Bio 121 Exam 2
Trace the steps involved in eukaryotic RNA processing.
1) 5'mRNA capping 2) poly A tail addition and cleavage (3' end processing) 3) Splicing of introns
types of metabolic pathways
1. Catabolic Pathway- release energy by breaking down complex molecules into similar compounds ■ (ex:) cellular respiration, breakdown of glucose in the presence of oxygen○ 2. Anabolic Pathways: consume energy to build complex molecules from simpler ones ■ (ex:) synthesis of a protein for amino acids
What is the net amount of ATP produced during cellular respiration
38 ATP molecules order of cellular respiration: Oxidation of glucose to pyruvate; oxidation of pyruvate; citric acid cycle; oxidative phosphorylation
Explain what a pedigree is and use examples to show how human traits follow Mendelian patterns of inheritance.
A pedigree shows relationships between family members and indicates which individuals have certain genetic pathogenic variants, traits, and diseases within a family as well as vital status. A pedigree can be used to determine disease inheritance patterns within a family.
spontaneous change
A spontaneous reaction is a reaction that occurs in a given set of conditions without intervention. Spontaneous reactions are accompanied by an increase in overall entropy, or disorder A spontaneous process is one that occurs on its own, without any energy input from the outside. For example, a ball will roll down an incline; water will flow downhill; ice will melt into water; radioisotopes will decay; and iron will rust.
Describe the process of secondary endosymbiosis and explain its role in eukaryotic history.
A symbiotic relationship where one organism lives inside the other is known as endosymbiosis. Primary endosymbiosis refers to the original internalization of prokaryotes by an ancestral eukaryotic cell, resulting in the formation of the mitochondria and chloroplasts. Secondary endosymbiosis occurs when a eukaryotic cell engulfs a cell that has already undergone primary endosymbiosis. They have more than two sets of membranes surrounding the chloroplasts.
Laws of Energy Transformation:
An isolated system is unable to exchange energy or matter with its surroundings An open system can transfer energy and matter between the system and its surroundings Thermodynamics- the study of energy transformations ● First Law- energy can be transferred and transformed, but can't be created or destroyed ● Second Law- every energy transfer/transformation increases the entropy of the universe ○ Living cells convert organized forms of energy to heat ○ Spontaneous processes occur without energy input
Describe what evidence a genome provides about evolutionary history
An organism's evolutionary history is documented in its genome Different genes can evolve at different rates, even in the same evolutionary lineage. As a result, molecular trees can represent short or long periods of time, depending on which genes are used.
Compare and contrast asexual and sexual reproduction with respect to inheritance of chromosomes by offspring.
Both result in the making of additional individuals. Asexual reproduction produces genetically identical offspring that inherits all their DNA from a single parent. The offspring of sexual reproduction show family resemblance, but siblings vary because they inherit different combinations of genes from the two parents.
Photosynthesis
Chloroplasts split water into hydrogen and oxygen, incorporating the electrons of hydrogen into sugar molecules. Photosynthesis is a redox process: is oxidized, and is reduced. The light reactions in the thylakoid membranes split water, releasing , producing ATP, and forming NADPH. The Calvin cycle in the stroma forms sugar from , using ATP for energy and NADPH for reducing power.
Discuss Mendel's laws of inheritance in relation to the behavior of chromosomes during meiosis and fertilization
Chromosome Theory of Inheritance: Mendelian genes have specific loci/positions on chromosomes, and chromosomes undergo segregation and independent assortment.
Use examples to show how genetic inheritance patterns can be affected by complete dominance, incomplete dominance, codominance, multiple alleles, pleiotropy, epistasis, and polygenic inheritance.
