Molecular Genetics Flashcards

Flashcards of key vocabulary and definitions from the Molecular Genetics lecture notes.

Frederick Griffith

Studied the bacteria responsible for bacterial pneumonia (Streptococcus pneumoniae); Injected two forms (strains) of the bacteria in mice.

Griffith's Conclusion

The protein coat on the smooth strain caused virulence.

Avery, MacLeod, and McCarty

Confirmed Griffith’s transforming principle; Proved DNA contains hereditary material.

Hershey and Chase

Used 32P to label the DNA and 35S for the protein coat of bacteriophages to determine if protein or DNA did the transforming.

Wilkins and Franklin

Used X-ray crystallography to study the shape of DNA; Franklin discovered sugar-phosphate backbones faced the outside and that DNA has a double-helix shape.

DNA Backbone

Alternating sugar and phosphate molecules with nitrogenous bases attached to the sugar.

DNA Strands

DNA strands are complementary, antiparallel, and written in the 5’ → 3’ direction.

DNA in Prokaryotes

One large circular strand packed tightly in the nucleoid region controlled by topoisomerase I and II.

Plasmids

Carry non-essential genes and can be copied and transmitted between cells.

Eukaryotic DNA Organization

DNA is wound around chunks of protein called histones in eukaryotes.

Semiconservative DNA Replication

Mechanism of DNA replication in which each newly synthesized DNA molecule is composed of one strand from the original strand and one newly synthesized strand.

Initiation (DNA Replication)

Part of DNA unwound to expose the bases for new pairing.

Elongation (DNA Replication)

Two new DNA strands assembled using parent strands as templates.

Termination (DNA Replication)

Replication process is completed, replication machine dismantled.

Origins of Replication

Replication always starts on specific parts of DNA called origins of replication, recognized by sequence.

Helicase

Unwinds the DNA by breaking the hydrogen bonds between nitrogenous base pairs

Topoisomerase

Used to prevent supercoiling (tangling) down the DNA strand.

Single-strand binding proteins

Coat the separate strands of DNA and prevents them from re-forming the double helix.

DNA polymerase III

Synthesizing new DNA in the 5’ to 3’ direction; needs a template to start with.

Primase

Makes an RNA primer to provide a 3’ end so DNA polymerase can work.

Leading Strand

The strand being created towards the replication fork is continuous.

Lagging Strand

Strand made in fragments called Okazaki Fragments using new primers for each segment.

Final Steps of DNA Replication

Lagging strands contain many small gaps and RNA primers; DNA polymerase I removes primers and fills in the gaps with DNA; other small gaps left are filled in by DNA ligase.

Helicase Function

Opens up DNA at the replication fork.

Single-Strand Binding Protein Function

Attaches to the DNA around the replication fork to prevent recoiling.

Topoisomerase Function

Found just ahead of the fork to prevent supercoiling.

Primase Function

Creates an RNA primer complementary to the DNA template strand.

DNA Polymerase III Function

Extends primers and makes new DNA.

DNA Polymerase I Function

Removes and replaces primers with DNA.

DNA Ligase Function

Seals gaps between DNA fragments.

End-Replication Problem

Ends cannot be fully copied, resulting in slow, gradual shortening of chromosome.

Telomeres

End of DNA strand with 5’TTAGGG3’ repeated hundreds to thousands of times acting as caps that protect the internal regions.

Telomerase

Enzyme that extends telomeres using RNA as a template; active in germ cells and some adult stem cells.

Cancer

When cells divide uncontrollably, ignores stop signals, avoids death, and results in tumor; caused by mutations.

Proofreading

DNA Polymerase can check their work with each base added, will remove wrong nucleotides and replaces it.

Mismatch Repair

Removes and replaces mispaired bases and corrects small insertion and deletions after new DNA has been made.

Direct Reversal

Some DNA-damaging chemical reactions directly undone by enzymes.

Base Excision Repair

Damage fixed by removal and replacement, only damaged base removed.

Nucleotide Excision Repair

Detects and corrects damage that distorts the double helix; fixes the addition of bulky chemical groups and some UV radiation damage.

Double-stranded Break Repair

Non-homologous end joining or homologous recombination used to repair. Linked to superhero origin stories, nuclear disasters

Non-Homologous Joining

Broken ends glued back together; messy and involves the loss or addition of a few nucleotides at the cut site; tends to produce a mutation, but better than losing an entire arm.

Homologous Recombination

Information from the homologous chromosome that matches the damaged one used for repair; cleaner and doesn’t usually cause mutations.

Central Dogma

Genetic information flows from DNA → RNA → proteins.

Transcription

Information coded in DNA is copied into RNA.

Translation

Information coded in the RNA is copied into amino acids.

RNA Polymerase

The main enzyme involved in transcription that uses a single DNA strand to synthesize a complementary RNA strand in 5’-3’ direction.

Initiation (Transcription)

RNA polymerase binds to a promoter region near the beginning of a gene, called the TATA box in eukaryotes; DNA strand separated.

Elongation (Transcription)

RNA polymerase “reads” the DNA and builds an RNA molecule out of complementary nucleotides; RNA carries same information as non-template (coding) strand.

Termination (Transcription)

Sequences called terminators signal completion of the RNA transcript; RNA releases from template strand.

