46 SEC TION II BIOCHEMISTRY BIOCHEMISTRY—CELLULAR

BIOCHEMISTRY—CELLULAR

Cell cycle phases Checkpoints control transitions between phases of cell cycle. This process is regulated by cyclins,
cyclin-dependent kinases (CDKs), and tumor suppressors. M phase (shortest phase of cell cycle)
includes mitosis (prophase, prometaphase, metaphase, anaphase, telophase) and cytokinesis
(cytoplasm splits in two). G1 and G0 are of variable duration.
REGULATION OF CELL CYCLE
Cyclin-dependent Constitutively expressed but inactive when not bound to cyclin.
kinases
Cyclin-CDK complexes Cyclins are phase-specific regulatory proteins that activate CDKs when stimulated by growth
factors. The cyclin-CDK complex can then phosphorylate other proteins (eg, Rb) to coordinate
cell cycle progression. This complex must be activated/inactivated at appropriate times for cell
cycle to progress.
Tumor suppressors p53 p21 induction CDK inhibition Rb hypophosphorylation (activation) G1-S
progression inhibition. Mutations in tumor suppressor genes can result in unrestrained cell
division (eg, Li-Fraumeni syndrome).
Growth factors (eg, insulin, PDGF, EPO, EGF) bind tyrosine kinase receptors to transition the cell
from G1 to S phase.
CELL TYPES
Permanent Remain in G0, regenerate from stem cells. Neurons, skeletal and cardiac muscle, RBCs.
Stable (quiescent) Enter G1 from G0 when stimulated. Hepatocytes, lymphocytes, PCT, periosteal cells.
Labile Never go to G0, divide rapidly with a short G1. Bone marrow, gut epithelium, skin, hair

hᵈ↑paam
Most affected by chemotherapy. follicles, germ cells.
""

wéᵈᵈÑan sm-iiʰin%?
"
MMM
Li-Fraumeni syndrome

naÉ↓mnÑⁿwon
DNA damage (loss of function)
p53
HPV E6 ,

Red
Breast
p21 BCL-2

G2 M
Sarcoma
Mit
osi
s Apoptosis
sis
Cell cycle arrest (intrinsic pathway)
ne
oki p21
Cy t

retinoblastoma
Cyclin
CDK
→
GO
Rb E2F
wngbaiooongm.ae
DNA

IN

Cyclin
ER
th
T

PH CDK
Sy

he ASE G1
ro
nt

sis G

S Rb P E2F
P
P Gene transcription
Rb, p53 modulate
G1 restriction point New DNA synthesis
?⃝
 BIOCHEMISTRY BIOCHEMISTRY—CELLULAR SEC TION II 47

Rough endoplasmic Site of synthesis of secretory (exported) proteins N-linked glycosylation occurs in the
reticulum and of N-linked oligosaccharide addition to eNdoplasmic reticulum.
lysosomal and other proteins. Mucus-secreting goblet cells of small intestine
Nissl bodies (RER in neurons)—synthesize and antibody-secreting plasma cells are rich in
peptide neurotransmitters for secretion. RER.
Free ribosomes—unattached to any membrane; Proteins within organelles (eg, ER, Golgi bodies,
site of synthesis of cytosolic, peroxisomal, and lysosomes) are formed in RER.
mitochondrial proteins.

Smooth endoplasmic Site of steroid synthesis and detoxification of Liver hepatocytes and steroid hormone–
reticulum drugs and poisons. Lacks surface ribosomes. producing cells of the adrenal cortex and
Location of glucose-6-phosphatase (last step in gonads are rich in SER.
both glycogenolysis and gluconeogenesis). -

Cell trafficking GOlgi is distribution center for proteins and lipids from ER to vesicles and plasma membrane.
Posttranslational events in O-oligosaccharides include modifying N-oligosaccharides on asparagine,
adding O-oligosaccharides on serine and threonine, and adding mannose-6-phosphate to proteins
for lysosomal and other proteins.
Endosomes are sorting centers for material from outside the cell or from the Golgi, sending it to
lysosomes for destruction or back to the membrane/Golgi for further use.
I-cell disease (inclusion cell disease/mucolipidosis type II)—inherited lysosomal storage disorder
(autosomal recessive); defect in N-acetylglucosaminyl-1-phosphotransferase failure of the
Golgi to phosphorylate mannose residues ( mannose-6-phosphate) on glycoproteins enzymes
secreted extracellularly rather than delivered to lysosomes lysosomes deficient in digestive
-

enzymes build-up of cellular debris in lysosomes (inclusion bodies). Results in coarse facial
M¥o
-
features, gingival hyperplasia, corneal clouding, restricted joint movements, claw hand deformities,

