Module 1 Vocab Flashcards
Gene
Specific nucleotide sequence that encodes a gene product that regulates the characteristics/ traits in an organism
Allele
Different varients of the same gene encoding for a slightly different phenotype
Chromosome
A condensed body of dsDNA in which genes are overlaid
Genome
The full set of chromosomes in a eukaryotic organism (23 in humans)
Heredity
Passing the genetic information from one generation to the next
Genotype
The two alleles of a gene that we inherit
Phenotype
The exhibited traits that are encoded in the genome
Karyotype
The full set of color coated chromsomes in a cell
Chromatin
DNA tightly packed around nucleosome protein complex, has a flexible structure
Nucleosome
The basic structure of chromatin organization formed by histones
Histones
Family of proteins rich in amine groups that come together to form nucleosomes
Histone Acetylation is associated with?
Open promotors/increased expression
Histone Deacetylation is associated with?
Tighter packing of nucleosomes
DNA methylation is associated with?
Inactivated DNA
DNA methylase
Adds the methyl (CH3) group to cytosine
Heterochromatin Specific Histone Modification
Allows for the formation and spread of heterochromatin, continues until it meets barrier DNA
X chromosome inactivation
Causes lyonization where a different x chromosome is inactivated in different embryonic cells causing a myraid of phenotype expression
Xist
X inactive specific transcript, inactivates an x chromosome
Epigenetics
Mechanism of gene regulation that can be stably inherite through mitosis, but is established without changing the DNA sequence
Co-IP
A method used to remove entire complexes of intact proteins with antibodies and magnetic beads
ChIP
Chromatin Immunoprecipitation is a technique used to determine specific regionis of DNA with specific chromatin modification through the use of antibodies and magnetic to purify DNA
Combinatorial Code
The difference in expression of genes in different cells of the same organism
Central Dogma of Genetics
Genetic information directs the synthesis of the final gene product
Transcription
The first step in gene expression, makes RNA 5’ to 3’ while reading DNA 3’ to 5’
mRNA
Messenger RNAs, code for proteins
rRNA
Ribosomal RNAs, form the core of the ribosome’s structure and catalyze protein synthesis
miRNA
Micro RNAs, regulate gene expression and targets complementary mRNA for destruction
tRNA
Transfer RNAs, serve as adaptors between mRNA and amino acids during protein synthesis
Promoter
A regulatory sequence located prior to the transcription start site that defines the direction of transcription and identifies the template DNA strand
RNA polymerase
A primer independent molecule that transcribes pre-mRNA transcripts, additionally has helicase activity, but lacks proofreading ability
RNA Polymerase I
Most rRNA genes
RNA Polymerase II
All protein-coding genes, miRNA genes, plus genes for other noncoding RNAs
RNA Polymerase III
tRNA genes, 5S rRNA gene, genes for many other small RNAs
Prokaryotic Promoters/Terminators
Have specific nucleotide sequences laid out in a specific 5’ -> 3’ direction for RNAP to recognize
Enhancer
Not part of a gene, but influences the rate of transcription, loop DNA to bind to transcription factors
Mediator
Coordinates between transcriptional activators/repressors and RNA polymerase
Transcription Factor
A small molecule that complexes to allow the start of transcription
Linker Scanning
A method to identify promoter elements important for function
Polycistronic mRNA
An mRNA that has multiple proteins encoded on it that generally have related functions (prokaryotes)
5’ capping
Capping enzyme complex (CEC) binds to RNAP and adds Guanine molecule to the 5’ end of an RNA molecule, marking it as mRNA and increases its half life
3’ Polyadenylation
Polyadenylate polymerase adds a poly A tail till it reaches a length of 250 A, provides, happens
Intron
A part of the eukaryotic gene that is removed during splicing
Exon
The part of the eukaryotic gene that is kept during splicing and is read to produce a protein
Alternative Splicing
Variable splicing of the same pre-mRNA to produce multiple different splice products
Splice donor/acceptor/branching site
Specific nucleotide sequences at the 5’, 3’ and a site upstream of 3’ end of introns that are conserved and guide spicing machinery
Spliceosome
Made of small nuclear ribonuclear protein with snRNA working as a ribozyme to excise introns
Trans-splicing
Splicing that pieces together transcripts from different gene loci
Self splicing introns
Some introns are self-splicing ribozymes that do not require other proteins to be spliced out of pre mRNA
Genetic Code
The rules by which the information in DNA is translated into amino acids via mRNA
Codon
A triplet of bases that encodes an amino acid
Charged tRNA
When the 3’ end of tRNA is covalently bound to its corresponding codon
Ribosome
Machinery of translation that exists in cytoplasm, RER, in the nucleolus, and the mitochondria; has a large and small subunit
Ribosome Sites
Exit (E), Peptidyl (P), and Aminoacyl (A) and are oriented 5’EPA3’ with respect to the mRNA
Translation Initiation Factors
Bind to the initiator tRNA and the small subunit of RNA and holds mRNA inplace before dissociating and the large ribosome subunit binds
Release Factor
The protein that binds to the stop codon of an mRNA transcript and intiates translation
Ribosome-binding sites
Sites within bacterial mRNA that allow ribosomes to bind and begin translation, each mRNA can have more than 1
Polysome
A series of ribosomes on one piece of mRNA spaced out as minimally as possible
Chaperon Proteins
Proteins that help properly fold newly synthesized partially folded proteins
PCR
Polymerase chain reaction, a technique used to amplify DNA, requiring primers, dNTPs, thermostable DNAP, the DNA to be amplified
qPCR
Quantitative or real-time PCR is in essence the same as normal PCR, but amplification of the DNA can be measured throughout the process
non-coding RNA
Target mRNA for destruction and regulate gene expression
UTR
Untranslated regions are regulatory sequences in mRNA, contain binding sites for transcription factors that mark for degradation and also have sequences that direct the frequency of translation
lncRNA
Long noncoding RNA, ~200 bases long, ~5000 different types but role is largely unknown
Dicer
Cuts dsRNA hairpins into 22 bp fragments that are loaded into the RISC complex for degradation
siRNA
Small interfering RNA, similar to miRNA, it is also cut by the DICER into 22 base sequences and binds to the RISC complex, but to degrade foreign RNA rather than mRNA
CRISPR
Cluster regualarly interspaced short palindromic repeats, gene sequence that makes the adaptive immune response in bacteria, it is specific and has memory; recognizes specific sequences in dsDNA and cuts both strands when complexed
Spacers
Non-repeat spacers derived from bacteriophages provides resistance against bacteriophages; get added close to the 5’ end of the CRISPR locus
Repeats
Identical palindromic sequences in the genome that make a hairpin loop like structure as a protein
Cas genes
Act as helicases and molecular scissors (endonucleases)
CRISPR-Cas System
The immune/ defense system of bacteria with memory and specificity passed on during binary fission; has been adapted for use in gene editing
Protospacers
Viral Genome that is degraded by Cas1-Cas2 into small fragments
PAM
Protospacer adjacent motif; site that allows Cas9 to distinguish foreign DNA from the bacterial genome, Cas9 cuts 5’ to the PAM site
HDR
Homology dependent repair, allows for precise gene repair
CRISPR-Cas9 Gene Drive
Gene drive makes modifications not only to the original organism, but all of its offspring as well, DNA from both parents is subsequently changed as a result in the offspring