Lecture Exam 2 Flashcards
Mendel’s Conclusion; aka Particulate Theory of Inheritance (5)
- Alternative versions of genes (alleles) account for variations in inherited characters
- For each character, an organism inherits two alleles, one from each parent; paired condition (of alleles) are restored by random fusion of gametes at fertilization
- If two alleles differ, then one (dominant) is fully expressed in the organism’s appearance; the other (recessive) has no noticeable effect on the organism’s appearance
- Law of Segregation: two alleles for each character segregate during gamete production
predicts that in a monohybrid (one factor) cross, the genotype of the F2 generation will approximate a 3:1 ratio (dominant to recessive) or a 1:2:1 ratio (homo-dom, hetero, homo-rec) - Law of Independent Assortment: each allele pair segregates independently during gamete formation via separate processes
Types of Crossing (3) + How
TEST CROSSING: lets you know what trait is dominant since you’re crossing the partially unknown (which requires at least ONE dominant allele) with a homo-rec (which can only pass on recessive alleles). THEREFORE, the phenotype of the offspring is dependent on the P/? (aka the partially unknown)
- Ie. If P/P then offspring will be P/p and all purple == OR == If P/p then offspring will be 1:1 ratio of purple to white.
- Can also use the Punnett square as a better visualization.
DIHYBRID CROSS: lets you hybridize for two traits.
– Consider:
P = Yellow; Round seeds x Green, Wrinkled seeds
F1 = All Yellow; Round
– Therefore, from the F1 generation, you know that Yellow and Round are the dominant alleles and that the offspring of this generation are all heterozygous.
– F2 generation is as follows → 9:3:3:1 ratio BUT still follows 3:1 ratio if genes are considered individually
== 9/16 Yellow; Round
== 1/16 Green; Wrinkled
== 3/16 Yellow; Wrinkled Novel combinations
== 3/16 Green; Round
** first two are the same combination as in the P generation; last two are novel combinations, with one gene dominant and the other recessive
TRIHYBRID CROSS:
Consider this:
– P = Yellow seed ; Round seed ; Long stem x Green seed ; Wrinkled seed ; Short stem
– F1 = Y/y ; R/r ; L/l
– F2 = UUUUUH → actually, don’t freak out. Just do your Punnett squares (separately, then multiply the ratios of what you want together).
Meiosis
- Interphase 1
- PMAT I
- Yield
- Interphase II
- PMAT II
Be sure to note all the things that happen here that DO NOT HAPPEN in mitosis.
Interphase I: chromosome replicates in S phase; centrioles in animals also replicate.
Prophase I: chromosomes condense; centrosomes move apart; tetrads form via synapsis; crossing over at chiasmata occurs; nuclear membrane and nucleoli disappear
– THINGS THAT HAPPEN HERE THAT DON’T HAPPEN IN MITOSIS: synapsis and crossing over
Metaphase I: tetrads align on metaphase plate; each homologue is attached to a kinetochore microtubule from the pole it faces
– THINGS THAT HAPPEN HERE THAT DON’T HAPPEN IN MITOSIS: kinetochore microtubules are no longer connected to both homologue; instead now only one per pole
Anaphase I: homologues move toward opposite poles by motor proteins; chromosomes are still doubled and the sister chromatids remain attached but are no longer identical
– THINGS THAT HAPPEN HERE THAT DON’T HAPPEN IN MITOSIS: sister chromatids are no longer alike due to crossing over
Telophase I: chromosomes arrive at spindle poles; (sometimes) the nuclear membrane will reappear; cytokinesis
– THINGS THAT HAPPEN HERE THAT DON’T HAPPEN IN MITOSIS: no reappearance of the nuclear membrane (usually)
At the end of Meiosis I, each daughter cell (there’s 4) is HAPLOID; chromosomes are still duplicated (therefore, still exist in the form of paired chromatids).
Interphase II: short; no DNA replication before Meiosis II
– no S phase as all the DNA was already duplicated in Interphase I.
Meiosis II: just like mitosis
Benefits of Meiosis
Meiosis REDUCES the chromosome SET number (and, therefore, the chromosome number).
GENETIC DIVERSITY
- Independent assortment (occurs in Metaphase 1), yielding unique combinations of chromosomes. There variations are the set up for Darwin’s “survival of the fittest” theory.
- Number of possible combos = 2n where n is the number of haploids → ie. for humans, n = 23 yields ~8 million
- Random fertilization in sexual reproduction → Therefore, number of possible combos is now SQUARED !! ~64 million combinations !!!