Transcription in Bacteria

All genes in the nucleoid are important and RNA can act as mRNA straight away.

Post-Transcriptional Modifications

Ends need to be modified with a 5’ cap and poly-A tail; needs to undergo splicing, where some parts are chopped out and remaining are stuck back together.

Introns

Intervening sequences that need to be removed.

Exons

Expressed sequences that are useful coding regions.

Splicing

Small nuclear ribonucleoproteins (snRNPs) combine with the pre-mRNA to form a spliceosome; causes intron to loop, bringing exons close together and cut out introns.

Alternative Splicing

Exons can be joined in different combinations increasing the number and variety of proteins encoded by a single gene; explains why humans, with 20k genes, can produce 100 000 proteins.

tRNAs

tRNAs are “bridges” that connect mRNA codons to the amino acids they encode; one end has anticodons to bind to specific sequences, aminoacyl-tRNA → chemically linked to a specific amino acid.

Ribosomes

Ribosomes are made up of rRNA and have two subunits (small and large) with three slots for tRNAs and are where polypeptides (proteins) are built.

Initiation (Translation)

Initiator tRNA binds to the small ribosomal subunit → methionine, binds to the 5’ end of mRNA cap, “walk” down mRNA in the 3’ direction, stops when it finds the start codon, large ribosomal subunit joins to form the initiation complex.

Elongation (Translation)

Initiator tRNA starts at P site, A site is the “landing site” for next tRNA, a tRNA matching the codons enters, peptide bond forms between MET and the new aa, ribosome moves down, initial tRNA is now in the E site, second tRNA in the P site, new tRNA enters A site

Termination (Translation)

Happens when a stop codon (UAA, UAG, UGA) enters the A site, recognized by release factors messes with the enzyme that normally forms peptide bonds, adds a water molecule to the end separates chain from the tRNA released.

Small Scale Mutations

Include mutations of an individual/small groups of base pair(s) and called point mutations.

Small-Scale Mutations

Differences in DNA of people within a population caused by point mutations referred to as single nucleotide polymorphisms (SNPs); effects can range from positive, negative, to no effect.

Frameshift Mutations

Reading frame shift multiple changes

Large-Scale Mutations

Involve multiple nucleotides, entire genes, or whole regions of chromosomes.

Duplication Mutations

Entire coding regions removed referred to as amplification; genes copied to multiple parts of the chromosome allowing for new functions of evolve while keeping original function retained on one gene.

Translocation Mutations

The movement of entire genes or sequences of DNA from one chromosome to another; some pieces of DNA move freely transposable elements and can enhance, disrupt, or modify gene expression.

Inversion Mutations

Portion of DNA molecule reverses direction and doesn’t usually correlate to loss of genetic material; gene can be compromised if break happens in the middle of a codon.

Spontaneous mutations

Caused by errors in DNA replication

Induced mutations

Caused by the effect of an environmental agent (mutagen).

Chemical Mutagens

Any chemical agent that can enter the cell nucleus and chemically alter DNA structure; can also cause mutations by mimicking a DNA nucleotide.

Radiation

UV radiation causes bonds to form between adjacent nucleotides forming a kink in the DNA backbone complicating replication and transcription and leads to certain types of skin cancer.

Sunscreen

Protects skin from the sun’s damaging rays, protects against three of the most common form of skin cancers, and reduces aging effects of the sun.

Radiation Cont.

Higher energy (ionizing) radiation can strip molecules of electrons and break bonds.

Genetic Engineering

The intentional production of new genes and alteration of genomes by substitution or introduction of new genetic material and bacteria are the most widely used.

Recombinant DNA

DNA strand created from two or more sources.

Restriction enzymes

Used to cut DNA at a specific location recognizing a specific sequence of nucleotides and cuts DNA into pieces called restriction fragments.

DNA LIGASE

Join together fragments of DNA and also used in DNA cloning; can join two different pieces of DNA with matching ends.

RESTRICTION MAPS

A diagram that shows restriction enzyme recognition sites and the distance between the sites (measured in base pairs).

THE POLYMERASE CHAIN REACTION

Aka PCR → process used to make a huge number of copies of a DNA sequence in a laboratory quickly and without the need for a host organism and only used to replicate a small portion of DNA.

THREE STEPS OF PCR

DNA heated, separated. Lower temps, DNA primers anneal to the strands. Two new DNA strands synthesized.

GEL ELECTROPHORESIS

PCR amplifies the DNA sequence, Gel electrophoresis separates the molecules (nucleic acids and proteins) using agarose gel.

Housekeeping genes

Continuously transcribed and translated

Regulatory DNA Sequences

Most bacteria have other regulatory sequences on top of the promoter and repressors bind to operators.

Regulatory Proteins

Come from regulatory genes and can be turned on or off by specific small molecules

Lactose and E. coli

E. coli has a love-hate relationship with it Uses it when other sugars are unavailable. Needs an operon Called the lac operon

Lac Operon Activation

Activation occurs upon meeting two conditions: Lactose is available; Glucose is not available. Detected by Lac repressor (lactose sensor) and CAP (glucose sensor)

Cyclic AMP (cAMP)

Regulatory protein that acts as a hunger signal when glucose levels are low; some transcription happens without CAP, but not a lot.

Tryptophan

An amino acid that E. coli need and can take it up from the environment or make its own.