Final Exam pt. 2 (from computer notes) Flashcards
True or False: the environment can modify the expression of phenotypes?
True.
In the mid-1900s, many scientists assumed proteins carried the information for inheritance, why?
Because of the greater complexity of proteins as compared to nucleic acids. Proteins have a much more varied 3-D structure as compared to the relatively uniform structure of DNA
What is the One-Gene-One-Enzyme hypothesis?
The first hypothesis surrounding genetics that each gene coded for a particular enzyme
What is the definition of a gene?
A unit of heredity on a chromosome that contains either:
1. The code for a protein molecule or one of its parts
2. The code for structural RNA molecule such as tRNA or rRNA
What is the One-Gene-One-Protein hypothesis?
The intermediate hypothesis of the idea that genes can code, not only for enzymes, nut also for types of proteins
What is the One-Gene-One-Polypeptide hypothesis?
The most recent hypothesis where some genes code for just of one the several polypeptides that make up a functional protein
In addition to genes that code for mRNAs, it was realized some genes code for structural ____
RNAs such as tRNAs and rRNAs
What is a mutation?
It is a permanent heritable change in genetic materal
True or False: mutations are the only source of new alleles?
True
What are the factors supplying variation in populations upon which natural selection can act?
o Independent assortment
o Recombination
o Mutations
o Random fertilization
True or False: Mutations are normally common events and exert little to no immediate effect on allele frequencies in populations?
False: Mutations are normally rare events and exert little to no immediate effect on allele frequencies in populations. But over evolutionary time scales, they are significant, as mutations have been accumulating for millions of years in all biological lineages
In many animals, mutations must affect cells in the _______ to be passed on to subsequent generations
Germ line
Somatic mutations do not have evolutionary significance in animals unless..?
It’s an animal capable of reproducing by cloning
Why do somatic mutations have a greater evolutionary significance in plants?
Because so many plants can reproduce vegetatively
True or False: Mutations are random events (unpredictable)?
True
True or False: all mutations are harmful?
False: Most mutations are harmful, but occasionally a beneficial one occurs
How do species reduce mutations?
Most species have mechanisms to repair damaged DNA, these mechanisms greatly reduce the prevalence of mutations
True or False: Mutations can occur both during DNA replication and after replication
True
What kind of mutation is a point mutation?
A small scale mutation
Describe point mutations
- Affects only one base pair in DNA
- They are base substitution mutations
- An incorrect base is submitted which then results in a change in the base sequence on both strands
What are the types of point mutations
- Silent mutations
- Missense mutations
- Nonsense mutations
- Deletions/insertions
Describe silent mutations
- If the amino acid coded for by a substitution is the same as the one coded for by the original codon
- This can happen because of the degenerate nature of the genetic code (i.e., more than one codon can code for the same amino acid)
- Silent mutations are also neutral mutations because the function of the encoded protein is not affected by the mutation
Describe missense mutations
- A base substitution
- Causes a change in a single amino acid in the encoded polypeptide
- This could also be a neutral mutation if there is no alteration in function of the encoded polypeptide
- Some have a dramatic deleterious effect on the function of the encoded protein
Describe nonsense mutations
- A substitution which converts a normal codon to a stop codon. This will cause translation to stop before the complete polypeptide encoded for by the normal allele is synthesized
- Results in a shortened polypeptide
- Very unlikely this shortened polypeptide will be functional
Describe deletions/insertions
- Addition or deletion of a nucleotides in a gene
- Results in a frameshift mutation
- Mutation shifts the reading frame on mRNA resulting in a completely different amino acid sequence on the polypeptide
- The seriousness of this type of mutation depends one where it occurs in the gene
- Less severe if one complete codon is added or deleted because this will not upset the reading frame downstream from the mutation.
What are the two possibilities that genes can code for?
- Messenger RNAs which code for proteins
- Functional RNA such as transfer RNAs and Ribosomal RNAs
What is the flow of gene expression?
DNA codes for mRNA (transcription) –> mRNA codes for proteins (translation) –> Proteins do not code for DNA or RNA
What is the role of helicase?
- DNA helicase unwinds the double helix by breaking H-bonds between the complementary nitrogenous base pairs in the rungs between the two strands
- This allows the two parental template strands to separate from each other
- As DNA helicase does its work, it causes the DNA double helix to twist more tightly in front of the moving replication fork
What is the role of topoisomerase (gyrase) and single-stranded binding proteins
- Alleviates the tightened coiling in front of the replication fork caused by helicase
- Breaks, swivels, and rejoins the DNA strands ahead of the moving replication fork, easing the tension
- Separated strands are prevented from coming together again behind DNA helicase by single-stranded binding proteins which bind to each separated parental strand
What is the role of primase?
