Bio251 Final Exam Study Guide Vocabulary Flashcards

Flashcards created from the provided lecture notes, focusing on key vocabulary terms and definitions to aid in exam preparation. The flashcards cover a range of topics including Molecular Analysis and Biotechnology, Epigenetics, Developmental Genetics and Immunology, Cancer Genetics, and Cumulative Topics from earlier in the semester.

Recombinant DNA

Techniques for locating, isolating, altering, and studying DNA segments, combining DNA from two organisms

Restriction enzymes

Recognize and cut DNA at specific nucleotide sequences, produced by bacteria

Restriction sites

Sequence recognized and cut by restriction enzymes, often palindromic sequences

Cohesive ends

Fragments with short, single-stranded overhanging ends, also called sticky ends

Blunt ends

Even-length ends from both single strands

Engineered nucleases

Protein consisting of part of a restriction enzyme that cleaves DNA, combined with another protein that recognizes and binds to a specific DNA sequence, custom designed to cut specific sequences

Zinc-finger nucleases

array of zinc-finger domains attached to a restriction enzyme, pairing of two ZFns increases specificity (a type of engineered nuclease)

Transcription activator like effector nucleases (TALEN)

protein of a type that normally binds to sequences in promoters is attached to a restriction enzyme (a type of engineered nuclease)

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)

series of palindromic sequences separated by unique spacers

Effector complex

cRNA and tracer RNA combined with Cas9 protein, recognizes protospacer-adjacent motif (PAM), unwinds DNA, and sgRNA pairs with and cuts DNA

Nonhomologous end joining

ends are joined without a template, which can introduce duplications and deletions, leading to frameshift mutations (a CRISPR-Cas9 system repair mechanism)

Gel electrophoresis

technique for separating charged molecules based on molecular size or charge, or both, nucleic acids stained with ethidium bromide or labeled prior

Probe

DNA or RNA molecule with a base sequence complementary to a sequence of interest, pairs with the target sequence

Polymerase chain reaction (PCR)

process with repeated steps of heating, primer annealing, and DNA synthesis by DNA polymerase

Gene cloning

amplify, alter, or manipulate sequences

Cloning vector

DNA molecule to which a foreign DNA fragment can be attached, allows foreign DNA into cells. Requirements: restriction enzyme site, origin of replication, selectable marker

Linkers

small synthetic DNA fragment with one or more restriction sites, attach to ends of DNA to insert into a vector

Expression vectors

vector containing DNA sequences like promoters, ribosome-binding sites, and transcription initiation/termination sites, allows inserted DNA to be transcribed and translated

Transformation

Screening cells for transformation success involves using a selectable marker in the plasmid and exposing cells to antibiotics

Dideoxy sequencing

uses a template to make new DNA with dNTPs and ddNTPs, synthesis stops when a ddNTP is used, products separated by gel electrophoresis

Illumina sequencing

a type of next-generation sequencing similar to dideoxy, uses fluorescent tags attached to dNTPs (color indicates base), and chemical terminators that can be reversed

DNA fingerprinting

Uses microsatellites (STRs) and PCR to identify individuals. Fragments separated by electrophoresis. Homozygotes show one peak, heterozygotes two peaks

Forward genetics

begins with a mutant phenotype and determines the gene causing it, traditional genetics study

Reverse genetics

begins with a gene of unknown function and induces mutations to determine effect on phenotype

Targeted mutagenesis

mutations are induced at specific locations to study effects, can use CRISPR-Cas9

Site directed mutagenesis

short sequence cut out with restriction enzymes and replaced with a short sequence with mutation, requires restriction sites around the target

Oligonucleotide directed mutagenesis

oligonucleotide used to introduce a mutant sequence when restriction sites are not available, acts as a primer for replication, results in a percentage of cells with the mutated plasmid

Transgene

foreign gene or DNA fragment carried in germ-line DNA, a form of reverse genetics

