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Biochemistry > Semester 1: Midterm 2 > Flashcards

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

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2
Q

What is a saturated fatty acid?

A

A fatty acid with no double bonds

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3
Q

The double bond of unsaturated fatty acids is usually in … confirmation

A

cis (trans can be found in bacteria)

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4
Q

What determines the boiling point of a fatty acid?

A

The more double bonds -> more soluble -> higher surface area -> higher boiling point

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5
Q

What are the essential fatty acids?

A

Arachidonic acid, linoleic acid, linolenic (two last used to make the first)

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6
Q

What is the composition of TAGs?

A

Three fatty acids in ester linkage with a single glycerol

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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

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8
Q

What are the reduced derivatives of cholesterol?

A

Bile acids

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9
Q

Primary bile acid

A
  • 24 carbons
  • 2-3 hydroxyl groups
  • Side chain that terminates in a carboxyl group
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10
Q

Secondary bile acid

A

Produced from primary bile acids by removing on of the hydroxyl groups

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11
Q

When does ARA (arachidonic acid) become essential in the diet?

A

If linoleic acid is deficient in the diet

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12
Q

What are eicosanoids?

A

The collective name for prostaglandind and the related compounds thromboxanes and leukotrienes

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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

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14
Q

What is a nucleoside composed of?

A

Base + pentose sugar

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15
Q

The backbone of the nucleic acid is made up from…?

A

Covalent phosphodiester bond between the nucleotides, going from3’ to 5’ end

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16
Q

How is adenine and thymine connected in DNA?

A

By two hydrogen bonds (+hydrophobic interactions)

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17
Q

How is cytosine and guanine connected in DNA?

A

By three hydrogen bonds (+hydrophobic interactions)

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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)
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19
Q

Differences between RNA and DNA

A
  1. RNA is smaller
  2. RNA contains ribose instead of deoxyribose
  3. RNA contains uracil instead of thymine
  4. RNA exists as a single strand
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20
Q

What are exonucleases?

A

Enzymes that work by cleaving nucleotides one at a time from the end of a polynucleotide chain

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21
Q

What are endonucleases?

A

Enzymes that cleave the phosphodiester bond within a polynucleotide chain

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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
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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

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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
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25
Q

What is the function of DNA ligase?

A

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

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26
Q

What proteins makes up the prepriming complex?

A
  • 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
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27
Q

Function of topoisomerase

A

Unlinks parental strands

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28
Q

What is leading and lagging strand?

A
  • Leading: Strand being copied in 5’-3’ direction (forward), continuously
  • Lagging: Retro-grade, DNA synthesized in short segments (Okazaki-fragments)
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29
Q

Function of Polymerase alpha?

A

(Eukaryotes)

  • Contains primase -> synthesize a short RNA primer
  • Initiates DNA synthesis on leading strand
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30
Q

Function of Polymerase beta?

A

(Eukaryotes)

- Repair (gap filling)

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31
Q

Function of polymerase gamma?

A

(Eukaryotes)

- Replicates mitochondrial DNA

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32
Q

Function of polymerase delta?

A

(Eukaryotes)

- Elongation of Okazaki fragments on lagging strand

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33
Q

Function of polymerase epsilon?

A

(Eukaryotes)

- Elongation of leading strand and complete DNA synthesis on this strand

34
Q

Why do we have replication bubbles in eukaryotes?

A

1) Replication is bidirectional

2) Replication proceeds from multiple origins in each chromosome

35
Q

Nucleosome structure

A

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
Q

DNA dependent RNA polymerase complex and each subunits function

A

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
Q

What are the promoter regions recognized by RNA pol sigma factor?

A
  • Pribnow box

- 35 sequence

38
Q

Termination of transcription in prokaryotes

A

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
Q

Inhibitors of transcription

A
  • 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
Q

Promotor regions in eukaryotic transcription

A
  • TATA/Hogness box (25n upstream)

- CAAT box (70-80n upstream)

41
Q

RNA pol I function

A

(eukaryotes)

Synthesizes the precursor of the large ribosomal RNAs (28s, 18s and 5.8s) in the nucleolus

42
Q

RNA pol II function + inhibitor

A

(Eukaryotes)
Synthesize the precursors of mRNA’s
Inhibited by alpha-amantin

43
Q

RNA pol III function

A

(Eukaryotes)

Produces the small RNAs, including tRNA

44
Q

How is the primary transcript of rRNA modified?

