Physeo Biochemistry

168 Pages·2019·22.291 MB·English

by  physeo.com

BIOCHEMISTRY
MEDICAL COURSE AND STEP 1 REVIEW
FIRST EDITION
Accompanies online videos taught by
Michael Christensen & Rhett Thomson
physeo.com
Copyright © 2019 by Physeo
All rights reserved. No part of this publication may be reproduced,
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methods, without the prior written permission of Physeo, except in
the case of personal study purposes.
TABLE OF CONTENTS
MOLECULAR ........................................................................................................................4
Section I - DNA Replication .........................................................................................................................................................4
Section II - DNA Repair ...............................................................................................................................................................7
Section III - Transcription .............................................................................................................................................................9
Section IV - Translation ..............................................................................................................................................................13
Section V - DNA Mutations ........................................................................................................................................................15
CELLULAR ..........................................................................................................................18
Section I - Cell Cycle ..................................................................................................................................................................18
Section II - Cell Structure ...........................................................................................................................................................21
Section III - Connective tissue ....................................................................................................................................................24
LABORATORY TECHNIQUES .........................................................................................28
Section I - PCR ...........................................................................................................................................................................28
Section II - Blotting Procedures ..................................................................................................................................................30
Section III - Flow cytometry .......................................................................................................................................................32
Section IV - Microarrays and ELISA ..........................................................................................................................................34
Section V - Karyotyping and FISH .............................................................................................................................................36
Section VI - CRISPR/Cas9 & Molecular Cloning ......................................................................................................................38
GENETICS ............................................................................................................................40
Section I - Genetics Overview ....................................................................................................................................................40
Section II - Imprinting and Uniparental Disomy ........................................................................................................................45
Section III - Linkage Disequilibrium ..........................................................................................................................................49
Section IV - Pedigrees.................................................................................................................................................................51
Section V - Hardy-Weinberg Principle .......................................................................................................................................54
Section VI - Autosomal Dominant Diseases ...............................................................................................................................56
Section VI.1 - Autosomal Dominant Diseases ............................................................................................................................58
Section VII - X-linked Diseases..................................................................................................................................................59
Section VII.1 - X-linked Recessive Diseases..............................................................................................................................61
Section VII.2 - Rett Syndrome ....................................................................................................................................................62
Section VIII - Autosomal Recessive Diseases ............................................................................................................................63
Section IX - Trinucleotide Repeat Disorders ..............................................................................................................................65
Section IX.1 - Huntington Disease .............................................................................................................................................68
Section IX.2 - Myotonic Dystrophy ............................................................................................................................................69
Section IX.3 - Fragile X Syndrome ............................................................................................................................................70
Section IX.4 - Friedreich Ataxia .................................................................................................................................................71
Section X - Autosomal Trisomies ...............................................................................................................................................72
Section X.1 - Down Syndrome ...................................................................................................................................................76
Section X.2 - Edwards Syndrome ...............................................................................................................................................77
Section X.3 - Patau Syndrome ....................................................................................................................................................78
Section XI - Sex Chromosome Disorders ...................................................................................................................................79
Section XI.1 - Turner Syndrome .................................................................................................................................................82
Section XI.2 - Klinefelter Syndrome ..........................................................................................................................................83
Section XII - Deletion syndromes ...............................................................................................................................................84
Section XII.1 - Cri-du-chat .........................................................................................................................................................86
Section XII.2 - Williams Syndrome ............................................................................................................................................87
Section XII.3 - DiGeorge Syndrome...........................................................................................................................................88
METABOLISM .....................................................................................................................91
Section I - Hexokinase & Glucokinase .......................................................................................................................................91
Section II - Glycolysis ................................................................................................................................................................93
