatty acids?
A
Arachidonic acid, linoleic acid, linolenic (two last used to make the first)
6
Q
What is the composition of TAGs?
A
Three fatty acids in ester linkage with a single glycerol
7
Q
What are the basic unit of cholesterol?
A
Sterols (structural lipids present in the mem. of most eukaryotic cells)
- Have 4 fused rings and a hydroxyl group
8
Q
What are the reduced derivatives of cholesterol?
A
Bile acids
9
Q
Primary bile acid
A
- 24 carbons
- 2-3 hydroxyl groups
- Side chain that terminates in a carboxyl group
10
Q
Secondary bile acid
A
Produced from primary bile acids by removing on of the hydroxyl groups
11
Q
When does ARA (arachidonic acid) become essential in the diet?
A
If linoleic acid is deficient in the diet
12
Q
What are eicosanoids?
A
The collective name for prostaglandind and the related compounds thromboxanes and leukotrienes
13
Q
What are nucleotides composed of?
A
1) A nitrogenous base (adenine, guanine, cytosine, thymine, uracil)
2) A pentose monosaccharide
3) 1-3 phosphate gorups
14
Q
What is a nucleoside composed of?
A
Base + pentose sugar
15
Q
The backbone of the nucleic acid is made up from…?
A
Covalent phosphodiester bond between the nucleotides, going from3’ to 5’ end
16
Q
How is adenine and thymine connected in DNA?
A
By two hydrogen bonds (+hydrophobic interactions)
17
Q
How is cytosine and guanine connected in DNA?
A
By three hydrogen bonds (+hydrophobic interactions)
18
Q
Structural forms of the double helix: A, B and Z forms
A
- B-form: Right handed helix with 10 residues per 360 degree turn of the helix (normal form)
- A-form: Dehydrated form of beta-form (11 per turn)
- Z-form: Left handed (12 per turn)
19
Q
Differences between RNA and DNA
A
- RNA is smaller
- RNA contains ribose instead of deoxyribose
- RNA contains uracil instead of thymine
- RNA exists as a single strand
20
Q
What are exonucleases?
A
Enzymes that work by cleaving nucleotides one at a time from the end of a polynucleotide chain
21
Q
What are endonucleases?
A
Enzymes that cleave the phosphodiester bond within a polynucleotide chain
22
Q
What are the functions of DNA polymerase I?
A
(Prokaryotes) Gap filling, following DNA replication, repair and recombination
- 3’-5’ exonuclease (proofreading)
- 5’-3’ exonuclease: Removes RNA primer when Pol III is in close proximity to it
- 5’-3’ polymerase activity
23
Q
What are the functions of DNA polymerase II?
A
(Prokaryotes) DNA proofreading and repair
Requires duplex DNA template and primer
- 3’-5’ exonuclease
24
Q
What are the functions of DNA polymerase III?
A
(Prokaryotes) Functions as the replication fork
- Catalyzes the highest rate of chain elongation in 5’-3’ direction
- 3’-5’ exonuclease: Proofreading
25
What is the function of DNA ligase?
Catalyzes the formation of a phosphodiester bond between a 3'hydroxyl at the end of one DNA strand and a 5'phosphate at the end of another strand
26
What proteins makes up the prepriming complex?
- DnaA protein: Binds to specific nucleotide sequence at origin of replication giving AT-rich regions in the origin to melt
- DNA helicase: Forcing dsDNA apart (unwinding double helix)
- SSB proteins (single-stranded DNA-binding): Cooperative binding to ssDNA - keeps strands apart
27
Function of topoisomerase
Unlinks parental strands
28
What is leading and lagging strand?
- Leading: Strand being copied in 5'-3' direction (forward), continuously
- Lagging: Retro-grade, DNA synthesized in short segments (Okazaki-fragments)
29
Function of Polymerase alpha?
(Eukaryotes)
- Contains primase -> synthesize a short RNA primer
- Initiates DNA synthesis on leading strand
30
Function of Polymerase beta?
(Eukaryotes)
| - Repair (gap filling)
31
Function of polymerase gamma?
(Eukaryotes)
| - Replicates mitochondrial DNA
32
Function of polymerase delta?
(Eukaryotes)
| - Elongation of Okazaki fragments on lagging strand
33
Function of polymerase epsilon?
