Molecular Biology Flashcards
Purines
A/G double ring structure with 4 nitrogen atoms
Pyrimidines
C/U/T single ring structure with 2 nitrogen atoms
Watson-Crick Model
DNA has right-handed double helix with H bonds between Bases (2 A-T, 3 C-G) in antiparallel orientation
Chargaff’s Rule
A = T, C = G
Annealing
AKA hybridization, binding of two complementary strands of DNA
34 angstroms
When the helix completes itself/completes a full turn (10 base pairs)
ds-DNA
chromosomes that store genome/genetic information (humans have 23 pairs, 46 total)
DNA gyrase
used by prokaryotes to make DNA more compact/sturdy (supercoil)
Histones
globular proteins used by prokaryotes to wrap DNA and form nucleosomes (DNA wrapped around octamer of histones)
Acetylation
loosens DNA from nucleosomes (Transcription)
Methylation
Inactivates chromosomes in eukaryotes
Euchromatin
Less dense, lighter regions of chromosomes when stained with chemicals (higher transcription rates and higher gene activity)
Centromere
Spindle fibers attach via kinetochores during cell division
Telomeres
Ends of chromosomes that prevent deterioration and fusion with neighboring chromosomes
Human genome
22 autosomes, 2 sex chromosomes
Intergenic regions
Regions of noncoding DNA (contribute to assembly of chromatin structure)
Nucleotide Variation
Single Nucleotide Polymorphisms, mutations that occur every ~1000 base pairs that cause specific traits/phenotypes
Copy-Number Variation
Structural Variations in genome lead to different copies of DNA sections
Repeated Sequences/Tandem Repeats
Short sequences of nucleotides repeated one after another, unstable if too short or if repeat is long`
Transcription
Process of reading DNA and writing information as mRNA (complementary to the DNA strand it read)
Translation
Reading of mRNA to create proteins
Codon
Nucleic acid word 3 nucleotide letters long (61 codons that specify 20 amino acids,)
AUG
start codon (methionine)
Retroviruses
Can make DNA from RNA using reverse transcriptase enzyme
DNA Replication
Synthesizing of new strand DNA using parental DNA as template
Helicase
Enzyme that separates tightly coiled DNA at nonrandom place (origin of replication ORI)
Topoisomerases
Cut one/both of the strands to unwrap the helix and prevent breakage
ssBP
single strand binding proteins protect unpackaged DNA (open complex)
DNA polymerase
synthesizes chain (from existing chain) – requires a primer (synthesized by primase) AND template (has to copy an old chain)
Elongation/Orientation of Replication
Daughter DNA is made 5’ to 3’ while template is read 3’ to 5’ –> completes this on both sides of the ORI
Hydrolysis of Pyrophosphate
Driving force thermodynamically of DNA replication
Replication Fork
Sites where unwinding continues after DNA polymerase proceeds in both directions away from ORI (Half of each template strand is replicated)
Leading/Lagging Strands
One continuous leading strand with a lagging strand that has Okazaki fragments (dependent on replication fork widening)
Leading strand = towards fork, lagging strand = away from fork
DNA ligase
Joins DNA fragments together after RNA primers replaced by DNA
Pro DNA Pol I
Adding nucleotides at RNA primer in 5’ to 3’ direction; slow processivity so about 400 base pairs from ORI, DNA pol III takes over; important for excision repair
Pro DNA Pol II
Backup for DNA Pol III (5’ to 3’ activity)
Pro DNA Pol III
Fast, accurate elongation of leading strand 5’ to 3’ activity (exonuclease/end works 3’ to 5’)
Proofreading Function
Ability of an enzyme to move backward to chop off an incorrect nucleotide
Pro DNA Pol IV/V
Not good at polymerase activity but stop other enzymes when repair pathways are activated
Pro vs Eu Replication
Prokaryotes only have one circular chromosome, duplicated genome looks like theta (theta mechanism)
Eukaryotic chromosome has several origins because of how long genome is - DNA looks like bubbles until joined/ligated together
Telomere Replication
No place on lagging strand to place primer, primer cannot be replaced - DNA cannot replicate end sequences
Telomeres are disposable repeats, eventually this telomere gets too short and cell becomes senescent (nondividing) or apoptosis
Hayflick limit
Number of times DNA can divide