- Synthesizes a short RNA primer to initiate a new DNA strand
- Builds an RNA primer in the 5’ to 3’ direction, the primer is antiparallel to the parental template strand, and it does have an exposed 3’ end
- Primase must remove the single-stranded binding proteins from the template strand before it can make the primer
- So initially, at a replication fork, primases make an RNA primer along each of the exposed parental template strands towards the expanding replication fork beside the leading strand template and away from the expanding replication fork beside the lagging strand template
- Once the primer is completed, primase detaches from the template strand and a DNA synthesizing enzyme called polymerase III attaches to the exposed 3’ end of the RNA primer
What is the role of ligase?
- Completes the covalent phosphodiester bond of the sugar-phosphate backbone that will repair the nick left by DNA polymerase I
- Then releases and leaves
- Adds nucleotides to a daughter strand that are complementary to the nucleotides on the parental template strand according to the AT/GC rule
DNA synthesis involves the formation of newly replicated DNA strands according to what rule?
The AT/GC rule
What were the three proposed models of DNA replication?
- Conservative mechanism
- Semiconservative mechanism
- Dispersive mechanism
What was the conservative mechanism in terms of DNA replication?
After the 1st replication of the two DNA molecules produced, one retains the two old parental strands, and the other is made up of the two newly synthesized replicated strands
What was the semiconservative mechanism in terms of DNA replication?
- Involves the complete separation of the two parental strands, which allows each parental strand to act as a template directing the synthesis of new complementary replicated strands
- The 1st replication results in two new DNA molecules, each with one old parental and one new replicated strand
What was the dispersive mechanism in terms of DNA replication?
The 1st replication results in both strands in each of the two DNA molecules produced made of segments of new DNA interspersed between segments of the old parental DNA
Which mechanism for DNA replication was found to be correct?
Experimental results supported the semiconservative mechanism model of DNA replication
Define epistasis
Epistasis is an interaction between two or more genes to control a single phenotype
In epistasis, alleles of one gene can ____ the expression of the alleles of another gene, with that come expected phenotypes will not appear among the offspring
Mask
Using planned crosses to study patterns in human inheritance is not possible, why?
Because mating can’t be controlled, and offspring sample sizes are too small. Also, human generation times are very long
Define/describe a pedigree chart
- Used to determine if a human trait is dominant or recessive and, also, if it is autosomal or X - Linked
- Is a family tree that displays members of a family affected by a genetic trait controlled by a single gene
- Used to track the inheritance of rare genetic diseases in humans
Describe the legend components of pedigree charts (what each symbol represents)
- Roman numerals stand for a generation in the family tree, digits stands for an individual
- Circles represent females, squares males
- Darkened circles/squares indicate an individual affected by the studied trait.
- Horizontal lines are used between a mated male/female pair
- A heterozygous individual may not be indicated or are indicated by ½ shading of the inside of a circle or square.
True or False: expected Mendelian ratios are not necessarily observed in individual human families because of small sample sizes
True
What is the common first step in analyzing whether the mode of transmission of a deleterious allele is autosomal or X-linked?
Determining whether males are most severely affected by the genetic disease.
Describe multiple alleles
When some genes have three or more alleles
What is a common example of a situation of multiple alleles
The human ABO blood group is an example of a trait controlled by a gene with three alleles, I^A, I^B, and i.
* I^A and I^B alleles are dominant to i
* A blood type is produced by I^AI^A and I^Ai
* B blood type is produced by I^BI^B and I^Bi
* AB blood type is produced by I^AI^B
* O blood type is produced by ii
Define codominance
Alleles have approximately equal effects in individuals making alleles equally detectable in the phenotypes of heterozygotes
What is the difference between codominance and incomplete dominance?
Codominance differs from incomplete dominance in those heterozygous individuals express both alleles simultaneously without any blending
Define incomplete dominance
- Incomplete dominance can occur because neither of the two alleles is fully dominant over the other
- This results in a phenotype in heterozygotes that is different from the phenotypes of both homozygotes, appearing to be a mixture intermediate between those of the two
Describe Testcrosses
- A cross involving an individual that shows a dominant phenotype but there is uncertainty about its genotype with another that is homozygous recessive for the trait being considered
- Testcrosses are also used to determine if two genes involved in a dihybrid cross are on the same chromosome or on different chromosomes
Describe blending inheritance
- Parents make equal genetic contributions to their offspring and that their genetic materials blend in their offspring
- Inherited traits of offspring were determined randomly, from a range bound by the traits found in their parents
- Freely mating populations over a period, should give rise to a genetically uniform population of individuals. Such an outcome is contradicted by every-day observations.
