First Aid for the USMLE Step 1 2022, 32nd Edition

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 32 SEC TION II Biochemistry   BIOCHEMISTRY—Molecular

` BIOCHEMISTRY—MOLECULAR

Chromatin structure DNA exists in the condensed, chromatin form to

fit into the nucleus. DNA loops twice around a
histone octamer to form a nucleosome (“beads
DNA double-helix on a string”). H1 binds to the nucleosome
and to “linker DNA,” thereby stabilizing the
chromatin fiber.
H1 histone DNA has ⊝ charge from phosphate groups.
(linker)
DNA Histones are large and have ⊕ charge from
lysine and arginine.
In mitosis, DNA condenses to form
Nucleosome Euchromatin Supercoiled chromosomes. DNA and histone synthesis
(H2A, H2B, structure occurs during S phase.
H3, H4) 2 Heterochromatin Mitochondria have their own DNA, which is
circular and does not utilize histones.

Metaphase
chromosome

Heterochromatin Condensed, appears darker on EM (labeled H Heterochromatin = highly condensed.

A
in A ; Nu, nucleolus). Sterically inaccessible, Barr bodies (inactive X chromosomes) may be
E thus transcriptionally inactive.  methylation, visible on the periphery of nucleus.
H  acetylation.
Nu

Euchromatin Less condensed, appears lighter on EM (labeled Eu = true, “truly transcribed.”

E in A ). Transcriptionally active, sterically Euchromatin is expressed.
accessible.
DNA methylation Changes the expression of a DNA segment DNA is methylated in imprinting.
without changing the sequence. Involved with Methylation within gene promoter (CpG islands)
aging, carcinogenesis, genomic imprinting, typically represses (silences) gene transcription.
transposable element repression, and X CpG methylation makes DNA mute.
chromosome inactivation (lyonization). Dysregulated DNA methylation is implicated in
Fragile X syndrome.
Histone methylation Usually causes reversible transcriptional Histone methylation mostly makes DNA mute.
suppression, but can also cause activation Lysine and arginine residues of histones can be
depending on location of methyl groups. methylated.
Histone acetylation Removal of histone’s ⊕ charge Ž relaxed DNA Thyroid hormone receptors alter thyroid
coiling Ž  transcription. hormone synthesis by acetylation.
Histone acetylation makes DNA active.
Histone deacetylation Removal of acetyl groups Ž tightened DNA Histone deacetylation may be responsible for the
coiling Ž  transcription. altered gene expression in Huntington disease.

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 Biochemistry   BIOCHEMISTRY—Molecular SEC TION II 33

Nucleotides Nucleoside = base + (deoxy)ribose (sugar).

Nucleotide = base + (deoxy)ribose + phosphate; 5′ end of incoming nucleotide bears the
linked by 3′-5′ phosphodiester bond. triphosphate (energy source for the bond).
α-Phosphate is target of 3′ hydroxyl attack.

Purines (A,G)—2 rings. Pure As Gold.

Pyrimidines (C,U,T)—1 ring. CUT the pyramid.
Thymine has a methyl.
Deamination reactions: C-G bond (3 H bonds) stronger than A-T bond
Cytosine Ž uracil (2 H bonds).  C-G content Ž  melting
Adenine Ž hypoxanthine temperature of DNA. “C-G bonds are like
Guanine Ž xanthine Crazy Glue.”
5-methylcytosine Ž thymine
Amino acids necessary for purine synthesis (cats
Uracil found in RNA; thymine in DNA. purr until they GAG):
Methylation of uracil makes thymine. Glycine
Aspartate
Glutamine
Purine (A, G) Pyrimidine (C, U, T)
Nucleoside
CO2 Carbamoyl Aspartate
Aspartate Glycine phosphate
C N C
Phosphate
N C N C
C N10–Formyl- O-
O P O-
C C tetrahydrofolate C C
N N N N O

N10–Formyl- Nitrogenous base CH₂

Glutamine
tetrahydrofolate

Deoxyribose sugar

Nucleotide

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 34 SEC TION II Biochemistry   BIOCHEMISTRY—Molecular

