2. Genes Flashcards
5’ –> 3’ Directionality
How DNA is written. The end 3’ carbon is attached to an OH group and the 5’ carbon end is attached to a phosphate group.
Activators and Repressors Proteins
Proteins that that regulate gene expression at transcription level. They bind to DNA close to promoter to activate or repress activity of RNA polymerase. Allosterically regulated by small molecules like cAMP.
Adenine (A)
one of the 4 nitrogenous base of DNA and RNA.
Anaphase
Sister chromatids split at centromeres and move toward opposite ends of the cell towards the centrioles. Cytokinesis also happens here.
Anaphase I
Separates the homologues from their partners.
Anaphase II
In females, activated when sperm penetrate secondary oocyte.
Anneal
PCR. Mixture is cooled, primers hybridize to complementary ends of the DNA strands.
Anticodon
set of neucleotides that is complementary to the codon, found on tRNA.
Antiparallel
The second strand of DNA, in a 3’ –> 5’ direction from the other strand going 5’ –> 3’. Bonded by hydrogen bonds between the bases.
Antisense Strand
The template strand that is translated from DNA to RNA. The nontranslated strand (called coding strand or sense strand) is the same sequence as the RNA strand.
Base-Pair Substitution Mutation
One bp is replaced by another. Transition or Transversion.
Base-Pairing (BP)
Length of DNA strand. Hydrogen bonds between the bases of the two strands of DNA double helix. A=T and C=G
Backward Mutation
Already mutated organism is reverted back to previous stage, typically its original state.
Bidirectional Replication
DNA replication is in both directions starting from the origin of replication.
Carcinogens
Mutagens that can cuase cancer.
Centromeres
group of proteins located toward the center of the chromosome
Centrioles
Inside centrosomes. Connected by spindle microtubles.
Centrosomes
There are two that moves to opposite ends of the cell when prophase begins.
Chiasma
A point where the two chromosomes are attached creating an “x” shape.
Chromatids
Each chromosome is made of two identical sister chromatids during the S phase.
Chromatin
the DNA/protein (histones) complex.
Chromosomal Mutation
Structure of a chromosome is changed.
Chromosome
A numbered Chromatin. There are 46.
Clone
Multiplied copy of the bacteria containing the vector (recombinant DNA).
Clone Library
To make a DNA library, take your DNA fragment (recombinant DNA), use a vector to insert it into a bacterium, and reproduce that bacterium like crazy. Now there are clones of bacteria with your DNA fragment.
Codon
Three consecutive nucleotide on mRNA that would translate into one AA.
Complementary DNA (cDNA)
The DNA that was reverse transcribed from mRNA. Add DNA polymerase and you get a double strand of DNA. This DNA contains no introns, since the mRNA was processed to take out the introns. Very helpful in science.
Complementary Strands
Two strands have to match up so that A can bind with T and C can bind with G.
Consensus Sequence
The most commonly found nucleotide sequence of a promoter recognized by the RNA polyermase of a given species. Variations causes RNA polymerase to bind less tightly and leff oten, making the genes transcribed less = less expressed.
Crossing Over
When homologous chromosomes exchange DNA sequences.
Cytokinesis
The actual separation of the cellular cytoplasm due to constriction of microfilaments about the center of the cell. Occurs in anaphase.
Cytosine
one of the 4 nitrogenous base of DNA and RNA.
Degenerative
More than one series of three nucleotide may code for any AA.
Deletion of BP
When bp is taken out of the sequence. May result in frameshift.
Deletion of Chromosome
Portion of the chromosome breaks off or loss during homologous recombination and/or crossing over.
Denatured
aka Melted. The two strands of DNA comes apart because the agent has disrupted their hydrogen bonds. About 95C is sufficient to denature any DNA sequence. Denatured DNA is LESS viscous, DENSER, and MORE able to absorb UV light.
Diploid
Means the cell has homologous pairs. 23 pairs, 46 chromosomes.
DNA
Deoxyribonucleic Acid. Nucleotides in chain.
