MCB2000 Exam 2 UF

Central Dogma of Molecular Biology

DNA -> RNA -> Protein (Replication -> Transcription -> Translation)

Chromosome

Cellular structure containing DNA, carrying hereditary information (genes)

Gene

Segments of DNA that encode functional products (RNA or protein)

Genome

The complete genetic information of a cell or virus

mRNA

Messenger RNA; carries the genetic code (codons) from DNA to the ribosome

tRNA

Transfer RNA; transports amino acids during protein synthesis and contains the anticodon

rRNA

Ribosomal RNA; combines with proteins to form ribosomes (the site of protein synthesis)

Replication

The process of copying DNA using a DNA template, producing DNA

Transcription

The process of synthesizing an RNA molecule using a DNA template

Translation

The process of synthesizing proteins using the genetic code encoded in mRNA

Template for Replication

Parental DNA strand

Template for Transcription

DNA strand

Template for Translation

mRNA molecule

Product of Replication

Two identical DNA molecules (semiconservative)

Product of Transcription

RNA molecule (mRNA, tRNA, or rRNA)

Product of Translation

Polypeptide / Protein

Complementary strands

DNA strands where base pairs match specifically (A pairs with T, C pairs with G via hydrogen bonds)

Anti-parallel

Describes the two strands of DNA running in opposite directions (one 5'->3' and the other 3'->5')

Semiconservative replication

DNA replication where each daughter molecule consists of one newly synthesized strand and one original parental strand

Double helix

The twisted ladder structure of DNA formed by two complementary, antiparallel strands

DNA gyrase

Enzyme that relaxes supercoiling ahead of the replication fork

DNA ligase

Enzyme that makes covalent bonds to join DNA strands (joins Okazaki fragments)

DNA polymerase

Enzyme that synthesizes new DNA strands by adding nucleotides in the 5' to 3' direction and has proofreading capability

RNA polymerase

Enzyme that uses a DNA template to synthesize RNA molecules during transcription

Helicase

Enzyme that unwinds and unzips double-stranded DNA at the replication fork

Viral genetic material

Can be DNA or RNA, and can be single-stranded or double-stranded

Location of DNA in eukaryotes

Found in chromosomes (nucleus), chloroplasts, and mitochondria

Location of DNA in prokaryotes

Found in the bacterial chromosome and plasmids

Operons

A cluster of several related genes under the control of a single promoter/operator, expressed together or not at all

Catabolite repression

A regulatory mechanism that allows bacteria to preferentially use glucose over other sugar sources (like lactose)

Ribosomes composition

Made of protein and ribosomal RNA (rRNA) molecules

Prokaryotic vs Eukaryotic ribosomes

Prokaryotes have 70S ribosomes while eukaryotes have 80S ribosomes; this difference allows certain antibiotics to target bacterial ribosomes without harming human cells

Recombinant DNA technology

The intentional modification of an organism's genetic material by inserting foreign DNA fragments

Purpose of cloning

To make multiple identical copies of a piece of DNA or an organism

RFLP (Restriction Fragment Length Polymorphism)

A technique where DNA is cut with restriction enzymes and separated by gel electrophoresis to analyze DNA patterns

Tools used to make Recombinant DNA

Restriction enzymes (to cut DNA), vectors like plasmids or viruses (to introduce DNA), and DNA ligase (to join DNA)

Gene library

A collection of cloned DNA fragments representing an organism's entire genome

Protoplast fusion

A method of joining plant, fungal, or bacterial cells by removing their cell walls to combine their genetic material

Gene gun

A physical method used to introduce foreign DNA into plant cells by shooting DNA-coated gold particles

Microinjection

A method of directly injecting DNA into a cell using a micro-pipette

Polymerase Chain Reaction (PCR)

A laboratory technique used to amplify specific DNA fragments exponentially

Synthetic DNA

Artificially synthesized DNA molecules created in the laboratory

Goal of the Genome Project

To sequence and map all the genes of an organism's genome

Nanotechnology

The manipulation of matter on an atomic, molecular, and supramolecular scale for various applications

Human microbiome in crime scene investigation

Using unique microbial fingerprints left behind on objects to link suspects to crime scenes

Agricultural products of recombinant DNA

Bt crops, herbicide-resistant crops, and frost-resistant plants

Spontaneous mutation

A mutation that occurs naturally without any added mutagen, due to occasional errors in DNA replication

Induced mutation

A mutation caused by physical or chemical agents known as mutagens

Base (Nucleoside) analogs

Chemical compounds structurally similar to normal nitrogenous bases that get incorporated into DNA and cause incorrect base pairing

Ionizing radiation (X-rays/Gamma rays)

Causes the formation of ions that can oxidize bases and break the sugar-phosphate backbone (double-strand breaks)

UV radiation

Causes the formation of harmful thymine dimers in DNA

Frameshift mutation

A mutation caused by the insertion or deletion of nucleotides not in multiples of three, shifting the reading frame

Missense mutation

A point mutation that results in a codon change leading to a different amino acid in the protein

