Molecular Biochem

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Protein malnutrition

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Kwashiorkor

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will see in kwashiorkor patient

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"MEALS":
malabsorption
edema
anemia
liver (fatty)
skin lesions
*clinical picture = small child with swollen belly

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energy malnutrition

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Marasmus

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see in Marasmus patient

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tissue/msucle wasting
loss of subcutaneous fat
variable edema

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nucleosome core

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H2A, H2B, H3, H4
2 each of these + charged histones

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charge of dna

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-

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nucleosome bead

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- charged DNA loops twice around nucleosome core

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only histone not in nucleosome core

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H1

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less condensed: heterochromatin or euchromatin

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euchromatin -
heterochromatin is more condensed

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transciptionally active: heterochromatin or euchromatin

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euchromatin -
heterochromatin is transcriptionally inactive

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anti-histone ab

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drug-induced sle

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purines

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A,G
"pure as gold"

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pyrimidines

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C,U,T
"cut the py"

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# of rings of purines

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2

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# of rings of pyrimidines

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1

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nucleotide with a ketone

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Guanine

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nucleotide with a methyl group

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thymine

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formation of uracil

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from deamination of cytosine

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unique nucleotide to rna

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uracil

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unique nucleotide to dna

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thymine

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nucleotide bond

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3'-5' phosphodiester bond

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pairs with highest melting point

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G-C
with 3 H bonds

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A-T bonds

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A=T, 2 H bonds

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amino acids necessary for purine synthesis

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Gly
Asp
Gln

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nucleotide =

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base pair + ribose + phosphate

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subsitute a purine for a purine or pyrimidine for a pyrimidine

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transition

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subsitute a purine for a pyrimidine or vise versa

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transversion

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each codon specifies only one amino acid

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unambiguous

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more than one codon may code for the same amino acid

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degenerate/redundant

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a.a. encoded by only 1 codon

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methionine

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read from a fixed starting point as a continuous sequence of bases

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commaless, nonoverlapping

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may not be commaless or nonoverlapping

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some viruses

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genetic code is conserved through evolution

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universal

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exceptions to being UNIVERSAL (4)

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mitochondria
archaebacteria
mycoplasma
some yeasts
*universal means genetic code is conserved throughout evolution

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mutation results in same aa

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silent

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serverity of damage of mutations: silent, nonsense, missense

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nonsense > missense > silent

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mutation results in changed aa

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missense

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mutation results in changed aa that is similar in chemical structure to mutated aa

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conservative

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mutation results in early stop codon

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nonsense

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mutation results in misreading of all nucleotides downstream

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frameshift
*causes early disease

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what mutation often results in a truncated protein

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frameshift

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where replication beigins in eukaryotes

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A-T rich base pairs

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nascent strand

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strand to be replicated

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daughter strand

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new strand to be made as a result of replication

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multiple origins of replication: eukaryote or prokaryote

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eukaryote

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single origin of replication: eukaryote or prokaryote

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prokaryote

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continuous dna synthesis on which strand

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leading

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discontinuous dna synthesis on which strand

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lagging (ogazaki)

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creates nicks in helix to relieve supercoils in dna replication

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dna topoisomerase

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denatures A-T bonds at beginning of dna replication

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dna-a

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unwinds dna (breaks helix)

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helicase

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phase of mitosis where dna replication occurs

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S phase

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enzyme of dna replication that makes an rna primer on which dnapIII can initiate replication

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primase

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5'->3' synthesis with
3'->5' exonuclease
enzyme in dna replication

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dnapIII

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enzyme that "proofreads" in dna synthesis

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exonuclease

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dna synthesis enzyme that degrades RNA primer and replaces with correct dna

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dnapI

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dna polymerase uses this to excise primers

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5'->3' exonuclease

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seals dna in dna synthesis

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dna ligase

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which enzyme forms the replication fork

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helicase

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stabilizes unwound helix

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SSB and DNA topoisomerase (creates nick in helix to relieve supercoils)

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steps in dna replication

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1. helicase unwinds
stabilized by ssb and
dna topoisomerase
2. leading strand synthesized continuously via DNAPIII
3. lagging strand synthesized discontinuously in ogasaki fragments
4. dnapI removes rna primer and replaces with correct dna
5. dna ligase seals break at ogasaki fragments to make continuous

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5' end of dna

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with phosphate group

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3' end of dna

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with hydroxyl group

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dna stabilization

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via H bonds and hydrophobic interactions

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diseases with imparied dna repair (5)

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1. ataxia-telangiectasia
2. xeroderma pigmentosa
3. fanconi anemia
4. bloom syndrome
5. hnpcc

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specific endonucleases release the oligonucleotide-containing damaged bases; while dna polymerase and ligase fill and reseal the gap, respectively

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nucleotide excision repair

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mutated nucleotide excision repair

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xeroderma pigmentosa

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dry skin with melanoma and other ca's; defective dna repair

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xeroderma pigmentosa

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

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base excision repair

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

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mismatch repair

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mutation in hereditary nonpolyposis colon cancer

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mismatch repair

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brings together 2 ends of dna fragments

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nonhomologous end joining

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direction of synthesis

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5' to 3'

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largest rna

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mrna

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most abundant rna

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rrna

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smallest rna

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trna

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rna polymerase I

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rrna

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rna polymerase II

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mrna

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rna polymerase III

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trna

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B,B,alpha

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zinc fingers

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opens dna at promoter site in transcription

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rna polymerase II

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inhibits rna polymerase

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alpha-amantin

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source of alpha-amantin

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cap mushrooms

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mRna initiation codons

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AUG
GUC (rarely)

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codes for methionine in eukaryotes

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AUG - start codon

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start codon in prokaryotes codes for....