(Eukaryotes)
| - Elongation of leading strand and complete DNA synthesis on this strand
34
Why do we have replication bubbles in eukaryotes?
1) Replication is bidirectional
| 2) Replication proceeds from multiple origins in each chromosome
35
Nucleosome structure
Histones and DNA:
- Two H2A, H2B, H3 and H4 form the structural core of the individual nucleosome "beads" (histone octamer)
- A segment of double helix DNA wound around core
36
DNA dependent RNA polymerase complex and each subunits function
Consisting of:
- 2 identical alpha subunits (binds regulatory sequences)
- 2 large beta (forms phosphodiester bonds) and beta' (binds DNA template) subunits
- Omega subunit
= often termed E -> associates with sigma to form holoenzyme (sigma factor allows RNA pol to recognize initiation site)
37
What are the promoter regions recognized by RNA pol sigma factor?
- Pribnow box
| - 35 sequence
38
Termination of transcription in prokaryotes
1) Rho-dependent: Rho factor migrates along behind RNA pol in 5'-3' direction until termination site is reached -> dissociation
2) Rho-independent: Requires that RNA has two structures, stable hairpin turn (with C and G rich sequence) and string of U's which when binding to A's of DNA template becomes weak -> separation
39
Inhibitors of transcription
- Rifampicin (binds beta subunit of bacterial RNA polymerase, blocks promotor clearance (elongation))
- Actinomycin D (intercalates between successive G=C base pairs in duplex DNA)
- Alpha amantin (inhibitor of RNA pol II)
40
Promotor regions in eukaryotic transcription
- TATA/Hogness box (25n upstream)
| - CAAT box (70-80n upstream)
41
RNA pol I function
(eukaryotes)
| Synthesizes the precursor of the large ribosomal RNAs (28s, 18s and 5.8s) in the nucleolus
42
RNA pol II function + inhibitor
(Eukaryotes)
Synthesize the precursors of mRNA's
Inhibited by alpha-amantin
43
RNA pol III function
(Eukaryotes)
| Produces the small RNAs, including tRNA
44
How is the primary transcript of rRNA modified?
Cleaved by ribonucleases to yield intermediate sized pieces of rRNA
- Methylation of pre-rRNA (45S)
- Cleavage to form mature rRNA: 18S, 5.8S, 28S
45
How is the primary transcript of tRNA modified?
An intron must be removed from the anticodon loop, and sequences at both 5' end and 3' end of molecule must be trimmed
46
How is the primary transcript of mRNA (hnRNA) modified?
1) 5'capping: 7-methyl-guanosine attached backwards to 5' terminal end of mRNA
2) Poly-A tail: Addition of 40-200 adenine nucleotides to 3'end
3) Removal of introns
47
Mechanism of splicing (removal of introns from mRNA primary transcript)
1) Primary transcript combines with snRNPs to form folded complex called a spliceosome
2) The 2'OH of an adenosine residue in the intron attacks and forms phosphodiester bond with the phosphate at the 5' end of intron 1
3) Newly freed 3'OH of upstream exon 1 forms phosphodiester bond with 5' end of downstream exon 2
4) Intron released
48
What are the subunits of eukaryotic and prokaryotic ribosomes?
Prokaryotic: 50S + 30S = 70S
Eukaryotic: 60S + 40S = 80S
49
Binding sites on ribosomes for tRNA
- A site: Binds incoming aminoacyl-tRNA during translation
- P site: Occupied by peptidyl-tRNA -> carries chain of AA that has already been synthesized
- E site: Occupied by the empty tRNA as it is about to exit the ribosome
50
Components needed for initiation of protein synthesis
1) The 2 ribosomal subunits
2) The mRNA to be translated
3) The aminoacyl-tRNA specified by the first codon in the message
4) GTP
5) Initiation factors facilitating the assembly of this initiation complex
51
How does the ribosome recognize the sequence initiating translation?