Section III - Pyruvate Metabolism ..............................................................................................................................................96
Section IV - The Tricarboxylic Acid Cycle ................................................................................................................................98
Section V - The Electron Transport Chain ................................................................................................................................100
Section VI - Gluconeogenesis ...................................................................................................................................................102
Section VII - Glycogen .............................................................................................................................................................104
Section VII.1 - Von Gierke & Cori ...........................................................................................................................................107
Section VII.1 - Pompe & Mcardle ............................................................................................................................................108
Section VIII - Fructose ..............................................................................................................................................................109
Section IX - Galactose ..............................................................................................................................................................112
Section X - Hexose Monophosphate Pathway ..........................................................................................................................114
Section XI - Fatty Acid Metabolism .........................................................................................................................................116
Section XII - Ketone Bodies .....................................................................................................................................................119
Section XIII - Ethanol Metabolism ...........................................................................................................................................121
Section XIV - Lipid Transport ..................................................................................................................................................123
Section XV - Homocysteine Metabolism .................................................................................................................................126
Section XVI - Purines & Pyrimidines .......................................................................................................................................128
Section XVII - Ammonia ..........................................................................................................................................................131
Section XVIII - Amino Acids ...................................................................................................................................................134
Section XIX - Lysosomal Storage Diseases ..............................................................................................................................137
Section XIX.1 - Tay-Sachs & Niemann-Pick Disease ..............................................................................................................139
Section XIX.2 - Fabry Disease .................................................................................................................................................140
Section XIX.3 - Metachromatic Leukodystrophy .....................................................................................................................141
Section XIX.4 - Krabbe Disease ...............................................................................................................................................142
Section XIX.5 - Gaucher Disease .............................................................................................................................................143
Section XIX.6 - Hurler & Hunter Syndrome ............................................................................................................................144
Section XX - Nutrition ..............................................................................................................................................................145
Section XX.1 - Thiamine .........................................................................................................................................................147
Section XX.2 - Riboflavin (B2) ...............................................................................................................................................148
Section XX.3 - Niacin (B3) .....................................................................................................................................................149
Section XX.4 - Pantothenic Acid (B5) .....................................................................................................................................150
Section XX.5 - Pyridoxine (B6) ...............................................................................................................................................151
Section XX.6 - Biotin (B7) ......................................................................................................................................................152
Section XX.7 - Folate (B9) ......................................................................................................................................................153
Section XX.8 - Cobalamin (B12) .............................................................................................................................................154
Section XX.9 - Vitamin C ........................................................................................................................................................155
Section XX.10 - Vitamin A ......................................................................................................................................................156
Section XX.11 - Vitamin D ......................................................................................................................................................157
Section XX.12 - Vitamin E ......................................................................................................................................................158
Section XX.13 - Vitamin K .......................................................................................................................................................159
Section XX.14 - Zinc ................................................................................................................................................................160
4
MOLECULAR
Section I - DNA Replication
E. Histone methylation → ↓ DNA transcription
I. DNA structure (Figure 2.1.1)
F. Histone acetylation → ↑ DNA transcription
A. DNA is complementary to the opposite strand
(cytosine pairs with guanine and thymine pairs
II. DNA replication (Figure 2.1.2)
with adenine).
A. Helicase separates the DNA at the replication
B. DNA wrapped around eight histones is called a
fork.
nucleosome.
B. Single-stranded binding proteins bind to
C. The first histone (H ) is responsible for linking
1 the DNA and prevent the two strands from
nucleosomes together.
reannealing.
D. Nucleosomes tightly packed together results in
C. The region where DNA replication begins is
the formation of a chromosome.
called the origin of replication.
1. Tightly packed → heterochromatin (not
D. Primase anneals to the 3’ end of the DNA and
accessible to transcription proteins)
synthesizes a primer.
2. Loosely packed → euchromatin
(transcriptionally active)
Figure 2.1.1 - DNA structure
5
E. DNA polymerase III binds to the primer and 2. Eukaryotic (topoisomerase I & II)
adds deoxynucleotides onto the 3’ end of the
a) Irinotecan
primer (eukaryotes perform this function via
b) Topotecan
DNA polymerase epsilon).
c) Etoposide
1. Synthesizes DNA in the 5’ → 3’ direction.
d) Teniposide
2. 3’ → 5’ exonuclease activity.
K. DNA polymerase I vs DNA polymerase III
F. The DNA strand being synthesized towards the
replication fork is called the leading strand. 1. DNA polymerase I (“DNA polymerase I only
goes in one direction”)
1. Synthesized continuously
a) 5’ → 3’ synthesis (“contrive at five”)
G. The DNA strand being synthesized away from
b) 5’ → 3’ exonuclease
the replication fork is called the lagging strand.