De novo pyrimidine Various immunosuppressive, antineoplastic, and antibiotic drugs function by interfering with
and purine synthesis nucleotide synthesis:
Pyrimidine base production Purine base production or Pyrimidine synthesis:
(requires aspartate) Ribose 5-P reuse from salvage pathway ƒ Leflunomide: inhibits dihydroorotate
(de novo requires aspartate, dehydrogenase
Glutamine + CO2 glycine, glutamine, and THF)
2 ATP
ƒ 5-fluorouracil (5-FU) and its prodrug
CPS2 (carbamoyl
phosphate capecitabine: form 5-F-dUMP, which inhibits
2 ADP + Pi + synthetase II) PRPP (phosphoribosyl
Glutamate pyrophosphate) synthetase thymidylate synthase ( dTMP)
Purine synthesis:
Carbamoyl ƒ 6-mercaptopurine (6-MP) and its prodrug
phosphate
Aspartate azathioprine: inhibit de novo purine
Leflunomide
6-MP, synthesis; azathioprine is metabolized via
PRPP
Orotic azathioprine purine degradation pathway and can lead to
acid
immunosuppression when administered with
UMP synthase UMP Mycophenolate, xanthine oxidase inhibitor
(impaired in IMP ribavirin
orotic aciduria) UDP ƒ Mycophenolate and ribavirin: inhibit inosine
ctas ide
reduucleot

Hydroxyurea AMP GMP monophosphate dehydrogenase

e
n

Purine and pyrimidine synthesis:

Ribo

dUDP CTP
ƒ Hydroxyurea: inhibits ribonucleotide
reductase
N5N10- dUMP
ƒ Methotrexate (MTX), trimethoprim (TMP),
Thymidylate

methylene THF
synthase

5-FU, and pyrimethamine: inhibit dihydrofolate

THF capecitabine
Dihydrofolate
DHF reductase ( deoxythymidine monophosphate
reductase dTMP [dTMP]) in humans (methotrexate),
bacteria (trimethoprim), and protozoa
MTX, TMP,
pyrimethamine (pyrimethamine)

CPS1 = m1tochondria, urea cycle, found in liver

and kidney cells
CPS2 = cytwosol, pyrimidine synthesis, found in
most cells

FAS1_2022_01-Biochem.indd 34 11/4/21 11:59 AM

 Biochemistry   BIOCHEMISTRY—Molecular SEC TION II 35

Purine salvage deficiencies

Nucleic acids Ribose 5-phosphate Nucleic acids

PRPP synthetase De novo synthesis
Nucleotides GMP IMP AMP
Cladribine, pentostatin
Lesch-Nyhan
syndrome
ADA
HGPRT APRT
Nucleosides Guanosine Inosine Adenosine
SCID
PRPP
Free bases Guanine PRPP Hypoxanthine Adenine
XO
Allopurinol
Xanthine
Febuxostat Degradation and salvage
XO
Uric acid
Urate oxidase (rasburicase)
Allantoin Excretion

ADA, adenosine deaminase; APRT, adenine phosphoribosyltransferase; HGPRT, hypoxanthine guanine phosphoribosyltransferase, XO, xanthine
oxidase; SCID, severe combined immune deficiency (autosomal recessive inheritance)

Adenosine deaminase ADA is required for degradation of adenosine One of the major causes of autosomal recessive
deficiency and deoxyadenosine.  ADA Ž  dATP SCID.
Ž  ribonucleotide reductase activity
Ž  DNA precursors in cells Ž  lymphocytes.
Lesch-Nyhan Defective purine salvage due to absent HGPRT, HGPRT:
syndrome which converts hypoxanthine to IMP and Hyperuricemia
guanine to GMP. Compensatory  in purine Gout
synthesis ( PRPP amidotransferase activity) Pissed off (aggression, self-mutilation)
Ž excess uric acid production. X-linked Red/orange crystals in urine
recessive. Tense muscles (dystonia)
Findings: intellectual disability, self-mutilation, Treatment: allopurinol, febuxostat.
aggression, hyperuricemia (red/orange “sand”
[sodium urate crystals] in diaper), gout,
dystonia, macrocytosis.

Genetic code features

Unambiguous Each codon specifies only 1 amino acid.

Degenerate/ Most amino acids are coded by multiple codons. Exceptions: methionine (AUG) and tryptophan
redundant Wobble—codons that differ in 3rd (“wobble”) (UGG) encoded by only 1 codon.
position may code for the same tRNA/amino
acid. Specific base pairing is usually required
only in the first 2 nucleotide positions of
mRNA codon.
Commaless, Read from a fixed starting point as a continuous Exceptions: some viruses.
nonoverlapping sequence of bases.
Universal Genetic code is conserved throughout Exception in humans: mitochondria.
evolution.