Gene therapy

direct transfer of genes into human patients to treat disease, can use vectors like retroviruses, adenoviruses, AAV, or CRISPR-Cas9

Epigenetics

changes in gene expression or phenotype that are potentially heritable but do not alter the underlying DNA sequences

Epigenesis

how an embryo develops, creation

Epigenome

epigenetic modifications within the genome of an individual

Methylation

addition of a methyl group (CH3). DNA methylation (on cytosine) represses transcription. Histone methylation can activate or repress transcription depending on location

Acetylation

addition of an acetyl group (CH3CO). Histone acetylation accelerates transcription by destabilizing chromatin, making DNA more available

Epigenetic marks

induced pluripotent stem cells retain some epigenetic marks

Xist

Transcription stimulated by Jpx on the inactive X chromosome. Coats the X chromosome, inactivating it, suppressed in the active X

lncRNA

lncRNAs can attract miRNAs so they are not available to bind to mRNA

Tsix

Expression stimulated by xite on the active X chromosome

Jpx

Jpx stimulates the transcription of Xist on the inactive X chromosome

Pluripotency

property of being undifferentiated with the capacity to form every type of cell in an organism

Induced pluripotent stem cells

somatic cells artificially induced to dedifferentiate and revert to pluripotent stem cells, retain some epigenetic marks

Paramutation

one allele of a genotype alters the expression of another allele, potentially heritably

Genomic imprinting

differential expression of genetic material depending on whether it is inherited from the male or female parent. It evolved to influence gene expression in offspring based on parent's diet/environment

Totipotent cell

cell that has the potential to develop into any cell type

Determination

cell becomes committed to a particular cell fate (what the cell becomes)

Egg-polarity genes

transcribed into mRNA during oogenesis, establish morphogen concentration gradients in the embryo, involved in establishing dorsal-ventral and anterior-posterior axes

Homeotic genes

determine the identity of segments, activated by protein concentrations from genes associated with segmentation

Morphogen

Egg-polarity genes establish morphogen concentration gradients in the embryo

Gap genes

segmentation genes that divide the embryo into broad regions. Mutation eliminates a group of segments

Pair-rule genes

segmentation genes that develop alternate segments. Mutations cause deletion of either even or odd numbered segments

Segmentation-polarity genes

segmentation genes that develop individual segments. Mutations cause deletion and replacement with a mirror image

Homeobox genes

encode DNA-binding proteins with a regulatory role in transcription. Hox genes are a type of homeobox gene

Hox genes

encode transcription factors that help determine the identity of body regions. Similar in fruit flies and mammals

Sepals

parts of a flower, whorl 1, controlled by Class A genes

Petals

parts of a flower, whorl 2, controlled by Class A and Class B genes

Carpels

parts of a flower, female reproductive whorl 4, controlled by Class C genes

Stamen

parts of a flower, male reproductive whorl 3, controlled by Class B and Class C genes

Class A genes

control flower development, expressed in whorl 1 (sepals) and whorl 2 (petals)

Class B genes

control flower development, expressed in whorl 2 (petals) and whorl 3 (stamen)

Class C genes

control flower development, expressed in whorl 3 (stamen) and whorl 4 (carpels)

Apoptosis

controlled, programmed cell death. DNA is degraded, nucleus/cytoplasm shrink, cell engulfed by macrophage, no release of contents. Involves caspases. Triggers include viral infection, DNA damage, mitochondrial damage, improperly folded proteins. Survival factors inhibit caspases

Necrosis

injured cells dying in an uncontrolled manner. Cell swells, bursts to release contents, causes inflammatory response

eyeless gene

controls eye development in fruit flies. Similar to small eye in mice and Aniridia in humans

Antigen

molecules that elicit an immune reaction

Antibodies

proteins that bind to antigens and mark them for determination by phagocytosis. Produced by B cells. Have heavy and light chains, constant and variable regions, binding sites. Diversity generated by somatic recombination and alternative splicing

