Feralis Ch 5 Flashcards
Law of Segregation
one member of each chromosome pair migrates to an opposite pole in anaphase I so that each gamete is haploid
i. Basically, each gamete is left with one copy of each allele
Law of Independent Assortment
the migration of homologues within one pair of homologous chromosomes does not influence the migration of homologues of other homologous pairs
Monohybrid cross
two organisms with variations at one gene of interest are crossed
Dihybrid cross
two organisms with variations at two genes of interest on different chromosomes are crossed
Test cross
when the genotype of an organism expressing the dominant phenotype is unknown, the unknown organism is crossed with a homozygous recessive organism to determine if the unknown is homozygous dominant, or heterozygous dominant
Punnett squares
a technique that uses probability rules to determine the outcomes of either monohybrid or dihybrid crosses and the subsequent expected frequencies
i. To set up a Punnett square, the genotype of both parents are listed outside the box, and the resultant combinations are written inside the boxes
Incomplete dominance
blending of expressions of alleles
i. For example, a red flower and white
flower are crossed to result in a unique heterozygous pink offspring
Codominance
both of the inherited alleles are completely expressed
i. For example, blood types A and B
or both can show as AB if expressed
Multiple alleles
blood groups have four possible phenotypes, the codominant A, codominant B, and O, leading to four possible genotypes and phenotypes
i. AO → type A
ii. BO → type B
iii. AB → codominant AB type
iv. OO → type O
Epistasis
the process in which one gene affects the phenotypic expression of a second gene. A common example of epistasis is fur pigmentation in mice → one gene controls the production of pigment by either turning on or turning off and the second gene controls the color or amount of color deposited in the fur. Therefore, if the first gene codes for no pigment, then the second gene has no effect
Pleiotropy
when a single gene has more than one phenotypic expression
i. One example of pleiotropy is a gene in pea plants that expresses for seed texture, but also influences the phenotype of starch metabolism and water uptake
ii. Another example of this is how
sickle cell anemia leads to different health conditions
a. Sickle cell anemia - A mutation
in the single gene responsible can result in the expression of multiple different health conditions: pain, stroke, high blood pressure, etc.
Polygenic inheritance
the interaction of many genes to shape a single phenotype with continuous variation such as height, skin color, or hair color
Linked genes
when two or more genes reside physically close to one another on the same chromosome and therefore cannot separate independently as they are inherited together
i. The closer two genes are on a chromosome, the less likely they are to be separated by genetic recombination (a process that occurs due to crossing over in meiosis I)
Chance of recombination between genes
Genes that are completely unlinked have a 50% chance of recombination, and the lower the percentage of recombination, the more likely the genes are linked/closer together
A greater recombination frequency means that the genes are located farther apart on the same chromosome, and therefore more likely to undergo recombination.
Linkage maps
Linkage maps can be generated to visualize recombination frequency in linked genes
Sex-linked genes
a type of linked gene that refers to a single gene residing on a sex chromosome that is inherited differently in males and females
i. One example of a sex-linked gene involves males. When a male (XY) receives an X chromosome from his mother, whether or not a dominant or recessive trait on the X chromosome is expressed depends on the mother as there is no copy on the Y chromosome
Sex-influenced genes
these differ from sex-linked genes in that the expression of genes can be influenced by the sex of the individual carrying the trait
i. For example, a female with the genotype Bb could be bald while a male with the same genotype is not
Genomic imprinting
Sex-influenced genes are similar to genomic imprinting, in which one allele, either paternal or maternal, is not expressed in the offspring. Genomic imprinting is also different from sex-linked genes since this is seen in autosomal chromosomes
Genomic imprinting causes genes to be expressed in a parent-of-origin-specific manner
Penetrance
describes the probability an organism with a specific genotype will express a particular phenotype
Complete penetrance
the genes for a trait are expressed in all of the population who have the gene
Incomplete penetrance
the genes for a trait are only expressed in a percentage of the population who have the gene
Variable Expressivity
this term describes the variation or range of phenotypes for a specific genotype
i. For example: the gene for red hair
could result in light hair, dark crimson hair, or any range of color in between.