FAS1_2022_01-Biochem.indd 35 11/4/21 11:59 AM

 36 SEC TION II Biochemistry   BIOCHEMISTRY—Molecular

DNA replication Occurs in 5′ Ž 3′ direction (“5ynth3sis”) in continuous and discontinuous (Okazaki fragment) fashion.
Semiconservative. More complex in eukaryotes than in prokaryotes, but shares analogous enzymes.
Origin of Particular consensus sequence in genome AT-rich sequences (such as TATA box regions)
replication A where DNA replication begins. May be single are found in promoters and origins of
(prokaryotes) or multiple (eukaryotes). replication.
Replication fork B Y-shaped region along DNA template where
leading and lagging strands are synthesized.
Helicase C Unwinds DNA template at replication fork. Helicase halves DNA.
Deficient in Bloom syndrome (BLM gene
mutation).
Single-stranded Prevent strands from reannealing or degradation
binding proteins D by nucleases.
DNA Creates a single- (topoisomerase I) or double- In eukaryotes: irinotecan/topotecan inhibit
topoisomerases E (topoisomerase II) stranded break in the helix topoisomerase (TOP) I, etoposide/teniposide
to add or remove supercoils (as needed due to inhibit TOP II.
underwinding or overwinding of DNA). In prokaryotes: fluoroquinolones inhibit TOP II
(DNA gyrase) and TOP IV.
Primase F Makes an RNA primer on which DNA
polymerase III can initiate replication.
DNA polymerase III G Prokaryotes only. Elongates leading strand DNA polymerase III has 5′ Ž 3′ synthesis and
by adding deoxynucleotides to the 3′ end. proofreads with 3′ Ž 5′ exonuclease.
Elongates lagging strand until it reaches Drugs blocking DNA replication often have a
primer of preceding fragment. modified 3′ OH, thereby preventing addition of
the next nucleotide (“chain termination”).
DNA polymerase I H Prokaryotes only. Degrades RNA primer; Same functions as DNA polymerase III, also
replaces it with DNA. excises RNA primer with 5′ Ž 3′ exonuclease.
DNA ligase I Catalyzes the formation of a phosphodiester Joins Okazaki fragments.
bond within a strand of double-stranded DNA. Ligase links DNA.
Telomerase Eukaryotes only. A reverse transcriptase (RNA- Upregulated in progenitor cells and also often in
dependent DNA polymerase) that adds DNA cancer; downregulated in aging and progeria.
(TTAGGG) to 3′ ends of chromosomes to avoid Telomerase TAGs for Greatness and Glory.
loss of genetic material with every duplication.
G 3'
E
DNA polymerase III 5'
Topoisomerase

C A
Helicase Origin of replication
Leading strand
B
Replication fork Lagging strand 3'
Okazaki fragment 5'
D
A
Area of interest Single-stranded RNA primer
Origin of replication binding protein
Leading strand Lagging strand I
F DNA ligase
Fork Fork Primase
movement movement
G
DNA polymerase III H
Lagging strand Leading strand
DNA polymerase I

FAS1_2022_01-Biochem.indd 36 11/4/21 11:59 AM

 Biochemistry   BIOCHEMISTRY—Molecular SEC TION II 37

DNA repair
Double strand
Nonhomologous end Brings together 2 ends of DNA fragments to 5´
Double strand break
3´ 5´
Double strand break

joining repair double-stranded breaks. 3´ 5´ 3´

5´
3´
Homology not required. Part of the DNA may be
lost or translocated. Nonhomologous end joining

Homologous Requires 2 homologous DNA duplexes. DoubleAstrand break Double strand break
5´ 3´ 5´ 3´
recombination strand from damaged dsDNA 3´ is repaired 5´ 3´
5´
5´
3´
using a complementary strand from intact 3´ 5´

homologous dsDNA as a template. Homologous recombination

Nonhomologous end joining
Defective in breast/ovarian cancers with BRCA1
or BRCA2 mutations and in Fanconi anemia.
Restores duplexes accurately without loss of
nucleotides. Homologous recombination

