O-linked: Ser/Thr

GalNAc-Ser(Thr)

membrane bound glycoslytransferases

enzymes in Golgi

no dol-P-P

not inhibited by tunicamycin

N-linked: Asn

2 GlcNAc + 3 Mannose

Dol-P-P

ER and Golgi enzymes

False, low Km = high affinity

(need less substrate to reach 1/2 max velocity)

Vmax will not change (if substrate is increased high enough it can overcome inhibition) 

 Km will increase (more substrate is required to compete with inhibitor and increase velocity)

10 TM domains

phosphoenzyme intermediate

function as monomers

Na/K (oubain sensitive)

H/K (maintains low gastric pH; Prilosec inhibits)

Ca (found at plasma membrane and on Sarcoplasmic reticulum (SERCA))

True or False: CFTR is an example of an ABC protein?

What are ABC protiens? Can you give an example?

True

ABC = ATP binding cassette

6 TM domains on each unit (12 TM domains total)

1 ATP binding site on each

Another example: MDR = multiple drug resistance transporters

ubiquitin-proteasome

lysosome

E3 (ubiquitin ligase)

i.e. the angel of cellular death

Which unit of the proteasome recognizes K48 polyubiquitin?

Which units are the barrel and cap?

19S caps (recognize K48)

20S barrel

True

mono--receptor trafficking to lysosomes

K48--to proteasome

K63--regulation of activity or location (not destruction)

active

APC = anaphase promoting complex is an E3 ubiquitin ligase that targets M-cyclin for degradation.

Thus M-cyclin cannot activate M-CDK and promote mitosis.

too many renal epithelial Na channels (ENaC)

infant hypertension

mutation is in the PY motif, which normally binds E3 ligase and leads to multiple monoubiquitination and lysosomal degradation of ENaC

4 superdomains (K channel 4 subunits)

6 TM segments each domain

S6 is activation gate

S4 is voltage sensor (moves outward upon depolarization)

inactivation gate

autoimmune disease against ACh-receptor

affects small muscles first

treat by blocking ACh esterase

NMJ: wide cleft

 few fold in post-synaptic membrane

debris in cleft

autoimmune against VG Ca channels

vesicles will dock at pre-synaptic membrane but not fuse g

et more AP and Ca will increase and eventually fire--> muscles get stronger with use

treat by inhibiting VG K channels

small cell carcinoma expresses the same VGCa channel, so the body makes antibodies to fight the cancer, often causing Lambert-Eaton

mutation in S1 head of myosin

heart responds to ineffective units by generating more (hypertrophy)

DHPR: on t-tubule (voltage gated)

RyR: on sarcoplasmic reticulum

Cardiac: Na/Ca exchanger contributes about 15% of Ca pumped out of cytoplasm and relies on the gradient established by Na/K pump (glycosides inhibit so AP prolonged)

SKM does not rely on Na/Ca exchanger

Kartagener Syndrome

(respiratory and fertility troubles)

immotile cilia caused by the improper arrangemnt of dynein in

microtubules (airway) and

flagella (sperm)

X-linked recessive disorder

mutation in dystrophin (spectrin-like actin anchoring protein)

muscle weakness

Which are actin based and which are intermediate filament based?

Adherens junction

Desmosome

Hemidesmosome

Focal adhesion

Adherens jn: joins actin bundles in neighboring cells

Desmosome: joins int. filaments in neighboring cells

Hemidesmosome: anchors IF to basal lamina

Focal adhesion: anchors actin to extracellular matrix

Integrins are calcium dependent receptors that link the ECM to the cytoskeleton.

What other molecules are required?

Name a process that depends on this linkage.

Linker proteins, such as talin, vinculin

cell crawling (requires focal adhesion complex)

hypoxanthine

(can cause AT to GC conversion)

xanthine

(reduced stability/ solubility)

uracil

(potential C(U)G to TA conversion)

thymine

(5-methyl C usually at promoter; if you lose this methylation, cannot recognize promoter)

Purines (A,G) nitrogen 9

Pyrimidines (C,U,T) nitrogen 1

True or false: Adenine forms H bonds at positions

2, 1, and 6.

G: 6,1,2

C: 2,3,4

1. OH- attacks 2' hydroxyl

2. 2' hydroxyl attacks 3' phosphate

3. 3' phosphate detaches from CH2-O on next nucleotide-sugar

4. Formation of cyclic phophodiester intermediate

5. mixture of 2' and 3' monophosphates and nucleotide-sugar that got kicked off

True:

A,G have 2,3,4,9 in minor groove

C,T have 1,2 in minor groove

1. increased G-C

2. increased salt concentration

3. increased cation valence (Mg2+ > Na+)

4. increased strand complimentarity

True or false:

AAGCTTTTTTCGAA is a tandem repeat?

Will it cause a hairpin?

False, this is a mirror repeat.

Only palindromes will cause hairpins.

"greasy" molecules that get between bases and cause mutations

ex: psoralens (sun-screen ingredient that caused skin cancer)

What causes gout?

How would you treat it?

Build up of uric acid in joints due to low solubility of purines (and their derivatives).

Allopurinol blocks production of xanthine and uric acid.