- Blending inheritance also fails to explain reappearing fully developed after skipping one or more generations
What are the factors that influence enzyme activity?
- Temperature
- pH
- Concentration of enzyme and substrates
- Other molecules, like inhibitors and activators
True or False: Proteins/enzymes assemble at high temperatures
False: Proteins/enzymes denature at high temperatures
What is a phototroph?
A type of autotroph, uses sunlight for energy
What is an autotroph?
Gets energy from light or inorganic chemicals
What was the Great Oxygenation Event (GOE)?
- Atmosphere accumulated oxygen over millions of years
- This oxygen was toxic to the anaerobic cells present
- This created one of the great extinctions in the history of the earth, but it also paved the way for eukaryotes
Describe modern day metabolism
- Respiration (catabolic), in the mitochondria (Sugars + O2 ATP + H2O)
- Photosynthesis (anabolic), in the chloroplasts (CO2 + H2O Sugars + O2)
Describe the ancient hypothesis for the start of metabolism
- Deep sea alkaline vents are porous chimneys form by precipitation of calcium carbonate. Warm nutrient rich alkaline vent water encounters acidic ocean water.
- Gradients of H2 create potential energy.
*Free energy from H+ flow used to make ATP
*Evidence of iron-sulfur proteins - Fe-S clusters are enzyme co-factors for Fe-S proteins. Fe-S proteins are crucial in all of today’s energy metabolism. Fe-S cluster bound to peptide chain
- Ancient bacteria pump H+ out of the cell to achieve the gradient. This mechanism still exists in some primitive prokaryotes
What was the likely scenario of abiogenesis?
Habitable world -> probiotic synthesis -> polymers, vesicles -> protocells (aka protobionts)
Describe a reciprocal cross
- Involves a set of mating where the mother’s phenotype in the first cross is the father’s phenotype in a second cross and the father’s phenotype in the first cross is the other’s phenotype in a second cross
- In Mendel’s pea plant crosses it did not matter which sex was providing the allele in the parental generation
what kind of sex determination system do humans have?
The X-Y system of sex determination
Which sex is heterogametic?
Males are the heterogametic sex – produce gamete with two types of sex chromosomes
Which sex is homogametic?
Females are the homogametic sex – produce gametes with only on type of sex chromosome
Which chromosome is larger, Y or X?
X
Which chromosome has more genes on it, Y or X?
X
Sex-linked genes on the X chromosome are said to be ____?
X-linked
The other 44 chromosomes in human cells are referred to as ______?
Autosomes
What is a Barr body?
In the cells of women, one of the X chromosomes is always inactivated to form a Barr body
True or False: it is random which X becomes inactivated?
True
What is the SRY gene?
Sex-determining region of the Y chromosome
All humans have the genes to produce both the male and female reproductive systems, but which system will develop is determined by?
Whether or not the protein produced by the SRY gene is expressed in the somatic cells of the embryo early in the embryo’s development
True or False: the SRY gene is an example of a pleiotropic gene?
True
What is hemophilia?
- The blood does not clot normally
- Women heterozygous for hemophilia are called carriers because they do not suffer from the disease but can pass the disease to their offspring
- Males are most severely affected by genetic diseases associated with genes on the X chromosome
Where and when does DNA replication take place?
Replication of DNA takes place in the nucleus in eukaryotes and in the cytoplasm in prokaryotes; takes place in the S phase of interphase in eukaryotes
Who carried out experiments in 1958 to confirm that DNA replication was semiconservative?
Matthew Meselson and Frank Stahl
What is polygenic inheritance?
Involves two or more genes affecting the outcome of a single trait
Traits subject to polygenic inheritance exhibit ..?
Continuous variation over a range of phenotypic expression
Phenotype in a population tends to have a normal ______ curve of continuous variation distribution pattern
Bell-shaped
What are some examples of human polygenic features?
Height
Weight
Skin colour
What kinds of effects during infancy and childhood can influence height in a population?
Nutrition and disease
True or False: Environmental factors typically can influence the expression of the phenotype in polygenic inheritance?
True
True or False: many different genotypes can produce the same expressed phenotype
True
True or False: alleles in polygenic inheritance so not have any additive effects?