DNA Helicase
Part of the replisome. Unwinds double helix and separate the double stranded DNA.
DNA Ligase
Enzyme that moves along the lagging strand to connect the okazaki fragments.
DNA Polymerase
Add nucleotides to an existing strand abd builds the new DNA strand. An enzyme. Reads original DNA strand in 3’->5’ making a 5’-3’ new strand. Exonulcease function, where it proofreads and remove wrong nucleotides. Nucleotides are added by hydrolysis of two phosphates group. This energy drives replication.
Duplications of Chromosome
DNA fragment breaks free of one chromosome and incorporates into a homologous chromosome. A form of mutation.
Double Helix
What the binding of the two complementary strands look like. The look of DNA. There are the major groove and the minor groove. Each groove spirals once around the double helix for every 10 bp.
Elongation
Second step of transcription. RNA polymerase transcribes a strand of DNA into RNA sequences.
Euchromatin
Areas where genes are actively being transcribed. Only in euk.
Exons
Linked together after introns are taken out. Makes the mature mRNA. Leaves nucleus to be translated to proteins.Avg number of exons per gene is 7. Sequences of DNA that code for exons are also called exons.
Five Steps of Replication
1) Helicase unzips the double helix 2) RNA polymerase builds a primer 3) DNA polymerase assembles leading and lagging strands 4) Primers are removed 5) Okazaki fragments joined (by DNA ligase)
Forward Mutation
An already mutated organism that is further mutated.
Frameshift Mutation
Deletions or Insertions occuring in multiples other than 3. Likely to result in completely nonfunctional protein.
Gametes (Germ Cells)
Product of meiosis.
Gene
DNA sequence that codes for rRNA, tRNA, mRNA. Gene is inherited.
Gene Expression in Prok vs. Euk
Prok: primary fxn is to respond to environmental changes. Euk: primay fxn is to keep at homeostasis. To control the intra- and extracellular environments of the cell.
Genetic Code
Nucleotide sequence (DNA) –> AA sequence (protein)
Genetic Recombination
Occurs during crossing over.
Genome
The entire DNA sequence of an organism. Only 1% of human genome codes for protein.
Guanine (G)
one of the 4 nitrogenous base of DNA and RNA.
Haploid
Cell that DOES NOT contain homologues.
Heterochromatin
Areas where genes are tightly packed, not really transcribed. Only in euk.
Histones
DNA that are not in used are wrapped tightly around these globular proteins.
Homologues
Two chromosomes that are partners and codes for the same traits. Humans have 23 pairs.
Initiation
First step of transcription. A group of proteins (initiation factors) finds a promotor on DNA strand and assembles a transcription initiation complex including the RNA polymerase.
Initiation Complex
small subunit, tRNA with meth AA signalling for the large subunit to join forming this complex.
Insertion
When bp is added into the sequence. May result in frameshift.
Interphase
Includes G1, S and G2.
Introns
Cut out from primary transcript mRNA. Stays in nucleus and gets degraded. Introns are usually longer than exons. Sequences of DNA that code for introns are also called introns.
Inversion Mutation
Orientation of a section of DNA is reversed on a chromosome.
Kinetochore
Protein structure and DNA located at the centromere of the joined chromatids of each chromosome.
Lagging Strang
Strand made of okazaki fragments.
Large Subunit
Part of ribosome. Made up of rRNA and separate proteins. 60S (euk) and 50S (prok)
Leading Strand
Continuous strand in DNA replication.
Meiosis
double nuclear division producing four haploid gametes.
Metaphase
Chromosomes align along the equator of the cell.
Metaphase I
homologues remain attached and move to the metaphase plate. Tetrads align.
Missense Mutation
A bp mutation. It occurs in AA coding sequence of a gene. It may or may not alter the AA sequence of a protein, the AA may or may not have esrious effects on the function of the protein.
Mitosis
Nuclear division without genetic change. Stages: PMAT.
Monocistronic
Euk: one RNA strand contains one gene.
mRNA
messenger RNA. Gets transcribed from DNA, moves to cytolsol for translation into protieins.