X-inactivation
during embryonic development in female mammals, one of the two inherited X chromosomes does not uncoil into chromatin, and remains as a dark and coiled compact body, which is referred to as a Barr body. Barr bodies are therefore not expressed, and only the genes on the other X chromosome that did uncoil are expressed.
i. It is important to understand that
either one of these two inherited X chromosomes can be inactivated. This process ultimately results in all of these genes in the female to not be expressed similarly. Moreover, all of the cells in a female mammal do not necessarily have identical function.
ii. A common example of x-inactivation is in Calico cats, where the characteristic black and orange fur coat depends on which copy of the X chromosome the cell chooses to leave active
Nondisjunction
describes when one or more chromosome pairs or chromatids fail to separate during mitosis. This commonly occurs during anaphase of mitosis, when two chromatids of a single chromosome fail to separate, or during anaphase of meiosis. In meiosis, recall there are two anaphases: homologous chromosomes fail to separate during meiosis I and sister chromatids fail to separate during meiosis II.
i. Depending on when nondisjunction occurs (in anaphase I, anaphase II, or mitotic anaphase), different outcomes can occur
Mosaicism
a phenomenon that occurs in cells that undergo nondisjunction in meiosis during embryonic development; fraction of body cells have extra or missing chromosomes
Polyploidy
when all chromosomes undergo meiotic nondisjunction and produce gametes with twice the number of chromosomes
a. Is common in plants
Point mutation
single nucleotide change causing either substitution, insertion, or deletion - the latter two which can cause a frameshift mutation.
A transition mutation involves conversion of a purine to purine or pyrimidine to pyrimidine.
A transversion mutation involves conversion of a purine to pyrimidine or vice versa.
Aneuploidy
a genome with extra or missing chromosomes, often caused by nondisjunction
Down syndrome
An example of aneuploidy
Trisomy 21
Turner syndrome
An example of aneuploidy
Turner syndrome is a genetic condition in which a female is either completely missing, or partly missing, an X chromosome, leading to the genotype XO. Turner syndrome also occurs as a result of nondisjunction, and the main genetic defect is the offspring is born with physical abnormalities.
Klinefelter’s Syndrome
An example of aneuploidy
Klinefelter’s Syndrome (XXY) is when a male is born with an extra X chromosome
Duplications
chromosome segments are repeated on the same chromosome, which can occur from unequal crossing over
Inversions
chromosome segments are rearranged in reverse orientation
Translocations
one segment of a chromosome is moved to another chromosome.
a. Can be reciprocal (two non-homologous chromosomes swap segments) or Robertsonian (one chromosome from a homologous pair becomes attached to another chromosome from a different pair). For example, an extra chromosome 21 attached to chromosome 14 can cause Down syndrome as well, due to the tripled 21 chromosome segment.
There is no gain or loss of genetic information in a reciprocal translocation, while there is a loss of genetic information in a Robertsonian translocation.
Chromosomal breakage
spontaneous or induced breakage of a chromosomal segment via mutagenic agents or X-rays
Mutagenic agents
include cosmic rays, X-rays, UV rays, radioactivity, chemical compounds including colchicine and mustard gas that can cause genetic mutations. Mutagenic agents are generally also carcinogenic
Colchicine functions by inhibiting spindle formation, which can cause polyploidy
Phenylketonuria (PKU)
Autosomal recessive condition
inability to produce the proper enzyme for phenylalanine breakdown, causing degradation product phenylpyruvic acid to accumulate
Cystic fibrosis
Autosomal recessive condition
fluid buildup in respiratory tracts
Tay-sachs
Autosomal recessive condition
lysosome defect in which cells can’t breakdown lipids for normal brain function
Huntington’s disease
Autosomal dominant condition
nervous system degeneration
Achondroplasia
Autosomal dominant condition
Causes dwarfism
Hypercholesterolemia
Autosomal dominant condition
excess cholesterol in blood that progresses into heart disease
Hemophilia
Sex-linked recessive condition
sex-linked recessive genetic condition causing abnormal blood clotting
Color blindness
Sex-linked recessive condition
primarily observed in males
Duchenne’s Muscular Dystrophy
Sex-linked recessive condition
progressive loss of muscle
Down’s Syndrome
Chromosomal disorder
trisomy 21
Turner’s Syndrome
Chromosomal disorder
deletion of X chromosome → XO genotype
Klinefelter’s Syndrome
Chromosomal disorder
extra X chromosome → XXY genotype
Cri du Chat
Chromosomal disorder
deletion on chromosome 5
Amniocentesis or chorionic villus sampling (CVS)
A fetus can be tested for genetic disorders via amniocentesis or chorionic villus sampling (CVS)
Extranuclear inheritance
extranuclear genes (genes present in organelles other than the nucleus) are found in mitochondria and chloroplasts
i. Defects in mitochondrial DNA can reduce a cell’s ATP production, and because mitochondrial DNA is inherited only from the mother, all related mitochondrial defects/ diseases are also inherited. Note that mitochondria have their own 70S ribosomes that make mitochondrial proteins within the mitochondria matrix.
