KAPLAN_USMLE_STEP_1_LECTURE_NOTES_2018_BIOCHEMISTRY_and_GENETICS

Part I ● Biochemistry

					3´ end
					A	OH		Activated amino
					C			acid is attached
					C			to 3´ OH.
			P	5´ end A
				C	A
				G	C
				C	G
				G	C
				G	C
				G	C				U A A
				G	C C G		G	C C
C C	G A C			U							A
		G A	G G
						G U	C	G G	T	ψ	C
U
					C
G G	D A G	C U	C G		A A	U
			U			G G
			C	G
			G	C
			G	C
			G	C
			Cm		A
			U		A
			C	A	U	Anticodon sequence (CAU)
						pairs with codon in mRNA.
		Figure I-3-10. Transfer RNA (tRNA)

RNA Editing

RNA editing is a process by which some cells make discrete changes to specific nucleotide sequences within a RNA molecule after its gene has been transcribed by RNA polymerase. Posttranscription editing events may include insertion, deletion, and base alterations of nucleotides (such as adenine deamination) within the edited RNA molecule. RNA editing has been observed in some mRNA, rRNA, and tRNA molecules in humans.

An important example is cytosine-to-uracil deamination in the apoprotein B gene. Apoprotein B100 is expressed in the liver, and apoprotein B48 is expressed in the intestines. In the intestines, the mRNA is edited from a CAA sequence to be UAA, a stop codon, thus producing the shorter apoprotein B48 form.

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Chapter 3 ● Transcription and RNA Processing

Recall Question

Which of the following is a co-transcriptional event in RNA synthesis?

A.Addition of a 7-methyl G cap

B.Splicing

C.Poly A tailing

Answer: A

Table I-3-2. Important Points About Transcription and RNA Processing

		Prokaryotic			Eukaryotic
Gene regions		May be polycistronic			Always monocistronic
		Genes are continuous coding regions			Genes have exons and introns
		Very little spacer (noncoding) DNA			Large spacer (noncoding) DNA between
		between genes			genes
RNA polymerase		Core enzyme: α2ββ′			RNA polymerase I: rRNA
					RNA polymerase II: mRNA; snRNA
					RNA polymerase III: tRNA, 5S RNA
Initiation of transcription		Promoter (–10) TATAAT and (–35)			Promoter (–25) TATA and (–70) CAAT
		sequence			Transcription factors (TFIID) bind promoter
		Sigma initiation subunit required to
		recognize promoter
mRNA synthesis		Template read 3′ to 5′; mRNA synthesized 5′ to 3′; gene sequence specified from coding
		strand 5′ to 3′; transcription begins at +1 base
Termination of transcription	Stem and loop + UUUUU			Not well characterized
	Stem and loop + rho factor
Relationship of RNA	RNA is antiparallel and complementary to DNA template strand; RNA is identical (except
transcript to DNA	U substitutes for T) to DNA coding strand
Posttranscriptional processing	None			In nucleus:
of hnRNA (pre-mRNA)				5′ cap (7-MeG)
				3′ tail (poly-A sequence)
				Removal of introns from pre-RNA
				• Alternative splicing yields variants of
					protein product
Ribosomes	70S (30S and 50S)			80S (40S and 60S)
	rRNA and protein			rRNA and protein
tRNA	Cloverleaf secondary structure
	• Acceptor arm (CCA) carries amino acid
	• Anticodon arm; anticodon complementary and antiparallel to codon in mRNA

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Part I ● Biochemistry

Review Questions

Select the ONE best answer.

1.The base sequence of codons 57-58 in the cytochrome β5 reductase gene is CAGCGC. The mRNA produced upon transcription of this gene will contain which sequence?

A.GCGCTG

B.CUGCGC

C.GCGCUG

D.CAGCGC

E.GUCGCG

2.A gene encodes a protein with 150 amino acids. There is one intron of 1,000 bps, a 5′-untranslated region of 100 bp, and a 3′-untranslated region of 200 bp. In the final processed mRNA, how many bases lie between the start AUG codon and the final termination codon?

A.1,750

B.750

C.650

D.450

E.150

Items 3–5: Identify the nuclear location.

