Chapter 5 (cont.

09/09/2015

Plant cells AND animal cells have mitochondria because they need to
utilize stored sugar
Nuclear porespores in between the 2 phospholipid bilayers in the
nuclear envelope
Cytosolactual fluid that occupies the actual space that is the
cytoplasm
Lysosomes bind to vesicles that have been through phagocytosis
Cytoplasmspace inside the cell
Cytosol-liquid that fills up the cytoplasm
Cytoskeleton-protein network inside the cytoplasm
Vesicles can be used for transport between members of the
endomembrane system
3 destination sequences: none, amino-terminal, internal
2 variations in signaling:
signal to be synthesized in the lumen (space between the folds in
the ER)
Hydrophobic tails in intermembrane spaceso proteins affiliate with
the hydrophobic tails so it can dissolve in the intermembrane space
Mitochondriaconducts respiratory reactions. Vesicles are sent here so
they can be incorporated into the membrane of the mitochondria
Chloroplastsinstead of an internal membrane like mitochondria, they
have thylakoids

L + D amino acids
Enantiomers of each other
H
H
|
|
HNCCOOH
HOOCCNH
|
|
R
R
Glycine is the one amino acid that cant be left or right-handed because
its R group is an H. In order to be an enantiomer, it has to have 4 different
substitutes. Glycine has only 3.

Everything except Glycine is a chiral amino acid

Chiral carbon is in the center
Saturated fats (all straight lines on phospholipid tails) increase Van der
Waals forces, so that makes it less cold-tolerant because increasing the
forces makes it freeze at a lower temperature
You want fewer saturated fats to decrease VDWF and therefore
decrease the freezing temp.
Urey-Miller experiment is important
Know the RNA hypothesis: scientists were torn between whether DNA
came first, or proteins first that did the chemical reactions and then DNA
was made for directions
RNA molecules can both code for genetic information and catalyze
reactionsexample: ribosomeRNA and protein put together. The RNA
helps catalyze the chemical reaction, protein synthesis.
Know how to draw an amino acid, know that glucose strung together
make carbohydrates, carbohydrates linked together make a triglyceride.
Know what a fatty acid looks like. Be able to do cis and transdraw and
explain.
The one spot you see a 55 connection between nucleotides is at the
5 cap, with 3 phosphates between them
45-55 multiple choice questions, maybe matching, 1 diagram A-E
bring #2 pencil, VCU ID, V number memorized
polyadenylation makes the poly-A tail
We have 5 cap and 3 poly-A tail to protect RNA so it lasts longer (only
has a 5 min half life)
Template strand35
Nucleotides are synthesized 53
Chromatinhow DNA is stored. How we consolidate DNA so it fits
inside the cell. DNA wrapped around the histone proteins.
Zwitteriona trait of amino acids
The OH from the COOH can lose its hydrogen and become a COO
The HN can become H2N+
Zwitterion is just a molecule that can have a positive or negative
charge on it, or even both at the same time
Peptide bond is between the amine and the carboxyl group
A-site, P-site and E-site
A-site: the ribosomal site most frequently occupied by aminoacyltRNA. The aminoacyl-tRNA in the A-site functions as the acceptor for the
growing protein during peptide bond formation.

P-site: the ribosomal site most frequently occupied by peptidyl-tRNA,

i.e. the tRNA carrying the growing peptide chain. The P-site is also referred
to as the puromycin sensitive site. Puromycin is an antibiotic which shows
similarities with a part of aminoacyl-tRNA. When puromycin is present in the
A-site, the peptide can be linked to puromycin via a peptide bond. Thus,
peptidyl-tRNA in the P-site is located in the puromycin sensitive site.
E-site: the ribosomal site harbouring decylated tRNA on transit out
from the ribosome.
Alternative splicing(RNA processing)in the nucleus
**who brings what? What does the TATA box do or initiate? What do
the general transcription factors initiate? What brings the general
transcription factors?
Transcriptionin the nucleus
Steps:
Double strand opens up into a transcription bubble
Initiated at the promoter sequence (TATA box)
Transcription activator proteins that are bound to the enhancer
sequence
RNA polymerase adds in the 35
RNA is synthesized in the 35 direction because it has to be put
together 53
Continues until RNA encounters the terminator sequence
Template strand is anti-sense because it runs 35
Non-template strand is sense because it runs in the 53 because it
makes sense p. 313
Splicingspliceosomes break apart
Attach the 5 cap and 3 poly-A tail
Donor site and acceptor site
Whats a lariat?
Whats a spliceosome?
Know the donor and acceptor sites
Translation
Elongation:
Start codon is at the P site, tRNA lands on the A site

Start codon moves to E site, tRNA moves to P site, and another tRNA
comes through the A site
Stop codonrelease factors bind to A site
Fig. 4.18***