ii. Mitochondrial DNA is also an exception to the universality of the genetic code
Hemizygous
Hemizygous is when one single copy of a gene is inherited instead of two.
i. One example of a hemizygous genotype is males, who have XY sex chromosomes, aka only a single copy of both X and Y genes inherited
ii. Important note - don’t confuse XY with homologous pairs
Phenotype and genotype ratios
Phenotype and genotype ratios are not necessarily the same - if there are multiple sets of alleles, treat each of the crosses individually and then multiply the individual probabilities to get the overall probability of one specific genotype outcome
Lethal gene
Imagine we cross Aa x Aa, and get 1 AA, 2 Aa, and 1 aa. If “aa” is lethal, our genotypic ratio would be AA and Aa present in a 1:2 ratio.
DNA
A, T, C, G; the hereditary information of the cell; contains a double helix with major and minor grooves
DNA backbone
consists of 5’ to 3’ phosphodiester bonds to form a sugar- phosphate backbone
RNA
A, U, C, G; has functional usage in the cell; varies per type (mRNA is linear, tRNA is in a clover shape, while rRNA is globular)
DNA replication
begins at origins of replication in the middle of a DNA molecule
DNA strands separate to form replication bubbles that expand in both directions. As thousands of these bubbles open up, replication speeds up and 3 billion base pairs can be replicated.
Origin of replication between eukaryote and prokaryote
Prokaryotes have one origin of replication while eukaryotes have multiple origins of replication
DNA Replication steps
- A second chromatid containing a copy of DNA is assembled during interphase
- Helicase is the enzyme that unwinds DNA, forming a Y shaped replication fork
- DNA polymerase moves from the 3’ → 5’ direction only, and synthesizes a new strand that is antiparallel (5’ → 3’)
- Primase is an enzyme that creates a small strip of RNA off of which DNA polymerase can work since it can only add to an existing strand
Semiconservative replication
DNA is replicated via semiconservative replication, in which one the two strands of DNA is always old and one is always new
S phase of interphase is when DNA is replicated. Therefore, in order to do so, DNA is unzipped and each strand serves a template for complementary replication
Helicase
Helicase is the enzyme that unwinds DNA, forming a Y shaped replication fork - Once DNA is unwound, we introduce several new enzymes to carry out replication
Single stranded binding proteins (SSBPs)
Single stranded binding proteins (SSBPs) attach to each strand of uncoiled DNA to keep them separate
Topoisomerases
Topoisomerases (like DNA gyrase) break and rejoin the DNA double helix of the replication fork, allowing the prevention of knots
ease tension of coiled DNA by introducing nicks and cuts into the DNA strand
DNA polymerase direction
DNA polymerase moves from the 3’ → 5’ (on template) direction only, and synthesizes a new strand that is antiparallel (5’ → 3’)
Leading strand
works continuously as more DNA unzips (synthesized 5’ → 3’)
Lagging strand
for the 5’ → 3’ template strand, the DNA polymerase has to go back to the replication fork and work away from it. It produces fragments piece by piece, and these fragments are called Okazaki fragments
DNA ligase connects Okazaki fragments
Primase
Primase is an enzyme that creates a small strip of RNA (RNA primer) off of which DNA polymerase can work since it can only add to an existing strand
RNA primer
Every Okazaki fragment has an RNA primer, and these RNA strips are later replaced with DNA by DNA polymerase I
a. DNA polymerase I replaces base pairs from the RNA primers and functions in DNA repair
b. DNA polymerase III is purely for replication
DNA polymerase I
has 3’ → 5’ exonuclease function, meaning that they can break the phosphodiester backbone on a single strand of DNA and remove a nucleotide. An exonuclease can only remove from the end of the chain.
also has 5’ → 3’ exonuclease function to remove the primer and replaces the primer with DNA nucleotides; polymerase I can also proofread in the 3’ → 5’ direction when laying down a new nucleotide strand
DNA polymerase III
has 3’ → 5’ exonuclease function, meaning that they can break the phosphodiester backbone on a single strand of DNA and remove a nucleotide. An exonuclease can only remove from the end of the chain.