E D

A

C

B

3.Transcription of genes by RNA polymerase 1

4.Euchromatin

5.Polyadenylation of pre-mRNA by poly-A polymerase

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Chapter 3 ● Transcription and RNA Processing

Answers

1.Answer: D. Since the sequence in the stem represents the coding strand, the mRNA sequence must be identical (except U for T). No T in the DNA means no U in the mRNA.

2.Answer: D. Only the coding region remains to be calculated 3 ×150 =450.

3.Answer: B. rRNA genes are transcribed by this enzyme in the nucleolus.

4.Answer: A. Less condensed chromatin, lighter areas in the nucleus. Darker areas are heterochromatin.

5.Answer: A. Polyadenylation of pre-mRNA occurs in the nucleoplasm. Generally associated with active gene expression in euchromatin.

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The Genetic Code,	4
ChapMutations,er Title
and Translation

Learning Objectives

Demonstrate understanding of the genetic code

Solve problems concerning mutations

Interpret scenarios about amino acid activation and codon translation by tRNAs

Demonstrate understanding of translation (protein synthesis)

Explain information related to inhibitors of protein synthesis

Interpret scenarios about protein folding and subunit assembly

Answer questions about how translation occurs on the rough endoplasmic reticulum

Demonstrate understanding of coand posttranslational covalent modifications

Solve problems concerning posttranslational modifications of collagen

TRANSLATION

The second stage in gene expression is translating the nucleotide sequence of a messenger RNA molecule into the amino acid sequence of a protein. The genetic code is defined as the relationship between the sequence of nucleotides in DNA (or its RNA transcripts) and the sequence of amino acids in a protein. Each amino acid is specified by one or more nucleotide triplets (codons) in the DNA.

During translation, mRNA acts as a working copy of the gene in which the codons for each amino acid in the protein have been transcribed from DNA to mRNA. tRNAs serve as adapter molecules that couple the codons in mRNA with the amino acids they each specify, thus aligning them in the appropriate sequence before peptide bond formation. Translation takes place on ribosomes, complexes of protein and rRNA that serve as the molecular machines coordinating the interactions between mRNA, tRNA, the enzymes, and the protein factors required for protein synthesis. Many proteins undergo posttranslational modifications as they prepare to assume their ultimate roles in the cell.

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Part I ● Biochemistry

THE GENETIC CODE

Most genetic code tables designate the codons for amino acids as mRNA sequences. Important features of the genetic code include:

•Each codon consists of 3 bases (triplet). There are 64 codons. They are all written in the 5′ to 3′ direction.

•61 codons code for amino acids. The other 3 (UAA, UGA, UAG) are stop codons (or nonsense codons) that terminate translation.

•There is one start codon (initiation codon), AUG, coding for methionine. Protein synthesis begins with methionine (Met) in eukaryotes, and formylmethionine (fMet) in prokaryotes.

•The code is unambiguous. Each codon specifies no more than one amino acid.

•The code is degenerate. More than one codon can specify a single amino acid. All amino acids, except Met and tryptophan (Trp), have more than one codon.

•For those amino acids having more than one codon, the first 2 bases in the codon are usually the same. The base in the third position often varies.

•The code is universal (the same in all organisms). Some minor exceptions to this occur in mitochondria.

•The code is commaless (contiguous). There are no spacers or “commas” between codons on an mRNA.

•Neighboring codons on a message are nonoverlapping.

First

Second Position

Third

Position

Position

U

C

A

G

(5' End)

(3' End)

UUU

}Phe

UCU

UAU

}Tyr

UGU

U

C

U

UUC

UCC

Ser

UAC

UGC}Cys

UUA

UCA

UAA

}Stop

UGA

Stop

A

UUG}Leu

UCG}

UAG

UGG

Trp

G

CUU

CCU

CAU

CGU

U

C

CUC

Leu

CCC

Pro

CAC} His

CGC

Arg

C

}

G

CUA

}

CCA

CAA

CGA

A

CUG

CCG}

CAG

Gln

CGG}

AUU

lle

ACU

AAU

}Asn

AGCAGU}Ser

U

C

A

AUC

ACC

AAC

AUA}

ACA

Thr

AAA

AGA

A

AUG

Met

ACG}

AAG}Lys

AGG}Arg

G

GUU

GCU

GAU} Asp

GGU

}

U

C

G

GUC

Val

GCC

Ala

GAC

GGC

Gly

A

GUA

GCA

GAA

GGA

GUG}

GCG}

GAG} Glu

GGG

G

Figure I-4-1. The Genetic Code

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Chapter 4 ● The Genetic Code, Mutations, and Translation

