Learning Objectives Flashcards
What is free energy?
the amount of work that can be extracted from a system
________ has the highest reduction potential
oxygen
4 types of kinetic energy
- radiant
- electric
- thermal
- mechanical
Potential energy is stored in … (4)
- redox pairs
- chemical bonds
- concentration gradients
- electric fields from charge separation
Equation relating electric potential and free energy
deltaG = -nFdeltaE
High energy phosphate bonds
P-O-P (ATP)
P-N (phosphocreatine)
C-O-P (phosphoenolpyruvate)
Solubility of nucleotide components
least to most: bases, nucleoside, nucleotide
Factors that affect Tm
- G-C ratios
- concentration
- pH
- chain length
Methods for attacking DNA metabolism
- synthesis of precursors (dNTPs)
- intercalation
- covalently binding base pairs
- topoisomerase
Eukaryote leading and lagging strand polymerases
leading strand: pol epsilon
lagging strand: pol delta
Diseases from mutations in DNA repair mechanisms
- Cockanye’s syndrome
- xeroderma pigmentosum
mutations in mismatch repair lead to ___________
Lynch Syndrome (hereditary non-polyposis colorectal cancer)
Components of the RNA Polymerase II Pre-Initiation Complex (4)
- RNA Pol II
- TATA box binding proteins
- general transcription factors
- mediator
What does TFIIH do?
facilitates nucleotide excision repair (adds PO4 to C-terminal domain of Pol II and acts as a helicase to open DNA strands
__________ recognizes the 5’ cap of mRNA for transport to the ribosome
translation factor elf4e
If a transcript has a 5’-methyl-G cap, it was made by ________
RNA Pol II
Steps for adding a 5’-cap to a pre-mRNA
- triphosphatase
- guanylyltransferase
- guanine-7-methyltransferase
Genetic diseases caused by splicing defects
- Marfan’s syndrome (fibrillin gene)
- spinal muscular atrophy (exon 7)
Reactions that make the mature 3’-end of mRNA
cleavage and polyadenylation
Poly-A tail is necessary for RNA polymerase complex to _____________________
detach from DNA (termination)
Hemophilia B Leyden
- X-linked disease that affects clotting (reduced factor IX gene)
- gets better at puberty because androgen receptor becomes active (binds overlapping sites at promotor)
4 major families of sequence-specific DNA binding proteins
- homeodomain (helix-turn-helix)
- zinc finger
- basic leucine zipper
- basic helix-loop-helix
Give an example of a disease where histone acetylation is altered
Rubinstein-Taybi syndrome (mutation in copy of CREB-binding protein gene; loss of HAT activity)
heterochromatin is mostly (hypo/hyperacetylated)
hypoacetylated (transcriptionally inactive)
Ways to regulate sequence-specific DNA-binding proteins
- control protein conformation by binding a ligand
- regulate entry into nucleus
- regulate amount of transcription factor in cell
- regulate binding to DNA
ways to control level of gene expression
- control mRNA export from nucleus
- control mRNA degradation
- control efficiency of translation
- control protein degradation
bacterial translation
- IF1 and IF3 bind to 30S subunit
- mRNA binds 30S subunit using Shine-Delgarno sequence
- IF2 delivers “initiator” tRNA to P-site to pair with AUG
- GTP hydrolysis releases initiation factor and binds 50S subunit
eukaryotic translation
- elf4E binds to 7-methyl guanosine cap on 5’ end of mRNA
- binding of other elFs and small ribosomal subunit
- large subunit joins, factors are released
- scanning through 5’ UTR to get to AUG so 5’ UTR can influence rate of process
What happens with IRE-BPs in high iron conditions?
IRE-BP’s are bound to FE, can’t bind IRE RNA
What happens with IRE-BPs in low iron conditions?
