bio lab midterm

liter

Basic unit of volume in the metric system

milliliter

1/1000 of a liter

microliter

- one millionth of a liter

- "ul"

concentration units

X, mols, m, %, g/L, ug/mL, mg/mL

DNA

- genetic information.

- made up of building blocks (legos), named A, G, T, C.

- genetic material made in the nucleus.

- made up of exons (contains info that gets translated into a protein) and introns (junk DNA).

mRNA

- lacks introns, it's the pre-mRNA after the splicing.

- known as mature mRNA.

pre-mRNA

- similar structure to DNA, exons, introns, and all.

- made up ribonucleotides (RNA building blocks).

tRNA

- transfer RNA; type of RNA that carries amino acids to the ribosome.

- bring the amino acid, matching the codon in the ribosome, over to add to the protein chain.

- translates/reads codons.

- has an anticodon on the bottom.

- each tRNA has an amino acid with a specific anticodon.

spliceosome

A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

ribosome

- Cytoplasmic organelles at which proteins are synthesized.

- connects the amino acid brought by the tRNA to the growing protein.

cDNA

a mirror of mRNA used to analyze the difference between gDNA and mRNA/cDNA.

- can determine what was spliced out of mRNA and difference in sequence length.

reverse transcription

- a process which allows you to synthesize DNA (cDNA) from mRNA, using the enzyme reverse transcriptase.

- convert mRNA into cDNA.

reverse transcriptase

An enzyme that converts RNA into DNA.

protein

- A large chemical structure that causes functions to occur.

- Made of amino acid monomers.

DNA polymerase

enzymes that create DNA molecules by assembling nucleotides

RNA polymerase

copies DNA into the pre-mRNA, works with the process of transcription.

polymerase chain reaction (PCR)

- a method that allows us to isolate and amplify specific sections of DNA.

1) denaturing - 95*C, double stranded DNA separates into single strands.

2) annealing - 55C-65C, primers attach to the sequence complementary to them in the single strand.

3) extension - 72*C, DNA polymerase attaches to the primers and extends the sequence.

Annealing

- 55C-65C, primers attach to the sequence complementary to them in the single strand.

- DNA strands are separated and are NOT double stranded anymore; can form bonds with other nucleotides now.

- primers attach to the single-stranded DNA.

denaturing

- 95*C, double stranded DNA separates into single strands.

- each long rectangle is one strand of DNA.

- two rectangles close together are double-stranded DNA.

extension

- 72*C, DNA polymerase attaches to the primers and extends the sequence.

- when TAQ (a DNA polymerase) binds to the primer and extends DNA strand.

- the new extended strand is completely complementary to the OG strand.

polymorphism

- two or more variant forms of a specific DNA sequence.

- different types include SNPs, Indels, and Transposable Elements.

insertion deletion (indel)

- when one or more nucleotides (base pairs) of DNA have been inserted or deleted from a DNA sequence.

- called both because we don't have the ancestral sequence to tell if it's been taken out or inserted.

- seen by a gap (dash).

- can be any size.

single nucleotide polymorphism (SNP)

- a change in a nucleotide base in a DNA sequence.

- refers to the location of the polymorphism than to a specific nucleotide that has been changed.

- the mutations are classified as synonymous/nonsynonymous or sense/missense/nonsense.

transposable element

- mobile pieces of DNA that can move and insert themselves in DNA.

- NOT a DNA replication error. - most identifiable at the end of a sequence.

- seen as a gap (dash).

- can be any size

- terminal inverted repeats

BLAST

website to view DNA sequence

multiple sequence alignment

A process that aligns three or more biological sequences (like proteins, DNA, or RNA) to identify homologous regions and infer evolutionary relationships

primers

- different for every PCR, short single stranded DNA sequence that primes the single-stranded DNA, so the DNA polymerase (TAQ) knows where to bind and start extending.

Taq

- Apart of the master mix, a DNA polymerase.

- Nucleotides for the polymerase to use during extension.

- Buffer to provide a good environment for DNA polymerase to work effectively.

negative control

- Control group where conditions produce a negative outcome. Negative control groups help identify outside influences which may be present that were not accounted for when the procedure was created.

- normally water

master mix

The solution that contains all the components--including enzymes, nucleic acids, and ions--to build new DNA.

gene expression

- the process of transcribing and translating DNA into a protein which can do stuff.

- also known as genetic information transfer.

antibiotic selection

The selection gene; a gene that ensures only transformed bacteria is left alive.

plasmid

- a circular strand of DNA that can be taken up by bacteria; the bacteria can express the genes located in the plasmid as its own DNA.

- must be Intronless.

bacterial transformation

- transform bacteria so they can perform new functions.

- inserting DNA into bacteria.

constitutive promoter

- An unregulated promoter that allows for continual transcription of its associated gene.

- always on

conditional promoter

Promoter activated under specific conditions.