BIOE2301 - Genetics & Molecular Biology

Virulence

the ability of a virus or a bacterium to cause damage to its host.

Deoxyribonucleic Acid (DNA)

a polymer that contains genetic information made of four different types of subunits called nucleotides. Each nucleotide contains a sugar (deoxyribose), a phosphate group, and one of four nitrogenous bases: either a double-ring purine (adenine or guanine), or a single-ring pyrimidine (cytosine or thymine).

Phosphodiester Bonds

covalent linkages between adjacent nucleotides in DNA. The phosphate on the 5′ carbon on the sugar ring of an incoming nucleotide is linked to the hydroxyl group on the 3′ carbon of the sugar of the last nucleotide in the growing polymer.

antiparallel

describes the opposing orientations of the two strands of double-stranded DNA. DNA polymers have direction and polarity, because at one end, the 5′ carbon of the sugar on the first nucleotide is not connected to any other nucleotide; while at the other end, the 3′ carbon of the sugar on the final nucleotide is not connected to any other nucleotide.

Complementary Base Pairing

formation of hydrogen bonds between specific bases (A/T and G/C) on antiparallel DNA strands. The two DNA strands in double-stranded DNA are complementary, and the base sequence of one strand predicts the base sequence of the other strand.

Semiconservative DNA Replication

each strand of a double-stranded DNA molecule is used as a template for synthesis of a complementary antiparallel DNA strand. Thus, after DNA replication, every double-stranded DNA molecule consists of one old strand (the template) and one newly synthesized strand.

Replication Fork

during DNA replication, a Y-shaped area where the top of the Y consists of two unwound DNA strands that are both used as templates for semiconservative DNA replication. The replication fork moves continually in the direction of the stem of the Y as the double-stranded DNA that constitutes the stem continually unwinds.

RNA Primer

during DNA replication, a short stretch of RNA synthesized by primase enzyme that initiates (primes) DNA synthesis.

DNA Polymerase

an enzyme complex that polymerizes DNA in the 5′ to 3′ direction by extending a primer bound to a DNA template. DNA polymerase III extends the RNA primers, and DNA polymerase I fills in the gaps after the RNA primers are removed.

Leading and Lagging Strand

During DNA replication, the leading strand is synthesized continuously in the 5′ to 3′ direction toward the unwinding replication fork. The lagging strand has a polarity opposite to that of the leading strand, and so it must be synthesized discontinuously as small Okazaki fragments that are ultimately joined into a continuous strand.

DNA Ligase

during DNA replication, the enzyme that stitches Okazaki fragments together by forming phosphodiester bonds between adjacent nucleotides.

Chromatin

complex of DNA and proteins in the cell nucleus. Some scientists consider certain RNA molecules associated with chromosomes also to be part of chromatin.

Histones

small DNA-binding proteins with a preponderance of the positively charged amino acids lysine and arginine; histones help compact DNA within chromatin.

Nucleosome

rudimentary DNA packaging unit, composed of DNA wrapped twice around the core histones, with two copies each of the four different histone proteins called H2A, H2B, H3, and H4.

Linker DNA

a stretch of ~40 base pairs of DNA that connects one nucleosome with the next. Histone H1 anchors the linker DNA to the nucleosome.

G Bands

alternating dark and light segments (1–10 Mb) of a chromosome as seen under a microscope after staining with Giemsa dye. An artist’s diagram of the microscopic image of G-banded chromosomes is called an idiogram.

P and Q Arm

short (P) and long (Q) intervals between a telomere and the centromere.

Telomeres

specialized terminal structures that ensure the maintenance and accurate replication of the two ends of each linear chromosome in eukaryotes.

Telomerase

an enzyme crucial to the successful replication of telomeres.

Restriction Enzyme

an enzyme used by bacteria to attack the genomes of bacteriophage by cutting foreign DNA at specific sequences, producing smaller, linear restriction fragments. Bacteria protect their own genomes from restriction enzymes by making modification enzymes that add methyl groups to specific nucleotides so that restriction sites are no longer recognized by the restriction enzymes.

Sticky vs. Blunt Ends

If a restriction enzyme cuts the two strands of DNA at phosphodiester bonds between the same base pairs, the ends of the restriction fragments are blunt. If the cuts are offset from each other, the restriction fragments have either 5′ or 3′ overhangs (depending on the enzyme). If the overhangs of any two fragments produced by an enzyme can base-pair with each other, the ends are sticky and compatible.

Plasmid

a small circular DNA molecule that can replicate within bacterial cells independently of the bacterial chromosome. Plasmid DNAs are often used as vectors to construct recombinant DNA molecules with relatively small inserts (An equation read as follows, less than 20kb) of foreign DNA.

Selectable Marker

gene carried on a vector that allows the selection of cells that contain recombinant DNA molecules.

Multiple Cloning Site (MCS)

a region within a cloning vector (like a plasmid or virus vector) that contains several unique restriction sites. These restriction sites are recognition sequences for specific restriction enzymes.

Molecular Cloning

isolation of large amounts of a given fragment of DNA that is joined in the test tube with a vector DNA, allowing propagation of the resultant recombinant DNA molecule. A preparation containing many identical copies of the same one recombinant DNA molecule is a DNA clone.

Genomic Library

long lived collection of cellular clones that contains copies of every sequence in the whole genome inserted into a vector (plasmid).

Gene Expression

The process by which information contained in genes is decoded to produce other molecules that determine the phenotypic traits of organisms.

Transcription

use of one strand of DNA (the template strand) by RNA polymerase to synthesize, from ribonucleotide subunits, a complementary strand of RNA (a transcript), whose sequence corresponds to the other DNA strand (the RNA-like strand).

Promoter

the DNA sequence in a gene to which RNA polymerase binds to initiate transcription.

Upstream and Downstream

terms describing directions or positions with respect to a gene. Upstream signifies the direction opposite to that traveled by RNA polymerase as it transcribes the gene, while the downstream direction is the direction in which RNA polymerase moves during transcription.

RNA Processing

events that occur in eukaryotic cells to change a primary transcript synthesized by RNA polymerase into a mature mRNA. These processing steps include: (i) addition of a run of As (a poly-A tail) near the 3′ end of the primary RNA, (ii) addition of a modified G nucleotide called a 5′ cap to the 5′ end of the RNA, and (iii) RNA splicing, the process by which long stretches of RNA called introns are removed and degraded, and the remaining RNA fragments, called exons, are connected together.

Mutation

a change in the base pair sequence of DNA. In multicellular organisms, mutations can occur in any cell, but they are heritable only if they are passed through the gametes.

Forward Mutation

mutation from a wild-type (normal) allele to a non-wild-type (mutant) allele is forward mutation.

Reverse Mutation

changing a mutant base pair sequence back to the wild-type sequence is reverse mutation or reversion, and the reverse mutants are called revertants.

Complementation Test

a genetic assay to determine whether two different recessive (relative to wild-type) loss-of-function mutations reside in the same gene. If an organism with the two mutant DNAs has a wild-type phenotype, the mutants complement one another, and each mutant DNA provides the function that the other lacks, and so the two mutations must reside in different genes. If a mutant phenotype is observed (no complementation), then the two mutations must be in the same gene; neither mutant DNA supplies the function that the other lacks.