False: there are additive effects of alleles in polygenic inheritance
Describe Sickle Cell Anemia
- The recessive deleterious allele for sickle cell anemia affects the structure of human hemoglobin molecules inside red blood cells
- Red blood cells in individuals homozygous for the recessive abnormal allele will develop a sickle shape when the cells enter the lower dissolved O2 levels within tissue capillaries
- Sickle cell disease has wide ranging pleiotropic effects on the human body
Define pleiotropy
The determination of several seemingly unrelated phenotypic traits by a single gene in a multicellular organism
The underlying mechanism of pleiotropy is that the pleiotropic gene codes for 1. _____ or 2. _____
- Product that is used in more than one cell type
- The product of the gene has a signaling function on various target cells (i.e., gene that codes for the insulin receptor protein on cell membranes)
True or False: Most single genes affect more than one observable trait
True
True or False: In humans a deleterious allele in just one gene will never cause widespread problems throughout the body
False: in humans a deleterious allele in just one gene can cause widespread problems throughout the body
Results of his dihybrid crosses led Mendel to propose what is now known as Mendel’s second law of inheritance: ?
The law of independent assortment of alleles
What is Mendel’s second law?
Alleles of genes on different (nonhomologous) chromosomes assort independently of each other during gamete formation
From his dihybrid cross, Mendel concluded the F1 individuals were produce how many different gametes during gamete formation?
Four different gametes ,in equal proportion
From his dihybrid cross, how many new phenotypes appeared in the F2 generation that were not present in the parental generation?
Two new phenotypes appeared
Where are these new genetic combinations appearing in the F2 coming from?
Due to the random orientation of maternal and paternal chromosomes in metaphase I of miosis
True or False: the way in which maternal and paternal chromosomes align at metaphase I occurs intentionally in F1 individuals
False: the way in which maternal and paternal chromosomes align at metaphase I occurs by chance in F1 individuals
What can produce different mixes of paternal and maternal chromosomes going to the poles in anaphase I in F1 individuals?
The random alignment at metaphase I
Define hybridization
Involves mating two individuals with different characteristics
Define allele
A contrasting alternative of a gene
Define phenotype
Observable properties of an individual as determined by genetics and the environment
Define cross-pollination
Pollination of a flower or plant with pollen from another flower or plant.
Define genotype
The genetic makeup of a cell or an individual usually with reference to a specific character under consideration.
True or False: alleles are discrete, unchanging units?
True
Who, all independently, rediscovered Mendel’s writings and laws; and who independently duplicated Mendel’s results in the late 1800s
Hugo de Vries, Carl Correns, William Spillman and Eric von Tschermak; and de Vries and Correns
What were the earliest fossils, and when do they date back to?
Stromatolites, mineral deposits made by cyanobacteria; the oldest ones date back to ~3.5 billion years ago
When was the earliest evidence life found to date?
~3.9 billion years ago
What was the earliest for evidence for life?
Radiocarbon dating of rocks from the ancient sea floor, there were lower levels of isotope 13C than expected
What was the evidence of the accumulation of oxygen in the atmosphere?
- Oxidized iron found in geological strata dating to ~2.5 billion years ago
- Due to the accumulation of oxygen in atmosphere from oxygenic photosynthesis
- True or False: LUCA would have shared the characteristics present in all modern cells
- If true, what would these characteristic entail?
- True
- Lipid bilayer, DNA -> RNA -> Protein, Ribosomes, Proteins are main structural/catalytic components, Energy transforming (i.e., metabolic) pathways
True or False: LUCA was psychrophilic?
False, it was thermophilic
Certain ancient archaeans live in extreme temperatures, these are called what?
Extremophiles
Describe Earth’s early atmosphere/climate
- Hydrogen (H2) carbon dioxide (CO2) ammonia (NH3) methane (CH4) water (H2O)
- Very little O2
- No ozone (O3) layer so strong UV radiation
- Lots of lightning, volcanoes, earthquakes, meteors, extreme temperature changes
Information flow structure in all extant earthlings?
DNA -> RNA -> Protein
Describe Oxygenic Photosynthesis
- Began in ancient cyanobacteria
- Like modern day photosynthesis
- Uses solar energy to capture CO2 and fix that into sugars
- Because H2O is split in order to get the charged H+ needed to create H+ gradients
- Prior to that, H2S was used for H+, but H2O is way more abundant than H2S
True or False: photosynthesis is the source of oxygen in the atmosphere?
True
Why did the first phototrophs rely on anaerobic metabolism?
Because there was only trace oxygen in the environment
Some extant phototrophic prokaryotes use anaerobic metabolism, what does this entail?
- Usage of solar energy to pump protons out of the cell
- ATP is made when protons move back in through ATP synthase enzyme
What where the endosymbiotic origins of chloroplasts?