Can proofread in the 3’ → 5’ direction, via its exonuclease function; if there is a mistake during replication, polymerase III will go back and replace a nucleotide
DNA Replication speed in prokaryotes vs eukaryotes
DNA Replication is almost 20x faster in prokaryotes than in eukaryotes, primarily because eukaryotes have more complex genomes
Methylation
In prokaryotes, the strand without any errors is methylated after it has been successfully replicated, so it doesn’t become accidentally repaired as proofreading is done.
Energy for DNA elongation
Energy for DNA elongation is provided by two additional phosphates that are attached to each new nucleotide. When the bonds holding the two extra phosphates are broken, the breakage provides chemical energy for the process, which is the same for DNA
Ligase
‘glues’ two strands of DNA together
Problems with replicating telomere
- There is not enough template strand for primase to attach
- When the last primase is removed, and in order to change from RNA to DNA, there must be another DNA strand in front of the RNA primer. However, DNA polymerase cannot build after removing the RNA primer, so ultimately that RNA primer is destroyed by enzymes that degrade the RNA left on the DNA. A section of the telomere is subsequently lost with each replication cycle.
i. Prokaryotes do not have this issue since their DNA is circular and doesn’t have telomeres
Telomerase
Enzyme that attaches to the end of the template strand and extends the template strand by adding a short repeating sequence of DNA that allows elongation of the lagging strand to continue. However, at the end of elongation, there will still not be enough of the strand for primase to attach, but this loss of an unimportant segment will not cause significant problems.
Carries an RNA template and binds to the flanking 3’ end of the telomere that compliments part of its RNA, and synthesizes to fill in over the rest of its template
mRNA and codons
a single stranded template; since there are 64 possible ways that four nucleotides can be arranged in triplet combinations (4 x 4 x 4), there are 64 possible codons. 61 of these codons code for amino acids, while the remaining 3 are stop codons. mRNA is also the least abundant RNA molecule due to its high turnover rate
3 stop codon codes
The three stop codons are UAA, UAG, and UGA which do not code for any amino acids
tRNA
A clover shaped transporter of anticodons; the C-C-A-3’ end of tRNA attaches to the amino acid being transported, and the other portion is the anticodon which base pairs with the codon from mRNA.
ii. tRNA’s clover shape is held together by hydrogen bonds (via intramolecular base pairing), and a distinguishing feature of tRNA is inclusion of unusual bases (methylinosine, pseudouridine, 4- thiouridine)
iii. tRNA is also the smallest of the RNA molecules
Wobbles
the exact base pair of the third nucleotide in the codon is often not required, allowing 45 different tRNA’s to base-pair with 61 codons that code for amino acids.
rRNA
the nucleolus is an assemblage of DNA actively being transcribed into rRNA, which come together to form ribosomes. A ribosome has three binding sites: one for mRNA, one for tRNA that carries the growing polypeptide chain (P site), one for the 2nd tRNA that delivers the next amino acid (A site), and one for the tRNA to exit after it has dropped off its amino acid
The ribosome is assembled in nucleolus but the large and small subunits are exported separately to the cytoplasm.
rRNA is the most abundant RNA molecule
rRNA is the most abundant RNA molecule - think r for ‘rich’, t for ‘tiny’ (tRNA), and m for ‘meager’ (mRNA)
Transcription steps
- Initiation
- Elongation
- Termination
Transcription - Initiation
RNA polymerase attaches to the promoter region on DNA and unzips the DNA into two strands. A promoter region for mRNA transcription often contains a repeating sequence of A and T nucleotides, called the TATA box.
i. The most common sequence of nucleotides at the promoter region is called the consensus sequence - variations from it cause less tight RNA polymerase binding, and therefore a lower transcription rate
ii. Note that the promoter is the site on DNA where RNA polymerase binds to initiate transcription, but it is not the start site, it’s actually just upstream of the start site!
