Molecular Bio Flashcards
What are the requirements of a chromosome?
Origin of Replication, telomere, centromere
DNA is basepairing is antiparallel because each strand’s sequence is complementary to partner. True or false?
true
Digestion with ___ break down DNA by cutting between nucleosomes and degrading the exposed DNA between nucleosome core particles (linker DNA)
nucleases
Each individual nucleosome core particle consists of __ histone proteins
8
Define pseudogenes
duplicated gene that has become irreversibly inactivated by multiple mutations
Describe what happens in gene duplication and divergence
both copies remain functional while diverging in sequence and pattern of expression
Name this DNA-binding motif:
simplest; two alpha helices connected by short chain of amino acids that make the turn at a fixed angle; longer helix portion = recognition module
helix-turn-helix
Name this DNA binding motif:
includes Zn atom; amino acid sequence drawn out looks like finger; binds to major groove
zinc finger domain
Name this DNA binding motif:
two alpha helical DNA binding domain; dimerizes through leucine zipper region; interactions between hydrophobic amino acid side chains at every 7 amino acids down one side of alpha helix: forms zipper structure; grabs DNA like clothespin
leucine zipper motif
Name this DNA binding motif:
consists of a short alpha chain connected by a loop to a second larger alpha chain; can occur as homodimers or heterodimers; three domains: DNA binding domain, dimerization domain, activation domain
helix-loop-helix
Describe regulation by RNA stability (2 things)
1 - decapping: exposed mRNA degraded from 5’ end
2 - mRNA degraded from 3’ end through poly-A tail and into coding region
____ ___ modifications are required by proteins to be functional
post translational
An apparatus that deliberately destroys aberrant protein is called what?
proteasome
In regards to specificity of protein degradation, there is one E1 ubiquitin activating enzyme and 1 proteasome but 30 E2 ubiquitin conjugating enzymes and hundreds of E3 accessory proteins. True or false?
true
Explain methylation and genomic imprinting
what genes get expressed (or not) from mom and dad
X-chromosome inactivation
even things out XX vs. XY - 2 X chromosomes vs 1 X chromosome
What are the 3 major transition checkpoints of the cell cycle
start: G1 to S
G2 to M
In M phase: anaphase and cytokinesis
True or false? activites of Cdks rise and fall during the cell cycle
true
Cdks are dependent on what proteins
cyclins
Without cyclin bound (inactive state) the active site of Cdk is blocked by a region of the protein called the __ ___
T loop
Phosphorylation of Cdk at T-loop fully activates enzyme. T or F?
true
What phosphorylates Cdk?
CAK
Name the effects of Wee1 and Cdc25 on Cdk-cyclin activities
Wee1: inactivates Cdk-cyclin by phosphorylation
Cdc25: removes phosphorylation, thus activating Cdk-cyclin
The 2 step process of chromosome condensation and resolution is brought about by what?
condensin
M-Cdk activates ____ to complete mitosis
APC/C
Chromosomes are attached to microtubules at the ____
kinetochore
Name the three forces that move chromosomes to opposite pole
1: depolymerization: major force pulls the kinetochore and chromosome toward the spindle pole. depolymerization of the plus end of the microtubule drives the pulling of the kinetochore poleward
2. microtubule flux: microtubules are moved toward spindle poles while being dismantled at minus end. tubular added at plus end while being removed at minus end
3. polar ejection force: kinesin-4, 10 motors on chromosomes interact with microtubules and transport chromosome from poles. results in push-pull phenomenon
Describe the intrinsic pathway of apoptosis
when cytochrome c is released from mitochondria, it binds to a protein called Apaf1 and forms apoptosome
What is the role of BH123 in apoptosis?