- Crossing over produces unique chromosomes that contain the genes from both parents. → There can be multiple crossovers per chromosome → → to infinity and beyond with genetic variation!
Blending Theory of Heredity
basically says that all the mixing of genes will result in a homogenous population
Assumes no new input of genetic material, therefore offsprings of subsequent generations will slowly become genetically similar
Once traits are blended, they cannot be separated again → think: mixed paint
Particulate Behavior of Genes
Inheritance is due to discrete factors (genes) that are passed on from generation to generation
Segregation and Assortment are RANDOM events that obey simple laws of probability
If F2 seed is planted, we will not be able to apriori predict the phenotype (basically, can’t theorize / calculate the outcome of the offspring) BUT can state that there will be a ¼ chance that it will have white flowers.
– Among a large sample size, about ¼ or 25% will have white flowers based on the 3:1 ratio. (Because small systems will have microcosms that will deviate the result from the ratio.)
** The larger the sample size, the closer results will fit the prediction.
Chromosome Theory of Inheritance + evidence
transmission of chromosomes paralleled transmission of genes in Mendel’s Theory → Mendel was rediscovered by scientists in the early 1900s and given credit posthumously
Genes are located on chromosomes
Chromosomes segregate and assort independently during meiosis
–
Evidence: working with Drosophila melanogaster (fruit fly)
- Easily cultured
- Breed like flies, therefore prolific – lots of offspring
- Short generation time, therefore have quick generational turnover (yields F2 in a few weeks)
- Have only 4 pairs of chromosomes, which are easily seen in a microscope
- 3 pair autosomes + 1 pair sex chromosomes
- Females X/X and males X/Y (heterogametic)
Discoveries:
- mutant genes
- linked genes
- parentals and recombinations
MUTANT GENES DISCOVERED
Mutation: the “not normal”; deviated from the regular phenotype; not necessarily dominant though
LINKED GENES DISCOVERED
Genes that are on the same chromosome
Therefore, do not segregate independently (ie. assort independently) and are INHERITED TOGETHER
Linkage: tendency for genes that are closer together to be inherited together
Note: dihybrid cross does not produce a dihybrid cross ratio in F2
PARENTALS AND RECOMBINANTS DISCOVERED
Parental: highest in number
Recombinants: aka novel combinations; arise due to crossing over in meiosis
Double crossing over yields double recombinants
Fruit Fly Denotation
Genes are named on the basis of the mutant phenotype
- If dominant, then capital; if recessive, then lowercase
- Wild type (aka “standard” strait) denoted by at +
- Ie. recessive white eye mutation = w ;; versus dominant red eye wild type = w+
- Remember! Mutant is the phenotype that is less present in the population
Homozygous if the alleles are the same → ie. sn+ // sn+
Heterozygous if the alleles are different
Hemizygous if the animal is a male and the allele maps to the X chromosome → ie. Xsn+ // Y or Xsn // Y → denotes situation based on X-linked or Y-linked genes in the male
Linked genes: found on same autosome; genetically linked, allowing for crossover → heterozygous = w sn // w+ sn+
Unlinked genes: found on different, non-homologous chromosomes; denotation has a semicolon separating them; allows for independent assortment → heterozygous = w // w+ ; sn // sn+
NOTE: DOUBLE LINED FRACTIONS IDENTIFY ONE FOR EACH STRAND → IE. TRAITS FOR ONE STRAND ARE ON TOP; TRAITS FOR THE OTHER STRAND ARE ON THE BOTTOM
Approaching three point crossover problems
Mapping genes: basically, look for the middle
Determining the map units in between genes
EXPECTING A DATA COLLECTION OF 8 VALUES
Top 2 = parentals
Lowest 2 = double recombinants → can also be zero!! Be careful!
Everything else = recombinants
Compare and contrast pairs of traits.