The TATA box is in eukaryotes, while in prokaryotes, it is termed the ‘Pribnow box’ (think P for P, Prokaryote Pribnow)
Transcription - Elongation
RNA polymerase unzips DNA and assembles RNA nucleotides using one strand of DNA as a template; Only one strand is transcribed, from the template = (-) antisense strand, while the other strand is the coding (+) sense strand for protection against degradation (Sense strand is same as mRNA being made except for U/T nucleotide)
Transcription is occurring in the 3’ to 5’ direction of the DNA template strand (but synthesis of the RNA strand is, as always, 5’ to 3’)
Transcription - Termination
occurs when RNA polymerase reaches a special sequence, often AAAAAA in eukaryotes
RNA synthesis vs DNA synthesis errors
RNA polymerase doesn’t have proofreading ability, therefore RNA synthesis has a much greater error level than that of DNA synthesis
mRNA Processing
Before leaving the nucleus, pre-mRNA undergoes several modifications:
- 5’ cap (5’ G-P-P-P-)
- A poly-A tail (-A-A-A…A-A-3’)
- RNA splicing
- Alternative splicing
5’ cap (5’ G-P-P-P-)
this sequence is added to the 5’ end of the mRNA; a guanine with 3 phosphate groups (GTP) provides stability for mRNA and a point of attachment for ribosomes
poly-A tail (-A-A-A…A-A-3’)
this sequence is attached to the 3’ end of the mRNA
The poly A tail consists of 200 A nucleotides that serve to provide stability and control the movement of mRNA across the nuclear envelope
i. In prokaryotes, the poly A tail actually
facilitates degradation!
RNA splicing
removes nucleotide segments from mRNA before mRNA moves into the cytoplasm via small nuclear ribonucleoproteins (snRNP’s). The spliceosome deletes the introns and splices the exons. Prokaryotes have no introns
Alternative splicing
allows different mRNA to be generated from the same RNA transcript by selectively removing differences of an RNA transcript into different combinations
mRNA Processing in eukaryotes vs prokaryotes
Prokaryotes generally have ready to go mRNA upon transcription. Only eukaryotes undergo the processing mentioned in this section. Because prokaryotes don’t need to process their mRNA first, translation can begin immediately and simultaneously. In both prokaryotes and eukaryotes, however, multiple RNA polymerases can transcribe the same template simultaneously
Translation
The assembly of polypeptides based on reading of new RNA in the cytoplasm with GTP used as the energy source. In general, an amino acid attaches to the 3’ end of a tRNA (termed an aminoacyl-tRNA) and one 1 ATP is converted to AMP per amino acid added the polypeptide chain.
- Initiation
- Elongation
- Termination
- Post-translation
Translation - Initiation
the small ribosome subunit attaches to the 5’ end of mRNA; a tRNA methionine attaches to the start sequence of mRNA (AUG), and the large ribosomal subunit attaches to form a complete complex. Requires 1 GTP.
Translation - Elongation
next tRNA binds to the A site, peptide bond formation occurs, and the tRNA without methionine is released. The tRNA currently in the A site moves to the P site (translocation) and the next tRNA comes into the A site to repeat the process. This requires 2 GTP per link.
Translation - Termination
when the ribosome encounters the stop codon (either UAG, UAA, or UGA), the polypeptide and the two ribosomal subunits all release due to a release factor breaking down the bond between tRNA and the final amino acid of the polypeptide
i. While the polypeptide is being
translated, amino acid sequences are determining the folding conformation, which is a process that requires assistance from chaperone proteins and 1 GTP
Translation - Post-translation
Translation begins on a free floating ribosome; a signal peptide at the beginning of the translated polypeptide may direct the ribosome to attach to the endoplasmic reticulum, in which case the polypeptide is injected into the ER lumen. If injected, the polypeptide may be secreted from the cell via the Golgi apparatus.
i. In general, post-translational modifications (addition of sugars, lipids, phosphate groups to the amino acids) may occur. However, the protein may be subsequently processed by the Golgi before it is functional
Translation directionality
Amino acids are placed starting from the 5’ end of the mRNA and move all the way down to the 3’ end. Corresponding tRNA codons are 3’ to 5’
Translation prokaryotes vs eukaryotes
Translation can occur simultaneously with transcription in prokaryotes, but not in eukaryotes. Multiple ribosomes may, however, simultaneously translate 1 mRNA
Start codon’s amino acid in eukaryotes vs bacteria
The amino acid for start codons in eukaryotes is methionine, while it in bacteria the amino acid for the start codon is n-formylmethionine rather than methionine
Redundancy or degeneracy
while the genetic code is universal for nearly all organisms, most amino acids have more than one codon specifying them, which is known as redundancy or degeneracy.