Mutagens
Physical or Chemical agents that INCREASES the frequency of mutation above frequencyof spontaneous (random errors) mutations.
Mutation
Any alteration in the genome (except for genetic recombination)
Nondisjunction
When centromere of any chromosome does not split in anaphase I or II. Results are trisomy 21.
Nonsense Mutation
If bp substitution, insertion, or deletion creates a STOP CODON. Very serious for the cell because they prevent the translation of a functional protein completely.
Northern Blot
Same technique as Southern Blot to identify RNA fragments.
Nucleolus
Site for rRNA manufacturing and assembling. Small and large subunits are exported separately to the cytoplasm.
Nucleosome
Made up of 8 histones.
Nucleotide (name the 3 components)
1) Phosphate Group, 2) Ribose (5-carbon sugar), 3) Nitrogenous base (A, T, G, C)
Nuclic Acid Hybridization
Technique scientists use to identify nucleotide sequences by binding a known sequence with an unknown sequence. DNA prefers to be double stranded and will look for a complementary partner. So the combinations are: DNA-DNA, DNA-RNA, and RNA-RNA.
Okazaki Fragments
Series of disconnected strands in the lagging strand of replication.
Oncogenes
Genes that cause cancer.
Oogonium
Undergoes meiosis.
Operon
The genetic unit consisting of the operator, promoter, and genes that contribute to a single prok mRNA. (polycistronic)
Origin of Replication
Location where DNA replication begins. Not at the end of a chromosome. There are several per euk chromosomes (this is why replication is so quick). Prok has only one origin of replication.
Palindromic
Reads the same backwards as forward. Makes up the Restriction Site or Recognition Sequence (where restriction enzyme cleaves).
Phosphodiester Bond
Link the nucleotide in DNA between the 3rd carbon of one deoxyribose and the 5th carbon of the other. This creates a sugar-phosphate backbone of a single strand of DNA.
Plasmid
Can be used as a vector, carries the recombinant DNA.
Point Mutation
When changes to a single base-pair of nucleotide in a double strand of DNA.
Polar Body
Smaller and degenerates. Primary oocyte produces secondary oocyte and one polar body. Secondary oocyte produces mature oocyte and 3 polar bodies. A way to conserve cytoplasm.
Poly-A Tail
added to the 3’ end of mRNA to protect from exonucleases.
Polycistronic
Prok: one RNA strand contains several genes.
Polymerase Chain Reaction (PCR)
Very fast cloning method. 1) 95C - denatures DNA. 2) 60C - primers hybridize. 3) 72C - activates polymerase, making double every time.
Post-Translational Modifications
Sugars, lipids, or phosphate groups may add to AA of protein newly synthesized. The polypeoptide may be cleaved in one or more places. Separate polypeptide may join to form the quaternary structure of a protein.
Primary Oocyte
Cell after replication of S phase. Replication occurs BEFORE BIRTH.
Primary Spermatocyte
Cell after replication of S phase.
Primary Transcript
The initial mRNA strand transcriped, unprocessed. Before processing occurs to cut out introns.
Name the 3 ways the primary transcript is processed.
1) addition of nucleotides. 2) deletion of nucleotides. 3) modification of nitrogenous bases.
Primer
Initiates the new strand of DNA in replication. RNA primer that’s ~ 10 ribonucleotides long. Built by primase, an RNA polymerase.
Probe
The radioactively labeled complementary sequence of the desired DNA fragment. It searches the library and the radiolabled cloans are identified by laying them over photographic film.
Prokaryote (# of copies of genes)
Only has one copy of each gene. Euk has more than one copy of some genes.
Promoter
A spot of DNA sequence that tells RNA polymerase where to begin transcription. These basepairs are noted with a - (negative numbers).
Prophase
Condensation of chromatin into chromosomes. Nucleolus and nucleus disappear. Centrioles move to opposite ends of cell, microtubles everywhere.
Prophase I
Homologous chromosomes line up, matching genes exactly. Crossing over occurs.
