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Biochemistry > Molecular > Flashcards

Molecular Flashcards

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1
Q

Heterochromatin

A

Condensed
Appears darker on EM
Transcriptionally inactive, sterically inaccessible
Barr bodies (inactive X chromosomes) are heterochromatin

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2
Q

Euchromatin

A

Less condensed
Lighter on EM
Transcriptionally active and sterically accessible

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3
Q

DNA methylation

A

Template strand cytosine and adenine are methylated in DNA replication, which allows MMR enzymes to distinguish between old and new strands in prokaryotes
DNA methylation at CpG islands represses transcription

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4
Q

Histone Methylation

A

Usually reversibly represses DNA transcription, but can activate it in some cases depending on methylation location

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5
Q

Histone Acetylation

A

Relaxes DNA coiling, allowing for transcription

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6
Q

Nucleoside

A

Base + (deoxy)ribose

Base + Sugar

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7
Q

Nucleotide

A

Base + (deoxy)ribose + phosphate

Linked by 3’-5’ phophodiester bond

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8
Q

Purines

A 
A & G
2 rings
PURe As Gold
GAG - amino acids necessary for purine synthesis
=Glycine, Aspartate, Glutamine
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9
Q

Pyrimidines

A

C, U, T
1 ring
CUT the PY (pie)
Deaminations of cytosine makes uracil (found in RNA)

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10
Q

Disrupting Pyrimidine Synthesis: Leflunomide

A

Inhibits dihydroorate dehydrogenase

Inhibits change Carbomoyl phosphate into orotic acid

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11
Q

Disrupting Pyrimidine Synthesis: Methotrexate, Trimethoprim & pyrimethamine

A

Inhibit dihydrofolate reductase
Decreases deoxy thymidine monophosphate in humans, bacteria and Protozoa
Inhibits change of DHF to THF

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12
Q

Disrupting Pyrimidine Synthesis: 5-Fluorouracil

A

Forms 5-F-dUMP, which inhibits thymidylate synthase (decreased dTMP)
Inhibits change from dUMP to dTMP

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13
Q

Disrupting Purine Synthesis: 6-Mercaptopurine

A

Inhibits de novo purine synthesis

Inhibits change of PRPP to IMP

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14
Q

Disrupting Purine Synthesis: Mycophenolate and Ribavirin

A

Inhibits inosine monophosphate dehydrogenase

Inhibits change from IMP to GMP

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15
Q

Disrupting both Purine and Pyrimidine synthesis: Hydroxyurea

A

Inhibits ribonucleotide reductase

Inhibits the change of UDP to dUDP

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16
Q

Adenosine deaminase deficiency

A

ADA is required for degradation of adenosine and deoxyadenosine
In ADA deficiency increase in dATP which is toxic for lymphocytes
One of the major causes of AR SCID

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17
Q

Lesch-Nyhan syndrome

A

Defective purine salvage due to absent HGPRT which converts hypoxanthine to IMP and guanine to GMP
Results in excess uric acid production and de novo purine synthesis
X-linked recessive
Findings: intellectual disability, self-mutilation, aggression, hyperuricemia (orange ‘sand’ in diaper), gout, dystonia
Treatment: allopurinol or febuxostat (second line)

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18
Q

Genetic code features: Unambiguous

A

Each codon specifies only 1 AA

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19
Q

Genetic code features: Degenerate/redundant

A

Most AA are coded my multiple codons

Exceptions: methionine and tryptophan encoded by only 1 codon (AUG & UGG)

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20
Q

Genetic code features: Commaless, non-overlapping

A

Read from a fixed starting point as a continuous sequence of bases
Exceptions: some viruses

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21
Q

Genetic code features: Universal

A

Genetic code is conserved throughout evolution

Exception in humans: mitochondria

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22
Q

DNA replication

A 
Eukaryotic DNA replication more complex than prokaryotes
DNA replication (in both) is semi conservative and involves both continuous and discontinuous (Okazaki fragment) synthesis
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23
Q

Origin of Replication

A

Particular consensus sequence of base pairs in genome where DNA replication begins
May be single (prokaryotes) or multiple (eukaryotes)
AT-rich sequences are found in promoters and origins of replication

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24
Q

Replication fork

A

Y-shaped region along DNA template where leading and lagging strands are synthesized