Silent mutations
when a mutation occurs, but the new codon still codes for the same amino acid, therefore the effect is “silenced”
Nonsense mutations
the new codon codes for a stop codon
Neutral mutations
there is no change in protein function
Missense mutations
a new codon codes for a new amino acid → can have minor or fatal results (as in sickle cell anemia where glu → val)
Proofreading
DNA polymerase checks base pairs
Mismatch repair
enzymes repair the errors DNA polymerase missed — mismatch repair deals with correcting mismatches between normal bases
Excision repair
enzymes remove nucleotides damaged by mutagens
Nucleotide excision repair
can be used to repair issues like thymine dimers
it removes a 12-24 nucleotide section.
nucleotide excision repair will chunk out an entire segment around the faulty base by nicking the entire surrounding phosphodiester backbone, not just the faulty base
Base excision repair
Base excision repair first chunks out just the faulty base, then the phosphodiester backbone around the base is cut out, then polymerase I does some 5’ to 3’ exonuclease cutting and fills in the gaps
Nucleosome
structured formed when DNA is coiled around bundles of 8-9 histone proteins, kind of like beads on a string
During cell division (interphase), however, chromatin exists as two types: Euchromatin, Heterochromatin
Euchromatin
Chromatin is loosely bound to nucleosomes; present when DNA is actively being transcribed
Heterochromatin
Areas of tightly packed nucleosomes where DNA is inactive and appears darker.
(i) Heterochromatin contains lots of satellite DNA (large tandem repeats of noncoding DNA concentrated at centromeres and ends of chromosomes)
Transposons (jumping genes)
DNA segments that can move to a new location on either the same or different chromosome. There are a two types of transposons:
i. Insertion sequences that consist of
only one gene that codes just for the enzyme that transports it (transposase)
ii. Complex transposons code for extra features: replication, antibiotic resistance
If either type of these transposons were inserted into another region, mutation results, which could have any degree of effect to the overall expression of the gene.
Pseudogenes
the human genome contains many types of DNA that do not actually code for proteins or RNA, and because most of the genome appears to be repetitive DNA, there are lots of transposable elements present as well.
Pseudogenes are former genes that
have accumulated mutations over a long time and no longer produce a functional protein
There are ~24,000 genes in the human genome, with a majority of the genome consisting of repetitive DNA
Virus
Consist of the following:
i. Nucleic acid - RNA or DNA that can
be double or single stranded
ii. Capsid - a protein coat that encloses
the nucleic acid
iii. Capsomeres - assemble to form the
capsid
iv. Viral envelope - surrounds capsid of
some viruses and incorporates phospholipids and proteins obtained from the cell membrane of the host
Bacteriophage
A virus that only attacks bacteria, is usually specific to a type of cell via viral surface proteins binding to specific receptors on the host cell of the species.
Host range
Host range is a term used to define the range of organisms or species a virus can attack
Viral replication
there are two cycles a virus can take when it needs to replicate
i. Lytic cycle
ii. Lysogenic cycle
Lytic cycle
When the virus penetrates the host cell membrane and uses host machinery to produce nucleic acids and viral proteins that are then assembled to make new viruses. These viruses then burst out of the cell and infect other cells
Lytic cycle - DNA viruses
Replicate by first replicating DNA and forming new viral DNA, which is then transcribed to produce viral proteins that combine with DNA to form new viruses
Lytic cycle - RNA virus
RNA serves as mRNA which is translated into protein. This protein and RNA assemble to form a new RNA virus
Lytic cycle - Retroviruses
Single stranded RNA viruses that use reverse transcriptase to make a DNA complement of their RNA by hijacking the host cell’s replicating machinery. This DNA is then used to manufacture mRNA or enter the lysogenic cycle (becoming incorporated into the host DNA)
(i) A common example of a retrovirus is HIV
Lysogenic cycle
When viral DNA is incorporated into the DNA of the host cell; there are two phases to the lysogenic cycle:
a. Dormant stage - the virus is referred to as a provirus (prophage if a bacteriophage) and remains inactive until an external stimuli triggers the virus
b. When triggered, the virus enters the lytic cycle, and follows the same steps as mentioned in the previous bullet
When a bacteriophage integrates itself into the host genome, it is a prophage, not an episome!