Single strand
Nucleotide excision Specific endonucleases remove the Occurs in G1 phase of cell cycle.
repair oligonucleotides containing damaged bases; Defective in xeroderma pigmentosum
DNA polymerase and ligase fill and reseal the (inability to repair DNA pyrimidine dimers
gap, respectively. Repairs bulky helix-distorting caused by UV exposure). Presents with dry
lesions (eg, pyrimidine dimers). skin, photosensitivity, skin cancer.
Base excision repair Base-specific Glycosylase removes altered base Occurs throughout cell cycle.
and creates AP site (apurinic/apyrimidinic). Important in repair of spontaneous/toxic
One or more nucleotides are removed by deamination.
AP-Endonuclease, which cleaves 5′ end. AP- “GEL Please.”
Lyase cleaves 3′ end. DNA Polymerase-β fills
the gap and DNA ligase seals it.
Mismatch repair Mismatched nucleotides in newly synthesized Occurs predominantly in S phase of cell cycle.
strand are removed and gap is filled and Defective in Lynch syndrome (hereditary
resealed. nonpolyposis colorectal cancer [HNPCC]).

UV exposure Pyrimidine dimer Deaminated C

T T
U G

A A G A

AP U
site
TT Endonucleases remove Glycosylase removes base Mismatched segment
G
damaged segment G removed
(AP site)

A A A
Endonuclease and lyase
G remove backbone segment

Newly replaced segment

T T C T
A A G A

Nucleotide excision repair Base excision repair Mismatch repair

FAS1_2022_01-Biochem.indd 37 11/4/21 11:59 AM

 38 SEC TION II Biochemistry   BIOCHEMISTRY—Molecular

Mutations in DNA Degree of change: silent << missense < nonsense < frameshift. Single nucleotide substitutions are
repaired by DNA polymerase and DNA ligase. Types of single nucleotide (point) mutations:
ƒ Transition—purine to purine (eg, A to G) or pyrimidine to pyrimidine (eg, C to T).
ƒ Transversion—purine to pyrimidine (eg, A to T) or pyrimidine to purine (eg, C to G).
Single nucleotide substitutions
Silent mutation Codes for same (synonymous) amino acid; often involves 3rd position of codon (tRNA wobble).
Missense mutation Results in changed amino acid (called conservative if new amino acid has similar chemical
structure). Examples: sickle cell disease (substitution of glutamic acid with valine).
Nonsense mutation Results in early stop codon (UGA, UAA, UAG). Usually generates nonfunctional protein. Stop the
nonsense!
Other mutations
Frameshift mutation Deletion or insertion of any number of nucleotides not divisible by 3 Ž misreading of all
nucleotides downstream. Protein may be shorter or longer, and its function may be disrupted or
altered. Examples: Duchenne muscular dystrophy, Tay-Sachs disease.
Splice site mutation Retained intron in mRNA Ž protein with impaired or altered function. Examples: rare causes of
cancers, dementia, epilepsy, some types of β-thalassemia, Gaucher disease, Marfan syndrome.
Original Silent Missense Nonsense Frameshift Frameshift
sequence mutation mutation mutation insertion deletion
T G

Coding DNA
5´
GAG GAA GTG TAG GA G GA C 3´

mRNA codon
5´
GAG GAA GUG UAG GAU GAC 3´
Amino acid Glu Glu Val Stop Asp Asp

Altered amino acids

Lac operon Classic example of a genetic response to an environmental change. Glucose is the preferred
metabolic substrate in E coli, but when glucose is absent and lactose is available, the lac operon is
activated to switch to lactose metabolism. Mechanism of shift:
ƒ Low glucose Ž  adenylate cyclase activity Ž  generation of cAMP from ATP Ž activation of
catabolite activator protein (CAP) Ž  transcription.
ƒ High lactose Ž unbinds repressor protein from repressor/operator site Ž  transcription.
Genes
CAP
Adenylate Lacl site P O LacZ LacY LacA
CAP cAMP cyclase Glucose DNA 5′ 3′

AUG AUG AUG

Messenger RNA
Binds CAP site, ATP
induces transcription
RNA
Lac operon STATE CAP polymerase
Low glucose
Lactose available
Lac genes strongly expressed
Lacl CAP site Promoter Operator LacZ LacY LacA Repressor protein
High glucose
o r, Lactose unavailable
e ra t o n Lac genes not expressed
Binds opnscripti
blocks tra
Low glucose
Repressor Lactose unavailable Lac genes not expressed
protein CAP
High glucose
site P O
Lactose available Very low (basal) expression
Allolactose Inactivated
(inducer) repressor