If the numbers match up then genetically UNLINKED
If the numbers are different from expected, then GENETICALLY LINKED
–
Recombination data can be used to map genes on a chromosome; constant and will never change within the species
Compare and contrast the double recombinant and the parent → Middle allele is the one that differs from the parent
Rewrite the given data to match this gene mapping
–
Recombination frequency is proportional to the “distance” between genes
Double crossover will yield an UNDERESTIMATE (meaning that the actual distance between the genes will be larger than the calculated) because they look similar to the parentals
Map units = number of recombinants over total number of progeny * 100
- Can substitute total number of progeny for (distance given)
- Aka centimorgans (cM); Related to probability that crossing over will occur between the two genes; larger distance = more likely to cross over
- Remember! Crossing over occurs at the distal ends of homologous chromosomes → contrast to linkage: tendency for genes close together on a chromosome to be inherited together
PHYSICALLY LINKED versus GENETICALLY LINKED
If the distance between two genes exceeds 50 map units (=50%), then they are considered to be UNLINKED (either bc they are v far apart on the same chromosome, therefore allowing for lots of crossover [thus act as unlinked], or on diff chromosomes)
Physically linked: on same chromosome
Genetically linked: can be detected by crossing
Ie. Mendel’s seed and flower color were PHYSICALLY LINKED but were too far apart and appeared to assort independently, thus was not considered genetically linked
SEX DETERMINATION
Chromosomal systems: common but not universal
Y chromosome: much smaller than the X; determines maleness
– Has SRY gene on Y: when activated, will create testosterone
– DAX1 on X inactivated → X/Y still male but sterile; extra on X/X then will develop testis
– Extra X chromosomes tolerated: X/X/X and X/X/Y
X Centered sex determination (fruit flies)
Ratio of X to autosomes determines femaleness
– X/X is female; X/Y is male; X/O is sterile male; X/X/X is dead
–
Environment systems: not a chromosomal system
– Temperature Dependent: temperature at which egg develops determines sex; some reptiles / turtle / alligators → concerns the temperature sensitive Dmrt1 gene that is expressed at lower temperatures, yielding a male; at higher temperatures, histones at Dmrt1 methylate, thus shutting down expression and yielding a female
– Location dependent: environmental sex determination in certain marine worms → male if the larva comes into contact with a female; becomes female if larva is alone on the seafloor
Note: the larva initially do not have a sex; their sex determination arises from their environment via contact with other larva
Sex Determination Animal Examples
Platypus: monotremes (basal mammal that lays yolky eggs); no SRY gene; sex chromosomes are not homologous to those of Eutherians
Many insects / few mammals → females are X/X, males are X/O (one less chromosome)
Birds / reptiles / moths / butterflies → Z/Z and Z/W system
- Females are heterogametic Z/W ; males are homogametic Z/Z
- No genes in common between mammalian X/Y and avian Z/W
Bees / ants / wasps / order hymenoptera → Haplodiploidy: specific type of chromosomal
- Males are haploid, called drone → Parthenogenesis: developed from unfertilized eggs
- Females are diploid → queen bee mates with drone (male); daughters share ¾ of their genes with each other (not ½ as in XY or ZW genes)
Streptococcus pneumoniae experiment
accidentally answered the question “what is genetic material”; injected S/R virus into mice
Initially, DNA (2 basic building blocks) was not accepted as genetic material because was too simple; proteins (4 basic building blocks) were more likely.
Premise: S killed mice (ie. caused disease); R did not; heat-killed S did not → combined heat killed S + living R, which killed mice BUT the blood revealed living S = concept of transformation.
- Transformation: uptake and expression of genetic material from surroundings; common in bacteria / prokaryotes but not in eukaryotes (sorry humans)
- Horizontal transformation of R into S as R took in heat-killed S
Due to transfer of genetic material from dead S to living R, the living R began expressing the genetic material from S, thus changing into the S phenotype
– Purified components from the heat-killed S revealed that only DNA transformed (not protein!)
T2 Bacteriophage
+ experiment
virus that affects E. coli
Programs host cell to make new virus, which lyse from the cell, thus destroying the host
Viruses don’t reproduce! They use the host cells to make more viruses.
Consists of a DNA encapsulated in a protein coat (called “capsule”) with a tail piece that can change shape in order to pierce the membrane of a target host cell, allowing for injection of the virus DNA
–
Experiment: how do you know that DNA is inserted (versus proteins)? ** Remember that viruses are made of both DNA and proteins.
- Grew E. coli and T2 together with 35S (radioactive blue stain for proteins) → incorporated into the phage protein (capsule)
- Grew E. coli and T2 together with 32P (radioactive stain for DNA, which has P groups)
Procedure:
1. Harvested the phage
2. Infected one group of bacteria with S-labelled phage and another group with the P-labeled phage
Samples blended to dislodge capsule
3. Centrifuged (capsules float; bacteria in pellet + whatever injected)
4. Check for location of radioactivity
Results:
- S labelled phage (protein stained) had radioactivity in the SUPERNATANT where the protein capsules were
- P labelled phage (DNA stained) had radioactivity in the PELLET where the DNA was
Name two important studies + some other important clues that led to the conclusion that DNA really was the genetic material (as opposed to proteins).
