Lecture 1 - 9 Terms Flashcards
What is a virus?
small pieces of nucleic acid. Can be DNA or RNA
What is a prion?
Misfolded proteins that can infect cells (a type of virus)
What is a viriod?
a bare piece of RNA that causes diseases in plants.
What is a genome?
An organisms complete set of DNA.
What is a transcriptome?
An organisms complete set of mRNA.
Genomics
the study of sequencing/assembling/analyzing genomes.
metagenomics
collecting environmental samples of earth and sequencing the bits of DNA/RNA found in soil.
Define a macromolecule.
a molecule with over 1,000 atoms. Often polymers.
Define small molecules
less than 1,000 atoms. often are monomers.
give examples of polymers.
starch, glycogen, cellulose, DNA/RNA, proteins, phospholipids.
give examples of monomers
monosaccharides (glucose, fructose, galactose), nucleotides, amino acids, ATP/ADP, GTP,GDP
What are chromosomes.
pieces of DNA and proteins linked to each other.
Define the term ploidy.
the number of sets of chromosomes in a cell. most animals are diploid, gametes are haploid.
what is a dyad?
a pair of sister chromatids. they will be separated during mitosis.
what is recombination?
when two sister chromatids swap genetic material while lined up on the metaphase plate. occurs during. Prophase I
what is aneuploidy?
an abnormal number of chromosomes.
what is trisomy?
one extra chromosome
What is monosomy?
a missing chromosome
Define translocations.
a DNA segment that is moved from one chromosome to a different chromosome (not a homologue)
what is an inversion?
a segment of DNA that is flipped. it will be coding backwards.
what is a deletion?
a segment of DNA is cut out of the DNA.
what is an insertion?
a segment of DNA is inserted into a different area on the same chromosome.
what is a centromere?
the middle of the chromosome. contains constitutive DNA (heterochromatin).
what is constitutive DNA?
Constitutive heterochromatin is the stable form of heterochromatin, i.e. it does not loosen up to form euchromatin, and contains repeated sequences of DNA called satellite DNA. It can be found in centromeres and telomeres, and is usually involved in structural functions.
define kinteochores.
a large protein complex that is encoded by the DNA within the centromere. It is where the microtubules will attach during metaphase.
what are telomeres?
a non-coding region at the end of some chromosomes. short repeated sequence of TTAGGGTTAGGG.
What is cellular senescence?
when a cell can no longer divide because it’s telomeres are too short. The cell will undergo apoptosis.
what is telomerase?
an enzyme with an RNA template that adds nucleotides to the 3’ end of the DNA template.
What is reverse transcription?
when DNA is synthesized from RNA.
What are cancer stem cells?
an adult stem cell that has mutated. Thus it bypasses regulatory factors controlling cell division.
What is alpha-satellite DNA?
found at the centromere. they encode the proteins that will form the kinetochore complex (where microtubules will bind to)
what are pseudo-genes?
genes that have become functionally inactive over periods of evolution.
define repeat elements.
repeating DNA segments that do not appear to serve a purpose (not used by the cell).
give an example of repeat elements.
Transposons/Transposible elements, microsatellite DNA
What are transposons?
they are DNA that can copy themselves and “jump” into other non-homologous chromosomes.
What is microsatellite DNA?
1-60 repeats that occur in succession 4-6 times. they vary across individuals, therefore they are used in forensics and paternity tests to find DNA matches. (Use PCR)
What are chromatin fibers?
coiled and condensed DNA that forms chromosomes. made of proteins (histones) and DNA.
What is euchromatin?
a state of DNA, where it is accessible for transcription.
What is heterochromatin?
a state of DNA, does not allow transcription to occur.
What is faculative heterchromatin?
DNA that can be condensed and uncondensed when needed.
Give an example of constitutive DNA.
alpha-satellite, telomeres, transposons, centromere
give an example of faculative heterochromatin.
Barr bodies and Transposons
Define the nuclear matrix.
a protein fiber network used to transport molecules and bind DNA to certain areas in the nucleus.
What is Topoisomerase II
A protein involved in unwinding DNA(along with DNA Helicase). since it is an enzyme it is able to “cut” DNA.
what are insulator proteins?
they act as a barrier on the outside of chromosomes so the backbone is not exposed. Prevents chromosomes from binding together.
Define the nuclear lamina
made of intermediate filaments and membrane proteins. Binds telomeres and also alpha-satellite DNA of the centromere.
What is a nucleosome?
made of histone octamer and DNA wrapped around the histone.
Define a nucleosome core particle.
aka Histone.
Name the major types of histones.
H2A, H2B, H3, and H4. H1 is a linker histone
What is MARS?
A DNA sequence with many “A” and “T” nucleotides that bind to the nuclear matrix proteins.
What is cohesin?
a ring-shaped protein occasionally maintain the loop-domains if there is damage to the DNA.
What is condensin?
a protein that DNA loops around during mitosis. Different from histones (but not really sure how).
What is epigenetics?
when the environment causes a phenotypic variation in an organism.
What is histone Deacetlyase?
an enzyme that removes an acetyl group. This causes the histone to wrap more tightly around the DNA, and thus inhibits transcription.