IRE-BP’s are not bound to FE, bind to IRE RNA, allowing synthesis of transferrin receptor
hydrophobic amino acids
glycine, alanine, valine, leucine, methionine, isoleucine, tryptophan, phenylalanine, proline
polar, uncharged amino acids
threonine, serine, cysteine, proline, asparagine, glutamine
polar, positively charged amino acids
histidine, lysine, arginine
polar, negatively charged amino acids
aspartate, glutamate
non=-polar aliphatic amino acids
glycine, alanine, valine, leucine, methionine, isoleucine
aromatic amino acids
tyrosine, tryptophan, phenylalanine
Bohr effect
pH difference causes different binding affinities
- high pH: high O2 binding (in lungs)
- low pH: low O2 binding (in tissue)
PCR is a good diagnostic test for…
- CF
- beta thalassemia
- Tay-Sachs
- HLA typing
plasmids
vectors for amplifying DNA sequences in bacteria
criteria during analysis of next-generation DNA sequencing data for SNP identification
- error rate
- coverage
- ploidy needs enough coverage to determine heterozygosity
competitive inhibition increases ______
Km
uncompetitive inhibitions lowers _____ and changes the apparent _____
Vmax, Km
mixed inhibition affects both _____ and ______
Vmax, Km
A good way to delay or prevent onset of Alzheimer’s would be to decrease ___________
beta-secretase
Minisatellites have _______ and are ___-rich
variable number tandem repeats, GC
Microsatellites have ______ and are ____-rich
short tandem repeat polymorphisms, CA
Euchromatin is (more/less) acetylated than heterochromatin
more
Tandem repeats are the basis for ____________
cytogenetic banding
Tandem repeats are found on chromosomes _________
1, 9, 16, Y
What is mosaicism?
an aberrant process in which cells with two different genetic complements are produced during mitosis after the zygote has already formed
What is the most common contiguous gene syndrome in humans?
DiGeorge’s Syndrome (absent or hypo plastic thymus and parathyroids, congenital heart disease)
What tests are done in the first trimester to check for chromosomal abnormalities?
- ultrasound measurement of nuchal folds
- B-hCG
- PAPP-A
What tests are doing in the second trimester to check for chromosomal abnormalities?
- B-hCG
- unconjugated estriol
- inhibin levels
How does x-chromosome inactivation work?
DNA methylation and modification of histones:
-XIST on inactive X transcribes RNA that spreads across X chromosome to coat it, modifying genomic structure to attract DNA methylators and HDACs
SRY gene and SOX9 lead to production of __________
anti-mullerian hormone
FGF9 leads to _____________________
differentiation of the testes
Androgen leads to development of the… (3)
- penis
- scrotum
- urethral opening of penis
5-alpha reductase deficiency
- XY
- autosomal recessive
- can’t convert testosterone to dihydroxytestosterone
46, XY: deletion of SRY is phenotypically ___________
female
46, XX: ectopic presence of SRY is phenotypically _________
male
Denys-Drash and Fraiser Syndrome involve sex reversal with 46 (XX/XY) and a mutation in ______
XY, WT1 gene (transcription factor for SRY)
A common symptom of Gaucher disease is __________
hepatosplenomegaly
In Gaucher disease, glucocerebrosidase activity is less than ____%
30%
Inheritance of Gaucher is ________________
autosomal recessive
Candidate gene association studies are best for _________________
common risk alleles with small to moderate effects
Genome wide association studies are best for ___________________
common alleles with small to moderate effects
Genetic linkage studies are best for _______________
uncommon alleles with strong effects in families
Three most commonly used types of DNA polymorphisms
- microsatellites
- SNPs
- CNVs
manifestation of PKU
hyperactivity, epilepsy, intellectual disability
PKU has (high/low) allelic heterogeneity
high
alpha-1 antitrypsin deficiency
inherited disorder, causes lung and liver disease
What enzyme is the primary target for alpha-1 antitrypsin deficiency?
elastase (a serum protease)
-alpha-1 antitrypsin inhibits elastase by irreversible binding so if it’s deficient, elastase breaks down elastin
Tay-Sachs Disease
destroys nerve cells in brain and spinal cord (CNS)
Tay-Sachs has a defect in the ability to get rid of ______________
ganglioside (defective HexA needed to metabolize GM2)
Alpha globin genes are located on chromosome ___ and beta globin genes are located on chromosome ____
16, 11
alpha globin cluster
zeta-alpha1-alpha2
beta globin cluster
epsilon-gamma G-gamma A-delta-beta
sickle cell amino acid change
glutamate to valine (A to T)
HbC amino acid change
glutamate to lysine
What are the two types of mutations known to cause hereditary persistence of fetal hemoglobin?