FAS1_2022_01-Biochem.indd 38 11/4/21 11:59 AM

 Biochemistry   BIOCHEMISTRY—Molecular SEC TION II 39

Functional Enhancer/
silencer Promoter 5´ UTR Open reading frame 3´ UTR Silencer
organization of a
eukaryotic gene Exon Intron Exon Intron Exon

DNA 5´ CAAT TATAAA GT AG GT AG AATAAA 3´

(coding strand)
CAAT Box TATA Box
Polyadenylation signal
Transcription start
Transcription
Exon Intron Exon Intron Exon

Pre-mRNA GU AG GU AG AAUAAA

Splicing
5´ cap
Protein coding region
Mature AAUAAA AAAAAA
mRNA
AUG start codon Stop
Poly-A tail
Translation

Protein

Regulation of gene expression

Promoter Site where RNA polymerase II and multiple Promoter mutation commonly results in
other transcription factors bind to DNA dramatic  in level of gene transcription.
upstream from gene locus (AT-rich upstream
sequence with TATA and CAAT boxes, which
differ between eukaryotes and prokaryotes).
Enhancer DNA locus where regulatory proteins Enhancers and silencers may be located close to,
(“activators”) bind, increasing expression of a far from, or even within (in an intron) the gene
gene on the same chromosome. whose expression they regulate.
Silencer DNA locus where regulatory proteins
(“repressors”) bind, decreasing expression of a
gene on the same chromosome.
Epigenetics Changes made to gene expression (heritable Primary mechanisms of epigenetic change
mitotically/meiotically) without a change in include DNA methylation, histone
underlying DNA sequence. modification, and noncoding RNA.

RNA processing Initial transcript is called heterogeneous nuclear mRNA is transported out of nucleus to be
(eukaryotes) RNA (hnRNA). hnRNA is then modified and translated in cytosol.
becomes mRNA. mRNA quality control occurs at cytoplasmic
The following processes occur in the nucleus: processing bodies (P-bodies), which contain
Cap Coding
5'
ƒ Capping of 5′ end (addition of exonucleases, decapping enzymes, and
Gppp 7-methylguanosine cap; cotranscriptional) microRNAs; mRNAs may be degraded or
3' ƒ Polyadenylation of 3′ end (∼200 A’s Ž poly-A stored in P-bodies for future translation.
HO-AAAAA
Tail
tail; posttranscriptional) Poly-A polymerase does not require a template.
ƒ Splicing out of introns (posttranscriptional) AAUAAA = polyadenylation signal. Mutation
Capped, tailed, and spliced transcript is called in polyadenylation signal Ž early degradation
mRNA. prior to translation.

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 40 SEC TION II Biochemistry   BIOCHEMISTRY—Molecular

RNA polymerases
Eukaryotes RNA polymerase I makes rRNA, the most I, II, and III are numbered in the same order
common (rampant) type; present only in that their products are used in protein
nucleolus. synthesis: rRNA, mRNA, then tRNA.
RNA polymerase II makes mRNA (massive), α-amanitin, found in Amanita phalloides (death
microRNA (miRNA), and small nuclear RNA cap mushrooms), inhibits RNA polymerase II.
(snRNA). Causes dysentery and severe hepatotoxicity if
RNA polymerase III makes 5S rRNA, tRNA ingested.
(tiny). Dactinomycin inhibits RNA polymerase in both
No proofreading function, but can initiate prokaryotes and eukaryotes.
chains. RNA polymerase II opens DNA at
promoter site.
Prokaryotes 1 RNA polymerase (multisubunit complex) Rifamycins (rifampin, rifabutin) inhibit DNA-
makes all 3 kinds of RNA. dependent RNA polymerase in prokaryotes.

Splicing of pre-mRNA Part of process by which precursor mRNA (pre-mRNA) is transformed into mature mRNA. Introns
typically begin with GU and end with AG. Alterations in snRNP assembly can cause clinical
disease; eg, in spinal muscular atrophy, snRNP assembly is affected due to  SMN protein
Ž congenital degeneration of anterior horns of spinal cord Ž symmetric weakness (hypotonia, or
“floppy baby syndrome”).
snRNPs are snRNA bound to proteins (eg, Smith [Sm]) to form a spliceosome that cleaves pre-
mRNA. Anti-U1 snRNP antibodies are associated with SLE, mixed connective tissue disease,
other rheumatic diseases.