g-wveio.T-a-ngm.su?Egtf.nI-ma:ngu&odon8
Key:
uuogbieñdapg
kyphoscoliosis, and plasma levels of lysosomal enzymes. Often fatal in childhood.
Signal recognition particle (SRP)
brane
Abundant, cytosolic ribonucleoprotein that
Clathrin a mem traffics polypeptide-ribosome complex
sm
Pla
Secretory from the cytosol to the RER. Absent or
vesicle
COPI Late Early dysfunctional SRP accumulation of
endosome endosome protein in cytosol.
COPII
Lysosome Vesicular trafficking proteins
Retrograde trans COPI: Golgi Golgi (retrograde); cis-Golgi
ER.
Anterograde
Golgi COPII: ER cis-Golgi (anterograde). nuoiidong
apparatus “Two (COPII) steps forward (anterograde); one
(COPI) step back (retrograde).”
Clathrin: trans-Golgi lysosomes; plasma
cis
membrane endosomes (receptor-
mediated endocytosis [eg, LDL receptor
Rough
endoplasmic
reticulum
activity]).
LAM www.tiboiotsois
↓↓
lioehtdhenmltsdl
Nuclear envelope

Liioiinoiibaohat :

TH protein
groin : Tltlipididtctuoag
48 SEC TION II BIOCHEMISTRY BIOCHEMISTRY—CELLULAR

Peroxisome Membrane-enclosed organelle involved in:

β-oxidation of very-long-chain fatty acids (VLCFA) (strictly peroxisomal process)
α-oxidation of branched-chain fatty acids (strictly peroxisomal process)
Catabolism of amino acids and ethanol phaingoaoaa , ethanol
Synthesis of cholesterol, bile acids, and plasmalogens (important membrane phospholipid,
especially in white matter of brain)
Nstthuong
Zellweger syndrome—autosomal recessive disorder of peroxisome biogenesis due to mutated PEX
genes. Hypotonia, seizures, hepatomegaly, early death.
Refsum disease—autosomal recessive disorder of α-oxidation buildup of phytanic acid due
to inability to degrade it. Scaly skin, ataxia, cataracts/night blindness, shortening of 4th toe,

lofhuyet~tudnguiong-kine .in
epiphyseal dysplasia. Treatment: diet, plasmapheresis.
NSTX
Adrenoleukodystrophy—X-linked recessive disorder of β-oxidation due to mutation in ABCD1
gene VLCFA buildup in adrenal glands, white (leuko) matter of brain, testes. Progressive
disease that can lead to adrenal gland crisis, progressive loss of neurologic function, death.

Proteasome Barrel-shaped protein complex that degrades damaged or ubiquitin-tagged proteins. Defects in the
ubiquitin-proteasome system have been implicated in some cases of Parkinson disease.

Cytoskeletal elements A network of protein fibers within the cytoplasm that supports cell structure, cell and organelle
movement, and cell division.
TYPE OF FILAMENT PREDOMINANT FUNCTION EXAMPLES
Microfilaments Muscle contraction, cytokinesis Actin, microvilli.
Intermediate Maintain cell structure Vimentin, desmin, cytokeratin, lamins, glial
filaments fibrillary acidic protein (GFAP), neurofilaments.
Microtubules Movement, cell division Cilia, flagella, mitotic spindle, axonal trafficking,
centrioles.

Microtubule
Dynactiy
Cylindrical outer structure composed of a Drugs that act on microtubules (microtubules
Positive
helical array of polymerized heterodimers get constructed very terribly):
end (+) of α- and β-tubulin. Each dimer has 2 GTP Mebendazole (antihelminthic)
Heterodimer bound. Incorporated into flagella, cilia, mitotic Griseofulvin (antifungal)
spindles. Also involved in slow axoplasmic Colchicine (antigout)
transport in neurons. Vinca alkaloids (anticancer)
Molecular motor proteins—transport cellular Taxanes (anticancer)
cargo toward opposite ends of microtubule. Negative end near nucleus.
Protofilament Retrograde to microtubule (+ −)—dynein. Positive end points to periphery.
Anterograde to microtubule (− +)—kinesin.
Negative Clostridium tetani toxin, herpes simplex virus, Ready? Attack!

d-
1¥
end (–) poliovirus, and rabies virus use dynein for
retrograde transport to the neuronal cell body.

uonvuén .