- large deletions (bring downstream enhancer closer to beta locus than gamma)
- promotor mutations destroy binding site of a repressor, relieving postnatal repression of gamma
clinical features of beta thalassemias
- dense skull/marrow expansion
- enlarged spleen
- osteopenia
Achondroplasia has ___% penetrance
100%
achondroplasia
- missense mutation of FGFR3 (gly to arg)
- gain of function (increases activity of protein interfering with skeletal development)
neurofibromatosis type I has a __________ mutation
loss of function (of a tumor suppressor gene)
tuberous sclerosis
- Autosomal dominant
- skin abnormalities, renal cysts, seizures, cognitive impairments, ADHD, autism
Tuberous sclerosis exhibits ________ penetrance and ________ expressivity
full, variable
Tuberous sclerosis has a __________ mutation on chromosomes ___ and ___
loss of function; 9,16
Osteogenesis imperfecta exhibits __________ expressivity
variable
clinical features of fragile x syndrome
- moderate intellectual disability with dysmorphic facial features
- autistic behavior, hand flapping
- aggression
- long face, large ears
X-linked dominant diseases
Fragile X, Rickets, Rett Syndrome
Lesch-Nyhan syndrome
- overproduction of uric acid (HPRT1 gene, recycling purines)
- X-linked recessive
- cerebral palsy
- self-injury
diseases of mitochondrial inheritance
- Kearns-Sayre syndrome: somatic mutation, single large deletion, eye paralysis, heart disease
- MELAS: mitochondrial encephalomyopathy, lactic acidosis, stroke-like episodes (stroke, seizures, muscle weakness)
- MERRF: myoclonic epilepsy with ragged-red fibers (muscle symptoms, seizures, dementia)
- Leber Hereditary Optic Neuropathy
characteristics of epigenetic phenomena (4)
- different gene expression pattern/phenotype, identical genome
- inheritance through cell division (even generations)
- like a switch (on/off)
- erase-able (interconvertible)
methylation only occurs on ___________
cytosine
diseases with loss of function mutation
- Duchenne muscular dystrophy (nonsense, frameshift)
- HNPP (deletion of gene)
- osteogenesis imperfecta type I (nonsense, frameshift)
diseases with gain of function mutation
- Hb Kempsey (missense)
- charcot marie tooth (duplication of PMP22)
8 steps where mutation can disrupt production of a normal protein
- transcription (thalassemia, HPFH)
- translation (thalassemia)
- polypeptide folding (hemoglobinopathy)
- post-translational folding (l-cell disease)
- assembly of holomeric protein (osteogenesis imperfecta)
- localization of polypeptide or holomer (familial hypercholesterolemia)
- co-factor or prosthetic group binding (homocystinurea)
- function of correctly folded protein (Hb Kempsey)
Fragile X syndrome consists of FXTAS triple repeats in the ___________
5’-UTR
During M phase of the cell cycle, (high/low) CDK (prevents/allows) buildup of the pre-replication complex
high, prevent
During S phase of the cell cycle, (high/low) CDK (prevents/allows) buildup of the pre-replication complex
low, allow
functions of epithelial tissues
- barrier to microorganisms and toxins
- selective transport into and out of body
- biochemical modification of molecules and metabolites
- special reception of stimuli
- self-renewal
What do desmosomes/adherence junctions regulate?