Complete dominance - phenotypes of the heterozygote and dominant homozygote are identical, the same dominant trait will affect each organism in the same way (ex. D = dark green; d = light green: Dd and DD will both be dark green leaves) Incomplete dominance - phenotype of F1 hybrids is between phenotypes of the two parental varieties (ex. Dd vs dd)Codominance - two dominant alleles affect the phenotype in separate, distinguishable ways (ex. S = smooth leaf; s = textured leaf: DdSs is a dark green smooth leaf) Multiple alleles - Three or more alternative forms of a gene (alleles) that can occupy the same locus. However, only two of the alleles can be present in a single organism. For example, the ABO system of blood groups is controlled by three alleles, only two of which are present in an individual. ADD BLOOD TYPES TO THIS QUIZLET Pleiotropy - When one single gene starts affecting multiple traits of living organisms, this phenomenon is known as pleiotropy. A mutation in a gene can result in pleiotropy. One example of pleiotropy is Marfan syndrome, a human genetic disorder affecting the connective tissues. Epistasis - a gene at one locus alters the phenotypic expression of a gene at a second locus ex. coat color in mice Polygenic inheritance - quantitative characters are those that vary in the population along a continuum; quantitative variation usually indicates polygenic inheritance, an additive effect of two or more genes on a single phenotype; ex: skin color in humans
Describe the structure of DNA and evidence that it is the genetic material.
DNA is a macromolecule consisting of two strands that twist around a common axis in a shape called a double helix. Evidence that it is the genetic material can be found in Hershey and Chase bacteriophage T2 experiments.
explain the structure of a dna molecule
DNA is made of two linked strands that wind around each other to resemble a twisted ladder — a shape known as a double helix. Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate groups. Attached to each sugar is one of four bases: adenine (A), cytosine (C), guanine (G) or thymine (T). DNA: A-T C-G RNA: A-U C-G T-A
List different types of alterations to chromosome number and structure, and explain how they can cause genetic disorders.
Deletions: A portion of the chromosome is missing or deleted. Duplications: A portion of the chromosome is duplicated, resulting in extra genetic material. Translocations: A portion of one chromosome is transferred to another chromosome. There are two main types of translocation. In a reciprocal translocation, segments from two different chromosomes have been exchanged. In a Robertsonian translocation, an entire chromosome has attached to another at the centromere. Inversions: A portion of the chromosome has broken off, turned upside down, and reattached. As a result, the genetic material is inverted. Trisomy: 21 is the duplication of chromosome 21 (three total) causing down syndrome, other examples are in the slides.
gene pairs
Diploid individuals - Genes have pairs of alleles on homologous chromosomes Homozygous - Two identical alleles Heterozygous - Two different alleles
Describe the events of interphase and the M phase.
During interphase, the cell grows and makes a copy of its DNA. During the mitotic (M) phase, the cell separates its DNA into two sets and divides its cytoplasm, forming two new cells.
Describe structural and functional adaptations of prokaryotes.
Earth's first organisms were likely prokaryotes The three most common shapes are spheres (cocci), rods (bacilli), and spirals Prokaryotes include Bacteria and Archaea. A prokaryotic cell consists of a single membrane and therefore, all the reactions occur within the cytoplasm. they are essential decomposers that recycle nutrients, if it wasn't for decomposers like prokaryotes we wouldn't have this cycling
organization of genetic material
Genes -Cells informational units -Made of DNA Chromatin -DNA and protein -Makes up chromosomes (eukaryotes) chromosomes -Allow DNA sorting I-nto daughter cells
gram positive vs gram negative cell wall
Gram-positive bacteria have relatively simple walls composed of a thick layer of peptidoglycan. The walls of gram-negative bacteria have less peptidoglycan and are structurally more complex, with an outer membrane that contains lipopolysaccharides (carbohydrates bonded to lipids). Gram staining is a valuable tool in medicine for quickly determining if a patient's infection is due to gram-negative or to gram-positive bacteria. has a double membrane.
haploid vs diploid cells
Haploid cells contain only one set of Chromosomes (n). Diploid, as the name indicates, contains two sets of chromosomes (2n) IDENTICAL Haploid cells are formed by the process of meiosis. Diploid cells undergo mitosis.
Explain the semi-conservative replication of DNA.
In this model, the two strands of DNA unwind from each other, and each acts as a template for synthesis of a new, complementary strand. This results in two DNA molecules with one original strand and one new strand.
Identify three checkpoints that control the cell cycle and explain how they operate.
Internal Checkpoints During the Cell Cycle: The cell cycle is controlled at three checkpoints. The integrity of the DNA is assessed at the G1 checkpoint. Proper chromosome duplication is assessed at the G2 checkpoint. Attachment of each kinetochore to a spindle fiber is assessed at the M checkpoint.