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25
Helicase
Unwinds DNA template at replication fork
26
Single-Stranded binding proteins
Prevent strands from reannealing
27
DNA topoisomerases
Crease a single or double stranded break in the helix to add or remove super oils Topo inhibitors: fluoroquinolones (topo II and IV in prokaryotes) and Etoposide/Teniposide (eukaryotic Topo II)
28
Primase
Makes an RNA primer on which DNA polymerase III can initiate replication
29
DNA pol III
Prokaryotic only Elongates leading strand by adding deoxy nucleotides to the 3' end (5'-3' synthesis) Elongates lagging strand until it reaches the primer of the preceding fragment 3'-5' exon unleash activity proof reads each added nucleotide
30
DNA pol I
Prokaryotic only Degrades RNA primer and replaces it with DNA Has same functions at DNA pol III but excises RNA primer with 5'-3' exonuclease
31
DNA ligase
Catalyzes the formation of a phosphodiesterase bond within a strand of dsDNA (i.e. Joins Okazaki fragments)
32
Telomerase
An RNA-dependent DNA polymerase that adds DNA to 3' ends of chromosomes to avoid loss of genetic material with every duplication Eukaryotes only Often dysregulated in cancer cells, allowing unlimited replication
33
Mutations in DNA: severity
Severity of damage: silent
34
Mutation in DNA: Transition
Purine to purine (A to G) or Pyrimidine to Pyrimidine (C to T)
35
Mutation in DNA: Transversion
Purine to Pyrimidine (A to T) or Pyrimidine to purine (C to G)
36
Silent mutation
Nucleotide substitution but codes for same (synonymous) AA | Often base change in 3rd position of codon (tRNA wobble)
37
Missense Mutation
Nucleotide substitution resulting in changed amino acid (called conservative if new AA is similar in chemical structure) E.g. Sickle cell disease - glutamic acid with valine
38
Nonsense Mutation
Nucleotide substitution resulting in early stop codon | Usually results in non-functional protein
39
Frameshift mutation
Deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream Protein may be shorter or longer and its function may be disrupted or altered E.g. Duchenne Muscular Dystrophy, Tay-Sachs disease
40
Splice Site mutation
Mutation at splice site - retained intron in mRNA - protein with impaired or altered function E.g. Rare causes of cancers, dementia, epilepsy and some types of beta-thalassemia
41
Lac Operon
Genetic response to environmental change | Glucose preferred metabolic substrate of E. Coli, but when absent and lactose is available can switch metabolism
42
Mechanism of shift: Lac Operon
Low glucose: increased adenylate cyclase activity to increase generation of cAMP from ATP causing activation of catabolite activator protein (CAP) and increase transcription High Lactose: unbinds repress or protein from repressor/operator site to increase transcription
43
Nucleotide excision repair
Single stranded repair Specific ending leases release the oligonucleotides containing damaged bases DNA pol and ligase fill and reveal the gap Repairs bulky helix-distorting lesions. Occurs in G1 phase of cell cycle Defective: xeroderma pigmentosum, which prevents repair of Pyrimidine dimers because of UV light damage
44
Base excision repair
Single stranded repair Base-specific glucose last removes altered base and creates AP site One or more nucleotides are removed by AP-endonuclease, which cleaves the 5' end Lyse cleaves the 3' end DNA polymerase Beta fills gap and DNA ligase seals it Throughout cell cycle Important repair of spontaneous/toxic deamination
45
Mismatch Repair
Single stranded repair Newly synthesized strand is recognized, mismatched nucleotides are removed, and the gap is filled and resealed Occurs mostly in G2 phase of cell cycle Defective: Lynch syndrome - hereditary non-polyposis CRC)
46
Nonhomologous end joining
Double strand repair brings together 2 ends of DNA fragments to repair dsDNA breaks No requirement for homology, some DNA may be lost Mutated in ataxia telangiectasia, Fanconi anemia
47
DNA/RNA/Protein synthesis direction
DNA and RNA - 5'-3' synthesis The 5' end of the incoming nucleotide bears the triphosphate (energy source) Drugs blocking DNA replication often have modified 3'OH preventing addition of the next nucleotide (chain termination) Protein: N-terminus to C-terminus
48
Start and Stop Codons: mRNA start codons
AUG Eukaryotes: codes for methionine which may be removed before translation is complete Prokaryotes: codes for N-formylmethionine (fMet) - stimulates neutrophil chemotaxis
49
Start and Stop Codons: mRNA stop codons
UGA UAA UAG
50
Promoter
Site where RNA pol II and multiple transcription factors bind to DN upstream from the gene locus (AT-rich region with TATA and CAAT boxes) Promoter mutation commonly results in dramatic decrease in gene transcription
51
Enhancer
Stretch of DNA that alters gene expression by binding transcription factors May be located close or far from or even within the gene
52
Silencer
Site where negative regulators (repressors) bind | May be located close, far from or within gene