BH 123 proteins become activated, form aggregation in mitochondrial outer membrane and induce release of cytochrome c - then apoptosome formed
Bcl2 proteins regulate intrinsic apoptosis. true or false?
true
note: Bcl2 is an anti-apoptotic protein
What is the role of BH3-only protein in apoptosis?
apoptotic stimulus
LAPs block caspases. true or false?
true
Anti-IAPs neutralize the IAPs and liberate what?
the caspases; leads to apoptosis
In regards to cancer genes, ___ involves single mutation event and activation of gene causing proliferation (dominant)
oncogenes
Describe tumor supressor genes and how they affect cancer
loss of function mutation. recessive - both alleles must be mutated
Heriditary form of Rb
loss of function or deletion of ONE copy of Rb in every cell- because defect is inherited
Sporadic form of Rb
since there are two normal alleles to begin with, need two sporadic mutations to occur
Describe the Apc mutation and how it can cause cancer
loss of function - Apc is a tumor suppressor gene
Gated Ion channels are common in ___ tissue
nervous
GPCRs use ___ transmembrane proteins
7-pass
Receptor tyrosine kinases are enzyme coupled. true or false?
true
Describe how a receptor tyrosine kinase receptor works
- RTK binds to SH2 of Grb2
- Grb2 also has SH3 domain
- SH3 of Grb2 binds to pralines of SOS which then binds to Ras
- Ras binds Raf and then rapid activation
___ subunits are compact and globular and are flexible structures 5-9 nm in diameter
actin
In treadmilling, the plus end remains in __ formation and the minus end adopts ___ formation
T;D
Nucleotide hydrolysis leads to ____
treadmilling
Treadmilling predominates in ___ filaments
actin
The following characteristics describe what:
long hollow cylinder; are made of tubulin, outer diameter 25nm, have one end attached to centrosome
microtubule
If nucleotide hydrolysis proceeds more rapidly than subunit addition, the cap is lost and the microtubule begins to shrink. This is called what?
catastrophe
GTP-containing subunits may still add to the shrinking end, and if enough add to form a cap, then microtubule growth resumes. This is called what?
rescue
dynamic instability predominates in ____
microtubules
the following characteristics describe what:
rope-like fiber; 10 nm diameter; help with mechanical strength
intermediate filaments
Describe the construction of intermediate filaments
alpha helical in monomer; coiled-coil dimer; staggered tetramer of two coil-coiled dimers
True or false? in intermediate filaments, there is no nucleotide binding site and structural polarity
true
Keratins impart mechanical strength by anchoring intermediate filaments at site of cell-cell contacts called ____ and cell-matrix contacts called _____
desmosomes; hemidesmosomes
In regards to accessory proteins for actin filaments, what does the ARP complex do?
nucleates assembly to form a web and remains associated with minus end
In regards to accessory proteins for actin filaments, what does cofilin do?
binds ADP-actin filaments, accelerates disassembly
In regardss to accessory proteins for microtubules, what does gamma-TuRC do?
nucleates assembly and remains associated with the minus end
Rac/Cdc42 = \_\_\_ actin Rho = \_\_\_ actin
dynamic; rigid
Rac activation promotes polymerization at the cell periphery leading to the formation of ___ extensions
lamellipodia
Cdc42 activation triggers actin polymerization and bundling to form ____
filopodia
Rho activation promotes both the bundling of actin filaments with ___ __ filaments into stress fibers and the clustering of interns and associated proteins to form focal contacts
myosin II
Name the junction:
seals gap between epithelial cells
tight
Name the junction:
connects actin filament bundle in one cell with that in the next cell
adherens
Name the junction:
connects intermediate filaments in one cell to those in the next cell
desmosomes
Name the junction:
allows the passage of small water-soluble molecules from cell to cell
gap
Name the junction:
anchors intermediate filaments in a cell to extracellular matrix
hemidesmosome
In regards to adhesion proteins, ___ mediate cell-cell connection and ____ mediate attachment of cells to matrix
cadherin; integrin
Adherents junctions often form a continuous ___ ___ close beneath the apical face of the epithelium, encircling each of the interacting cells in the sheet
adhesion belt
Each sealing strand of tight junction is composed of a long row of ___ pass transmembrane adhesion proteins embedded in each of the two interacting plasma membranes
4
two main tight junction proteins are what?
claudin and occludin
Gap junction is spanned by channel forming protein called what?
connexin
note: 6 connexin protein subunits
Gap junctions couple cells both electrically and metabolically. True or false?
true
Intracellular linkage of integrin to actin is mediated by ___
talin
What are FAK molecules and what do they do?
cytoplasmic protein tyrosine kinase; they autophosphorylate each other and make docking sites for Src-family kinases
Describe the structure of a proteoglycan
long polysaccharide/core complex linked to extensive hyaluronic acid chain
describe the triple helix of collagen
each chain twists to left; twist helically around each other to the right
Procollagen triple helix is formed where?