L. DNA polymerase III
1. Synthesized discontinuously resulting in the
formation of Okazaki fragments. 1. 5’ → 3’ synthesis
H. DNA polymerase I (eukaryotes perform removal 2. 3’ → 5’ exonuclease
of primers via DNA polymerase delta) removes
M. Telomerase
the RNA primers and replaces them with DNA.
1. Telomere: region at the end of a
1. Synthesizes DNA in the 5’ → 3’ direction.
chromosome
2. 5’ → 3’ exonuclease activity.
2. Telomerase: enzyme that adds DNA to the
I. DNA ligase joins the Okazaki fragments 3’ end of chromosomes to prevent the loss
of genetic material with every duplication.
J. Topoisomerases remove supercoils in DNA.
1. Prokaryotic (topoisomerase II & IV)
a) Fluoroquinolones
Figure 2.1.2 - DNA replication
6
REVIEW QUESTIONS ?
3. A 76-year-old male is admitted to the hospital
1. A new experimental drug is found to inhibit
for community acquired pneumonia. A sputum
histone deacetylase. How will this drug most
culture is obtained in hopes of isolating the
likely alter transcription?
pathogen and determining antibiotic sensitivity.
As the organism grows, its DNA is extracted and
• Acetylation of histones → ↑ transcription
analyzed. Detailed analysis of fragments from
• Deacetylation of histones → ↓ transcription
partially replicated DNA reveals the presence
• Deacetylase is an enzyme that removes
acetyl groups on histones of ribose sugar molecules with an increased
• The drug described inhibits deacetylase number of hydroxyl modifications. These
→ ↑ number of acetylated histones → ↑ fragments are most likely degraded by what
transcription enzyme during DNA replication?
• “Detailed analysis of fragments from par-
tially replicated DNA reveals the presence
of ribose sugar molecules with an increased
number of hydroxyl modifications.” →
referencing RNA (ribose contains one more
hydroxyl group than deoxyribose)
• During DNA replication RNA is present in
the form of primers
• RNA primers are degraded by the enzyme
2. A pathologist is studying DNA from staph aureus
DNA polymerase I
wound infections. She isolates an enzyme and
studies its activity during DNA replication. She
finds that this particular enzyme possesses 5’ to
3’ exonuclease activity. What enzyme has she
most likely isolated?
• DNA polymerase I has 5’ to 3’ exonuclease
activity
7
Section II - DNA Repair
C. Mismatch repair (Figure 2.1.5)
I. Single strand DNA repair
1. In eukaryotes, replicated DNA is normally
A. Nucleotide excision repair (Figure 2.1.3)
proofread by DNA polymerases. However,
1. Repairs bulky DNA alterations such as
when this repair mechanism fails, mismatch
pyrimidine dimers (UV radiation).
repair enzymes act as a “backup” repair
2. Endonucleases removes nucleotides. mechanism.
3. DNA polymerase fills in the empty space. 2. The replicated daughter strand of
DNA normally contains nicks in the
4. Sealed by ligase.
phosphodiester bonds which distinguishes
5. Defective in xeroderma pigmentosum.
it from the parent strand of DNA. Two
B. Base excision repair (Figure 2.1.4) proteins (MutS and MutL) slide along the
daughter strand until the nick is found.
1. Repairs non-bulky DNA alterations
such as deamination, depurination, or 3. Exonuclease 1 is recruited to the MutS/
alkylation (carcinogenic exposure, aging, MutL complex and degrades a segment of
neurodegeneration). DNA that includes the mismatched base.
2. Glycosylase recognizes and cleaves the 4. The gap region is stabilized by single
altered base resulting in an empty sugar- stranded DNA binding proteins.
phosphate region known as an apurinic or
5. DNA polymerase delta fills in the empty
apyrimidinic (AP) site.
space moving in the 5’ → 3’ direction.
3. Endonuclease cleaves the 5’ end of the AP
site.