53
RNA pol I: eukaryotes
Makes rRNA (most numerous RNA, rampant)
54
RNA pol II: Eukaryotes
Makes mRNA (largest RNA, massive) Opens DNA at the promoter site Alpha-amanitin, found in Amanita phalloides (death cap mushrooms) inhibits RNA pol II and causes severe hepatoxicity if ingested
55
RNA pol III: Eukaryotes
Makes 5S rRNA, tRNA (smallest RNA, tiny)
56
RNA pol: Prokaryotes
Multisubunit complex makes all three kinds of RNA Rifampin: inhibits RNA pol in prokaryotes Actinomycin D: inhibits RNA pol in both pro and eu
57
RNA processing (eukaryotes)
Initial transcript = heterogeneous nuclear RNA - modified to mRNA In the nucleus: capping of 5' end (7-methylguanosine cap), polyadenylation of 3' end (AAUAAA - signal), splicing out of introns = mRNA Then mRNA transported out of nucleus into cytosol for translation Quality control in P-bodies
58
Chromatin Structure
DNA exists in the condensed, chromatin form in order to fit into the nucleus Negatively charged DNA loops 2x around positively charged his tone octamer to form nucleosides (beads on a string) Histones rich in AA lysine and arginine H1 binds to the nucleosome and to linker DNA thereby giving stabilization In mitosis, DNA condenses to form chromosomes DNA and histone synthesis occur during S phase
59
Splicing of pre-mRNA
1. Primary transcript combines with small nuclear ribonucleoproteins and other proteins to form the spliceosome 2. Lariat-shaped (looped) intermediate is generated 3. Lariat is released to precisely remove intron and join two exons Ab to spliceosome like snRNPs (anti-Smith Ab) are highly specific for SLE Anti-U1 RNP Ab are highly associated with mixed CT disease
60
Exon
Contain actual genetic information for coding proteins Different exons are frequently combined by alternative splicing to produce larger numbers of unique proteins Abnormal splicing variants are implicated in oncogenes is and many genetic disorders (e.g. Beta-thalassemia)
61
Intron
Are intervening non-coding segments of DNA | Stay in the nucleus once spliced out
62
MicroRNAs
Small, noncoding RNA molecules that post-transcriptionally regulate protein expression Introns can contain miRNA genes They have multiple mRNA targets, typically related to complementary base pairing: miRNA - degradation or inactivation of target mRNA - decreased translation into protein Abnormal expression of miRNAs contribute to certain malignancies (e.g. By silencing an mRNA from a tumor suppressor gene)
63
tRNA: Structure
Secondary structure cloverleaf form with anticodon end is opposite 3' aminoacyl end All tRNAs have CCA (Can Carry Amino acids) at 3' end along with a high percentage of chemically modified bases The AA is covalently bound to the 3' end of the tRNA
64
tRNA: T-arm
Contains the ribothymidine, pseudouridine, cytidine sequence necessary for tRNA-ribosome binding
65
tRNA: D-arm
Contains dihydrouidine residues necessary for tRNA recognition by the correct aminoacyl tRNA synthetase
66
tRNA: Acceptor stem
The 5' CCA 3' is the amino acid acceptor site
67
tRNA: Charging
Aminoacyl-tRNA synthetase (1 per AA; matchmaker; uses ATP) scrutinizes AA before and after it binds to tRNA If incorrect bond is hydrolyzed The AA-tRNA bond has energy for formation of a peptide bond Am is harmed tRNA reads usual codon but inserts the wrong AA
68
tRNA: Wobble
Accurate base pairing is usually required only in the first 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd 'wobble' site may code for the same tRNA/AA (as a result of degeneracy of the genetic code)
69
Protein synthesis: Initiation
Initiated by GTP hydrolysis Initiation factors help assemble the 40S ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal 60S subunit assemble with the complex ATP-tRNA (Activation = charging) GTP-tRNA (Gripping and Going places = translocation)
70
Ribosomal Subunits
Eukaryotic: 40S + 60S = 80S (Even) PrOkaryotic: 30S + 50S = 70S (Odd)
71
Protein Synthesis: Elongation
1. Aminoacyl-tRNA binds to A site (exception: initiator methionine) 2. rRNA (ribozyme) catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A site 3. Ribosome advances 3 nucleotides toward 3' end of mRNA, moving peptidyl tRNA to P site (translocation)
72
Ribosome Sites
A site = incoming Aminoacyl-tRNA P site = accommodates growing Peptide E site = holds Empty tRNA as it Exits
73
Protein Synthesis: termination
Stop codon is recognized by release factor and completed polypeptide is released from ribosome
74
Post translational modifications: trimming
Removal of N or C-terminal propeptides from zymogen to generate mature protein E.g trypsinogen to trypsin
75
Posttrasnlational modifications: Covalent alterations
Phosphorylation, glycosylation, hydroxylation, methylation, acetylation and ubiquitination
76
Chaperone protein
Intracellular protein involved in facilitating and/or maintaining protein folding E.g. Yeast heat shock proteins are expressed at high temps to prevent protein denaturing/misfolding

Biochemistry (6 decks)

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