Module 3 genetics

minimal medium

Medium that contains the nutrients required by only prototrophic bacteria—typically a carbon source, essential elements such as nitrogen and phosphorus, certain vitamins, and other required ions and nutrients.

complete medium

A medium that contains all the substances required by bacteria for growth and reproduction. Auxotrophic mutants can grow on a complete medium.

Colony

Clump of genetically identical bacteria derived from a single bacterial cell that undergoes repeated rounds of division.

plasmid

Small, usually circular DNA molecule that is distinct from the bacterial chromosome; capable of replicating independently of the bacterial chromosome.

episome

Plasmid capable of replicating freely and able to integrate into a bacterial chromosome.

F (fertility) factor

Episome of E. coli that controls conjugation and gene exchange between E. coli cells. The F factor contains an origin of replication and genes that enable the bacterium to undergo conjugation.

conjugation

Mechanism by which genetic material can be transferred from one bacterium to another. In conjugation, two bacteria lie close together, and a connection forms between them. A plasmid, or sometimes a part of the bacterial chromosome, passes through this connection from one cell to the other.

transformation

Mechanism by which DNA found in the environment is taken up by a cell. After transformation, recombination may take place between the introduced genes and those of the bacterial chromosome.

transduction

Type of gene exchange that takes place when a virus carries genes from one bacterium to another. After it is inside the cell, the newly introduced DNA may undergo recombination with the bacterial chromosome.

pilus (pili)

Extension of the cell membrane of some bacteria that allows conjugation to take place. When a pilus on one cell makes contact with a receptor on another cell, the pilus contracts and pulls the two cells together.

competence

The ability to take up DNA from the environment (to be transformed).

transformant

Cell that has received genetic material through transformation.

contransformation

Process in which two or more genes are taken up together during cell transformation.

horizontal gene transfer

Transfer of genes from one organism to another by a mechanism other than reproduction.

restriction-modification system

A type of bacterial defense that uses restriction enzymes to cleave foreign DNA. The bacteria protects its own DNA from cleavage by modifying the sequences recognized by the restriction enzymes.

CRISPR-Cas system

A system used by bacteria and archaea as a defense against foreign DNA. Has been adapted for use as a molecular tool for precisely cutting DNA, providing a powerful way of editing the genome.

CRISPR array

A series of repeated DNA sequences called clustered regularly interspaced short palindromic repeats located in the bacterial or archaeal chromosome. Fragments of foreign DNA are inserted into the array; these are later transcribed into CRISPR RNA.

Cas proteins

Proteins that function in CRISPR-Cas systems. Combine with crRNA to form an effector complex that cleaves DNA at specific base sequences.

protospacer adjacent motifs (PAM)

Adjacent DNA sequence required for binding by a CRISPR-Cas effector complex; the complex associates with the PAM and unwinds the DNA nearby.

virus

Noncellular replicating structure consisting of nucleic acid surrounded by a protein coat; can replicate only within a host cell.

virulent phage

Bacteriophage that reproduces strictly through the lytic cycle and kills its host cell.

temperate phage

Bacteriophage that can undergo the lysogenic cycle, in which the phage DNA integrates into the bacterial chromosome and remains in an inactive state.

prophage

Phage genome that is integrated into a bacterial chromosome.

plaque

Clear patch of lysed cells on a continuous layer of bacteria on the agar surface of a petri plate; each plaque represents a single original phage that multiplied and lysed many cells.

generalized transduction

Transduction in which any gene may be transferred between bacteria by viruses.

specialized transduction

Transduction in which genes near special sites on the bacterial chromosome are transferred from one bacterium to another; requires lysogenic bacteriophages.

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transducing phage

Phage that contains a piece of the chromosome of its bacterial host inside the phage coat.

transductant

Bacterial cell that has received genes from another bacterium through transduction.

cotransduction

Process in which two or more genes are transferred together from one bacterial cell to another by a virus. Only genes located close together on a bacterial chromosome will be cotransduced.

retrovirus

Virus that injects its RNA genome into a host cell, where reverse transcription produces a complementary, double-stranded DNA molecule from the RNA template; the DNA copy then integrates into the host chromosome to form a provirus.

reverse transcriptase

Enzyme that can synthesize complementary DNA from either an RNA or a DNA template.

provirus

A viral genome incorporated into a host chromosome.

integrase

Enzyme that inserts prophage, or proviral, DNA into a host chromosome.

oncogene

Dominant-acting gene that stimulates cell division, leading to the formation of tumors and contributing to cancer; arises from a mutated copy of a normal cellular gene (proto-oncogene).

antigenic drift

The appearance of new strains of a rapidly evolving virus because of mutations.

antigenic shift

Major change in a viral genome through the reassortment of genetic material from two different strains of the virus.

nucleotide

Repeating unit of DNA or RNA made up of a sugar, a phosphate, and a nitrogenous base.

chargaffs rule

Rules developed by Erwin Chargaff and his colleagues concerning the ratios of bases in DNA.

transforming principle

Substance responsible for transformation. DNA is the transforming principle

isotopes

Different forms of an element that have the same number of protons and electrons but differ in the number of neutrons in the nucleus.

x-ray diffraction

Method for analyzing the three-dimensional shape and structure of a chemical substance in which crystals of the substance are bombarded with X-rays, which hit the crystals, bounce off, and produce a pattern of spots on a detector. The pattern of the spots produced on the detector provides information about the molecular structure.

ribose

Five-carbon sugar in RNA; has a hydroxyl group attached to the 2'-carbon atom.

deoxyribose

Five-carbon sugar in DNA; lacks a hydroxyl group on the 2'-carbon atom

nitrogenous base

Nitrogen-containing base that is one of the three parts of a nucleotide

purine

Type of nitrogenous base in DNA and RNA. Adenine and guanine are purines.

pyrimidine

Type of nitrogenous base in DNA and RNA. Cytosine, thymine, and uracil are pyrimidines.