Purine
Adenine and Guanine. Two-ring structures
Pyrimidines
Cytosine and Thymine. One-ring structures
Recombinant DNA
Artificially recombined. Two DNA fragments cleaved by the same endonuclease are joined regardless of the origin of the DNA. Ex: human DNA and a dog’s DNA.
Reduction Division
Meiosis I. Number of chromosome is reduced to half the number.
Replication Fork
Where replisome (groups of proteins involved in replication) attaches to chromosome and begins DNA replication.
Restriction Enzymes
Digest (cut) nucleic acid only at certain nucleotide sequences called “restriction site” or “recognition sequence.”
RFLP
“Restriction Fragment Length Polymorhisms.” Identifies individuals (instead of genese like the other techniques). Able to do this because everyone has different restriction sites at varying distances.
Ribosome
made up of rRNA and protein. It provides the site for translation to take place.
RNA
Ribonucleic acid. Differences from DNA: 1) C2 has -OH group (not deoxygenated) 2) Single stranded 3) Uracil, pyrimidine, instead of Thymine.
RNA Polymerase
Initiation: Part of the transcription initiation complex that binds to promotor and begins transcription. Unzips DNA double helix. Elongation: Then it transcribes DNA sequences into RNA nucleotides in elongation. Moves in 3’-5’ making a 5’-3’ RNA strand. Slower than DNA replication. No proofreadig mechanism. Prok: has 1 RNA polymerase. Euk: has 3 RNA polymerase for the 3 types of RNA.
rRNA
ribosomal RNA. Made in nucleolus. Combines with proteins to form ribosomes. Directs synthesis of protins.
Secondary Oocyte
Product of Telophase I. 23 chromosomes. Cells are HAPLOID. One of the two identical cells is a polar body.
Secondary Spermatocytes
Product of Telophase I. 23 chromosomes. Cells are HAPLOID.
Semiconservative DNA Replication
A new double strand of DNA contains one strand from the original DNA and one newly synthesized strand.
Semidiscontinuous Replication
One continuous strand and one lagging strand with okazaki fragments.
Signal Peptide
A 20 AA sequence near the front of the translated polypeptide that signals to the SRP (signal-recognition particle) to carry the ribosome with polypeptide to a receptor protein on the ER. polypeptide continues to be made and protein is either released into the lumen of ER (then secreted from the cell via the Golgi) or partially attched to the ER becoming a membrane protein. Signal peptide is then removed by an enzyme. Signal peptides also targets to mitochondria, nucleus or other organelles.
Small Subunit
Part of ribosome. Made up of rRNA and separate proteins. 40S (euk) and 30S (prok)
snRNPS
These are enzyme-RNA complexes called “nuclear ribonucleoproteins.” They recognize nucleotides sequences at the ends of the introns. The snRNPS associate with proteins to form a spliceosome which cut the introns and link the exons.
Southern Blotting
To identify target fragments of known DNA sequence in a large population of DNA.
Name 5 Steps of Southern Blotting
1) chop up some DNA at restriction fragments. 2) Use an electric field to spread out pieces according to size and denature the fragments. 3) blot it onto a membrane. 4) add a radioactive probe made from DNA or RNA. 5) visualize with radiographic film.
Spermatogonium
Undergoes meiosis.
Spindle Apparatus
In prophase. Consists of aster, kinetochore microtubules growing from centromeres, and sindle microtubles.
Spindle Microtubles
Connecting two centrioles.
SSB Tetramer
Proteins that hold the lagging strand to not fold back onto itself so that it can be replicated. Aka helix destabilizer proteins.
What is the Start Codon?
AUG (Methionine)
Stop Codons
UAA, UAG, UGA.
Telomeres
Repeated 6 nucleotide units from 100-1,000 long that protect chromosomes from being eroded through repeated rounds of replication.
Telophase
Nuclear membrane reforms followed by the reformation of the nucleolus. Chromosomes decondense. Cytokinesis continues.
Telophase I
Nuclear membrane reform, cytokinesis occur.