dad
 BIOCHEMISTRY BIOCHEMISTRY—CELLULAR SEC TION II 49

Cilia structure 9 doublet + 2 singlet arrangement of Kartagener syndrome—autosomal recessive

microtubules A .
Basal body (base of cilium below cell
dynein arm defect immotile cilia loirgdichuyei
dysfunctional ciliated epithelia. Findings:
membrane) consists of 9 microtubule developmental abnormalities due to impaired
triplets B with no central microtubules. migration and orientation (eg, situs inversus C ,
Axonemal dynein—ATPase that links peripheral hearing loss due to dysfunctional eustachian
9 doublets and causes bending of cilium by tube cilia); recurrent infections (eg, sinusitis,
VLTL
differential sliding of doublets. ear infections, bronchiectasis due to impaired
Gap junctions enable coordinated ciliary ciliary clearance of debris/pathogens); Khang
movement. infertility ( risk of ectopic pregnancy due to Sinh
dysfunctional fallopian tube cilia, immotile Chong
spermatozoa). Lab findings: nasal nitric oxide nhteoñ
(used as screening test).
tñong
A B C
Dynein
arm R L
Microtubule
A
Microtubule
B
Nexin

Sodium-potassium Na+-K+ ATPase is located in the plasma 2 strikes? K, you’re still in. 3 strikes? Nah, you’re
pump membrane with ATP site on cytosolic side. For out!
each ATP consumed, 2 K+ go in to the cell Cardiac glycosides (digoxin and digitoxin)
(pump dephosphorylated) and 3 Na+ go out of directly inhibit Na+-K+ ATPase indirect
the cell (pump phosphorylated). inhibition of Na+/Ca2+ exchange [Ca2+]i
cardiac contractility.

Extracellular
3Na+ 2K+
space

Plasma
membrane
P
Cytosol 2K+
3Na+ ATP ADP P
50 SEC TION II BIOCHEMISTRY BIOCHEMISTRY—CELLULAR

COLLAGEN
Collagen Most abundant protein in the human body. Type I - Skeleton
Extensively modified by posttranslational Type II - Cartilage
modification. Type III - Arteries
Organizes and strengthens extracellular matrix. Type IV - Basement membrane
pianos SCAB
Type I Most common (90%)—Bone (made by Type I: bone, tendone.
osteoblasts), Skin, Tendon, dentin, fascia, production in osteogenesis imperfecta type I.
gia-cmo.ec
cornea, late wound repair.

a-pgtma.CO
Type II Cartilage (including hyaline), vitreous body, Type II: cartwolage.
nucleus pulposus.
Type III Reticulin—skin, blood vessels, uterus, fetal Type III: deficient in vascular type of Ehlers-
tissue, early wound repair. Danlos syndrome (threE D).
Type IV Basement membrane (basal lamina), lens. Type IV: under the floor (basement membrane).
Defective in Alport syndrome; targeted by
autoantibodies in Goodpasture syndrome.

Collagen synthesis and structure

Synthesis—translation of collagen α chains
Fibroblast Preprocollagen
Pro α-chain backbone (Gly-X-Y)
(preprocollagen)—usually Gly-X-Y (X and
Y are proline or lysine). Collagen is 1⁄3
Nucleus
OH
Hydroxylation of proline and glycine; glycine content of collagen is less
OH lysine (requires vitamin C)
Collagen mRNA - variable than that of lysine and proline.
Sugar
Glycosylation
Hydroxyproline is used for lab quantification
Cytoplasm OH
OH of collagen.
RER
Hydroxylation—hydroxylation

Golgi
Procollagen ⑦ri3cai
Triple helix formation (“hydroxCylation”) of specific proline
and lysine residues. Requires vitamin C;
deficiency scurvy.
Exocytosis
Glycosylation—glycosylation of pro-α-chain
Extracellular
hydroxylysine residues and formation of
space procollagen via hydrogen and disulfide
0 Cleavage of procollagen
C- and N-terminals
bonds (triple helix of 3 collagen α chains).
_ Problems forming triple helix osteogenesis
Tropocollagen
imperfecta.
Formation of cross-links Exocytosis—exocytosis of procollagen into
(stabilized by lysyl oxidase) extracellular space.
Proteolytic processing—cleavage of
Collagen fiber
disulfide-rich terminal regions of procollagen

scurvy / insoluble tropocollagen.

vooimaqhmanisatngddgayvo Cross-linking—reinforcement of many

staggered tropocollagen molecules by

gaii⑨
C
tweet vitamin covalent lysine-hydroxylysine cross-linkage
(by copper-containing lysyl oxidase) to make
collagen fibrils. Cross-linking of collagen
increases with age. Problems with cross-
linking Menkes disease.
 BIOCHEMISTRY BIOCHEMISTRY—CELLULAR SEC TION II 51
taoxbattoan puff
Osteogenesis Genetic bone disorder (brittle bone May be confused with child abuse.
imperfecta disease) caused by a variety of gene defects Treat with bisphosphonates to fracture risk.
A
(most commonly COL1A1 and COL1A2). Patients can’t BITE:
Most common form is autosomal dominant Bones = multiple fractures
with production of otherwise normal type I I (eye) = blue sclerae nanhaingm.ae
collagen (altered triple helix formation). Teeth = dental imperfections
Upper Manifestations include: Ear = hearing loss raingbattoan
extremity Multiple fractures and bone deformities
B
(arrows in A ) after minimal trauma (eg,
during birth)
Blue sclerae B due to the translucent
connective tissue over choroidal veins
Some forms have tooth abnormalities,
including opalescent teeth that wear easily
due to lack of dentin (dentinogenesis
imperfecta)
Conductive hearing loss (abnormal ossicles)