Telomerase
Adds repetitive nucleotide sequences to chromosome ends (contains RNA primer and reverse transcriptase)
Germline Mutations
Can be passed onto offspring
Somatic Mutations
Occur in somatic cells and cannot be passed onto offspring
Physical Mutagens
Ionizing radiation ex. X ray (causes DNA breaks)- one side reparable, both sides irreparable
UV light cause pyrimidine dimers that distort DNA backbone - reparable
Chemical Mutagens
Chemical compounds that can cause mutation, Chemicals covalently alter bases or if they look like base pairs can insert themselves into DNA
Biological Agent Mutagens
Viruses, transposons, DNA polymerase making mistakes can all cause mutations
Point mutations: Transitions, Transversions, Missense, Nonsense, Silent Mutation
Transitions - purine substituted for purine or pyrimidine for pyrimidine
Transversions - purine for pyrimidine or vice versa
Missense - one amino acid replaced by another amino acid
Nonsense - one amino acid replaced by a stop codon
Silent Mutation - codon changed for new codon (but both code for same amino acid)
Frameshift Mutations
Insertions/Deletions that change reading frame of protein
Inversion Mutation
Segment of a chromosome is reversed end to end
Amplification Mutation
Segment of chromosome duplicated
Translocation and Rearrangement Mutations
Recombination between non-homologous (not belonging to the same chromosome/containing the same genetic information)
Loss of heterozygosity
Diploid organisms have two copies of each gene (so a mutation in one can be tolerated if other is normal) but deletion removing the normal copy creates a loss of heterozygosity
Hemizygous
A locus where there is only one gene copy within a diploid organism
Transposons
Mobile genetic elements that can jump around the genome (eukaryotic - degenerative retroviruses)
Cause inversions, deletions and rearrangements
Types of Transposons
IS Element
Complex
Composite
IS Element - transposase gene with inverted repeat sequence on both sides
Complex - has additional genes
Composite - two similar or identical IS elements with central region in between
Transposase
Can cut and paste into any new genetic location
Haploinsufficiency
Diploid organism has only a single functional copy of a gene and this is not enough to support the normal state
Good/Bad Mutation
Anemia - mutation within hemoglobin, but heterozygotes are malaria-resistant
DNA Repair
Developed mechanisms to help deal with DNA damage
Direct Reversible
Main mechanism of DNA repair in humans, directly reversible damage (ex. UV-induced pyrimidine photodimers)
Homology-Dependent Repair
Excision
Post-Replication
Mutations can be repaired using the undamaged strand
Before DNA replication = excision repair (removes defective bases/nucleotides and replaces them)
After DNA replication = post-replication repair (mismatch repair pathway MMR targets based pairs not repaired by polymerase)
Myelation
Bacterial Post-Replication Repair for only old strands
Double Strand Break (DSB) Repair
Double strand breaks caused by reactive oxygen species, cells use homologous recombination and nonhomologous end-joining (can lead to deletions or translocations)
Homologous Recombination
One sister chromatid helps repair DSB in another
Nonhomologous End Joining
Cells that are not dividing do not have the ability to use sister chromatids (no backup chromosome)
Instead broken ends stabilized and DNA ligase connects fragments
RNA
ribonucleic acid - single stranded, containing uracil, extra hydroxyl group makes RNA polymer less stable (nucleophilic attack of the backbone phosphate group)
mRNA
contains information carried to the ribosome (can be translated into protein)
monocistronic (one gene one protein) in eukaryotes
polycistronic (one gene many proteins) in prokaryotes
5’ UTR
5’ Region in mRNA not coded for protein that is important for initiation and regulation of transcription
Open Reading Frame (ORF)
Start and stop codon located after 5’UTR
hnRNA
first RNA transcribed from DNA (immature precursor to mRNA in eukaryotes). Cap, tail, splicing makes hnRNA into mature mRNA
Non-coding RNa
tRNA rRNA snRNA miRNA/siRNA piRNA ncRNA
RNA not translated into proteins
tRNA - transfer RNA, translates genetic code & carries amino acids from cytoplasm to ribosome to be added to growing protein