- Photosynthetic bacteria became chloroplasts
- Horizontal gene transfer: occurred for millions of years as the endosymbiotic relationship deepened
True or False: the endomembrane system may be derived from plasma membrane
True
Describe eukaryotes and aerobic respiration
- Sugars + O2 ATP + H2O (mitochondria)
- Endosymbiotic origins of mitochondria and chloroplasts
Define monohybrid
Hybridizing for a single trait
The location of a gene on a chromosome is called the ____?
Gene locus
Define transcription factors
Transcription factors include proteins that initiate and regulate the transcription of other genes
What is Mendel’s First Law of inheritance?
The Law of Segregation: Alleles of a gene segregate independently of each other during gamete formation
True or False: alleles segregate during mitosis?
False: alleles segregate during meiosis
Mapping is based on what assumption?
That crossing over is just as likely to occur at any point along a chromosome
The closer the two genes are together, there are ____ points at which crossing over can occur between them
Fewer
Map units can only provide us with values for the _______ between genes on a chromosome
Relative distance
Recombinant frequencies will suggest the alleles of these two genes are assorting independently if each other if genes are more than ____ map units apart
50 or more map units
Genetic Linkage Mapping is not useful for what?
Studying organisms with long generation times or species in which you cant carry out experimental experiments
____________________ , obtained from test crosses of F1 dihybrids, can be used to map the linear order of genes on the same chromosomes
Recombinant frequencies
When alleles of different genes tend to stay together during meiosis the genes are said to be?
Linked
Define recombinants
- Phenotypes with a different combination of traits than the original parents
- An individual chromosome, meiotic product or individual that possess a new combination of alleles due to crossing over
In linked genes recombination is produced by the crossing over process in what stage of meiosis?
Prophase I
Define parental gametes
Gametes that maintain the original linkage of genes (alleles) in the chromosomes of the parental generation
Define recombinant gametes
- Responsible for the appearance of the nonparental phenotypes in test cross offspring
- Those in which the original linkage is undone due to exchange of chromosomal pieces during crossing over in meiosis
Define genetic recombination
A change in the combination of alleles of genes in each chromosome, meiotic product or individual
What is the Oparin-Haldane hypothesis?
Reducing atmosphere
1. There was very little O2, meaning that the atmospheric conditions were reducing
2. Thus lots of complex electron rich molecules could form: amino acids and other organic molecules common to life came to be
3. Later Hydrogen cyanide and formaldehyde was added and all of the building blocks formed (fatty acids, phospholipids, amino acids, ribose, deoxyribose, glucose, etc) but NOT polymers
What are the building blocks of life?
- Fatty acids
- Phospholipids
- Amino acids
- Ribose
- Deoxyribose
- Glucose
Describe the RNA world Hypothesis
- Life began with RNA
- RNA can store information and catalyze reactions
- Can form complex secondary structures
- RNAs with enzymatic activity are still in existence
- At some point RNA functions were replaced by DNA and proteins
What is an example of an RNA with enzymatic activity?
Ribozymes: RNAs that forms complex secondary structures that can catalyze simple reactions
At some point, RNA functions are replaced by DNA and proteins. What functions did they each respectively replace?
- DNA takes over role in info storage, as its much more stable and can last for millions of years. Since it is double stranded, it can repair itself much easier
- Proteins take over catalytic functions
Describe Clay Surface Polymerization
- Clay acts as a catalytic surface for polymer formation
- Monomers are forced together due to: electrical charges on surface holding monomers in place and surfaces being very close together (nanometers)
- Holding close together increases probability of monomers matching up just right to from bonds
When two genes are close together on the same chromosome, alleles F1s received from their parents tend to be transmitted together during gamete formation in F1s, what is this process called?
This process is called linkage
Which three scientists carried out a dihybrid cross in sweet peas in 1908?
Bateson, Punnett, and Saunders
The dihybrid cross in 1908 showed results from the sweet pea plantings did not correspond with predictions of inheritance based on independent assortment. Bateson and Punnett were unable to clarify the inheritance of these traits in sweet peas, when was this resolved?
- It wasn’t until Morgan, discovered gene linkage in 1911, that it was realized that the genes were inherited as linked gens located on the same homologous chromosomes
- As it turns out, these genes are close together on the same chromosomes, not on a different chromosome as was the case with genes used by Mendel on his dihybrid cross
What is a test cross?
Dihybrid x homozygous recessive
So, when doing crosses with dihybrid, how do you decide if you are dealing with gene pairs that are on different chromosomes or on the same chromosome?