tightness of specific cell junctions
Hemidesmosomes contain __________ that provide membrane attachment to epithelia and connect __________ to ____________
integrins; connective tissue, the lamina
Focal adhesions connect basal lamina to ___________
intracellular components inside epithelial cells
One regulatory protein of epithelial stem cells is ______
wnt
Wnt inhibits ____________ by binding at the cell surface and setting off a signaling cascade
differentiation
Name the two most common pathogens in CF lungs
- staph
- pseudomonas
Without CFTR, cells have elevated levels of import of ____ into epithelia
Na+
Ivacaftor is a CFTR _________ for people with at least one G551D mutation
potentiator
Lumacaftor/ivacaftor is a CFTR _________ and _________ for people with two copies of _______ mutation
corrector, potentiator; F508del
Motile cilia are …
- multiciliated
- differentiated
Sensory cilia detect _________ stimuli
physical (mechanical strain, temperature, osmolality, gravity), light, and chemical
____ ligand binds to patched, extrudes it from the cilium, allowing for __________ protein to activate the GLE transcriptional activator
hedgehog, smoothin
The hedgehog ligand contributes to _________ and _________ formation and neurogenesis
limb, bone
Bardet-Biedl syndrome has a problem with _______________
ciliary-trafficking (transport problem)
Lymphocytes make __________ when activated
antibodies
What is the function of myofibroblasts?
exert pressure on an area to restrict blood loss and close a wound; die after wound heals
Chondrocytes form from _________ and secrete _____________
mesenchymal cells, cartilaginous ECM
The chondrocytic matrix is covered with ____________
perichondrium
Hyaline cartilage is made of ___________ and _______ that promote hydration and flexibility
proteoglycans, GAGs
Two processes that lead to bone formation
- intramembranous ossification (directly from mesenchymal cells)
- endochondrial ossification (template cartilaginous bone)
Osteoporosis leads to a decrease in _________ due to a defect in _________________
bone mass, resorption/formation coupling
Rickets cause an abnormal increase in ____________ by interfering with mineralization
uncalcified osteoid
The tunica intima is made mostly of _________________
stratified squamous epithelium
The tunica media and tunica adventitia are made largely of _____________
smooth muscle, collagen
The tunica intima of elastic arteries is made largely of…
- endothelial cells
- fibroblasts
- connective tissue
A portal system goes from _____________ to _______________
capillary bed, capillary bed
Titin connects the _______ to the _______ in the sarcomere
Z line, M line
Epimysium surrounds a _________
muscle
Perimysium is a connective tissue that surrounds __________
each muscle fascicle
Endomysium is a connective tissue that surrounds and invests __________
muscle cells
How is skeletal muscle tension graded?
- frequency of APs fired
- number of motor units recruited for contraction
What are satellite cells?
specialized stem cells that produce new skeletal muscle cells (instead of replacing cells, they fuse to form larger muscle fibers - good to build muscle when exercising)
How is cardiac and smooth muscle tension graded?
- cell length
- neurotransmitter/hormone receptor activity
Hedgehog signaling leads to…
- limb formation
- bone formation
- neurogenesis
Bardet-Biedl proteins faciliate…
vesicle transport to and within the cilium (receptor transport)
Fibrillars
interact end-to-end and bundle together to form fibers
fibril-associated collagens
- attached to fibrillars
- connect to basal tissue, underlie epithelium
network-forming collagens
-form thin sheet networks inside basal lamina
Osteoclasts derive from…
monocytes in the blood that differentiate
Parathyroid stimulates Ca _______ and bone _________
release, resorption
Calcitonin stimulates Ca ________ and bone _________
decreased Ca release, deposition
_____________ of the myosin light chain controls the actin-myosin interaction in smooth muscle
phosphorylation
T/F: Smooth muscle lacks both a tropomyosin complex and t-tubule system
true
You see a young, healthy athlete with a murmur and personal/family history of sudden cardiac death. You suspect…
hypertrophic cardiomyopathy
Myostatin is normally made and secreted by muscles as a (positive/negative) feedback for muscle growth
negative
Malignant hyperthermia is a __________ disorder
dominant
Malignant hypothermia has a(n) ______ mutation
RyR1
If a patient in surgery has masseter spasms and hyperthermia, you should think about _____________
malignant hyperthermia
If a patient has malignant hyperthermia, you should give them _____________
dantrolene
In classic DMD, cardiomyopathy is seen in ________ cases by age 18
most/all (close to 100%)
Elastin is secreted by __________
fibroblasts
50% of non-small cell lung cancers are ____________
adenocarcinomas
What genes are commonly mutated in hypertrophic cardiomyopathy?
sarcoplasmic genes
What is the mechanism for increasing muscle length?