rRNA - ribosomal RNA component of the ribosome (catalytic function) AKA ribozymes
snRNA - small nuclear RNA form complexes in spliceosome
microRNA/small interfering RNA -function in RNA interference to help increase or decrease translation
PIWI interacting RNA - prevent transposons from moving
Long ncRNAs help control transcription
Transcription
Synthesis of RNA using DNA as a template
Begins at specific spot on chromosome (start site) that begins polymerization using RNA polymerase called promoter
Template-driven polymerization
Involved in both replication and transcription (driving force is removal of pyrophosphate/ negative delta G)
Template Strand
Single strand of the DNA template that encodes a particular mRNA molecule (AKA non-coding, transcribed, or antisense strand)
Coding Strand
AKA sense strand that has the same sequence as transcript with T instead of U
Three Stages of Transcription
Initiation
Elongation
Termination
Initation
RNA polymerase holoenzyme binds to dsDNA promoter and then unwinds and binds to ssDNA promoter (close to open complex)
Elongation
Elongates RNA chain processively with one polymerase complex synthesizing entire RNA molecule
RNA polymerase moves along in transcription bubble (where DNA double helix is unwound)
Termination
Signal that tells polymerase to fall off DNA and release the RNA (sometimes with the help of a protein called rho)
Differences Between Prokaryotic/Eukaryotic Transcription (There are 4)
Location:
Pro - transcription and translation in cytoplasm
Eu - transcription in nucleus while translation in cytoplasm (nonsimultaneous)
Primary Transcript
Pro - mRNA, ready for translation
Eu - hnRNA (modified before translation)
RNA Polymerase
Pro - only one RNA polymerase
Eu - 3 types (I - transcribes rRNA, II- transcribes hnRNA/mRNA, II - transcribes tRNA)
Transcription itself
Translation
Synthesis of polypeptides according to mRNA where tRNA brings specific amino acids
tRNA
Transfer RNA - step and loop structure with anticodon that recognizes mRNA codon to be translated. also has amino acid receptor site
Wobble Hypothesis
61 codons expect 61 distinct tRNA molecules, but there are usually fewer than 45 (suggests some tRNA molecules bind to more than one codon (first and second codon-anticodon normal, third is flexible)
Amino Acid Activation
Peptide bonds not thermodynamically favorable, reaction coupling (ATP hydrolysis) done to allow amino acids to attach
Amino acid reacts with ATP to form aminoacyl AMP, then Ppi group hydrolyzed
Aminoacyl AMP is destroyed to load to tRNA where aminoacyl-tRNA synthetase enzymes specific to each amino acid
Ribosome
Composed of polypeptides/ rRNA chains and has small and large subunit
80S, 40S subunit and 60S large subunit (large one has 28S rRNA molecule that has ribozyme function)
Binding sites:
A - tRNA delivers amino acid
P - growing polypeptide chain is located
E - empty tRNA sits before release
Epigenetics
Changes in gene expression due to differences outside of DNA sequencing
DNA Methylation and Chromatin Remodeling
Eu - turns off gene expression
Pro - alters gene expression (promoting/inhibiting transcription)
Gene Dose
Increasing number of copies of a gene can increase expression
Genomic Imprinting
When one allele of a gene is expressed (either maternal or paternal)
X Chromosome Inactivation
Females have 2 X chromosomes, (one inactive). Humans its by random choice which X is inactivated (have highest levels of DNA methylation)
Bacterial Regulation Mechanisms
Anabolic Enxymes - inhibited in excess product (repressible enzymes)
Catabolic enzymes - activated in excess substrate (inducible enzymes)
Ex. TRP vs Lac operon respectively
Lac Operon
Inducible, involving lactose catabolism (contains Z, Y, A genes)
When lactose is present, lac repressor falls off which allows lactose catabolism
TRP operon
Presence of tryptophan, repressor protein binds to the operon, operator turned off
Post-Translational Modification
Proteins Folded, modified, transported by molecular chaperones
Fidelity
Accuracy (Transcription has less fidelity than Replication)
mRNA half-life
Means mRNA remains in cell longer and more protein is consequently translated