Types of Energy
Kinetic Energy- energy associated with motion Thermal Energy- kinetic energy associated with random movement of atoms or molecules Potential Energy- energy that matter possesses because of its location or structure Chemical Energy- potential energy available for release in a chemical reaction
Explain Mendel's two laws of inheritance.
Mendel's Laws of Heredity are usually stated as 1) The Law of Segregation: Each inherited trait is defined by a gene pair 2) The Law of Independent Assortment: Genes for different traits are sorted separately from one another so that the inheritance of one trait is not dependent on the inheritance of another.
Describe how mitochondria participate in aerobic respiration.
Mitochondria are organelles whose membranes are specialized for aerobic respiration. The matrix of the mitochondria is the site of Krebs Cycle reactions. The electron transport chain and most ATP synthesis rely on the compartments created by the inner membrane of the mitochondria. everyhting except gylocolsis occurs in the mitochondria
mitosis
Mitosis involves the seperation of chromosomes; once chromosome is duplicated into two, they are called sister chromatids. The chromatids then get split at the opposite ends of the cell; cell divides; each seperated chromatid becomes chromosomes again, all together make chromatin.
Mitosis vs. Meisosis
Mitosis: DNA replication followed by one division, resulting in two identical daughter cells each with 46 chromosomes (2n) Meiosis: DNA replication is followed by two divisions, so that there are four daughter cells with genetic variation, each with 23 chromosomes (n)... these are sex cells which can fuse to form a zygote
Explain how the redox reactions of respiration yield energy by oxidizing organic fuels.
Organic fuel molecules are oxidized during cellular respiration. Respiration, the oxidation of glucose and other molecules in food, is a redox process. In a series of reactions, glucose is oxidized and oxygen is reduced. The electrons lose potential energy along the way, and energy is released. ○ Chemical reactions that transfer electrons between reactants (oxidation- reduction reactions) ■ Oxidation- a substance loses electrons, or is oxidized ■ Reduction- a substrate gains electrons, or is reduced ● Reducing agent- electron donor ● Oxidizing agent- electron receptor ○ In cellular respiration... O2 is reduced Glucose is oxidized
Trace the sequence of events during the light-dependent reactions that convert solar energy to chemical energy.
Photosynthesis Light energy - Is converted to chemical energy (carbohydrates) Hydrogen from water - Reduce carbon Oxygen from water - Is oxidized, forming molecular oxygen In light-dependent reactions, the energy from sunlight is absorbed by chlorophyll and converted into chemical energy in the form of electron carrier molecules like ATP and NADPH. Light energy is harnessed in Photosystems I and II, both of which are present in the thylakoid membranes of chloroplasts.
Identify sources of genetic diversity in prokaryotes.
Rapid reproduction (they don't reproduce sexually), mutation, and genetic recombination promote genetic diversity in prokaryotes
Describe the inheritance patterns displayed by sex-linked genes and the effects of X inactivation in female mammals.
Sex-linked diseases are passed down through families through one of the X or Y chromosomes. X and Y are sex chromosomes. Dominant inheritance occurs when an abnormal gene from one parent causes disease, even though the matching gene from the other parent is normal. The abnormal gene dominates. X-inactivation ensures that females, like males, have one functional copy of the X chromosome in each body cell. Because X-inactivation is random, in normal females the X chromosome inherited from the mother is active in some cells, and the X chromosome inherited from the father is active in other cells. If an X-linked mutation results in the absence of a certain protein, a cell which has inactivated the wild-type, X-chromosome will experience problems from the protein absence, possibly resulting in growth disadvantage of that cell, or even cell death, which will result in selection against mutant cells.
Explain transcription, including a description of important molecules involved in the process.
Synthesizes messenger RNA (mRNA) Transcription is the process in which a gene's DNA sequence is copied (transcribed) to make an RNA molecule. RNA polymerase is the main transcription enzyme. Transcription begins when RNA polymerase binds to a promoter sequence near the beginning of a gene (directly or through helper proteins).
Describe ecological roles played by prokaryotes.
The carbon cycle is maintained by prokaryotes that remove carbon dioxide and return it to the atmosphere. Prokaryotes play a major role in the nitrogen cycle by fixing atomspheric nitrogen into ammonia that plants can use and by converting ammonia into other forms of nitrogen sources
phylogenetic trees
The evolutionary history of a group of organisms can be represented in a branching diagram
Distinguish among the levels of chromatin packing in a eukaryotic chromosome.