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formyl-methionine (f-met)

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mrna stop codons

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UGA, UAA, UAG

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binds promoter sequence of dna in transcription

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rnapII

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intial steps of transcription (3)

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1. ranpII binds promoter sequence of dna (tata and caat box)
2. dna unwinds and forms "transcription bubble"
3. rnapII moves along "sense" strand, adding ribonucleotides to growing strand of mrna

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site where rna polymerase and other transcription factors bind to DNA upstream from gene locus

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promoter

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site of promoter

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A-T rich upstream sequence with TATA and CAAT box

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mutation resulting in dramatic decline in amount of gene transcribed

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promoter mutation

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stretch of dna that alters gene expression by binding transcription factors

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enhancer

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operator

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site where negative regulators (repressors) bind

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contain the actual genetic information coding for a protein

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exons

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intervening noncoding segments of dna

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introns

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different exons can be combined to make unique proteins in different tissues

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alternative splicing

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primary transcript combines with snRNP's to form.....

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spliceosome

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intermediate formed to spliceosome

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lariat-shaped intermediate that is released to remove introns and join 2 exons

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steps in splicing (3)

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1. primary transcript combines with snRNPs to form spliceosome
2. lariat-shaped intermediate is generated
3. lariat is released to remove introns and join 2 exons

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location of rna processing

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at nucleus

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process after transcription

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rna processing -
1. capping at 5' end
2. poly a tail at 3' end
3. splice out introns

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capped and tailed transcript

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mRNA

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initial transcript before rna processing is called....

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hnRNA (heterogeneous nuclear RNA)

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only step of rna processing that does not occur at the nucleus (instead at the cytoplasm)

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capping on 5' end

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added during capping

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7-methyl-G
add methyl group on c7
and add guanesine

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end that is capped

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5'

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end with poly-a tail

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3'

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function of poly-a tail

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protects genes from degradation
guides rna to 30s to read 3' end

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how many A's in the poly-A tail

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~200 A's added to 3' end

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# of nucleotides in trna

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75 - 90

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cloverleaf shaped rna

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trna

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sequence at 3' end of trna

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CCA

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location of anticodon

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in middle loop - opposite 3' end

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end of amino acid covalent bond in trna

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3' end of trna

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attaches aa to 3' end of trna

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aminoacyl-trna synthetase

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scrutinizes aa before and after it binds to trna

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aa-trna synthetase

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if aa bound to trna is incorrect, bond is hydrolyzed by

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synthetase (aa-trna synthetase)

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aa-trna bond has this for formation of peptide bond

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energy

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mischarged trna

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reads usual codon
interts wrong amino acid

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ACC at 3' end of trna codes for......

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Met

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"wobble" position

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3rd nucleotide of an mrna codon

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says that accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon

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"wobble" theory

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3 main steps of protein synthesis

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1. initiation
2. elongation
3. termination

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location of protein synthesis

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ribosome

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occupies A site

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trna of next aa to be added to the growing polypeptide

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occupies P site

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trna containing growing peptide chain

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helps assemble the 30s ribosomeal subunit with the initiator tRNA

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IF initiation factor

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released when mrna and ribosomal subunit assemble with the complex

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IF initiation factor

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codon recognized by initiator trna

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AUG

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occurs during Initiation of protein synthesis

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IF's help assemble the 30s ribosomal subunit with the initiator tRNA. then if's are released when mRNA and ribosomal subunit assemble with the complex

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during elongation, aminoacyl trna binds to.....

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A site

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during elongation, catalyzes peptide bond formation, transfering growing polypeptide to amino acid in A site

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peptidyl transferase

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energy needed for tRNA activation

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ATP (charging)

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energy needed for tRNA translocation

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GTP

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ribosome advances 3 nucleotides toward 3' end of rna

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during elongation, to move peptidyl RNA to p site

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completed protein is released from ribosome when stop codon enters a site

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TERMINATION step of protein synthesis

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holds Empty tRNA as protein exits

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E site

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3 steps of elongation

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1. aminoacyl tRNA binds A site
2. peptidyltransferase catalyzes peptide bond formation, transfers growing popypeptide to amino acid in A site
3. ribosome advances 3 nucleotides toward 3' end of RNA, moving peptidyl RNA to P site

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Termination

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stop codon enters a site. complete protein is released from ribosome. protein is dislocated. empty trna occupies E site

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posttranslational modifications (3)

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trimming
covalent alteration
proteasomal degradation

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removal of N- or C- terminal pro-peptides from zymogens to generate mature proteins

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trimming

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phosphoylation, glycosylation, and hydroxylation

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covalent alterations

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attachment of ubiquitin to defective proteins to tag them for breakdown

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proteosomal degradation