7.012 Final Exam Preparation
Exam 4
 Cell Structure
o Prokaryotic vs. Eukaryotic Cell Structure
Eukaryotes
Plasma Membrane
Cytoplasm
Nucleus
Membrane-bound
organelles
Cell Wall
Ribosome
Chromosomes/DNA
Flagellum
Prokaryotes
Yes
Yes
Yes
Yes
Yes
Yes
No
No
Only plants, fungi
Yes
Yes
No
Yes
Yes
Yes
Yes

o Eukaryotic Organelles
 Endoplasmic Reticulum: membranes in the cytoplasm, half of
which are dotted by ribosomes (rough ER) that produce proteins,
and half of which are smooth ER that produce lipids
 Golgi Body: vesicle complex involved in secretion and
intracellular transport, performs post-transcriptional modifications
like glycosylation
 Peroxisome: break down fatty acids, and reduction of reactive
oxygen species
 Mitochondria: releases energy to create ATP
 Nucleus: contains chromosomes (chromatin (DNA wrapped
around histones) folded into distinct threads)
 Lysosome: breaks down food and old cell organelles
o Cell membrane
 Functions: selectively permeable barrier, transport in and out of
cell, maintain homeostasis, cell signaling and communication
 Structure: composed of phospholipids and proteins
o Size limitation in cells
 Large surface area to volume ratio is important since a cell dictates
nutrient requirements relative to volume
 Nucleo-cytoplasmic ratio
 As size of cell increases, risk of damage to cell membrane also
increases
 Need sufficient support structures within cell


Protein Localization
o Protein localization is the process by which proteins find their way to
proper cell places, directed based on amino acid sequence.
o To function properly in a cell, proteins need:
 To be in right location
 Right chemical environment to fold properly
 Post-translational modifications
o All proteins are made in cytoplasm by ribosomes
o Other proteins made for other cellular components can reach destination
by co-translational import or post-translational import
o Secretory pathway: ER  Golgi Apparatus  Plasma Membrane 
Excreted
o All proteins that localize to ER, golgi, or lysosome and all transmembrane
proteins of the plasma membrane and secreted have the characteristics:
 Signal sequence at N terminus
 Cytoplasm: no signal sequence
 ER retention tag: RDEL at C-terminus
 Nuclear localization signal: NLS in middle
 Secreted: signal sequence at N-terminus
 Transmembrane: stop-transfer anchor sequence in center
with signal sequence at N-terminus
 Translocation stops when SRP binds signal sequence and brings
mRNA, the nascent peptide with emerging signal sequence, and
ribosome to ER
 Translation continues when signal sequence is translocated to the
ER and rest of protein threads into the ER co-translationally
Microbes: Viruses
o General structure of viruses
o Life Cycles of Viruses
 Lysogenic Cycle (non-virulent/temperate infection): following
integration of phage DNA into the host cell genome with the
phage-encoded integrases (becomes a prophage) and replicates
passively with the cell, and may cause the cell to exhibit different
properties.


Lytic Cycle (virulent infection): following injection into the host
cell, the phage genome synthesizes early proteins that break down
host DNA, allowing the phage to take control of cellular
machinery. From there, host cell synthesizes the remaining
proteins to create new daughter phages. Once a critical mass is
reached and the phage enzymes weaken the cell enough, the cell
will lyse, releasing all the new daughter phages into the
bloodstream to infect other cells.
Induction: If a bacterium containing prophages is subject to
stressors, the prophage can enter the lytic cycle spontaneously in a
messy manner where it can leave DNA portions behind or take
host DNA portions with them (transduction = process by which
antibiotic resistance and toxin genes can be spread through a
bacteria population)
o Early and Late Genes
 Early gene expression



Via cellular RNA polymerase II and cellular transcription
factors that bind to early promoters and promote synthesis
of early pre-mRNAs.
 Alternative splicing can yield different proteins that play
roles in the viral life cycle:
o Replication of the viral genome
o Regulation of viral gene expression by typically
activating late gene transcription and autoregulating
 Altering host-cell metabolism by activating pathways that
induce cell entry into S phase for cellular DNA synthesis.
Late gene expression
 Late genes transcribed and translated to give rise to late
proteins that encode structural proteins of the virus (capsid,
matrix, envelope proteins).
Microbes
SOURCES
https://www.technologynetworks.com/immunology/articles/lytic-vs-lysogenicunderstanding-bacteriophage-life-cycles-308094