MUTATIONS

A mutation is any permanent, heritable change in the DNA base sequence of an organism. This altered DNA sequence can be reflected by changes in the base sequence of mRNA, and, sometimes, by changes in the amino acid sequence of a protein. Mutations can cause genetic diseases. They can also cause changes in enzyme activity, nutritional requirements, antibiotic susceptibility, morphology, antigenicity, and many other properties of cells.

A very common type of mutation is a single base alteration or point mutation.

•A transition is a point mutation that replaces a purine-pyrimidine base pair with a different purine-pyrimidine base pair. For example, an A-T base pair becomes a G-C base pair.

•A transversion is a point mutation that replaces a purine-pyrimidine base pair with a pyrimidine-purine base pair. For example, an A-T base pair becomes a T-A or a C-G base pair.

Mutations are often classified according to the effect they have on the structure of the gene’s protein product. This change in protein structure can be predicted using the genetic code table in conjunction with the base sequence of DNA or mRNA. A variety of such mutations is listed in Table I-4-1. Point mutations and frameshifts are illustrated in more detail in Figure I-4-2.

Table I-4-1. Effects of Some Common Types of Mutations on Protein Structure

	Type of Mutation			Effect on Protein
	Silent: new codon specifies same			None
	amino acid
	Missense: new codon specifies			Possible decrease in function;
	different amino acid			variable effects
	Nonsense: new codon is stop codon			Shorter than normal; usually nonfunc-
				tional
	Frameshift/in-frame: addition or			Usually nonfunctional; often shorter
	deletion of base(s)			than normal
	Large segment deletion (unequal			Loss of function; shorter than normal
	crossover in meiosis)			or entirely missing
	5′ splice site (donor) or 3′ splice site			Variable effects ranging from addition
	(acceptor)			or deletion of a few amino acids to
				deletion of an entire exon
	Trinucleotide repeat expansion			Expansions in coding regions cause
				protein product to be longer than
				normal and unstable.
				Disease often shows anticipation in
				pedigree.

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Part I ● Biochemistry

Normal

A T G G C A A T T C G T T T T T T A CCT A T A G G G

DNA

coding strand

Met

Ala

Ile

Arg

Phe Leu

Pro

Ile

Gly

Amino Acid

Silent

A T G G C A A T T C G T T T T T TG

CCT A T A G G G

DNA

coding strand

Mutation

Met

Ala

Ile

Arg

Phe Leu

Pro

Ile

Gly

Amino Acid

Missense

A T G G C A A T T C G T T T T T C A CC T A T A G G G

DNA

coding strand

Mutation

Met

Ala

Ile

Arg

Phe Ser

Pro

Ile

Gly

Amino Acid

Nonsense

A TG G C A A T T C G T T T T T G A CC T A T A G G G

DNA

coding strand

Mutation

Met

Ala

Ile

Arg

Phe

Stop

Amino Acid

Frameshift

A T G G C A A T T C G T T T T T A C CT A T A G G G

DNA

coding strand

Mutation

(1bp deletion)

Met

Ala

Ile

Arg

Phe Tyr

Leu

Amino Acid

Stop

Figure I-4-2. Some Common Types of Mutations in DNA

Large Segment Deletions

Large segments of DNA can be deleted from a chromosome during an unequal crossover in meiosis. Crossover or recombination between homologous chromosomes is a normal part of meiosis I that generates genetic diversity in reproductive cells (egg and sperm), a largely beneficial result. In a normal crossover event, the homologous maternal and paternal chromosomes exchange equivalent segments, and although the resultant chromosomes are mosaics of maternal and paternal alleles, no genetic information has been lost from either one. On rare occasions, a crossover can be unequal and one of the two homologs loses some of its genetic information.