Streptococcus pneumoniae experiment; from Frederick Griffith and (later) Avery et al.
T2 Bacteriophage and E. coli experiment; from Hershey and Chase
DNA composition (ratios of nitrogen bases A:G:T:C) are species specific (ie. will vary from species to species since no two species will be the same) BUT strange regularity of amount of A = amount of T and amount of G = amount of C → Base Pairs (aka Chargaff’s rules) from Erwin Chargaff
1950s - DNA officially accepted as Genetic Material
Watson-Crick Model of DNA Structure
+ what does it mean to be double stranded
X-Ray Crystallography Photo method (from Rosalind Franklin): specimen is crystallized and examined with x ray beams, which result in a scattering of light that can then be caught by photosensitive film → the scatter pattern that results can be inferred
Led to deduction of the DNA Double Helix: 2 nm wide; 2 strands (2 poly nucleotides entwined) → 10 layers of nitrogenous bases (pairs) in one turn of the helix, where one full turn is made every 3.4 nm
–
Each strand consists of sugar-phosphate backbone
Strands are held together by H-bonds between the nitrogen bases
For two bases to fit in the space, has to be Pyrimidine (one ring) with Purine (double ring) → can’t be pyr-pyr bc too small / doesn’t fill space of 2nm, can’t be pur-pur bc too big / overfills space of 2nm
Explains Chargaff’s Rules since A-T and G-C theory is held up (equal each other and fill up space) → A/G are pyrimidines, T/C are purines
DNA Directionality
both strands are antiparallel to each other, thus operate in different chemical directions → because of base pairing rules, if we know the base sequence of one strand, we can predict the base sequence of the opposite strand (aka complementary!)
3’ is considered “longer / business” end because it has the capacity to form long carbon chains due to the HYDROXYL GROUP on the THIRD CARBON of the nucleotide sugar; also the location of phosphodiester linkages → allows for (weak) hydrogen bond attractions between the strands, hence creating the double helix form
5’ is considered the “shorter / hanging out end because the PHOSPHATE GROUPs do not interact with anything in the strand / environment besides being attached to the FIFTH CARBON of the nucleotide sugar
DNA Replication Models
+ types of replication
replication occurs during the S phase of the cell cycle
DNA strands separate → each strand serves as a template for constructing new complementary strand; deoxyribonucleoside triphosphates attach to new strand, matching base of template according to the base pairing rules
–
Types of Replication: the winner and the losers + why they lost
- Conservative: strands are replicated separately but come back together, thus yielding the original strand joined back together and a completely new strand made from combining the replicas
- Dispersive: strands are more or less randomly distributed as original or synthesized; aka splicing information into each “new” strand
- Semiconservative: proven theory; one strand is from the original, the other is the newly synthesized – (from reader) as double helix replicates, daughter molecules will consist of one strand from the original molecule and one newly synthesized strand
Meselson and Stahl experiment
Tested which of the three models were correct by double replicating the strands in order to differentiate them from one another + compare
Procedure:
1. Used bacteria cultured in a medium containing 15N (heavy nitrogen; therefore DNA synthesized will be heavier) – remember that nitrogen is incorporated into the bases
2. Bacteria transferred to a medium containing 14N
DNA Sample centrifuged after 20 minutes (which is after the first replication) and again after 40 minutes (second replication)
Prediction and Results: original DNA model is of higher density than its replicas
- Conservative predicted that there would be heavy and light density DNA present and no intermediates → eliminated because intermediates were present after the first replication
- Dispersive predicted intermediates after the first replication BUT also predicts that the DNA density should become lighter after the second replication → eliminated because intermediate density does not change
- Semiconservative predicted that intermediates after the first replication BUT also predicts that the densities will not change after the second replication → proven
DNA Replication
Rapid and accurate despite having about 6 billion bases in the human genome
DNA polymerase: synthesizes; super accurate (makes about 1 mistake in a billion bases, therefore only 6 mistakes in the entirety of genome replication); however, cannot initiate
– New DNA is created from 5’ to 3’ at a rate of 50 nucleotides / s (but there’s a lot working at once)
Origins of Replication: lots of different types in eukaryotes but there’s a specific sequence of nucleotides that act as a marker in prokaryotes
- 2 strands separate at the origin of replication
- - Problem: DNA polymerase can add new nucleotides only to an existing 3’-OH therefore CANNOT INITIATE
- - Solution: RNA primer attaches to the complementary sequence at the origin of replication to which the DNA polymerase can extend; DNA primase can then make a primer out of it (teamwork!) - Replication bubble formed as helicase unwinds
- - Creation of replication fork
- - Creation of leading strand (continuously replicated in 5’ to 3’ direction) and lagging strand (discontinuously replicated because need to be in 5’ to 3’ direction)
- —- Lagging strand requires additional primers and DNA polymerases but still unable to fill in the gaps in between, aka Okazaki fragments (about 100 to 200 nucleotides long)
- —- DNA polymerase will remove the primers it meets (after the first) but gap still present
- —- DNA ligase comes in to seal the P-sugar backbone with a covalent bond; basically creates a phosphodiester linkage - Elongation continues via helicase until replication forks from adjacent regions meet
Why is RNA used instead of DNA as a primase??