A

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
Q

How is the primary transcript of tRNA modified?

A

An intron must be removed from the anticodon loop, and sequences at both 5’ end and 3’ end of molecule must be trimmed

46
Q

How is the primary transcript of mRNA (hnRNA) modified?

A

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
Q

Mechanism of splicing (removal of introns from mRNA primary transcript)

A

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
Q

What are the subunits of eukaryotic and prokaryotic ribosomes?

A

Prokaryotic: 50S + 30S = 70S
Eukaryotic: 60S + 40S = 80S

49
Q

Binding sites on ribosomes for tRNA

A
  • 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
Q

Components needed for initiation of protein synthesis

A

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
Q

How does the ribosome recognize the sequence initiating translation?

A
  • 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
Q

Role of eukaryotic initiation factors: eIF2

A

GTP-binding protein interacts with eIF3 and members of eIF4. Binds tRNA

53
Q

Role of eukaryotic initiation factors: eIF3

A

Binds to ribosomal subunit-mRNA complex

Preventing large ribosomal subunit from binding small subunit before it’s ready to commence elongation

54
Q

Role of eukaryotic initiation factors: eIF4

A

Unwinds tRNA at 5’end

55
Q

Elongation factors in prokaryotes:

A
  • 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
Q

Elongation factors in eukaryotes:

A
  • 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
Q

What is a signal sequence?

A

A short (3-60AA long) peptide chain that directs the transport of a protein

58
Q

What is co-translational translocation?

A

The process of exporting proteins from the cell through the rER membrane

59
Q

The process of co-translational translocation

A

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
Q

What is KDEL?

A

Retention signal sequence for ER resident proteins

61
Q

What are the role of chaperones in the ER?

A

Helps in folding, refolding of denatured proteins, preventing misfolded proteins from leaving the ER

62
Q

What is the role of SNARE proteins?

A

Mediate fusion of vesicles with membranes

v-snare on vesicle, t-snare on membrane

63
Q

What is the role of coat proteins? Types?

A

Vesicle producing proteins

  • COPI: Golgi -> ER (retrograde transport)
  • COPII: ER -> Golgi (anterograde transport)
  • Clathrin: Golgi -> lysosomes
65
Q

What type of bond keeps nucleotides together?

A

3’-5’ phosphodiester bonds

66
Q

What is the correct base pairing for mRNA from this noncoding/antisense (template) strand: CGTCATGTA

A

GCAGUACAU

67
Q

How is RNA polymerase different from DNA polymerase?

A
  • 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
Q

All DNA polymerase a catalyze elongation of the primer strand in …… direction, copying the template strand in a….. direction

A

5’ to 3’, 3’ to 5’

69
Q

Start codon for translation

A

AUG (codes for met)

70
Q

Stop codon for translation

A

UAA, UAG, UGA

71
Q

What causes a frame shift mutation?

A

Either an insertion or a deletion of a nucleotide

72
Q

Ames test

A
  • Culture of his- Salmonella

- Medium lacking histidine

73
Q

Amino acid activation for tRNA

A

AA+tRNA+ATP –> Aminoacyl-tRNA+AMP+2Pi

74
Q

Single base changes (point mutations)

A
  • Transitions: Pyrimidine/purine changed to different pyrimidine/purine
  • Transversions: Pyrimidine to purine or the other way around
75
Q

What is a missense effect?

A

Occurs when a different AA is incorporated at the corresponding site in the protein molecule

76
Q

What is a nonsense codon?

A

Can occur after a point mutation, will lead to the premature termination of translation

77
Q

Cyclin D

A
  • 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
Q

Function of Rb protein (retinoblastoma protein)

A

Binds and inactivates E2F

79
Q

Cyclin E, A and CDK2

A

Initiation of DNA synthesis in early S phase

80
Q

Cyclin B and CDK1

A

Transition from G2 to M phase

81
Q

DNA double strand breaks can be repaired by..

A
  • Homologous recombination (HR) –> S, G2 and M phases

- Nonhomologous end-joining (NHEJ) –> G0/G1 phase

82
Q

Tumor suppressor p53 function

A

Delays transit through cycle (checkpoints G1 and 2)

83
Q

p21 function

A

CDK-cyclin inhibitor

Biochemistry (9 decks)

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