- Shine-Dalgarno sequence: Purine rich sequence, 6-10 bases upstream of AUG codon (prokaryotes)
- Eukaryotes: 40S subunit binds cap structure at 5' end of mRNA
52
Role of eukaryotic initiation factors: eIF2
GTP-binding protein interacts with eIF3 and members of eIF4. Binds tRNA
53
Role of eukaryotic initiation factors: eIF3
Binds to ribosomal subunit-mRNA complex
| Preventing large ribosomal subunit from binding small subunit before it's ready to commence elongation
54
Role of eukaryotic initiation factors: eIF4
Unwinds tRNA at 5'end
55
Elongation factors in prokaryotes:
- EF-T4 : Mediates entry of aminoacyl-tRNA to a free site of ribosome
- EF-T5 : Guanine nucleotide exchange factor for EF-T4. Catalyzing the release of GDP from EF-T4
- EF-6 : Catalyzes translocation of tRNA and mRNA down the ribosome at the end of each round of polypeptide elongation
56
Elongation factors in eukaryotes:
- eEF-1: alpha- entry of aminoacyl-tRNA to free site of ribosome. beta4- Guanine nucleotide exchange factor for alpha, catalyzing release of GDP
- eEF-2: Catalyzing translocation of the tRNA and mRNA down the ribosome at the end of each round of polypeptide elongation
57
What is a signal sequence?
A short (3-60AA long) peptide chain that directs the transport of a protein
58
What is co-translational translocation?
The process of exporting proteins from the cell through the rER membrane
59
The process of co-translational translocation
1) N-terminus of signal sequence being recognized by SRP (signal recognition particle)
2) Protein-ribosome complex transferred to an SRP receptor on ER (2 binding sites: one for signal sequence and one for A-site in ribosomes)
3) Protein inserted into translocon (Sec61 channel- mem. bound protein)
4) Protein covered by a chaperone protein - folded and modified
60
What is KDEL?
Retention signal sequence for ER resident proteins
61
What are the role of chaperones in the ER?
Helps in folding, refolding of denatured proteins, preventing misfolded proteins from leaving the ER
62
What is the role of SNARE proteins?
Mediate fusion of vesicles with membranes
| v-snare on vesicle, t-snare on membrane
63
What is the role of coat proteins? Types?
Vesicle producing proteins
- COPI: Golgi -> ER (retrograde transport)
- COPII: ER -> Golgi (anterograde transport)
- Clathrin: Golgi -> lysosomes
65
What type of bond keeps nucleotides together?
3'-5' phosphodiester bonds
66
What is the correct base pairing for mRNA from this noncoding/antisense (template) strand: CGTCATGTA
GCAGUACAU
67
How is RNA polymerase different from DNA polymerase?
- Only works on one strand
- Has its own helicase activity
- Does not need priming (primase)
- Does not proofread product (RNA)
- RNA doesn't stay bound following synthesis
68
All DNA polymerase a catalyze elongation of the primer strand in ...... direction, copying the template strand in a..... direction
5' to 3', 3' to 5'
69
Start codon for translation
AUG (codes for met)
70
Stop codon for translation
UAA, UAG, UGA
71
What causes a frame shift mutation?
Either an insertion or a deletion of a nucleotide
72
Ames test
- Culture of his- Salmonella
| - Medium lacking histidine
73
Amino acid activation for tRNA
AA+tRNA+ATP --> Aminoacyl-tRNA+AMP+2Pi
74
Single base changes (point mutations)
- Transitions: Pyrimidine/purine changed to different pyrimidine/purine
- Transversions: Pyrimidine to purine or the other way around
75
What is a missense effect?
Occurs when a different AA is incorporated at the corresponding site in the protein molecule
76
What is a nonsense codon?
Can occur after a point mutation, will lead to the premature termination of translation
77
Cyclin D
- Appears in late G1 phase and allows progression to S phase
| - Activates CDK4 and 6 (together with cyclin D forming an active serine-threonine protein kinase)
78
Function of Rb protein (retinoblastoma protein)
Binds and inactivates E2F
79
Cyclin E, A and CDK2
Initiation of DNA synthesis in early S phase
80
Cyclin B and CDK1
Transition from G2 to M phase
81
DNA double strand breaks can be repaired by..
- Homologous recombination (HR) --> S, G2 and M phases
| - Nonhomologous end-joining (NHEJ) --> G0/G1 phase
82
Tumor suppressor p53 function
Delays transit through cycle (checkpoints G1 and 2)
83
p21 function
CDK-cyclin inhibitor
