Block 1 - Making Parts (L6-7) Flashcards
The nucleus has — that codes for —- proteins.
DNA, 30,000
How is DNA typically stored?
in a dispersed form called chromatin, where the nucleic acids are spooled around histone proteins
the chromatin supercoils into chromosomes during cell division
What are the components of DNA?
- deoxyribose sugar
- phosphate
- on of the four bases: adenine, thymine, guanine, and cytosine
What are the differences between nucleosides, nucleotides, and nucleic acids?
nucleoside: base and sugar
nucleotide: nucleoside and phosphate
nucleic acids: a sequence of linked nucleotides
What are the bases vs. the nucleosides?
bases: adenine, thymine, guanine, and cytosine
nucleosides: adenosine, thymidine, guanosine, and cytidine
Each strand of DNA contains info for…
replicating the other strand and protein structure
What are the two processes needed for protein synthesis?
transcription (DNA to mRNA)
translation (mRNA to protein)
What are the base pairs?
AU/AT and GC
What two things are different about RNA structure than DNA structure?
RNA has a ribose instead of a deoxyribose, and uracil instead of thymine
Where does transcription take place?
the nucleus
Why does mRNA move out of the nucleus while DNA stays in the nucleus?
RNA is not as resistant to hydrolysis
What are the steps of transcription?
- DNA strands unwind and separate
- DNA strand containing the specific gene serves as a template strand
- RNa nucleotides are matched to complementary DNA bases
- mRNA molecule is complete and DNA rewinds
During transcription, DNA is read in the —– direction and RNA is made in the ——- direction.
DNA read in the 3’-5’ direction
RNA made in the 5’-3’ direction
What does RNA polymerase do?
location where the new bases are added to the template strand and form the new mRNA strand
Describe RNA splicing
introns (parts that are not the protein’s code) are removed and exons (parts that code the protein) are joined together to make the complete mRNA
Where does translation occur?
ribosomes in the cytoplasm
mRNA has 3 letter segments called —– that…
3 letter segments called codons,
code for an amino acid
tRNA has 3 letter segments called —– that…
3 letter segments called anticodons,
are complimentary to the mRNA codon
What bond connects the amino acids during translation?
peptide bonds
The DNA in every cell is…
the same
How is gene expression regulated?
different types of cell express different genes, which causes specialization (the genes are the same, just different ones are expressed)
What is the promotor in translation?
DNA sequence upstream of (before) the start of a gene where the RNA polymerase binds
What are transcription factors?
proteins that bind to the promotor to augment the binding of RNA polymerase (control if that gene is able to be transcribed)
Where does transcription start?
the start codon of the coding sequence (not the promoter region, that’s just where the RNA polymerase binds)
What are the 5 control points for protein?
- transcriptional control
- RNA processing control
- RNA transport control
- translation control
- protein activity control
It is important to control protein synthesis because faults can cause…
defective proteins which lead to many disorders
Mutant sodium channels that have defective inactivation can cause…
hyperkalemic periodic paralysis, long QT syndrome, and inherited epilepsy
Do all proteins turnover at the same rate?
No - different proteins have different rates, and the same protein can even have different turnover rates in different tissues
What is the half-life?
time to decay to half of its initial value
What is a common way to study protein synthesis and degradation?
labeled methionine incorporation:
incubate cells with 3H-methionine and measure the incorporation into the target protein, then immunoprecipitate using an antibody that binds the target, separate with electrophoresis, and look for radioactivity from the 3H
What is pulse-chase?
more accurate way to study protein synthesis and degradation
1. pulse - incubate cells with 3H-methionine to allow incorporation into the target protein
2. chase - incubate cells with nonradioactive methionine and watch the disappearance of the labeled target protein
Proteins are degraded by —— which is compartmentalized in two ways:
proteolysis, compartmentalized by lysosomes or proteasomes
What are lysosomes? Describe their composition.
membrane-bound compartments with various hydrolases, including proteases, and a low pH
Contrast the things that lysosomes and proteasomes degrade.
lysosome: long-lived cytosolic proteins, integral membrane proteins in secretory and endosomal vesicles
proteasome: short-lived cytosolic proteins, ER membrane proteins
What allows lysosomes and endosomes to have a low pH?
proton pumps called V-ATPase shift H+ into them via primary active transport
How are proteins headed for the lysosomes tagged?
single molecule of ubiquitin (mono-uniquitination)
Lysosomes degrade both…
extracellular materials taken in by endocytosis, and cellular material shifted in via cytoplasmic vesicles
What is autophagy? What are the steps?
cell mechanism for disposing of large particles
1. envelopment
2. sealing
3. merging with a lysosome
3. resulting residual body
What is crinophagy? How does it occur?
process for the degradation of secretory proteins that have gone beyond their “shelf life”
lysosomes fuse with old secretory vesicles and degrade their contents
What is inside lysosomes, and how does it get there?
they contain many different hydrolytic enzymes
precursors are tagged with mannose-6-phosphate in the golgi, trans golgi receptors divert the enzyme precursors to endosomes and lysosomes where they are activated
What is the basic structure of a proteasome?
protein subunits assemble into a proteolytic machine, and proteolysis sites line the inside of the narrow chamber
regulatory complexes guard the openings to allow access only to selected, unfolded polypeptides
What do proteasomes degrade?
key substrates, abnormal and misfolded proteins, and some degrade antigens
(always in response to signaling cascades or at specific transitions in the cell cycle)
Describe the detailed structure of a proteasome
- main core and a cap at each end
- core is the 20S proteasome, which has 28 subunits arranged in 4 7-member rings (alpha are the top and bottom, beta are the middle two)
- proteolytic sites on the beta rings face the inner chamber
How are unneeded or damaged proteins marked for destruction by a proteasome?
covalent attachment of chains of a small protein called ubiquitin (polyubiquinated)
How do proteins and ubiquitin link?
Describe the link and the process
side chain amino acid groups of lysine on the target protein covalently link to the C-terminus of uniquitin (a glycine)
- ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2), and ubiquitin protein ligase (E3)
- one ATP is hydrolyzed for every ubiquitin molecule attached to the target protein
Describe the ubiquitin conjugation mechanism
- E1 activates ubiquitin
- E2 carries ubiquitin
- E3 attaches ubiquitin to the substrate
- mono (lysosome) poly (proteasome)