Prions
are not viruses or cells, but are infectious, mis-folded versions of proteins in the brain that cause normal versions of proteins to also become mis-folded. Prions are fatal, and are implicated in diseases such as Mad Cow disease, kuru, scrapie in sheep, and Creutzfeldt-Jakob disease
Viroids
Very small (even smaller than viruses!) circular RNA molecules that infect plants. These do not encode for proteins, but replicate in host plant cells via host enzymes, and cause errors in the regulatory systems of plant growth
Bacteria
Bacteria are prokaryotes with no nucleus or organelles, consist of a single circular double stranded DNA molecule (that is tightly condensed and called a nucleoid), and have no histones or other associated proteins.
Because bacteria lack a nucleus, they also lack microtubules, spindles, and centrioles
Binary fission
bacteria reproduce via this method in which the chromosome replicates, the cell divides into two cells, and each cell now holds the exact same copy of the original chromosome
Bacteria - Plasmids
Short, circular DNA outside of chromosomes that carry genes that are beneficial, but not essential for survival
Plasmids are what help bacteria gain characteristics like antibiotic resistance
Bacteria - Plasmids - Episomes
Episomes are plasmids that can incorporate into bacterial chromosomes
Genetic exchanges
there are three main ways bacteria can exchange information with each other or their surroundings
- Conjugation
- Transduction
- Transformation
Conjugation
Donor bacteria produces a bridge (pilus) and connects to the recipient bacteria; this allows the donor to send a chromosome or plasmid to the recipient, thus allowing recombination to occur
a. An F plasmid allows a pilus to form, and a once the recipient (F-) receives the F plasmid from the donor (F+), it is now F+ and can donate this plasmid as well
b. Pili are also used for cell adhesion!
Transduction
DNA is introduced into a genome via virus. When the virus is assembled during the lytic cycle, some bacterial DNA is incorporated in the place of viral DNA. When the virus infects another host, the bacterial DNA part that it delivers can recombine with the resident DNA.
Transformation
Bacteria take in DNA from surroundings and incorporate it into the genome
Operon
Region of DNA that controls gene transcription and consists of:
i. Promoter - sequence of DNA where
RNA polymerase attaches to begin
transcription
ii. Operator - region that can block
action of RNA polymerase if occupied
by repressor proteins
iii. Structural genes - DNA sequences
that code for related enzymes
iv. Regulatory genes - located outside
of operon region, and produce repressor proteins. Others produce activator proteins that assist the attachment of RNA polymerase to the promoter region
Lac operon (E. coli)
Controls the breakdown of lactose; the regulatory gene produces an active repressor that binds to the operator and blocks RNA polymerase
The lac operon consists of three lac genes (Z, Y, A), which code for the following:
a. B-galactosidase that converts lactose → glucose and galactose b. Lactose permease that transports lactose into the cell c. Thiogalactoside transacetylase
When lactose is available, lactose binds to the repressor, and inactivates it → therefore allowing RNA polymerase to transcribe the genes.
Moreover, lactose induces the operon, and enzymes that the operon produces as a result are termed “inducible enzymes”. An adaptive enzyme or inducible enzyme is an enzyme that is expressed only under conditions in which it is clearly of adaptive value, as opposed to a constitutive enzyme which is produced all the time. The Inducible enzyme is used for the breaking-down of things in the cell.
cAMP
The lac operon isn’t only controlled by lactose, however. The important signaling molecule cAMP plays a regulatory role as well:
iii. When glucose is low, cAMP is high. This cAMP binds to a CAP binding site of the promoter, which enhances the binding and transcription via RNA polymerase, allowing for lactose to be broken down.
iv. If lactose AND glucose are high, the operon is shut off. This is because cAMP is low, and doesn’t bind to CAP. Bacteria uses one sugar at a time, and prefers glucose.
