Usmle Step 1: Biochemistry 1

Front 1

Fat/Water soluble vitamins

Back 1

- fat soluble - A, D, E, K
- water soluble - B(s), C, Biotin, folate

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Vitamin A

Back 2

- retinol is vitamin A, so think Retin-A
- deficiency: night blindness, dry skin
- function: constituent of visual pigments (retinal)

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Vitamin B1

Back 3

- thiamine
- spell beriberi ber1ber1
- deficiency: beriberi and wernicke-korsakoff syndrome
- function: in thiamine pyrophosphate, a cofactor for oxidative decarboxylation of alpha-ketoacids

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Vitamin B2

Back 4

- riboflavin
- deficiency: angular stomatitis, cheilosis, cornela vascularization
- function cofactor in ox/redox of FADH2 (FAD and FMN are derived from riboFlavin)

Front 5

Vitamin B3

Back 5

- niacin
- deficiency: Pellagra - Diarrhea, Dermatitis, Dementia
- function: constituent of NAD+/NADP+. derived from tryptofan using B6

Front 6

Vitamin B5

Back 6

- pantothenate
- deficiency: dermatitis, enteritis, alopecia, adrenal insufficiency
- function: constituent of CoA and fatty acid synthase (Pantothen-A is Co-A)

Front 7

Vitamin B6

Back 7

- pyridoxine
- deficiency: convulsions, hyperirritability, peripheral neuropathy
- function: converted to pyridoxal phosphate and required for synthesis of niacin.

Front 8

Vitamin B12

Back 8

- cobalamin
- deficiency: macrocytic megaloblastic anemia; neurologic symptoms, glossitis
- function: cofactor for homocysteine methyltransferase
- deficiency usually caused by malabsorption, lack of IF (pernicious anemia), or absence of terminal illeum (Crohn's disease)

Front 9

Folic acid

Back 9

- deficiency: macrocytic, megaloblastic anemia
- function: coenzyme (THF) for 1-carbon transfer - important for DNA/RNA synthesis
- FOLate from FOLiage

Front 10

Biotin

Back 10

- deficiency: dermatitis, enteritis - caused by antibiotic use and excessive raw eggs (AVIDin in egg whites AVIDly binds biotin).
- function: cofactor for carboxylations

Front 11

Vitamin C

Back 11

- ascorbic acid
- deficiency: scurvy - swollen gums, bruising, anemia, poor wound heeling
- function: necessary for collagen synthesis, facilitates iron absorption, necessary to convert dopamine to NE

Front 12

Vitamin D

Back 12

- D2 consumed in milk
- D3 formed in sun-exposed skin
- 25-OH D3 is storage form
- 1,25-OH D3 (calcitriol) is active form

- deficiency: rickets in children, osteomalacia in adults, hypocalcemic tetany
- function: intestinal absorption of Ca and phosphate

Front 13

Vitamin E

Back 13

- deficiency: fragile erythrocytes (E is for Erythrocytes), neurodysfunction
- function: antioxidant (protects erythrocytes from hemolysis)

Front 14

Vitamin K

Back 14

- Deficiency: neonatal hemorrhage (infants have sterile intestines thusly cant synthesize vitK)
- Function: Catalyzes gamma-carboxylation of glutamic acid residues (concerned w/ blood clotting)
- VitK synthesized by bacteria so deficiency can result from antibiotics
- K for Koagulation (Warfarin is a vitamin K antagonist)

Front 15

Zinc deficiency

Back 15

- Delayed wound healing, hypogonadism, ↓ adult hair (axillary, facial, pubic); may
predispose to alcoholic cirrhosis.
- zinc deficiency makes you less like wolverine

Front 16

Ethanol metabolism

Back 16

- NAD+ oxidizes alcohol to acetate (via alcohol dehydrogenase and acetaldehyde dehydrogenase
- NAD+ is limiting reagent

Front 17

ethanol hypoglycemia

Back 17

- Ethanol metabolism ↑ NADH/NAD+ ratio in liver, causing diversion of pyruvate to lactate and OAA to malate, thereby inhibiting gluconeogenesis and leading to hypoglycemia. This altered NADH/NAD+ ratio is responsible for the hepatic fatty change (hepatocellular steatosis) seen in chronic alcoholics (shunting away from glycolysis and toward fatty acid synthesis, which normalizes the ratio).