- If you get a 1:1:1:1 phenotypic ratio in the offspring, you conclude the alleles of the two genes are assorting independently of each other, so, the genes are on different chromosomes
- If you get a phenotypic ratio where most of the offspring have the parental phenotypes and only a few offspring have the nonparental phenotypes, you can conclude the two genes are linked and are on the same homologous chromosomes
Why do we use testcrosses?
To decide if the genes in question in the F1 dihybrids are:
1. On different chromosomes (i.e., assorting independently)
2. Or on the same chromosome (i.e., genetically linked)
What are recombinant gametes responsible for?
The appearance of the nonparental phenotypes in test cross offspring
What is the formula for free energy ad spontaneous reactions?
ΔG = ΔH -TΔS
What is the full name for ATP?
Adenosine triphosphate?
ATP cycle
- Energy is released during the formation of ATP + Pi
- Energy is released during the formation of ADP + P. This reaction releases free energy, so it is exergonic
Importance of enzymes?
- Enzymes force substrates into the transition state 2. Enzymes lower the activation energy for a reaction
- Enzymes reduce the free energy of the transition state
Protein monomers consist of __ different amino acids; whereas DNA monomers consist of just __ nucleotides
20, 4
What was the end result of the Hershey-Chase experiment?
Confirms that DNA is the genetic material
What was the Hershey-Chase experiment?
In 1952, Alfred Hershey and Martha Chase used radioactively labeled T2 viral phages to infect cells of the bacterium Escherichia coli
Describe the Hershey-Chase experiment
Hershey and Chase prepared two radioactively labeled batches of T2 phages:
1. In one batch the protein was labeled; in the other batch the DNA was labeled
2. The two batches of phages were introduced into separate cultures. The two cultures were allowed enough time for the phages in the cultures to fully infect the bacteria
3. Each culture of infected bacteria was then mixed in a blender to shear the phage coats off the surfaces of the bacteria. The two batches were then analyzed to identify where the radioactivity was
4. If it was DNA that was the genetic material, then only phages with radioactive DNA should be able to produce new phages with radioactive. This was true
5. It was concluded that it was the phage DNA that contained the genetic material necessary
Describe metabolism
- Carried out largely by enzymes
- Catabolism or Anabolism
Define Catabolism
The breaking down of something (e.g., cellular respiration, glycolysis)
Define Anabolism
The building of something (e.g., photosynthesis, lipid synthesis)
Describe enzymes
- Biological catalysts that create, destroy, or modify
- Catalyze reactions that otherwise would happen slowly or not at all
Describe enzyme-substrate complex
When a substrate enters the active site of the enzyme
What are the two models for enzyme function?
- Lock and Key model
- Induced fit model
Who proposed the lock and key model?
Mario Lock and Luigi Key
Lock and Key vs. Induced Fit models
The lock and key model states that the active site of an enzyme precisely fits a specific substrate. The induced fit model states that the active site of an enzyme will undergo a conformational change when binding a substrate, to improve the fit.
What are the two major types of energy?
Kinetic and potential
Describe thermodynamics
- Describes energy and its transformation
- Looks as things as a system and its surroundings
Biological systems are what kind of systems?
Open systems: they exchange matter and energy with surroundings
Describe the relation between matter and energy
- E = mc^2
- Matter and energy are interchangeable
- They are different forms of the same thing
What is the First Law of Thermodynamics?
Energy cannot be created or destroyed, only transformed or transferred
What is the Second Law of Thermodynamics?
- Energy and matter move from ordered to disordered (they will naturally spread out over time (e.g., diffusion, heat loss)
- Called entropy (S)
Second Law of Thermodynamics and the entropy of the universe
The entropy of the universe is constantly increasing
Laws of Thermodynamics and the universe
First Law: the energy of the universe is constant
Second Law: the entropy of the universe in continuously increasing
Describe spontaneous processes
- Do not require continuous input of energy to proceed
- “Spontaneous” has no relation to the speed of the process
- If there is a loss in energy, the reaction is considered spontaneous
True or False: whether a reaction is spontaneous or not is determined by the free energy of a system?
True
Define Gibbs Free Energy (G)
The amount of energy of a system available to do work
What symbol is used to represent the change in free energy?
ΔG
If there is no change in free energy, what is ΔG; what does this imply?
ΔG =0; the process/reaction is at equilibrium
What is ΔG if there is a loss/gain in free energy?
Loss: ΔG is negative, spontaneous, exergonic
Gain: ΔG is positive, nonspontaneous, endergonic
What determined the free energy of a system?
The combination of temperature of the surroundings, and the entropy/enthalpy of a system
Describe enthalpy
- The heat content of a system, based on amount and strength of atomic bonds
- Changes in enthalpy referred to as ΔH
- Either Exothermic or Endothermic
What is the ΔH when a reaction is exo/endothermic?
