Biology Class 3 Flashcards
Nucleoside vs nucleotide
nucleoside includes just the sugar and base, while nucleotide also includes the phosphates
Bond formed between two nucleotides
phosphodiester bond
Monomer of nucleic acids
Nucleotides/nucleosides
Important facts about nucleic acids
- 5’-3’ synthesis
- Antiparallel & complementary
- Phosphodiester bond
Pyrimidine vs Purine
Pyrimidine: Cytosine, thymine, uracil
- 6 C ring
Purine: Adenine & Guanine
- 6 C & 5 C ring
Bases in DNA vs RNA
DNA: Adenine, guanine, cytosine, thymine
RNA: Adenine, guanine, cytosine, uracil
How many H bonds hold a AT bond vs GC bond
2, 3 respectively
U pairs with A
Genome
All the DNA in an organism
Genome: Prokaryotes vs Eukaryotes
Prokaryote: one singular circular DNA genome
Eukaryote: 23 pairs of linear chromosomes (46 chromosomes)
How is the Prokaryote genome protected?
- Methylation - methylates chromosome to protect from own RE
- Supercoiling - Gyrase helps with supercoiling and helps compact the chromosome
How do Eukaryotes form chromosomes?
- DNA is wrapped around 8 histone molecules & forms a nucleosome
- Condenses to form chromatin
- Further condenses to form chromosome
Euchromatin vs Heterochromatin
Euchromatin
- unwound, active, light staining
Heterochromatin
- wound, inactive, dark staining
Centrosome
Region of the chromosome
- attaches spindle fibers
- connects sister chromatids after replications
Telomeres
- End of chromosomes
- Short sequence repeats
- Allows ends of chromosomes to loop around & bp with itself and allows it to stabilize the chromosome
Central Dogma
DNA (transcription) –> RNA (translation) –> Protein
What are the stop and start codons
Start: AUG (Met)
Stop: UAG,UAA,UGA
Human Genome
- 46 chromosomes
- ~21,000 genes
- 3 billion nucleotidesLarge intergenic regions (regions that don’t code for proteins)
Different types of point mutations
Missence- codon for aa becomes new codon for new aa (effect: change aa)
Nonsense: codon for aa becomes STOP codon (effect: shortened protein)
Silent: Codon for aa becomes new codon for same aa (effect: no effect)
Sources of Mutations
Polymerase Errors
Endogenous damage (a. ROS b. Physical Damage)
Exogenous Damage (a. radiation b. chemicals)
Transposons
Polymerase Errors
- Point mutations
- Small repeats
- Insertions/deletions (small, frameshift)
Endogenous Damage
- Oxidized DNA
- Cross-linked bases
3, Double or single stranded breaks
Exogenous Damage
- UV radiation (pyrimidine dimers T-T or T-C)
- > usually repaired by direct reversal by white light - X-Rays = double stranded breaks & translocations
- Chemicals = can lead to physical damage or to intercalation (insertion of molecules into bases of DNA)
Transposons
- Insertions/deletions (large)
- Inversions
- Duplications
Transposon Structure
Inverted repeats on both sides with transposae in center
Transposase
enzyme that cuts out transposon to relocate it somewhere else
Types of Transposons
- IS Element: composed of regular transposon structure
- Complex transposon: composed of transposae with some other genes flanked with inverted repeats
- Composite transposon: composed of 2 transposae with central region in middle
How do transposons contribute to genomic variation?
- Transposase gene codes for the “cut & paste” transposae enzyme
- Transposae cuts transposon out & pastes it somewhere else
Effect of ONE transposon vs TWO
If one transposon is inserted in:
Intergenic region, then likely no problems
Coding region, then could disrupt the gene & cause less proteins to be formed
If two transposons are inserted in:
Same direction - DNA loops around and causes both to pair up & delete some coding area (therefore loss of genetic info)
Opposite direction - DNA loops around and pair with each other BUT coding area is flipped (therefore less problematic, gene inversion, chromosome rearrangement)
Inversions
Piece of DNA is flipped
Amplifications
Region of gene is duplication therefore the amount of mRNA increases = increases proteins therefore disrupts homeostasis
Translocations
Due to faulty DNA repair (non-homologous end joining) or abnormal recombination between non-homologous chromosomes. Can cause gene fusion
DNA Repair
Direct Reversal: Use white light to reverse damage
Mismatch Repair Pathway: DNA polymerase & endonucleases do this; repairs DNA polymerases mistakes that happen DURING DNA replication; uses methylated strand as template to fix mismatch
Base/Nucleotide Excision Repair: removes & replaces bad nucleotide DURING DNA replication
Homology - directed Repair: intact DNA helps fix DS break that happen AFTER replication; use sister chromatid as template to repair broken strand & does it through homologous crossing over