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Kwashiorkor vs. marasmus

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- Kwashiorkor: protein malnutrition (small child with swollen belly) resulting in skin lesions, edema, liver malfunction (fatty change).
- Marasmus: energy malnutrition resulting in tissue/muscle wasting, loss of subcutaneous fat, and variable edema
- Kwashiorkor results from a protein-deficient MEAL: Malnutrition, Edema, Anemia, Liver (fatty)

Front 19

Chromatin structure

Back 19

- neg. charged DNA loops twice around histone octomer(2 each of the positively charged H2A, H2B, H3, and H4) to form nucleosome bead.
- H1 ties nucleosomes together in string

Front 20

Heterochromatin

Back 20

- condensed, transcritionally inactive

Front 21

Euchromatin

Back 21

- less condensed, transcriptionally active

Front 22

Nucleotides

Back 22

- purines (A,G): PURe As Gold
- pyrimidines (CTU): CUT the PY
- G-C bonds (3HB) stronger than A-T bonds (2HB) --> higher G-C content leads to higher melting temp.

Front 23

Transition

Back 23

- substituting purine for purine or pyrimidine for pyrimidine

Front 24

Transversion

Back 24

- substituting purine for pyrimidine or vise versa

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Silent mutation

Back 25

- same AA, often base change in 3rd position of codon (tRNA wobble)

Front 26

Missense mutation

Back 26

- changed AA
- if conservative: new AA is similar to original

Front 27

Nonsense mutation

Back 27

- change results in stop codon
- STOP the NONSENSE!

Front 28

Frame shift mutation

Back 28

- change resulting in misreading of all nucleotides downstream, usually resulting in a truncated protein

Front 29

Eukaryotic DNA replication

Back 29

- multiple origin sites

Front 30

Prokaryotic DNA replication

Back 30

- single origin site
- bidirectional: continuous on leading strand and okazaki fragments on lagging strand

Front 31

Helicase

Back 31

- enzyme which unwinds DNA at replication fork

Front 32

DNA topoisomerases

Back 32

- create a nick in the helix to relieve supercoils

Front 33

primase

Back 33

- makes an RNA primer on which DNA polymerase III can initiate replication

Front 34

DNA polymerase III

Back 34

- elongates the chain by adding deoxynucleotides to the 3' end (leading strand, 5'-3')
- elongates lagging strand until it reaches primer of preceding fragment
- 3'-5' exonuclease activity "proofreads" each added nucleotide

Front 35

DNA polymerase I

Back 35

- degrades RNA primer and fills in the gap with DNA

Front 36

DNA ligase

Back 36

- seals
- connects Okazaki fragment to lagging strand

Front 37

Nucleotide excision repair

Back 37

- specific endonucleases release the oligonucleotide-containing damaged bases
- DNA polymerase and ligase fill and reseal the gap, respectively
- this enzyme is mutated in xeroderma pigmentosum (dry skin with melanoma and other cancers, "children of the night"), which prevents repair of thymidine dimers

Front 38

Base excision repair

Back 38

- specific glycosylases recognize and remove damaged bases
- AP endonuclease cuts DNA at apyrimidinic site
- empty sugar is removed and the gap is filled and resealed

Front 39

mismatch repair

Back 39

- unmethylated, newly synthesized string is recognized
- mismatched nucleotides are removed
- gap is filled and resealed

Front 40

Nonhomologous end joining

Back 40

- brings together two ends of DNA fragments

Front 41

DNA/RNA/protein synthesis direction

Back 41

- DNA/RNA are synthesized 5'-3'
- mRNA is read 5'-3'
- protein synthesis is N to C

Front 42

Types of RNA

Back 42

- Massive, Rampant, Tiny
- mRNA is largest
- rRNA is the most abundant
- tRNA is the smallest