Exothermic: ΔH is negative
Endothermic: ΔH is positive
Define activation energy
The amount of energy required to reach the transition state.
When is energy released?
During the formation of ADP + Pi
Define energy coupling
When the energy produced by one reaction or system is used to drive another reaction or system.
Quick summary of the ATP cycle
- ATP + H2O (creates energy for cellular work for endergonic processes) –> ADP + Pi
- ADP + Pi (energy from catabolism) —> ATP
True or False: enzymes lower the activation energy for a reaction?
True, they do this by forcing things into the transition state
True or False: enzymes have pH optima consistent with their environment?
True
True or False: enzymes do not have optimal temperatures?
False; for animals, optimal activity is body temperature because proteins/enzymes denature at high temperatures
True or False: enzyme and substrate concentrations influence reaction rates?
True
What are the three steps in translation?
Initiation, elongation, and termination
Describe the initiation stage of translation
- First step of the initiation stage is the binding together of an initiator tRNA, methionine, and a small ribosomal subunit
- The initiator tRNA has the anticodon UAC
- The small ribosomal subunit with its tRNA binds initially to the mRNA at the mRNA’s 5’ end
- The small ribosomal subunit scans along the mRNA, until it lines up over the ‘start codon’ on the mRNA
- Base-pairing occurs between the tRNA anticodon and the start codon AUG on the mRNA. This pairing establishes the correct ‘reading frame’ for translation of the codons
- A large ribosomal subunit now binds onto the small subunit
- The completed ribosome has three sites that can accommodate tRNAs: E, P and A sites
Why is establishing the correct reading frame essential in the initiation stage of translation?
Establishing the correct reading frame is essential as there is no punctuation along the mRNA that separates one codon from the rest
Describe the elongation stage of translation
- Elongation cycle adds one new amino acid at a time
- At the beginning of each cycle, a polypeptide chain is held by the tRNA in the P site at the end of the cycle, the polypeptide chain is again held by a new tRNA in the P site
- The chain increases in length by one amino acid during each cycle
- At the beginning of the first elongation cycle, the P site is occupied by a charged tRNA with methionine attached to it
The E and A sites are empty
o A tRNA with a new amino acid enters the empty A site with an anticodon complementary to the codon exposed in the A site
o Peptidyl transferase in the large subunit catalyzes the formation of a peptide bond between the two amino acids attached to the two tRNAs held in the P and A sites
Catalyst is a catalytic rRNA, a ribozyme
o The tRNA in the P site releases its attachment to its amino acid, resulting in the growing polypeptide now being held by the tRNA in the A site
o The ribosome now translocates along the mRNA a distance of three nucleotides in the 5’ to 3’ direction
o This shifts the uncharged tRNA in P site into the E site and the charged tRNA in the A site into the P site, leaving the A site empty
o The uncharged tRNA in the E site exits the ribosome
o Empty A site is now ready to receive a new tRNA bringing in the next amino acid to be added to the polypeptide chain
o This ends of one elongation cycle, with the new polypeptide chain again held by a new tRNA in the P site
o This elongation cycle is repeated over and over, growing the polypeptide chain one amino acid at a time
Define probionts
Aggregate of abiotically produced organic molecules surrounded by non unit membrane
Describe an autotroph
An organism that can produce its own food using light, water, carbon dioxide, or other chemicals
Define panspermia
The theory that life on the earth originated from microorganisms or chemical precursors of life present in outer space and able to initiate life on reaching a suitable environment.
Define extremophile
a microorganism, especially an archaean, that lives in conditions of extreme temperature, acidity, alkalinity, or chemical concentration.
Define astrobiology
The branch of biology concerned with the study of life on earth and in space
Describe symbiosis
Symbiosis in which one of the symbiotic organisms lives inside the other
Define symbiosis
Symbiosis is any type of a close and long-term biological interaction between two different biological organisms
Define genome
A genome is the complete set of genetic information in an organism.
Describe horizontal gene transfer (HGT).
The mobility of genetic information between unrelated species, known as horizontal gene transfer (HGT), is a dynamic and persistent phenomenon that can have immediate or delayed effects in the recipient host
Describe the endosymbiotic theory of the origin and evolution of mitochondria and chloroplasts.
The Endosymbiotic Theory states that the mitochondria and chloroplast in eukaryotic cells were once aerobic bacteria (prokaryote) that were ingested by a large anaerobic bacteria (prokaryote). The aerobic bacteria were initially free-living prokaryotes, before being ingested by anaerobic bacteria
Describe the lines of evidence that support the endosymbiotic theory of the origin and evolution of mitochondria and chloroplasts.
