Key Terms from Bioinformatics & Molecular Biology (Video Notes)

A set of vocabulary flashcards covering key concepts, terms, and definitions from the video notes.

Computational biology

Development of methods and software tools for understanding biological data; analysis, prediction, and modeling of biological data with computers; combines biology, computer science, information engineering, mathematics, and statistics.

Bioinformatics

Field applying computational approaches to manage and interpret biological data; aims to interpret biological information and enable efficient access to data.

Cell

Fundamental working unit of every living system; all organisms are composed of cells and every organism has cells capable of independent functioning.

Prokaryotic cell

Single-celled organism with no nucleus and no membrane-bound organelles; typically has a single circular DNA molecule.

Eukaryotic cell

Cell that can be single or multicellular; contains a nucleus and membrane-bound organelles; linear chromosomes.

Nucleus

Membrane-bound organelle that houses DNA in eukaryotic cells and is a key site for transcription.

Chromosome

Threadlike structure in the nucleus made of DNA; carries genes and packages genetic material.

DNA (Deoxyribonucleic acid)

Molecule that stores genetic information; double-stranded; bases are Adenine (A), Cytosine (C), Guanine (G), and Thymine (T).

RNA (Ribonucleic acid)

Single-stranded nucleic acid that transfers genetic information and provides templates for protein synthesis; bases are Adenine (A), Cytosine (C), Guanine (G), and Uracil (U).

mRNA (Messenger RNA)

RNA molecule that carries genetic information from DNA to the ribosome for protein synthesis.

tRNA (Transfer RNA)

RNA molecule that delivers specific amino acids to the ribosome during translation; contains an anticodon that pairs with codons on mRNA.

rRNA (Ribosomal RNA)

RNA component of ribosomes; provides structural scaffolding and catalyzes peptide bond formation during protein synthesis.

Protein

Polypeptide chains formed from amino acids; perform a wide range of cellular functions including enzymes, signaling, structure, and transport.

Amino acids

20+ building blocks of proteins; encoded by the genetic code; side chains determine properties (charged, polar, hydrophobic, etc.).

Central Dogma

Principle that genetic information flows from DNA to RNA to protein.

Genome

The complete set of genetic material present in an organism or cell.

Gene

Discrete unit of hereditary information located on chromosomes; DNA sequence that encodes instructions to make a protein or RNA.

Genotype

The genetic makeup of an organism; the set of genes possessed.

Phenotype

The observable physical and physiological traits of an organism resulting from gene expression and environment.

Open Reading Frame (ORF)

DNA region that has the potential to be translated into a protein; starts with a start codon and ends with a stop codon.

Promoter

Regulatory DNA sequence upstream of a gene that controls the initiation of transcription.

5' cap

Modified guanine nucleotide added to the 5' end of eukaryotic mRNA to protect from degradation and assist in translation.

Poly-A tail

Series of adenine nucleotides added to the 3' end of eukaryotic mRNA; enhances stability and export from the nucleus.

Exon

Coding sequences in a gene that remain in mature mRNA after splicing.

Intron

Non-coding sequences within a gene that are removed during RNA splicing.

Splicing

Process of removing introns and joining exons to form mature mRNA.

Alternative splicing

Process by which a single gene can produce multiple mRNA variants by including/excluding different exons, increasing protein diversity.

Coding strand vs template strand

Coding (sense) strand has the same sequence as mRNA (T replaced by U); template (antisense) strand is used by RNA polymerase to synthesize mRNA.

Transcription

Process of copying a gene's DNA sequence into an RNA transcript by RNA polymerase.

Translation

Process of converting an mRNA sequence into a polypeptide chain at the ribosome.

Codon

Triplet of nucleotides in mRNA that encodes a specific amino acid or a stop signal.

Anticodon

Triplet in tRNA that pairs with a codon on mRNA to insert the correct amino acid during translation.

Ribosome

Ribonucleoprotein complex that synthesizes proteins by translating mRNA; consists of rRNA (structural scaffolding) and proteins.

DNA polymerase

Enzyme that replicates DNA, copying the DNA during cell division.

RNA polymerase

Enzyme that synthesizes RNA from a DNA template during transcription.

Restriction enzymes

Enzymes that cut DNA at specific recognition sequences; used to cut DNA into fragments for cloning and analysis.

Ligation

Joining of DNA fragments by forming phosphodiester bonds between ends; used to fuse DNA pieces.

Polymerase Chain Reaction (PCR)

Process to massively replicate DNA sequences by separating the two strands and adds the DNA primer. DNA polymerase builds new DNA from the primer starting point.

Clone-by-Clone sequencing

Genome sequencing approach: break genome into large clones, map them, cut into overlaps (~500 bp), sequence, and assemble.

Whole-genome shotgun sequencing

Genome sequencing approach: break genome into small pieces, sequence them, and reassemble to form the full genome.

Sequence assembly

Process of reconstructing the original DNA sequence by aligning overlaps among fragments; complex due to repeats and errors.

Mutation

Change in a DNA sequence; can be beneficial (good), harmful (bad), or neutral (silent).

Phylogenetic tree

Diagram showing evolutionary relationships among species based on genetic data.

Genetic code / Standard Genetic Code

Table mapping codons (triplets) in mRNA to amino acids or stop signals; universal to most organisms.

DNA base pairing rules

A pairs with T; C pairs with G in DNA. In RNA, A pairs with U.

RNA base pairing rules

A pairs with U; C pairs with G in RNA.

Spliceosome

Complex that carries out RNA splicing, removing introns and joining exons during mRNA processing.

RNA secondary structure

Predicted base-pairing pattern within an RNA molecule; influences function and is not always uniquely determined.

Codon table

Reference that associates each codon with its corresponding amino acid or stop signal in translation.