4. Lyase removes the sugar-phosphate region.
5. DNA polymerase fills in the empty space
with the correct sugar.
6. Sealed by ligase.
Figure 2.1.3 - Nucleotide excision repair Figure 2.1.4 - Base excision repair
8
6. Sealed by ligase. REVIEW QUESTIONS ?
7. Defective in Lynch syndrome (hereditary
nonpolyposis colon cancer). 1. A 53-year-old male presents with a two month
history of cough, fatigue, and weight loss. He
II. Double strand endorses a 45-pack-year smoking history. CT
scan of the chest reveals an irregular mass
A. Caused by ionizing radiation
near the inferior lobe of the right lung. Biopsy
B. Homologous end joining samples are obtained. Further analysis reveals
malignant cells with heavily alkylated regions of
1. Sister chromosome is used as a template to
DNA. What are the first three enzymes normally
repair the double stranded break.
associated with repairing this type of damaged
C. Nonhomologous end joining
DNA?
1. Many proteins required for fixing the broken
• This patient has lung cancer and the malig-
strands of DNA.
nant cells contain heavily alkylated regions
2. Nonhomologous because the sister of DNA
chromosome is NOT used. • Base excision repair is responsible for
repairing non-bulky DNA alterations (deami-
3. ↑ risk of errors
nation, depurination, or alkylation)
4. Associated with Fanconi anemia and ataxia
• Carcinogenic exposure (i.e. smoking) can
telangiectasia
cause non-bulky DNA alterations
• Glycosylase, endonuclease, and lyase are
the first three enzymes associated with base
excision repair
2. A 40-year-old female presents with two months
of bloody vaginal discharge. She states that her
cycle normally occurs every 28 days and flow
normally lasts 3-4 days. Two years ago she had
an ovarian malignancy surgically removed. The
physician confirms a diagnosis of endometrial
carcinoma. However, he suspects a genetic
condition as the underlying cause and orders
a fecal occult blood test which comes back
positive. DNA analysis of malignant tissue would
most likely reveal cytosine-rich regions of DNA
pairing with what other base?
• Ovarian, endometrial, and likely colon
cancer (positive fecal occult blood test) →
Lynch syndrome
• Lynch syndrome is due to mutations of DNA
mismatch repair genes
• Normally cytosine pairs with guanine
• A defect in mismatch repair → cytosine ab-
normally paired with adenine and thymine
rather than guanine
Figure 2.1.5 - Mismatch repair
9
Section III - Transcription
B. Pre-mRNA is synthesized in the 5’ → 3’ direction
I. Overview (Figure 2.1.6)
from the template strand of DNA.
A. Transcription is a process whereby mRNA is
C. A molecule of modified guanine is added to the
synthesized using DNA as a template.
5’ end of the pre-mRNA (5’ cap).
B. Prokaryotes: DNA → mRNA → protein
D. Several adenine molecules are added to the 3’
C. Eukaryotes: DNA → pre-mRNA → mature end of the pre-mRNA (poly-A tail).
mRNA → protein
E. The introns are removed through a process
D. Promoter: located before the gene and known as splicing to form mature mRNA.
facilitates the binding of RNA polymerase to this
region
III. Splicing
E. Enhancer: increases the rate of transcription
A. Introns are removed by structures called
F. Silencer: decreases the rate of transcription spliceosomes.
1. Small nuclear ribonucleoproteins (snRNPs) +
II. Transcription (Figure 2.1.7) protein = spliceosome.
A. RNA polymerase binds to the promoter region. B. The intron nucleotides directly adjacent to the
exons are important for proper splicing.
1. Eukaryotes have three types of RNA
polymerases C. An intermediate intron structure is formed
called a Lariat intermediate.
a) RNA polymerase I: rRNA (nucleolus)
b) RNA polymerase II: mRNA (inhibited by D. Alternative splicing is a process whereby one
amatoxins) gene may produce multiple types of mature
mRNA molecules and ultimately multiple types
c) RNA polymerase III: tRNA and other
of proteins.
RNA
2. Prokaryotes
a) One RNA polymerase performs all
functions (inhibited by antibiotics)
Figure 2.1.6 - Transcription and translation overview