Primary transcript combines with 5′ splice site U1 snRNP Branch point 3′ splice site
small nuclear ribonucleoproteins
U2 snRNP
(snRNPs) and other proteins to
form spliceosome. 5′ O P GU A AG P O 3′
Exon 1 Intron Exon 2

Spliceosome

Cleavage at 5′ splice site; lariat-

shaped (loop) intermediate is
generated. UG
P A
OH 3′ AG P O
Exon 1 Exon 2

Mature mRNA
Cleavage at 3′ splice site; lariat
is released to precisely remove
intron and join 2 exons.
P +
Exon 1 Exon 2 UG
P A
AG OH 3′

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 Biochemistry   BIOCHEMISTRY—Molecular SEC TION II 41

Introns vs exons Exons contain the actual genetic information Introns are intervening sequences and stay
coding for protein or functional RNA. in the nucleus, whereas exons exit and are
Introns do not code for protein, but are expressed.
important in regulation of gene expression. Alternative splicing—can produce a variety
Different exons are frequently combined by of protein products from a single hnRNA
alternative splicing to produce a larger number (heterogenous nuclear RNA) sequence (eg,
of unique proteins. transmembrane vs secreted Ig, tropomyosin
variants in muscle, dopamine receptors in the
brain, host defense evasion by tumor cells).

Exon 1 Exon 2 Exon 3 Exon 4 Exon 5 Exon 6

5′ 3′
DNA 3′ 5′

Transcription

hnRNA 5′ 3′
1 2 3 4 5 6
Splicing Alternative splicing

mRNA 5′ 3′ 5′ 3′ 5′ 3′
1 2 4 5 6 1 3 5 6 1 3 4 5 6

Translation

1 5 1 5 1 5
Proteins 6 6 6
4 4
2 3 3

FAS1_2022_01-Biochem.indd 41 11/4/21 11:59 AM

 42 SEC TION II Biochemistry   BIOCHEMISTRY—Molecular

tRNA
Structure 75–90 nucleotides, 2º structure, cloverleaf form, anticodon end is opposite 3′ aminoacyl end. All
tRNAs, both eukaryotic and prokaryotic, have CCA at 3′ end along with a high percentage of
chemically modified bases. The amino acid is covalently bound to the 3′ end of the tRNA. CCA
Can Carry Amino acids.
T-arm: contains the TΨC (ribothymidine, pseudouridine, cytidine) sequence necessary for tRNA-
ribosome binding. T-arm Tethers tRNA molecule to ribosome.
D-arm: contains Dihydrouridine residues necessary for tRNA recognition by the correct aminoacyl-
tRNA synthetase. D-arm allows Detection of the tRNA by aminoacyl-tRNA synthetase.
Attachment site: 3′-ACC-5′ is the amino acid ACCeptor site.
Charging Aminoacyl-tRNA synthetase (uses ATP; 1 unique enzyme per respective amino acid) and
binding of charged tRNA to the codon are responsible for the accuracy of amino acid selection.
Aminoacyl-tRNA synthetase matches an amino acid to the tRNA by scrutinizing the amino acid
before and after it binds to tRNA. If an incorrect amino acid is attached, the bond is hydrolyzed.
A mischarged tRNA reads the usual codon but inserts the wrong amino acid.
Structure Charging Pairing
(aminoacylation) (codon-anticodon)
Amino acid Amino acid
O O
Attachment site OH 3´ 3´ 3´
A A A
C C C
C C C

5´ 5´ 5´

IF2
T-arm
D-arm ATP AMP + PPi (initiation factor)
D D D
C Ψ T
Aminoacyl-tRNA C Ψ T C Ψ T
D D D
synthetase
Variable arm

Anticodon
loop U A C U A C Anticodon (5´-CAU-3´) U A C
Wobble
position C C C A U G A U A C
mRNA
Codon
(5´-AUG-3´)

Start and stop codons

mRNA start codon AUG. AUG inAUGurates protein synthesis.
Eukaryotes Codes for methionine, which may be removed
before translation is completed.
Prokaryotes Codes for N-formylmethionine (fMet). fMet stimulates neutrophil chemotaxis.
mRNA stop codons UGA, UAA, UAG. UGA = U Go Away.
Recognized by release factors. UA A = U Are Away.
UAG = U Are Gone.