Non-homologous end-joining: patch the ends & ligase the DNA bc intact is better than broken; used for DS breaks too; no sister chromatids because happens BEFORE replication or in cells where replication doesn’t happen; can be mutagenic
4 Rules & requirements to carry out replication
- Semiconservative (one strand is old, one strand is new)
- 5’ - 3’
- Requires a primer
- Requires a template
Helicase
Unwinds DNA
Topoisomerase
Cuts DNA, relaxes supercoiling
Primase
Synthesizes the RNA primer
DNA polymerase
Replicates DNA, proofreads, removes primer
Ligase
Links okazaki fragments
DNA Replication
- At origin of replication, Helicase binds and so does Topoisomerase
- RNA primer makes DNA in 5’-3’ direction while reading in 3’-5’
- DNA polymerase binds to primer & what makes DNA and elongates
- Removes RNA primer and replaces with DNA
- Ligase hooks okazaki fragments together
Prokaryotic DNA Replication vs Eukaryotic DNA replciation
- Only 1 origin of replication
- 5 DNA polymerases
- goes through Theta replication
- Multiple origins
- Replication bubbles
- several DNA polymerases composed of complex multisubunit enzymes
DNA polymerases in prokaryotes
DNA Polymerase I:
- low processivity
- slow 5’-3’ polymerase AND 3’-5’ exonuclease
- also a 5’-3’ exonuclease to remove primer
- adds nucleotides at RNA primer
- DNA excision repair
DNA Polymerase II:
- 5’-3’ polymyerase AND 3’-5’ exonuclease
- back up for DNA polymerase III
- DNA repair
DNA Polymerase III:
- high processivity
- fast 5’-3’ polymerase AND 3’-5’ exonuclease
- adds nucleotides at ~400 bp downstream of ORI
- main replicating enzyme
- no known fx in DNA repair
DNA Polymerase IV:
- error prone 5’-3’ polymerase activity
- DNA repair
DNA Polymerase V:
- error prone 5’-3’ polymerase activity
- DNA repair
Telomerase
Elongates telomeres on parent strand of DNA
- Includes its own RNA template
- Reverse transcriptase activity (DNA from RNA)
DNA vs RNA
DNA
- double stranded
- double helix
- thymine
- one type of DNA
- Deoxyribose
RNA
- single stranded
- Lots of different 3D shapes
- uracil
- multiple types of RNA
- ribose
3 primary types of RNA
ribosomal RNA
messenger RNA
transfer RNA
Others:
heterogenous nuclear RNA (hnRNA)
micro RNA (miRNA)
small interfering RNA (siRNA)
How does transcription work?
- RNA polymerase binds at promoter and downstream at start site is where mRNA is made
- RNA polymerase continues until it reaches stop site
- RNA polymerase falls off at this point & mRNA leaves
- DNA binding proteins bind to operator region (repressor - prevents more mRNA, enhancer - more mRNA)
Transcription regulation
- Promoter
Strong - lots of RNA
Weak - less amount of RNA - DNA binding proteins
Repressors
Enhancers
Prokaryote vs Eukaryote transcription
Prokaryotes
- Transcription and translation happens at same time
- Polycistronic
- No mRNA processing
- 1 RNA polymerase
Eukaryotes
- Transcription happens in nucleus & translation happens in cytoplasm
- Monocystronic
- mRNA processing: 5’ g cap, 3’ a tail, splicing
- 3 RNA polymerases (rRNA, mRNA, tRNA)
xtRNA^y translates to..
x = type of a.a. that's attached y = type of tRNA
How many ATPs to load a.a. onto tRNA
2 ATP
What enzymes attaches amino acids to tRNA?
aminoacyl tRNA synthetase
Wobble Hypothesis
First two anticodon pairs bind normally (Watson-Crick pairing), third anticodon is more flexible
5' Base in anticodon (tRNA) --> 3' Base in mRNA G --> C or U C --> G U --> A or G A --> U I -->A,U or C
- Sometimes adenine can be converted to inosine for more flexibility
What happens in ribosomes?
Protein synthesis
Prokaryotic vs Eukaryotic ribosomes
Prokaryotic
Large subunit - 50 s
Small subunit - 30 s
Total - 70 s
Eukaryotic
Large subunit - 60 s
Small subunit - 40 s
Total - 80 s
What does svedberg mean?
Svedberg tells you how fast it sediments (bigger the # = faster it sediments
- Not addidtive because other factors affect sedimentation rates
Translation process
- mRNA (first codon) is present in the P site while the first tRNA is present in the A site
- tRNA will translocate to A site and initiate translation
- tRNA #2 will bind to codon at empty A site with a.a. attached
- tRNA #2 and #1 a.a will bond and tRNA #1 now exits and tRNA will have 2 amino acids
- Continue the process until termination codon is detected in A site
How to determine how many ATP is required for x amino acids?
of amino acids x 4 = # of ATP needed
1 ATP for initiation
1 ATP for termination
2 ATP per tRNA loading
1 ATP for A site binding (1 less than original a.a)
1 ATP for translocation (1 less than original a.a)
Post translational Modification
- Protein folding
- aided by chaperonins - Covalent modification
- phosphorylation, glycosylation, disulfide bridges, etc - Processing (most enzymes are made in non-active stage)
- cleavage to activate protein (eg. zymogens)
Pepsinogen (zymogen) —> pepsin (active protein)