DNA polymerase is very active; can incorporate nucleotide triphosphate; if it makes a mistake, can back up and correct it – super accurate tho
DNA Primase that is put down is prone to errors – if used to replicate genome then sooo many mutations would occur
Use RNA instead because there’s a chemical difference from DNA – can be erased with good DNA → “it’s a matter of conserving the integrity of the DNA” – Jim Baxter 2018
RNA primase makes mistakes too but it doesn’t matter because of amplification + the DNA can get replace it
What is DNA?
Contains the information needed to construct the primary structure of proteins.
Genes: encodes information for one polypeptide or structural RNA
– Not all genes are “on” in all cells or at all times
Need a mechanism to selectively express specific genes without expressing all the genes on a chromosome (basically, how to turn something on or off)
Eg. Liver cells are different from neurons because even though the DNA content of the cells are the same, different proteins are present and thus yield a different gene expression
Central Dogma of Biology
DNA → RNA → Protein
Overview: DNA can undergo replication or can be transcribed into RNA (intermediate), which can be translated into a different language that codes for proteins!
DNA = Genomic DNA encodes the information needed for life and for differentiating one species from another
RNA = Information from the genome, representing only a small fraction of the total DNA content, is transcribed into mRNA for further processing
Protein = Information in a portion of the mRNA sequence (aka coding sequence) is used to guide the synthesis of a specific protein
Gene expression: production of polypeptide or structural RNA encoded for by a gene → “active” protein or RNA required; usually one gene per one polypeptide or RNA BUT can be extended
DNA versus RNA
2 polynucleotides (double stranded) – 1 polynucleotide (which can fold to form double stranded portions if complementary, but typically single stranded)
Deoxyribose sugar – ribose sugar
Thymine – Uracil
Transcription
RNA polymerase II used to separate DNA strands and DOES NOT need priming; however, less accurate than DNA polyermase
Adds and links together ribonucleotides in a 5’ to 3’ direction according to the sequence in the template and base pairing rules
Non template strand will be identical (due to complementation to the template) to the RNA being produced (which also complements the template strand)
Note: Eukaryotes have 3 types of RNA polymerase; I and III are mostly transcribed for structural RNAs, ie. ribosomal RNA
Three Stages of Transcription
- Initiation: general transcription factors (GTF) bind to the specific nucleotide sequence in the promotor
- - Promoter: aka “switch”; can change the environment only when GTF binds to it, thus allowing RNA polymerase to attach to the initiation site and allowing transcription to begin
- - TATA box: TA box rich region in the promoter of eukaryotes where TATA transcription factor binds → one of the first to bind, thus allowing others to bind after it because the of the induced environment change - Elongation: RNA polymerase separates the DNA into two strands, the directionality of which determines which will be the template for RNA because the RNA nucleotides are linked in a 5’ to 3’ direction; processes at a rate of 30 to 50 nucleotides / s
- - Newly made RNA will peel away from the template and DNA strands reanneal - Termination: RNA polymerase proceeds until the terminator sequence is reached/transcribed, which will form a hairpin loop (aka “proles”) to push the DNA polymerase off (ends transcription)
In eukaryotes: will often be AAUAAA
Translation
mRNA → amino acid sequence
Direct correspondence of linear sequences of codons in mRNA and amino acid sequences of polypeptides
Important players:
- Ribosomes
- mRNA (product from post transcriptional processes)
- tRNA: aka transfer RNA; structural
- Aminoacyl-tRNA synthetases (specific class of enzymes):
- Lots and lots of enzymes