recruiting myoblasts and increasing number of nuclei
Roles of mitochondria in cell death (4)
- generate ROS
- regulate cytosolic Ca
- supply energy to the cell
- release cytochrome c
Cilia contain (actin/microfilaments/microtubules)
microtubules
______ cleaves the two cells in half during mitosis
actin
Connective tissue is (loose/tight)
loose
Components of connective tissue
- collagen
- elastin
- fibroblasts
- proteoglycans
- GAGs
- lymphocytes
Epithelia have (big/small) nuclei
big
The nuclei of lymphocytes stains (light/dark) because…
dark; the chromatin is compact
The nucleus of fibroblasts is…
flat, long, isolated
The CT skin dermis contains (high/low) cell density and (light/dark) nuclei stain
low, light
The CT of the small intestine has (high/low) cell density and (light/dark) nuclei stain
high, dark
Calcified bone has a _________ stain
dense
Osteocytes are embedded in a _________
lacunae
Osteoclasts have ___ nuclei, (dark/light) stain, and are (large/small) cells
2+, dark, large
Skeletal muscle have ___ nuclei located _________ and stains _______
2, on the periphery, light
Causes of down syndrome (3)
95% trisomy 21
3-4% Robertsonian translocation
1% mosaicism
High __________ heterogeneity in patients with beta thalassemia means that most people are _____________________
allelic; compound heterozygotes
Fis1 and Drp are used for ___________
fission
Mfn and OPA1 are used for _________
fusion
How is the ATP transported out of the mitochondria once made?
via ATP-ADP antiporter
___________ tissues are avascular
epithelial
Key proteins of tight junctions are ________ and __________
occludins, claudins
Adherence junctions link _______________ and other adapter/signaling proteins in the cytoplasm
actin filaments
Desmosomes contain cadherins that like to _____________ and other adapter proteins
intermediate filaments
Epithelial cells directly connect to basal laminae by attachment of ___________ and _________ on the basal surface of the epithelial cell to basal lamina
hemidesmosomes, focal adhesions
Homozygous dominant inheritance for achondroplasia is ___________
lethal
Genetic linkage studies assume that multiplex families…
share genome segments that are disproportionately co-inherited
Multiple testing corrections must be included for ____________________
gene association studies
What markers are typically used in genetic linkage studies?
microsatellites
The first test confirming diagnosis of PWS is __________________
methylation testing
In Huntington’s, what is the significance of excessive repeated sequences?
formation of a novel property toxic protein
A patient with alpha-thalassemia major produces ______ and ______ but no _________
Bart’s hemoglobin, HbH; fetal Hb
recurrence risk of having a child with Trisomy 21
1/100 + age-related risk
FISH can determine ____________
karyotype (ie: amniocentesis + FISH for trisomy 21)
When a disease is rare, you can assume that 2pq estimates ____
2q
Paternal error in meiosis I results in __________ and paternal error in meiosis II results in ___________
XXY, XYY
Pharmacogenetics is the _____________________
examination of individual alleles and their differences
When in the cell cycle are CDK levels high?
S and M phases
The large subunit of a ribosome contains the _________
peptidyl transferase center
ATP contains a _____________ bond
phosphoanhydride
DNA polymerase cannot initiate synthesis of new strands of DNA without _____________
an RNA primer
RNA primers are removed by __________ pol I
5’-3’
In screening for CF in newborns, blood tests measure _________________
immunoreactive trypsinogen
Lesch-Nyhan disease is caused by a defect in ________________
recycling purines
(acidic/basic) pH decreases melting temperature
basic
What is an example of DNA base methylation?
cytosine to 5’-methylcytosine
What is an example of deamination of DNA bases?
cytosine deaminated = uracil
-if uracil gets methylated, get thymine
siRNA vs. miRNA
siRNA: perfect match, cleaves RNA
miRNA: imperfect match, inactivates RNA
Primase catalyzes ___________ to begin DNA replication
addition of the RNA primer
_____ is the cofactor for ligase in eukaryotes and _____ is the cofactor for ligase in prokaryotes
ATP, NAD+
RNA Pol I makes ____, RNA Pol II makes ____, and RNA Pol III makes _____
rRNA; miRNA, snRNA, mRNA; tRNA
In fragile X, methylated DNA recruits __________
HDACs, silencing transcription
Beta-thalassemia involves a mutation in the ___________
TATA box (CATA to CATG)
Gamma-delta-beta thalassemia involves a mutation in _________________
the locus of control region
What are the two classes of DNA activators/repressors?