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start codon

Back 43

- AUG

Front 44

stop codon

Back 44

- UGA, UAA, UAG
- UGA = U Go Away
- UAA = U Are Away
- UAG = U are Gone

Front 45

promoter

Back 45

- site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus (AT-rich upstream sequence with TATA and CAAT boxes)
- promoter mutation commonly results in dramatic decrease in amount of gene transcribed

Front 46

enhancer

Back 46

- stretch of DNA that alters gene expression by binding transcription factors
- may be located close to, far from, or even within (in an intron) the gene whose expression it regulates

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silencer

Back 47

- site where negative regulators (repressors) bind

Front 48

Eukaryotic RNA polymerase

Back 48

- I, II, and II are numbered as their products are used in protein synthesis

- RNA polymerase I makes rRNA
- RNA polymerase II makes mRNA
- RNA polymerase III makes tRNA

- RNA polymerase II is inhibited by alpha-amanitin (found in death cap mushrooms)

Front 49

Prokaryotic RNA polymerase

Back 49

- RNA polymerase makes all 3 kinds of RNA

Front 50

RNA processing

Back 50

1. capping on 5' end
2. polyadenylation on 3' end
3. splicing out of introns

- initial transcript is called heterogenous nuclear RNA (hnRNA)
- processed transcript is called mRNA

Front 51

Splicing of pre-mRNA

Back 51

1. primary transcript combines with snRNPs and other proteins to form spliceosome
2. lariat-shaped intermated is generated
3. larait is released to remove intron precisely and join 3 exons

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introns vs exons

Back 52

- introns are spliced out
- exons are kept and therefore expressed
- INtrons stay IN the nucleus while EXons EXit and are EXpressed

Front 53

tRNA wobble

Back 53

- Accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd “wobble” position may code for the same tRNA/amino acid.

Front 54

tRNA structure

Back 54

- amino acid bound to 3' end
- aminoacyl-tRNA synthetase catalyzes AA-tRNA binding and proofreads AA-tRNA pair yielding selectivity

Front 55

Protein synthesis

Back 55

- A, P, E sites
- A site accepts incoming tRNA
- P site catalyzes AA-AA peptide bond formation
- E site holds empty tRNA as it exits

- initiation: initiation factors help assemble the 40S ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal subunit assemble with the complex
- elongation: A, P, E sites
- termination: protein released by hydrolysis

Front 56

Ribosomal subunit sizes

Back 56

- eukaryotes (even): 80S → 60S + 40S
- prokaryotes (odd): 70S → 50S + 30S

Front 57

Posttranslational modifications

Back 57

- trimming: removal of N- or C-terminal propeptides from zymogens to generate mature proteins
- covalent alterations: Phosphorylation, glycosylation, and hydroxylation
- proteasomal degradation: attachment of ubiquitin to defective proteins to tag them for breakdown

Front 58

Cell cycle

Back 58

- G1, S, G3, M

Front 59

Mitosis

Back 59

- prophase, metaphase, anaphase, telephase

- CDKs: constitutive and inactive
- Cyclins: phase specific, activate CDKs
- Cyclin-CDK complexes: must be both activated and inactivated for cell cycle to progress
- Rb/p53 tumor suppressors normally inhibit G1-to-S progression; mutations in these genes result in unrestrained growth

Front 60

Rough endoplasmic reticulum

Back 60

- site of synthesis of secretory proteins
- site of N-linked oligosaccharide addition to many proteins

- nissl boddies (in neurons) synthesize enzymes and peptide neurotransmitters
- free ribosomes synthesize cytosolic/organellar proteins

- mucus secreted goblet cells and immunoglobbin secreting plasma cells have lots of RER

Front 61

Smooth endoplasmic reticulum

Back 61

- site of steroid synthesis and detoxification of drugs/poisons
- liver hepatocytes and steroid hormone-producing cells of the adrenal cortex are rich in SER

Front 62

Golgi apparatus (functions)

Back 62

- distributes proteins/lipids from ER to plasma membrane, lysosomes and secretory vesicles
- targeting modifications

Front 63

I-cell disease

Back 63

- failure of addition of mannose-6-phosphate to lysosome proteins in the golgi apparatus; enzymes are secreted outside the cell instead of being targeted to the lysosome