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TUGAS BIOLOGI SEL MOLEKULER

1. Ikatan Basa nitrogen dengan magnesium pada RNA Polimerase II.

(Yang et. al., 2006)


Location and models of action for the RNAP active center. (A) The active center
performing Pi-stimulated RNA hydrolysis. Catalytic Mg2+ ions are indicated. (B)
Nucleotidyl transfer reaction. The dotted lines represent coordination bonds. Arrows
indicate the migration of electron density. (C and D) Models for Pi action in
hydrolytic RNA cleavage and RNA phosphorolysis, respectively. (E and F) Structural
models for C and D, respectively.
All RNAP reactions proceed through an Sn2 mechanism (13⇓–15), which involves
two Mg2+ ions (Fig. 1) chelated by an invariant aspartate triad of β′ subunit residues
(D460, D462, and D464). One Mg2+ ion (Mg-I) saturates the active center, whereas
the other (Mg-II) binds transiently and must be recruited through additional
coordination for each round of catalysis (13). In the nucleotidyl transfer reaction Mg-
II is stabilized by chelation with phosphate groups of the NTP substrate. In transcript
cleavage it is coordinated with carboxylate residues of Gre or TFIIS transcription
cofactors, which approach the active center through the secondary channel, or by the
triphosphate residue of noncognate NTP substrate bound at the E-site of the active
center (13). In RNA synthesis Mg-I activates the 3′-hydroxyl of the terminal RNA
residue and the α-phosphate of an NTP substrate for nucleophilic attack, whereas Mg-
II promotes release of pyrophosphate (Fig. 1B). The two Mg2+ ions switch roles for
RNA hydrolytic cleavage. Thus, Mg-II activates the attacking water and Mg-I aids in
release of the leaving group (Fig. 1C). In addition to the above-mentioned aspartate
triad, two neighboring acidic residues, βE813 and βD814, as wel l as a basic cluster
(βK1073, βR678, βR1106, and β′R731), are engaged in both substrate binding and
catalysis (11, 13, 16

2. Membran plasma nukleus (inner dan outer) tersusun atas fosfolipid


bilayer

( Enyedi & Niethammer, 2017)


The critical function of the nuclear membranes is to act as a barrier that
separates the contents of the nucleus from the cytoplasm. Like other cell membranes,
each nuclear membrane is a phospholipid bilayer permeable only to small nonpolar
molecules (see Figure 2.27). Other molecules are unable to diffuse through the
bilayer. The inner and outer nuclear membranes are joined at nuclear pore complexes-
the sole channels through which small polar molecules and macromolecules pass
through the nuclear
envelope (Figure 9.2). As discussed in the next section, the nuclear pore complex
is a complicated structure that is responsible for the selective traffic of proteins and
RNAs between the nucleus and the cytoplasm. (Cooper & Hausman, 2007)

3. T-RNA berikatan dengan asam amino.

Charged tRNA

The amino acid is attached by an ester bond ( R - O - R ) between


the carboxyl group and the 3'-A of the terminal ribonucleotide of the amino acceptor
stem of the tRNA. The 3' stem of the tRNA is always a single-stranded 3'-ACC

Figure © 2010 PJ Russell, iGenetics 3rd ed.; all text material © 2012 by Steven M.
Carr
4. M-rna dan ribosom

Interactions between the ribosome and mRNA in the P site. (A) Hydrogen bonds to
the phosphates of nucleotides +1 and +3 of mRNA shown from the perspective of the
30S head. The position of G1401 and a fully hydrated Mg2+ have been removed for
clarity. (B) Coordination of a fully hydrated Mg2+ to 16S rRNA and the backbone of
mRNA, shown from the perspective of the subunit body. (C) View of (F obs − F calc)
difference electron density in the electronegative pocket between the backbone of P-
site mRNA and helix-44 nucleotides 1494–1498 in 16S rRNA. The position of
A1493 is already adjusted to fit the electron density. (D) Nucleotides +4 through +6
of the mRNA, along with two Mg2+ ions, modeled into the electron density in C
followed by refinement.
Ribosome interactions with the P-site ASL. (A) Closing of the P-site cleft when
compared with the 30S ribosome structures (9). Changes in the distance between
C1400 and G966 and between G966 and ASL are indicated by arrows and distances.
The position of the very C terminus of protein S9 is indicated. The view is from the
aminoacyl-tRNA site in the small subunit. (B) Stereoview of the averaged (3F obs −
2F calc) difference electron density for the 30S contacts to the ASL shown in A.
Electron density for mRNA nucleotides +4 through +6 has been removed for clarity.
The density indicated by an asterisk is disconnected from that for protein S9 and
therefore has not been assigned. (C) Minor groove interactions among G1338,
A1339, and the P-site ASL. The view is from the right in A, i.e., from the perspective
of the 50S subunit.

(Berk et. al. 2006)


Proposed mechanism for phosphodiester cleavage of ribosome- bound mRNA by
YafQ. The second A-site nucleotide or A+5 stacks with Phe91 (double arrows)
orienting the mRNA optimally for in-line attack at the scissile phosphate. His50 or
His63 functions as a general base to abstract the 2 -proton of the 2 -OH of mRNA
residue A+5 and His87 stabilizes the 5 -leaving group as a general acid. Asp67
interacts with His87 to shift its pKa to facilitate leaving group stabilization. The
specific role of Asp61 is unclear although it does appear important for overall
function.
(Maehigasi et. al., 2015)
5. Eksport dan Import molekul dari dan ke nukleus

Figure 12–13 How GTP hydrolysis by Ran in the cytosol provides directionality to
nuclear transport. Movement through the NPC of loaded nuclear transport receptors
occurs along the FG-repeats displayed by certain NPC
proteins. The differential localization of Ran-GTP in the nucleus and Ran-GDP in the
cytosol provides directionality (red arrows) to both nuclear import (A) and nuclear
export (B). Ran-GAP stimulates the hydrolysis of GTP to produce Ran-GDP on the
cytosolic side of the NPC (see Figure 12–12).

Figure 12–12 The compartmentalization of Ran-GDP and Ran-GTP. Localization of


Ran-GDP in the cytosol and Ran-GTP in the nucleus results from the localization of
two Ran regulatory proteins: Ran GTPaseactivating protein (Ran-GAP) is located in
the cytosol, and Ran guanine nucleotide exchange factor (Ran-GEF) binds to
chromatin and is therefore located in the nucleus. Ran-GDP is imported into the
nucleus by its own import receptor, which is specific for the GDP-bound
conformation of Ran. The Ran-GDP receptor is structurally unrelated to the main
family of nuclear transport receptors. However, it also binds to FG-repeats in NPC
channel nucleoporins