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 Biochemistry   BIOCHEMISTRY—Molecular SEC TION II 43

Protein synthesis
Initiation 1. Eukaryotic initiation factors (eIFs) identify Eukaryotes: 40S + 60S Ž 80S (even).
the 5′ cap. Prokaryotes: 30S + 50S Ž 70S (prime).
2. eIFs help assemble the 40S ribosomal Synthesis occurs from N-terminus to
subunit with the initiator tRNA. C-terminus.
3. eIFs released when the mRNA and the
ATP—tRNA Activation (charging).
ribosomal 60S subunit assemble with the
GTP—tRNA Gripping and Going places
complex. Requires GTP.
(translocation).
Elongation Aminoacyl-tRNA binds to A site (except for
initiator methionine, which binds the P site), Think of “going APE”:
requires an elongation factor and GTP. A site = incoming Aminoacyl-tRNA.
rRNA (“ribozyme”) catalyzes peptide bond P site = accommodates growing Peptide.
formation, transfers growing polypeptide to E site = holds Empty tRNA as it Exits.
amino acid in A site. Elongation factors are targets of bacterial toxins
Ribosome advances 3 nucleotides toward 3′ (eg, Diphtheria, Pseudomonas).
end of mRNA, moving peptidyl tRNA to P
site (translocation). Shine-Dalgarno sequence—ribosomal binding
site in prokaryotic mRNA. Recognized by 16S
Termination Eukaryotic release factors (eRFs) recognize the
RNA in ribosomal subunit. Enables protein
stop codon and halt translation Ž completed
synthesis initiation by aligning ribosome with
polypeptide is released from ribosome.
start codon so that code is read correctly.
Requires GTP.
60/50S

40/30S

M
R
M
Initiation M M H

Initiator tRNA
U A C

U A C 5´ A U G C A U G A U 3´ U A C G U A
mRNA
E P A
5´ A U G C A U G A U 3´
E P A
S Ribosome moves left to
right along mRNA

M Elongation M
H
U G A

G U A U A C

U A C Q G U A
Termination
A U G C A U G A U A U G C A U G A U
5´ 3´ 5´ 3´
E P A E P A

Posttranslational modifications
Trimming Removal of N- or C-terminal propeptides from zymogen to generate mature protein (eg,
trypsinogen to trypsin).
Covalent alterations Phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination.

Chaperone protein Intracellular protein involved in facilitating and maintaining protein folding. In yeast, heat
shock proteins (eg, HSP60) are constitutively expressed, but expression may increase with high
temperatures, acidic pH, and hypoxia to prevent protein denaturing/misfolding.

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 44 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 is 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 Ž p21 induction Ž CDK inhibition Ž Rb hypophosphorylation (activation) Ž 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
Most affected by chemotherapy. follicles, germ cells.

Cell cycle arrest

p21 Cyclin
GO
Cyclin
CDK CDK
DNA damage Rb, p53 modulate G1
p21
G1 restriction point
th
ow
Gr

is
M

es
Li-Fraumeni syndrome

kin
to
(loss of function) Cy

Mito
p53

sis
HPV E6
IN TERPH

BCL-2 BCL-XL
Rb P
DNA

P
P
BAX/BAK
AS
Sy n

Rb E2F S
E
t he

is
s

Caspase activation E2F G2

Gene transcription
Apoptosis
(intrinsic pathway)

FAS1_2022_01-Biochem.indd 44 11/4/21 11:59 AM

 Biochemistry   BIOCHEMISTRY—Cellular SEC TION II 45

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 Hepatocytes and steroid hormone–producing
reticulum drugs and poisons. Lacks surface ribosomes. cells of the adrenal cortex and gonads are rich
Location of glucose-6-phosphatase (last step in 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 GOlgi 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 Ž failure of the
Golgi to phosphorylate mannose residues ( mannose-6-phosphate) on glycoproteins Ž enzymes
secreted extracellularly rather than delivered to lysosomes Ž lysosomes deficient in digestive
enzymes Ž buildup of cellular debris in lysosomes (inclusion bodies). Results in coarse facial
features, gingival hyperplasia, corneal clouding, restricted joint movements, claw hand deformities,
kyphoscoliosis, and  plasma levels of lysosomal enzymes. Symptoms similar to but more severe
than Hurler syndrome. Often fatal in childhood.
Key: Signal recognition particle (SRP)—abundant,
brane
cytosolic ribonucleoprotein that traffics
mem polypeptide-ribosome complex from the
Clathrin sma
Pla
Secretory cytosol to the RER. Absent or dysfunctional
vesicle
COPI Late Early SRP Ž accumulation of protein in cytosol.
endosome endosome