ER/Golgi Complex
Procollagen is then cleaved outside of cell where it self-assembles into a what?
collagen fibril
aggregation of fibrils forms fiber
What is the defective enzyme in scurvy?
prolyl hydroxylase
What is the defective enzyme in ehlers-Danlos VI?
lysl hydroxylase
What is the purpose of doing an SDS-PAGE?
separating proteins by size
Why would you do Mass Spec?
identify unknown proteins
Why would you do a western blot?
to analyze specific proteins
Which ELISA is necessary for HIV test?
indirect
What is an example of a sandwich ELISA?
pregnancy test
Why would you use nuclear magnetic resonance?
to analyze protein structure
Plasmids are cloning vectors. true or false?
true
How do cDNA clones work?
DNA copy of mRNA; use reverse transcriptase
What is pcr used for?
to detect altered genes or foreign DNA
What does CSI utilize?
STRs
True or false? mitochondria are more dynamic in high energy cells
false, less dynamic. become more fixed in high energy cells where they are packed tightly between myofibrils
Do mitochondria retain their own DNA?
yes
Mitochondria transfer RNAs are highly variable. changes in mt tRNAs have been linked to over 200 disease states. true or false?
true
Accumulation of ___ generated by the respiratory chain can cause mito DNA damage
ROS
note: ROS increase with age, and the brain is particularly susceptible
list the layers of the epidermis
granular, prickle, basal, basal lamina
Olfactory receptors are what type of receptor?
G protein coupled receptor
Describe the flow of action potential from olfactory receptor
relayed via axon to brain to glomeruli
Where are glomeruli found?
olfactory bulbs
Define totipotency
ability of a cell to give rise to all cells of an organism, including embryonic and extra embryonic tissues ex: zygote
Define pluriptoency
ability of a cell to give rise to all cells of the embryo and subsequently adult tissues ex: embryonic stem cells
define multipotency
ability of a cell to give rise to different cell types of a given lineage ex: adult stem cells
true or false? founder stem-cell populations stay small; transit amplifying divisions let them generate and renew a big adult structure
true
Explain the immortal strand hypothesis
to combat passing on mutation, stem cells divide asymmetrically, passing down a template parental strand
How are ES cells derived?
what for zygote to become blastocyst and then take inner cell mass and culture on plate
True or false? Adult stem cells are tissue specific
true
give the function of the following types of RNAs:
tRNA; snRNA; snoRNA; miRNA; siRNA
tRNA: adaptor between mRNA and AAs
snRNA: splicing of pre-mRNA
snoRNA: chemically modify rRNAs
miRNA: regulate gene expression - block translation of specific mRNAs
siRNA: turn off gene expression
Explain eukaryotic transcription initiation
TFIID binds to TATA box; recruitment of other TFs; formation of transcription initiation complex; Phosphorylation of CTD by TFIIH = elongation
The genetic code is degenerate. True or false?
True
What is the anticodon loop on a tRNA molecule?
a set of 3 consecutive nucleotides that pair with a complementary codon in an mRNA molecule
What is the 3’CCA terminal region of a tRNA molecule?
the region which binds the AA that matches the corresponding codon
Some tRNAs require accurate base-pairing only at the first two positions of the codon and can tolerate a mismatch at the third (wobble) position. This wobble base pairing explains why…..
so many of the alternative codons for an AA differ only in their third nucleotide
UAA, UAG and UGA are what type of codons
stop codons
Protein transfer/transport to various compartments is guided by ___ signals. Signal ___ remove signal after protein reaches final destination
sorting; peptidases
Nuclear transport is ___, ___, and ____
bidirectional, selective, and gated