}
Ehlers-Danlos type Faulty collagen synthesis causing A B
syndrome hyperextensible skin A , hypermobile joints B ,
daatan and tendency to bleed (easy bruising).

not Multiple types. Inheritance and severity vary.

Can be autosomal dominant or recessive. May
be associated with joint dislocation, berry and
aortic aneurysms, organ rupture.
Hypermobility type (joint instability): most
common type. tatngvot
Classical type (joint and skin symptoms):
caused by a mutation in type V collagen (eg,

dqngmacfiman
COL5A1, COL5A2).
Vascular type (fragile tissues including vessels
[eg, aorta], muscles, and organs that are prone
to rupture [eg, gravid uterus]): mutations in
type III procollagen (eg, COL3A1).

Menkes disease X-linked recessive connective tissue disease caused by impaired copper absorption and transport
due to defective Menkes protein ATP7A (Absent copper), vs ATP7B in Wilson disease (copper
Buildup). Leads to activity of lysyl oxidase (copper is a necessary cofactor) defective collagen.
be
Results in brittle, “kinky” hair, growth and developmental delay, hypotonia, risk of cerebral
aneurysms.

Wilson
Curitreonggan
:
52 SEC TION II BIOCHEMISTRY BIOCHEMISTRY—LABORATORY TECHNIQUES

Elastin
d-air hot Stretchy protein within skin, lungs, large arteries, elastic ligaments, vocal cords, epiglottis,
ligamenta flava (connect vertebrae relaxed and stretched conformations).
Rich in nonhydroxylated proline, glycine, and lysine residues, vs the hydroxylated residues of
collagen.
Single Tropoelastin with fibrillin scaffolding.
elastin Stretch
Relax Cross-link
Cross-linking takes place extracellularly and gives elastin its elastic properties.
molecule
Broken down by elastase, which is normally inhibited by α1-antitrypsin.
α1-Antitrypsin deficiency results in unopposed elastase activity, which can cause COPD.
Changes with aging: dermal collagen and elastin, synthesis of collagen fibrils; cross-linking
remains normal.
NST
'
thudding
A Marfan syndrome—autosomal dominant (with variable expression) connective tissue disorder
affecting skeleton, heart, and eyes. FBN1 gene mutation on chromosome 15 (fifteen) results in
defective fibrillin-1, a glycoprotein that forms a sheath around elastin and sequesters TGF-β.
Findings: tall with long extremities; chest wall deformity (pectus carinatum [pigeon chest] or
pectus excavatum A ); hypermobile joints; long, tapering fingers and toes (arachnodactyly); cystic
medial necrosis of aorta; aortic root aneurysm rupture or dissection (most common cause of
death); mitral valve prolapse; risk of spontaneous pneumothorax. date, eoñgngu:c hot
toy
Homocystinuria—presentation similar to Marfan syndrome with pectus deformity, tall stature,
arm:height ratio, upper:lower body segment ratio, arachnodactyly, joint hyperlaxity, skin
get
hyperelasticity, scoliosis.
Marfan syndrome Homocystinuria
INHERITANCE Autosomal dominant Autosomal recessive
INTELLECT Normal Decreased
VASCULAR COMPLICATIONS Aortic root dilatation Thrombosis
LENS DISLOCATION Upward (Marfan fans out) Downward

BIOCHEMISTRY—LABORATORY TECHNIQUES

Polymerase chain Molecular biology lab procedure used to amplify a desired fragment of DNA. Useful as a diagnostic
reaction tool (eg, neonatal HIV, herpes encephalitis).
5' 3' 5' 3' 5' 3'

5' 3' 3' 5'

DNA primer
dNTP
Repeat
3' 5' 5' 3'
Double-stranded DNA
3' 5' 3' 5' 3' 5'

Denaturation—DNA is heated to ~95°C to separate the strands.

Annealing—Sample is cooled to ~55°C. DNA primers, a heat-stable DNA polymerase (Taq),
and deoxynucleotide triphosphates (dNTPs) are added. DNA primers anneal to the specific
sequence to be amplified on each strand.
Elongation—Temperature is increased to ~72°C. DNA polymerase attaches dNTPs to the
strand to replicate the sequence after each primer.
Heating and cooling cycles continue until the amount of DNA is sufficient.