- sequence-specific DNA binding proteins
- cofactors
Zinc finger proteins include _________ and ___________ receptors
androgen, estrogen
Swi and sf are examples of __________________
ATP-dependent chromatin remodelers (open chromatin, expose DNA for binding via hydrolysis)
Rubenstein-Taybi syndrome involves a mutation in ______ binding protein, activating a ____
CREB, HAT
What is interferon stimulation?
Cells make interferons in response to viral RNA and the interferons bind to other cells to downregulate their translation
piRNAs are involved in ________________
mobile element silencing
steps to detecting HbS mutation in Sickle Cell
- digest patient’s DNA with MstII restriction enzyme
- electrophorese
- Southern blot
What does exome sequencing detect?
novel coding SNPs among patients with the same rare Mendelian disorder
____% of the genome is GC rich and ____% of the genome is AT rich
38%, 54%
alternate vs. adjacent segregation
alternate: centromeres of homologues go to opposite poles
adjacent: adjacent centromeres go to same pole
In primordial germ cells, ….
females = (maternally/paternally) methylated
males = (maternally/paternally) methylated
females = (maternally) methylated males = = (paternally) methylated
FISH probes detect small deletions, such as in __________ or ____________
Down Syndrome, leukemia
Locus specific identifier FISH probe
deletion/duplication of chromosomes
-p53, cancer
chromosomal microarrays can detect __________ and ___________ but not ______________
deletions and duplications, not translocations
pharmacokinetics (4)
absorption, distribution, metabolism, excretion of drugs
CYP3A
drug: cyclosporine (immunosuppressant)
inhibitors: grapefruit juice, ketoconazole
inducer: rifampicin
_______________ make up the bulk of the ECM in CT
fibroblasts
What type of tissue is a gland?
epithelial
Steps of smooth muscle contraction
- Ca binds to calmodulin
- Ca-calmodulin activate CaM kinase
- phosphorylation of myosin light chain head
- power stroke
____________ allow capillaries and post-capillary venues to contract despite having no smooth muscle
pericytes
Maturity onset diabetes is an example of _____________
variable expressivity
(a-/a-) is more common in ___________ and (aa/–) is more common in ____________
Africans, SE Asians
You need to know the __________ for FISH
genetic sequence (because you have to know what the complement should bind to)
T/F: Most ECM in bone is calcified
true
Von-Hippel Lindeau has __________ penetrance and ____________ variable expressivity
high, high
Why is administering insulin and glucose a good treatment for hyperkalemia?
facilitates glucose uptake into cell, bringing K+ with it (activates Na-K pump)
What is the function of the S5/6 domains of Nav/Kv ion channels?
form ion-conducting pathway and selectivity filters
The safety factor for an action potential is _________ at the branch point
lowest
What is a karyopherin?
importin/exportin
-shuttles cargo across the nuclear envelope
Intrinsic mechanism for apoptosis
- Bim cancels effect of Bcl-2
- Bax and Bak activated
- cytochrome c leaves mitochondria, interacts with Apaf-1
- activates caspase 9, caspase 3, apoptosis
extrinsic mechanism for apoptosis
- cytotoxic T cells up regulate CD95L/FasL
- ligand cross-links to infected cell
- recruits FADD adapter
- caspase 8, caspase 3, apoptosis
___________ is a drug that stabilizes microtubules, shutting down mitosis
paclitaxel
What is the role of abiraterone on prostate cancer?
-blocks CYP17 (androgen production in tumor?
What is the role of enzalutamide in prostate cancer?
-inhibits nuclear translocation
Two types of fibrillar proteins
collagen, elastin
Two types of matrix metalloproteases (MMPs)
fibronectin, laminin (participate in remodeling ECM)