Adenine (A)

Purine base in DNA and RNA.

guanine (G)

Purine base in DNA and RNA.

cytosine (C)

Pyrimidine base in DNA and RNA.

thymine (T)

Pyrimidine base in DNA and RNA.

uracil (U)

Pyrimidine base in RNA, but not normally in DNA.

nucleoside

Ribose or deoxyribose sugar bonded to a nitrogenous base.

phosphate group

phosphorus atom bonded to four oxygen atoms; one of the three components of a nucleotide.

deoxyribonucleotide

Basic building block of DNA, consisting of deoxyribose, a phosphate group, and a nitrogenous base.

ribonucleotide

Basic building block of RNA, consisting of ribose, a phosphate group, and a nitrogenous base.

phosphodiester linkage

A strong covalent bond that joins the 5'-phosphate group of one nucleotide to the 3'-hydroxyl group of the next nucleotide in a polynucleotide strand

polynucleotide stand

Series of nucleotides linked together by phosphodiester bonds

5’ end

End of a polynucleotide chain at which a phosphate group is attached to the 5' -carbon atom of the sugar in the nucleotide

3’ end

End of a polynucleotide chain at which an OH group is attached to the 3' -carbon atom of the sugar in the nucleotide

antiparallel

The orientation of the two polynucleotide strands of the DNA double helix in opposite directions

complementary DNA strands

Nucleotide strands of DNA in which each purine on one strand pairs with a specific pyrimidine on the opposite strand (A pairs with T, and G pairs with C

B-DNA

Right-handed helical structure of DNA that exists when water is abundant; the secondary structure described by Watson and Crick and probably the most common DNA structure in cells.

A-DNA

The orientation of the two polynucleotide strands of the DNA double helix in opposite direction

Z-DNA

Secondary structure of DNA characterized by 12 bases per turn, a left-handed helix, and a sugar– phosphate backbone that zigzags back and forth. 

transcription

Process by which RNA is synthesized from a DNA template.

translation

Process by which a protein is assembled from information contained in mRNA.

replication

Process by which DNA is synthesized from a single-stranded nucleotide template.

central dogma

Concept that genetic information passes from DNA to protein in a one-way information pathway

reverse transcriptase

Synthesis of DNA from an RNA template.

RNA replication

Process in some viruses by which RNA is synthesized from an RNA template.

supercoiling

Tertiary structure that forms when strain is placed on a DNA helix by overrotation or underrotation. See also positive supercoiling, negative supercoiling

relaxed state of DNA

Energy state of a DNA molecule when there is no structural strain on the molecule.

positive supercoiling

Tertiary structure that forms when strain is placed on a DNA helix by overrotating.

negative supercoiling

Tertiary structure that forms when strain is placed on a DNA helix by underrotating.

topoisomerase

Enzyme that adds or removes rotations in a DNA helix by temporarily breaking nucleotide strands; controls the degree of DNA supercoiling.

nucleoid

Bacterial DNA confined to a definite region of the cytoplasm.

euchromatin

Chromatin that undergoes the normal process of condensation and decondensation in the course of the cell cycle.

heterochromatin

Chromatin that remains in a highly condensed state throughout the cell cycle; found at the centromeres and telomeres of most chromosomes

non-histone chromsomal protein

One of a heterogeneous assortment of nonhistone proteins in chromatin

nucleosome

Basic repeating unit of chromatin, consisting of a core of eight histone proteins (two each of H2A, H2B, H3, and H4) and about 146 bp of DNA that wraps around the core about two times.

linker DNA

Stretch of DNA separating two nucleosomes.

topologically associated domain (TADs)

Large regions of spatially interacting chromatin; may contain tens of thousands to millions of bp of DNA. Within a TAD, regions of chromatin lie in close proximity and interact with one another but are separated in space from other TADs. Help to control gene expression in eukaryotic cells.

epigenetic change

stable alteration of chromatin structure that may be passed on to descendant cells or individuals. Phenomena due to alterations in DNA that do not include changes in the base sequence; often affects the way in which DNA sequences are expressed. Such alterations are often stable and heritable in the sense that they are passed to descendant cells or individuals

telemetric sequence

Sequence found at the ends of a chromosome; consists of many copies of short, simple sequences repeated one after the other.

shelterin

Multiprotein complex that binds to telomeres and protects the ends of the DNA from being inadvertently repaired as a double-stranded break in the DNA.

C-value

Amount of DNA per cell in an organism.

C-value paradox

The absence of a relation between the C-values (genome sizes) of eukaryotes and organismal complexity

unique-sequence DNA

DNA sequence that is present only once or, at most, a few times in the genome.

gene family

Set of genes that are similar in sequence and that arose through duplication events; often encode different protein products.

repetitive DNA

DNA sequences that exist in multiple copies in a genome.

moderately repetitive DNA

A major class of repetitive DNA, which typically consists of sequences from 150 to 300 bp in length that are repeated thousands of times.

tandem repeats

Type of moderately repetitive DNA in which sequences are repeated one after another; tend to be clustered at specific locations on a chromosome.

interspersed repeats

repeated sequences that are scattered throughout the genome

short interspersed element (SINE)

Short DNA sequence repeated many times and interspersed throughout the genome.

long interspersed element (LINE)

Long DNA sequence repeated many times and interspersed throughout the genome.

highly repetitive DNA

DNA that consists of short sequences that are present in hundreds of thousands to millions of copies that are repeated in tandem and are clustered in certain regions of chromosomes.