Nonsense mutation

A point mutation that introduces a premature stop codon, resulting in a truncated protein

Mutagen/Carcinogen example

Nitrous acid; causes adenine to bind with cytosine instead of thymine, or chemical agents like benzo[a]pyrene that cause cancer

Vertical gene transfer

The transfer of genetic material from an organism to its offspring

Horizontal gene transfer

The transfer of genes between independent, mature organisms (e.g., transformation, transduction, conjugation)

Plasmids in antibiotic resistance

Small circular DNA pieces that frequently carry antibiotic resistance genes and spread them via horizontal gene transfer

Yeast, plant, and mammalian cells in gene products

Used as host expression systems to properly fold and produce complex eukaryotic proteins and vaccines

Ti Plasmid

A plasmid from Agrobacterium tumefaciens used as a vector to genetically modify plants

Differences between bacteria and viruses

Bacteria are living cellular organisms with cell walls, ribosomes, and independent metabolism; viruses are acellular infectious entities requiring a host cell

Obligate intracellular parasites

Organisms/entities that cannot reproduce outside their host cell; includes viruses, chlamydias, and rickettsias

Essential virus components

Every virus must have genetic material (DNA or RNA) and a protein coat (capsid); some also have an envelope and spikes

Transforming viral infection

An infection where viruses cause cells to become cancerous or immortalized

Persistent viral infection

A disease process that occurs gradually over a long period and is typically fatal

Latent viral infection

An infection where the virus remains dormant inside the host cell without producing symptoms for long periods (e.g., cold sores, shingles)

Lysogenic viral infection

Viral DNA integrates into the host bacterial chromosome as a prophage and is replicated along with the host DNA

Lytic viral infection

A viral life cycle that culminates in the lysis (rupture) of the host cell and release of new virus particles

Tissue/Cell culture / Monolayer

In vitro growth of cells used to cultivate viruses since viruses always require a living host cell

Three ways viruses are cultivated

Living animals, embryonated eggs, and cell cultures

Order of virus life cycle

Adsorption, penetration, un-coating, biosynthesis, maturation (assembly), and release

Adsorption

The process where a virus attaches specifically to host cell receptors

Uncoating

The step where a virus loses its capsid protein coat to release its viral genome inside the host cell

Assembly (Maturation)

The step where viral nucleic acids and capsid proteins are put together to form new virions

One step growth cycle

A graph measuring virus concentration over time during a single infection cycle to study viral replication dynamics

Congenital infections

Infections passed from mother to fetus (e.g., rubella, CMV, Zika)

Virus shapes

Helical, polyhedral (icosahedral), and complex; icosahedral morphology is unique to viruses

Viruses in cancer

Certain oncogenic viruses integrate their DNA into host chromosomes and disrupt normal cell cycle regulation (e.g., HPV causes cervical cancer, Hepatitis B/C causes liver cancer)

Viruses to treat cancer (Oncolytic viruses)

Genetically engineered viruses designed to selectively infect and kill cancer cells without harming healthy tissue

Plaque assay

A laboratory technique used to detect and quantify viable viruses by counting clear zones (plaques) on a cell monolayer

CPE (Cytopathic Effect)

Visible structural changes in host cells caused by viral invasion (e.g., cell rounding, lysis, inclusion bodies)

Phage conversion (Lysogenic conversion)

The process where a bacterium acquires new traits, including disease-causing toxins, from a prophage

Extra Chromosomal DNA

Genetic elements outside the main chromosome, such as plasmids, mitochondrial DNA, and chloroplast DNA

Reverse transcription

The synthesis of DNA from an RNA template, carried out by the enzyme reverse transcriptase

Endonuclease vs Exonuclease activity

Endonucleases cut DNA internally; exonucleases remove nucleotides from the ends of DNA strands

Mutagens

Chemical or physical agents that cause mutations

Carcinogens

Agents that can cause cancer

Ames Test

A bacterial assay used to identify chemical carcinogens based on their ability to cause back-mutations

Genomic library

A collection of all the cloned DNA fragments of an organism's genome

Gel electrophoresis

A technique used to separate DNA fragments based on size using an electric field

Vectors

DNA molecules (such as plasmids or viruses) used as vehicles to artificially carry foreign genetic material into another cell

Subunit vaccine

A vaccine consisting of only specific antigenic fragments/proteins of a pathogen rather than the whole organism

DNA vaccine

A vaccine that uses a nonpathogenic plasmid containing genes for a pathogen's antigens

Gene therapy

The introduction of normal genes into cells to correct genetic disorders

Gene silencing

A mechanism like RNA interference (using siRNAs) that blocks or destroys mRNA to prevent gene expression

Shotgun sequencing

A rapid sequencing method where DNA is randomly broken into small segments, sequenced, and reassembled by computer algorithms

Metagenomics

The study of genetic material recovered directly from environmental or clinical samples (microbiome analysis)

Capsid

The protein coat surrounding a virus's genetic material

Spike

Glycoprotein projections on the surface of some viruses used for host cell attachment

Envelope

A lipid bilayer membrane surrounding the capsid of some viruses