COPII Vesicular trafficking proteins

Lysosome ƒ COPI: Golgi Ž Golgi (retrograde); cis-Golgi
Retrograde trans Ž ER.
Anterograde ƒ COPII: ER Ž cis-Golgi (anterograde). “Two
Golgi (COPII) steps forward (anterograde); one
apparatus (COPI) step back (retrograde).”
ƒ Clathrin: trans-Golgi Ž lysosomes; plasma
membrane Ž endosomes (receptor-mediated
cis
endocytosis [eg, LDL receptor activity]).
Rough
endoplasmic
reticulum

Nuclear envelope

FAS1_2022_01-Biochem.indd 45 11/4/21 11:59 AM

 46 SEC TION II Biochemistry   BIOCHEMISTRY—Cellular

Peroxisome Membrane-enclosed organelle involved in:

ƒ β-oxidation of very-long-chain fatty acids (VLCFA) (strictly peroxisomal process)
ƒ α-oxidation of branched-chain fatty acids (strictly peroxisomal process)
ƒ Catabolism of amino acids and ethanol
ƒ Synthesis of bile acids and plasmalogens (important membrane phospholipid, especially in
white matter of brain)
Zellweger syndrome—autosomal recessive disorder of peroxisome biogenesis due to mutated PEX
genes. Hypotonia, seizures, jaundice, craniofacial dysmorphia, hepatomegaly, early death.
Refsum disease—autosomal recessive disorder of α-oxidation Ž buildup of phytanic acid due
to inability to degrade it. Scaly skin, ataxia, cataracts/night blindness, shortening of 4th toe,
epiphyseal dysplasia. Treatment: diet, plasmapheresis.
Adrenoleukodystrophy—X-linked recessive disorder of β-oxidation due to mutation in ABCD1
gene Ž 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 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 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 ƒ Mebendazole (antihelminthic)
Heterodimer bound. Incorporated into flagella, cilia, mitotic ƒ Griseofulvin (antifungal)
spindles. Also involved in slow axoplasmic ƒ Colchicine (antigout)
transport in neurons. ƒ Vinca alkaloids (anticancer)
Molecular motor proteins—transport cellular ƒ Taxanes (anticancer)
cargo toward opposite ends of microtubule. Negative end near nucleus.
Protofilament ƒ Retrograde to microtubule (+ Ž −)—dynein. Positive end points to periphery.
ƒ Anterograde to microtubule (− Ž +)—kinesin.
Negative Clostridium tetani toxin, herpes simplex virus, Ready? Attack!
end (–) poliovirus, and rabies virus use dynein for
retrograde transport to the neuronal cell body.

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 Biochemistry   BIOCHEMISTRY—Cellular SEC TION II 47

Cilia structure Motile cilia consist of 9 doublet + 2 singlet arrangement of microtubules (axoneme) A .
Basal body (base of cilium below cell membrane) consists of 9 microtubule triplets B with no
central microtubules.
Nonmotile (primary) cilia work as chemical signal sensors and have a role in signal transduction
and cell growth control. Dysgenesis may lead to polycystic kidney disease, mitral valve prolapse,
or retinal degeneration.
Axonemal dynein—ATPase that links peripheral 9 doublets and causes bending of cilium by
differential sliding of doublets.
Gap junctions enable coordinated ciliary movement.

A B
Dynein
arm
Microtubule
A
Microtubule
B
Nexin

Doublets
Triplets

Primary ciliary Also called Kartagener syndrome. Autosomal recessive. Dynein arm defect Ž immotile cilia Ž
dyskinesia dysfunctional ciliated epithelia.
Developmental abnormalities due to impaired migration and orientation (eg, situs inversus A , hearing
A
loss due to dysfunctional eustachian tube cilia); recurrent infections (eg, sinusitis, ear infections,
R L bronchiectasis due to impaired ciliary clearance of debris/pathogens); infertility ( risk of ectopic
pregnancy due to dysfunctional fallopian tube cilia, immotile spermatozoa).
Lab findings:  nasal nitric oxide (used as screening test).

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 Ž indirect
the cell (pump phosphorylated). inhibition of Na+/Ca2+ exchange Ž  [Ca2+]i Ž
 cardiac contractility.

Extracellular
3Na+ 2K+
space

Plasma
membrane
P
Cytosol 2K+
3Na+ ATP ADP P

FAS1_2022_01-Biochem.indd 47 11/4/21 11:59 AM