α-thalassemia is a well-known example of a genetic disease in which unequal crossover has deleted one or more α-globin genes from chromosome 16. Cri-du- chat (mental retardation, microcephaly, wide-set eyes, and a characteristic kittenlike cry) results from a terminal deletion of the short arm of chromosome 5.

Mutations in Splice Sites

High-Yield

Mutations in splice sites affect the accuracy of intron removal from hnRNA during posttranscriptional processing. If a splice site is lost through mutation, spliceosomes may:

•Delete nucleotides from the adjacent exon

•Leave nucleotides of the intron in the processed mRNA

•Use the next normal upstream or downstream splice site, deleting an exon from the processed mRNA

Mutations in splice sites have now been documented in many different diseases, including β-thalassemia, Gaucher disease, and Tay-Sachs.

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Chapter 4 ● The Genetic Code, Mutations, and Translation

β-Thalassemia

There are two genes for the beta chain of hemoglobin. In β-thalassemia, there is a deficiency of β-globin protein compared with α-globin. A large number of β-globin mutations have been described, including gene deletions, mutations that slow the transcriptional process, and translational defects involving nonsense and frameshift mutations. Other mutations involve β-globin mRNA processing (more than 70% of the β-globin gene is not encoding information and eventually must be spliced out), such as splice site mutations at the consensus sequences. Also, mutations within intron 1 create a new splice site, resulting in an abnormally long mRNA.

A 9-month-old infant of Greek descent was brought to the hospital by his parents because he became pale, listless, and frequently irritable. The attending physician noted that the spleen was enlarged and that the infant was severely anemic. His face had “rat-like” features due to deformities in the skull.

β-thalassemias are found primarily in Mediterranean areas. It is believed that, similar to sickle cell anemia and glucose-6-phosphate dehydrogenase deficiency, the abnormality of red blood cells in β-thalassemia may protect against malaria. Splenomegaly is due to the role of the spleen in clearing damaged red cells from the bloodstream. The excessive activity of the bone marrow produces bone deformities of the face and other areas. The long bones of the arms and legs are abnormally weak and fracture easily. The most common treatment is blood transfusions every 2–3 weeks, but iron overload is a serious consequence.

Trinucleotide Repeat Expansion	High-Yield

The mutant alleles in certain diseases, such as HuntingtonMEDIUMdisease,YIELDfragile X syndrome, and myotonic dystrophy, differ from their normal counterparts only in the number of tandem copies of a trinucleotide. In these diseases, the number of repeats often increases with successive generations and correlates with increasing severity and decreasing age of onset, a phenomenon called anticipation. For example, in the normal Huntington allele, there are 5 tandem repeats of CAG in the coding region. Affected family members may have 30–60 of these CAG repeats. The normal protein contains 5 adjacent glutamine residues, whereas the proteins encoded by the disease-associated alleles have 30 or more adjacent glutamines. The long glutamine tract makes the abnormal proteins extremely unstable. A major clinical manifestation of the trinucleotide repeat expansion disorders is neurodegeneration of specific neurons.

The expansion of the trinucleotide repeat in the mutant allele can be in a coding region or in an untranslated region of the gene.

Table I-4-2. Two Classes of Trinucleotide Repeat Expansion Diseases

	Translation repeat disorders
				Untranslated repeat disorders
	(polyglutamine disorders)
	Huntington disease: (CAG)n			Fragile X syndrome: (CGG)n
	Spinobulbar muscular atrophy: (CAG)n			Myotonic dystrophy: (CTG)n
				Friedreich’s ataxia: (GAA)n

Clinical Correlate

Huntington disease, an autosomal dominant disorder, has a mean age-of- onset in decade 4. Symptoms appear gradually and worsen over about 15 years until death occurs. Mood disturbance, impaired memory, and hyperreflexia are often the first signs, followed by abnormal gait, chorea (loss of motor control), dystonia, dementia, and dysphagia.

Cases of juvenile onset (age <10) are more severe and most frequently occur when the defective allele is inherited paternally. About 25% of cases have late onset, slower progression, and milder symptoms.

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