Humoral immunity

production of antibodies by B cells

Cellular immunity

depends on T cells

Clonal selection

process where appropriate lymphocytes (B/T cells) recognizing an antigen divide, leading to a primary immune response. Memory cells remain for a faster secondary response upon re-exposure

Primary immune response

production of antigen-specific B and T cells following the first exposure to an antigen, part of clonal selection

Secondary immune response

faster and stronger response upon re-exposure to an antigen due to memory cells

Memory cells

cells that remain in circulation after the primary immune response, allowing a faster response if the same antigen reappears

T cells

involved in cellular immunity. Have receptors that bind both histocompatibility antigens (MHC) and specific foreign antigens. Release molecules to destroy target cells

B cells

involved in humoral immunity, produce antibodies

Multiple sclerosis

an autoimmune disease where the body attacks its own tissues

Lupus

an autoimmune disease where the body attacks its own tissues

Insulin dependent diabetes mellitus

an autoimmune disease where the body attacks its own tissues

T cell receptors

have alpha and beta chains held by disulfide bonds, variable region binds antigen. Alpha chain has V, J, C segments; Beta chain has V, D, J, C segments. Undergo somatic recombination

Immunoglobulin

another name for antibody

Somatic recombination

process in mature lymphocytes where V segments move to a new location near J segments, generating antibody and T cell receptor diversity

Immune rejection

can occur with organ transplants if MHC antigens don't match, immune cells attack the foreign organ

MHC antigens

Major Histocompatibility Complex antigens. Proteins that provide identity to an individual's cells. T cell receptors bind both MHC and foreign antigens. Matching MHC antigens is important for organ transplants

Histocompatibility

related to MHC antigens, compatibility between donor and recipient cells

Benign tumor

groups of cells that cannot spread to other parts of the body

Malignant tumor

tumor consisting of cells that invade other tissues, serious cancers

Metastasis

movement of cells that separate from malignant tumors to other sites, where they form new tumors

Oncogenes

mutated proto-oncogenes that contribute to cancer development. Often encode proteins in signal transduction pathways

Proto-oncogenes

normal cellular genes that are important for cell division and growth, can mutate into oncogenes. Drivers that contribute to cancer development

Tumor-suppressor genes

normal cellular genes that inhibit cell division or promote apoptosis. Mutation or loss contributes to cancer development. Examples include p53 and RB

Aneuploidy

abnormal number of chromosomes

Translocation

chromosomal rearrangement where a segment of one chromosome is moved to another. Can be a type of chromosomal abnormality associated with cancer

Duplication

chromosomal abnormality where a segment of a chromosome is repeated

Deletion

chromosomal abnormality where a segment of a chromosome is lost

Inversion

chromosomal abnormality where a segment of a chromosome is reversed

Clonal evolution

process where tumor cells accumulate mutations over time, and those with advantageous mutations (drivers) outgrow others, leading to increased proliferation and malignancy

Loss of heterozygosity

when an individual is heterozygous for a tumor suppressor gene, but the normal allele is lost or inactivated in a somatic cell, leaving only the mutated allele

Haploinsufficiency

when a single functional copy of a gene is not sufficient to maintain normal function, often relevant for tumor suppressor genes where one mutated copy can increase cancer risk

Cyclin

proteins that regulate the cell cycle. Their concentration increases during specific cell cycle stages. They combine with CDKs to activate cell cycle transitions

Cyclin-dependent kinases (CDKs)

enzymes that bind to cyclins to regulate cell cycle transitions. They phosphorylate target proteins

Signal transduction pathway

external signals trigger a cascade of intracellular reactions producing a specific response. In cancer, proteins encoded by oncogenes are often involved. Steps involve receptor components: extracellular, transmembrane, and intercellular domains

Angiogenesis

formation of new blood vessels, which tumors require to grow and metastasize