What is histone acetylase Transferase?
an enzyme that attaches an acetyl group to the histone. causes the histone to unwind from the DNA, and thus makes the DNA transcriptionally available/active.
What is a barrier DNA sequence?
a sequence of DNA that prevents histones from turning an entire chromosome into heterochromatin.
What is a gene?
the smallest unit of heredity.
What is an open reading frame (ORF)?
a continuous stretch of codons encoding a polypeptide. in other words, a piece of mRNA that will become a polypeptide.
Define polymerases.
multi-unit enzymes that add nucleotides onto a complimentary strand of RNA from a DNA template.
What is a core promoter?
Found upstream of the transcriptional start site, it is where RNA-POL II will bind prior to transcription. Within the core promotor is the TATA box (and also the Start codon)
What is TBP?
TATA-Binding Protein. it is the first protein to bind to the promotor.
What is TAFs?
TBP-Associated Factors, proteins associated with TBP to form the Pre-Initiation Complex.
What is TFIID?
Transcription Factor II D is a multiprotein assembly. It recognizes the core promotor sequence TATA.
What is TFIIH?
Transcription Factor II H acts as a protein kinase. (This means it adds a phosphate group to another molecule, usually a protein).
What is a Poly-A Tail?
a long chain of Adenine nucleotide added to an mRNA molecule.
What is CTD?
Carboxyl-Terminal Domain, found at the end of a polypeptide chain. Acts as a scaffold for other proteins to bind to.
What is Poly-A Ribonuclease?
an enzyme that gradually degrades the Poly-A Tail.
What is an oligo dT?
a single stranded sequence of deoxythymine.
What is heterogenous nuclear RNA?
hnRNA is the same thing as pre-mRNA. this means it contains introns that require splicing.
What are exons?
a fragment of nucleic acid that codes for proteins (this is usually where genes are found)
What is a consensus sequence?
a sequence of nucleotides that are commonly found at a specific region of DNA/RNA.
Give an example of consensus sequence.
Splice site, TATA box,
Define a spliceosome.
A large ribonucleoprotein complex found primarily within the nucleus. made of snRNPs and other proteins.
What are snRNPs?
small nucleic RiboNucleicAcids that are bound to U-proteins
Define splicer enhancer proteins.
a protein that binds to an enhancer site found within the intron.
What is a codon?
A triplet base pair of mRNA.
what is an anticodon?
A triplet base pair of tRNA that is complimentary to the codon of mRNA.
What is a synonymous substitution?
a silent mutation.
what is a non-synonymous substitution?
a mutation that results in altering the structure/function of a protein.
Define Aminoacyl-tRNA Synthetases
aaRS, an enzyme that attaches the appropriate amino acid onto its corresponding tRNA. Requires ATP.
what is Aminoacyl-tRNA?
a tRNA molecule with an amino acid attached to it.
What are snoRNPs?
Small Nucleolar RiboNucleoProtein Particles, help to process rRNA
What is translation?
the process of turning mRNA into a protein.
What is initiation Factor 1?
promotes the attachment of mRNA to 30s Subunit
What is initiation Factor 2?
IF2 is a GTP binding protein. it guids fMET-tRNA to the “P”-site.
What is initiation Factor 3?
IF3 prevents the large ribosomal subunit from binding to the small subunit during initiation.
What is initiation in reference to Translation?
the assembly of the ribosome. occurs at the beginning of the coding region in mRNA.
what is elongation in reference to translation?
elongation is the bonding of amino acids to produce a polypeptide chain.
What is Peptidyl Transferase?
a piece of ribosome that is made of RNA. A ribozyme.
name the stop codons in translation.
UAA, UAG, UGA
What is release factor?
RF, inserted into “A” spot after ribosome encounters stop codon. it mimics tRNA anticodon.
Define Polyribosomes/Polysomes.
they are a complex of multiple ribosomes on an mRNA strand allowing for simultaneous translation.
What is a “shotgun” library?
describes the way DNA are fragmented into “shrapnel” in order for the pieces to be sequenced.
what are ddNTPs?
DiDeoxyriboNucleoside Triphosphates. They do not contain a 3’ OH group.
give an example of ddNTPs.
ddATP, ddGTP, ddCTP, ddTTP
Define a proteome.
the inventory of all the proteins present in a cell, tissue, organism
Define the nuclear envelope.
two membranes separated by nuclear space. They are fused together at sites forming a nuclear pore.
What is the nuclear lamin?
The inner surface of the nuclear envelope. made of intermediate filaments.
Define the Nuclear Localization Signal.
NLS, a sequence of positively charged amino acids within a protein. This “tag” is recognized by proteins in the nuclear pore, allowing the protein to enter the nucleus.
What are importins?
proteins that recognize the nuclear localization signal. they assist proteins into the nucleus.
What are exportins?
proteins within the nuclear pore that recognize nuclear export sequence/signal. they assist proteins out of the nucleus.
What are FG proteins?
Proteins with repeats of Phenylalanine and Glycine. Because of their lack of order, they make “wiggly snake” movements