X-linked error in purine metabolism (purnine salvage)

lack enzyme HPRT (hypoxanthine-guanine phophoribosyl transferase)

1. developmental delay

2. ataxia

3. renal malfunction--orange purine crystals in feces

False: they are about 300 bp (10-30 bp/repeat)

(highly repetitive DNA is 5-100 bp/ repeat but can stretch to 10,000 bp long)

True

(none are in non-transcribed control elements)

carrier

she may have mild symptoms associated with FXTAS

Remnants of transposable elements that can act as sites of homologous recombination are _____?

Can you give an example?

LINES

mutation in LDL receptor LINES yields hypercholosterolemia

False!

98% is non-coding (2% coding)

But is it really junk DNA?

False;

siRNA is from dsRNA

(miRNA formed from hairpins by Drosha enzyme)

type I: single strand nick

type II: double strand break

paternally

(if active maternal gene is deleted, Angelman syndrome results)

True or false: The SNRPN gene is maternally imprinted?

What will deletion of the non-imprinted gene yield.

True

deletion of the active paternal SNRPN region yields PWS

becterial artificial chromosome

(although if YAC were a choice, you could "gripe" it)

false,

RT yields only cDNA

more than one sequence arrangement within a population for a given locus

(i.e. multiple alleles or number of repeats)

1. require primer (DNA or RNA)

2. require template

3. synthesize 5' to 3' direction

False

eukaryotes 50 bp/ sec

prokaryotes 1000 bp/ sec

PCNA (proliferating cell nuclear antigen) was discovered in patients with systemic lupus erythematosis (SLE) and is a marker of cell proliferation.

It is the "sliding clamp" of human DNA replication, which keeps Polymerase bound.

Rad51

BRCA1, BRCA2

homologous recombination

The problem is that joining ends may produce non-disjunction events.

False,

methylation signals the old strand

Proteins that bind to mismatched DNA and cut opposite to the methylated strand.

(HINT: in E.coli: MutL, MutS)

nucleotide excision repair (

involves exinuclease = endonuclease of large chunk around error)

decreased

(not well translated due to extra repeats yet not hypermethylated like in full mutation)

FXTAS is associated with all of the following except: intention tremor

ataxia

macroorchidism

cognitive decline

autonomic dysfunction

False.

The RNA is a compliment of the template (or non-colding) strand.

diverse

low

nucleoplasm

rRNA

Pol I

True or false: The E.Coli Promoter region contains

-35 and -10 sequences recognized by the sigma factor.

TATA

CpG

Pol II

elongation

unwinds

Ser 5

True or false: Sequence specific transcription factors can form homo- or heterodimers. They interact with BOTH the major and minor groove.

An example of this is MyoD in muscle cells.

False!

St. John's Wort catalyses many enzymes to control detoxification, including metabolism of many drugs. This makes the drugs less effective (including birth control, ladies!)

True

(HYPOacetylation leads to tight DNA)

mutation in intron 3 (downstream of exon 3)

causes exon 3 to be skipped

smaller, less-functional protein

autosomal dominant

severe short stature

EF-G (requires GTP hydrolysis).

EF-G resembles EF-Tu GTP-aatRNA, so it binds the A site and displaces it to the P site (molecular mimicry)

e = eukaryotic

IF = initiation factors

eIF = eukaryotic initiation factors

EF = elongation factors (eEF in eukaryotes)

RF = release factors

eRF = eukaryotic (only 1 because it recognizes all 3 STOP codons)

*see page 153 of syllabus for a list*

The efficiency of translation in bacteria is determined by:

1. lack of ___ structure

2. strength of complimentarity of _____ _______ sequence.

3. choice of initiation codons (name the 2)

1. secondary

2. Shine-Dalgarno

3. AUG of GUG (AUG 10X more efficient)

false,

phos-4E-BP promotes synthesis by leaving eF4E (can bind eIF4G and promote synthesis)

In cancer, eIF4E can be overexpressed, exceeding 4E-BP, and becoming uncontrolled.

decrease PKR

increase mutant eIF2

Chronic myeloid leukemia

(HINT: chromosome translocation disorder)

chromosome 9/22 translocation

(Philadelphia chromosome forms)

Abl is an oncogene tyrosine kinase

Bcr now in front of Abl and stops auto-inhibition (Abl overexpressed)

Gleevec inhibits

EGF --- EGF-R (erbB)

SHC

grb 2

SOS

ras

raf

MEK

ERK

myc, jun

cyclin D

erbB--EGF-R can undergo oncogenic conversion and will no longer require EGF.

Name 2 diseases associated with this receptor.

glioblastoma

non-small cell lung carcinoma

phosphorylate

increase

(phos-RB leaves E2F up to its own devices--evil laugh)

If ATM is lost, p53 is not phosphorylated.

What happens next?

non-phos p53 is quickly degraded with MDM2 ubiquitin ligase, so it cannot bind the p21 promoter, which keeps RB in check.

Thus, RB goes and gets itself phosphorylated and E2F runs amuk.

True

ATM blocks the MDM angel of death and p53 stays around, chilling with it's homeboy p21.

 p21 gets all dominant on CDK and cyclin, so they can't mess with RB.

No evil phosphates come between RB and E2F

= happy genome

False

dominant is a gain of function from aggregates of misfolded protein

(recessive is degraded protein, loss of function)