The fact that they are able to function on their own, but cannot survive outside the cell
Transition state
The hypothetical state that is mid-way between reactants and products, poised at a point where the reaction is as likely to go forward to products as it is to fall back to reactants.
Define cofactor
A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme’s role as a catalyst (a catalyst is a substance that increases the rate of a chemical reaction). Cofactors can be considered “helper molecules” that assist in biochemical transformations.
Describe what occurs when ATP is hydrolyzed (in terms of reactants and energy).
A water molecule binds to the ATP molecule, causing it to break down in a catabolic reaction that separates one of the phosphate groups from the rest of the molecule. This converts the ATP into a molecule of adenosine diphosphate (ADP) and a free phosphate group (Pi)
Describe how cells use ATP to couple reactions.
Cells use ATP to perform work by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions.
Direction of synthesis is in what direction?
The 5’ to 3’ direction
At each replication fork, one strand is synthesized as a continuous strand towards the replication fork alongside the leading strand template. This continuous strand is called the..?
Leading strand
The other strand is synthesized away from the replication fork alongside the lagging strand template in fragments called ______________. Fragments will later be joined together to complete the __________
Okazaki fragments. lagging strand.
Lagging strand is produced by?
Discontinuous synthesis.
Describe the role of DNA polymerase III
- DNA polymerase III removes single-stranded binding proteins and begins to build a daughter strand by adding DNA nucleotides to the daughter strand in the 5’ to 3’ direction
- Sliding clamp holds DNA polymerase onto the template strand
- DNA polymerase III, once attached to primer, synthesizes the leading strand continuously towards the moving replication fork
- On the other side of the replication fork, each RNA primer is synthesized in the opposite direction, away from the replication fork
- DNA polymerase III attaches to a newly synthesized primer and synthesizes DNA away from the replication fork only for a short distance, producing a short piece of new DNA attached to an Okazaki fragment
Describe the role of DNA polymerase III is lagging strand synthesis
- DNA polymerase III must detach from the fragment it’s synthesizing because it encounters the RNA primer of a previously synthesized Okazaki fragment
- It then releases from the fragment it has been synthesizing, leaving an Okazaki fragment in place
- A new primase can then associate with the newly exposed template nucleotides and begins to remove single strand binding proteins and adding RNA nucleotides to the produce a new primer
- A DNA polymerase III has attached to the new primer and begins to complete the new Okazaki fragment
Describe the role of DNA polymerase I
- Attaches to Okazaki fragment 2 at its 3’ end and begins to remove nucleotides on the RNA primer of the fragment 1, replacing the RNA nucleotides with DNA nucleotides in the 5’ to 3’ direction
- When DNA polymerase I encounters the first DNA nucleotide of fragment 1, the enzyme detaches from fragment 2 and leaves
- But, the enzyme leaves a nick in the sugar-phosphate backbone of the lagging strand between the fragments 2 & 1
What is the role of DNA polymerase 1 vs 3?
- DNA polymerase 3 is the main enzyme catalyzing the 5’→3’ polymerization of DNA strand during replication.
- Whereas DNA polymerase 1 is the main enzyme for repair, removal of primers and filling the gaps in the lagging strand.
What is the main difference among mRNA tRNA and rRNA
- mRNA carries the coding instructions of an amino acid sequence of a protein
- tRNA carries specific amino acids to the ribosome to form the polypeptide chain
- rRNA is associated with proteins to form ribosomes.
Where does transcription occur?
- Occurs in the cytoplasm in prokaryotes
- Occurs in the nucleus in eukaryotes
Transcription of a gene occurs in three stages: ?
Initiation, elongation, and termination
Define transcription
The synthesis of an RNA molecule complementary to a portion of a strand of DNA (gene) acting as a template
Which RNA sequence below is complementary to the given DNA sequence 5’TTAAGGCC3’ ?
- Rewrite the DNA sequence so that it is antiparallel to the four options
- Answer: 5’GGCCUUAA3’
Describe the initiation phase of transcription
- Gene consists of a promoter and a transcription unit
- Eukaryotes have a TATA box within their promoter consisting of 30 base pairs of Ts and As upstream from the transcription start point
- The transcription unit is a stretch of DNA used to describe a primary transcript (the RNA molecule). Only one of the transcription unit strands will serve as a template strand for transcription
- First, transcription factor proteins bind to the promoter in the TATA box. Transcription factors recruit the enzyme RNA polymerase to the beginning of the transcription unit