Trp operon (E. coli)
Produces enzymes for tryptophan synthesis; regulatory genes produce an inactive repressor, which allows RNA polymerase to produce enzymes.
i. When tryptophan is available, we no longer need to synthesize it internally: it binds to an inactive repressor and activates the repressor, which binds to the operator and blocks RNA polymerase.
i) Tryptophan is a co-repressor here
Repressible enzymes
Are when structural genes stop producing enzymes only in the presence of an active repressor. Unlike repressive enzymes, some genes are constitutive (constantly expressed) either naturally or due to mutation
Regulation of Prokaryotic Gene Expression
Operon, lac operon (E. coli), Trp operon (E. coli), Repressible enzymes
Regulation of Eukaryotic Gene Expression
Regulatory proteins, Nucleosome packing, RNA Interference, Human genome
Regulatory proteins
Repressors and enhancers/activators that influence RNA polymerase attachment to the promoter region.
i. Utilizing the presence or absence of activators allows for cell type-specific transcription (for example: a liver versus a lens cell transcribe different genes)
Nucleosome packing
Involves regulation at the chromosome level
i. Methylation of histones - results in
tighter packing that prevents transcription
ii. Acetylation of histones - uncoils
chromatin, encouraging transcription
iii. Direct DNA methylation - epigenetic control of DNA that can be inherited and usually leads to lower expression
Methylation is also used in X- inactivation and on DNA bases to repress gene activity.
Also, while histone methylation usually prevents transcription, it can sometime activate transcription as well
RNA Interference
noncoding RNA (ncRNA) plays a role in controlling gene expression as well! Some are even involved in chromatin modification.
Micro RNA (miRNA), Short interfering RNA (siRNA)
Micro RNA (miRNA)
A type of RNA interference
Single stranded RNA molecules that bind to complementary RNA sequences and either degrades the mRNA target or blocks its translation
Single stranded endogenous
Short interfering RNA (siRNA)
A type of RNA interference
Function similarly to miRNA, aside from a subtle difference between the precursors.
The major difference between siRNAs and miRNAs is that the former are highly specific with only one mRNA target, whereas the latter have multiple targets.
Regulates gene expression by endonucleolytic cleavage
Exogenous double stranded RNA
Human genome
97% of human DNA does not code for protein product, but rather non-coding DNA
i. Non-coding DNA includes regulatory
sequences, introns, tandem repeats, and repetitive sequences that are never transcribed
ii. Tandem repeats are abnormally long stretches of back to back repetitive sequences within an affected gene (e.g. Huntington’s).
DNA polymerase VS RNA polymerase
DNA polymerase is for replication
RNA polymerase I is for rRNA
RNA polymerase II is for transcription
RNA polymerase III is for translation
Southern vs Northern vs Western blot
Southern - DNA
Northern - RNA
Western - Protein
SNOW DROP
Karyotyping
Method to view an organism’s chromosomes
PCR
Amplifies a sequence of DNA into many copies
Gel electrophoresis with agarose gel
Separates DNA molecules by molecular weight. Large molecules are slower than small molecules.
Polyacrylamide gel electrophoresis (PAGE)
PAGE separates proteins based on charge, not by mass (which is what gel electrophoresis does)
Molecules travel from negative to positive end
DNA is a negatively charged polymer
Type A blood donate and receive
Antibodies for B antigens
Receive A or O blood
Donate to A or AB
Type B blood donate and receive
Antibodies for A antigens
Receive B or O blood
Donate to B or AB
Type AB blood donate and receive
No antibodies for B nor A antigens
Receive A, B, AB or O blood
Donate to AB
Type O blood donate and receive
Antibodies for A and B antigens
Receive O blood
Donate to A, B, AB and O
DNA cloning
Mass produce a protein by inserting human genes into bacteria
- Obtain eukaryotic mRNA from gene of interest. Use mRNA because bacteria cannot process introns. mRNA does not have introns.
- Convert mRNA back to DNA so it can be inserted to bacterial DNA.
- Use restriction enzyme to create sticky ends in the plasmid so that we can place gene of interest into bacteria and seal with ligase
- Use heat/ CaCl2 to shock bacteria into incorporating the plasmid in a process called transformation
number of amino acids
20 total, 9 essential
Transfection
Introducing genetic material into eukaryotic cells by making pores in their plasma membrane so they can uptake the surrounding medium