Termination
Last step of transcription. Requires a special termination sequence (stop codon) and special proteins to dissociate RNA polymerase from DNA.
Tetrads
Four chromatids. Appears during crossing over.
The Central Dogma
DNA (transcribed) –> RNA (translated) –> Protein. This is how genes are expressed.
Thymine (T)
one of the 4 nitrogenous base of DNA. Replaced as Uracil in RNA.
Traits
Coded by chromosome.
Transcription
Manufacturing RNA from DNA template. Takes place in nucleus and mitochondrial matrix (bc DNA cannot leave these two locations)
Translation
mRNA directs protein synthesis.
Translocation
ribosome shifts 3 nucleotides along the mRNA toward the 3’ end. Part of elongation step of protein synthesis.
Translocation Mutation
A segment of DNA from one chromosome is exchanged for a segment of DNA on another chromosome.
Transposons
DNA segments that can excise themselves from a chromosome and reinsert at another location. It has capability to copy itself and move, or copy and stay. Transposition is one mechanism by which a somatic cell of a multicellular organism can alter its genetic makeup without meiosis.
tRNA
transfer RNA. Collects AA in cytosol, transfer to ribosomes to make protein.
Vector
A bateriophage or plasmid that transfer the recombinant DNA into a cell, or from one bacterium to another.
Western Blot
Detect particular PROTEIN with ANTIBODIES in a mixture of proteins.
Steps of Western Blot
1) Electrophoresis to separate by size. 2) Blot onto membrane. 3) Primary antibody, specific to protein of interest added to bind to protein. 4) Secondary antibody binds to primary for visualization. 5) Rxn catalyzed to produce color or visible product.
Wild Type
Original, unmutated, state of an organism.
Where does post-transcriptional modication of mRNA occur in euk?
In the nucleus. Posttranscriptional processing allows for additional gene regulation.
5’ Cap on mRNA
The cap is placed using GTP even before the euk mRNA is completely transcribed. Cap serves as an attachment site in protein synthesis and as protection against degradation by exonucleases.
3’ End on mRNA
End is polyadenylated with a poly A tail. Protect from exonucleases.
Methylation
Bacteria adds a -CH3 to their DNA to protect from being cut up into fragments. Bacteria has enzymes to cut viral DNA into fragments as to deactivate it. Methylation is usually associated with inactivated genes.
Sticky Ends
Restriction enzymes cut the two strands unevenly, leaving complementary single stranded ends. Helps hybridization. Phosphodiester bonds of fragments joined by DNA ligase.
Unambiguous
Any single series of 3 nucleotide will code for ONLY ONE AA.
How many AA are there?
20!
P Site
Peptidyle site. tRNA with meth AA sits in this site and signals for the large subunit to form initiation complex. Starts the initiation step of making a protein.
A Site
Aminoacyl site. Next tRNA with AA sits here, connects to the existing tRNA in Psite via dehydration rxn. This is elongation step.
E Site
tRNA moves to here to exit ribosome so elongation step can continue.
Gene Mutation
Alteration in the sequence of DNA nucleotides in a SINGLE gene.
Transition Mutation
Purine to purine OR Pyrimidine to pyrimidine.
Transversion Mutation
Purine to Pyrimidine or vice versa.
Growth Phase 1 (G1)
Just divided, now needs to grow in size. RNA synthesis, protein synthesis.
Synthesis Phase (S)
Triggered by cell size, ratio of cytoplasm to DNA. Replicating DNA. Cell STILL only have 23 pairs of homologous chromosomes, or 46 chromosomes. Organelles and proteins are produced more slowly.
Growth Phase 0 (G0)
After G1, if cell is not big enough to go to S phase. Not part of interphase. It’s a nongrowing phase. This phase allows for the differences in length of the cell cycle. Some cells, like mature neurons and muscle cells stay here permanently.
Growth Phase 2 (G2)
Cell prepares to divide. RNA, organelles, and protein actively synthesized.
Meiosis II
Appears like mitosis. Produces haploid gametes each with 23 chromosomes.