The first level of packing is achieved by the winding of DNA around a protein core to produce a "bead-like" structure called a nucleosome. The second level of packing is the coiling of beads in a helical structure called the 30 nm fiber that is found in both interphase chromatin and mitotic chromosomes.
prokaryote structure compared to eukaryotes
The genome of a prokaryote is structurally different from a eukaryotic genome and in most cases has considerably less DNA. Prokaryotes typically have one circular chromosome (Figure 27.9), whereas eukaryotes usually have several to many linear chromosomes. In addition, in prokaryotes the chromosome is associated with many fewer proteins than are the chromosomes of eukaryotes. Also unlike eukaryotes, prokaryotes lack a nucleus; their chromosome is located in the nucleoid, a region of cytoplasm that is not enclosed by a membrane. In addition to its single chromosome, a typical prokaryotic cell may also have much smaller rings of independently replicating DNA molecules called plasmids (see Figure 27.9), most carrying only a few genes.
Explain how linkage of genes and crossing over affect inheritance.
The inheritance of the linked genes takes place during sexual reproduction in the meiosis phase. Linked genes have very few chances of recombination because they do not allow any crossing over. Genetic linkage results in the inheritance of two genes at the same time.
Describe the laws of probability and use them to solve complex genetics problems.
The law of probability tells us about the probability of specific events occurring. The law of large numbers states that the more trials you have in an experiment, then the closer you get to an accurate probability.
Explain how the light-independent reactions use the chemical energy stored during the light-dependent reactions to fix carbon.
The light-independent reactions (Calvin cycle) use stored chemical energy from the light-dependent reactions to "fix" CO2 and create a product that can be converted into glucose. The ultimate goal of the light-independent reactions (or Calvin cycle) is to assemble a molecule of glucose.
Explain the alternation of fertilization and meiosis in different types of sexual life cycles, using the terms haploid, diploid, and zygote.
The process of meiosis produces unique reproductive cells called gametes, which have half the number of chromosomes as the parent cell. Fertilization, the fusion of haploid gametes from two individuals, restores the diploid condition. Thus, sexually reproducing organisms alternate between haploid and diploid stages. The fertilized egg, which has one set of chromosomes from each parent, is the zygote.
Identify the ways in which sexual life cycles generate genetic variation that contributes to evolution.
The three main sources of genetic variation arising from sexual reproduction are: Crossing over (in prophase I) Random assortment of chromosomes (in metaphase I) Random fusion of gametes from different parents.
energy coupling
The use of an exergonic process to drive an endergonic one. the hydrolysis of ATP - the reaction of ATP and water yields the inorganic phosphate and ADP and releases energy
Trace the pathway of glucose oxidation during glycolysis
The word glycolysis means "sugar splitting," and that is exactly what happens during this pathway. Glucose, a six-carbon sugar, is split into two three-carbon sugars. These smaller sugars are then oxidized and their remaining atoms rearranged to form two molecules of pyruvate. (Pyruvate is the ionized form of pyruvic acid.) occurs in the cytosol
How are multiple polypeptides made in bacteria and in eukaryotes?
This occurs when multiple ribosomes translate a single mRNA simultaneously- forms polyribosome/ polysome. Polyribosomes allow many polypeptides to be synthesized simultaneously, which makes the process more efficient. In bacteria, transcription and translation are coupled to make the process more streamlined, while in eukaryotes the two processes are separated by the nuclear envelope.
List the cellular components and molecules involved in translation, and describe the process
Translation involves "decoding" a messenger RNA (mRNA) and using its information to build a polypeptide, or chain of amino acids. Initiation ("beginning"): in this stage, the ribosome gets together with the mRNA and the first tRNA so translation can begin. Elongation ("middle"): in this stage, amino acids are brought to the ribosome by tRNAs and linked together to form a chain. Termination ("end"): in the last stage, the finished polypeptide is released to go and do its job in the cell.
change in free energy
a measure of energy that is available to do work. The free energy of a system changes during energy transfers such as chemical reactions, and this change is referred to as ΔG The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously We can think of free energy as a measure of a system's instability—its tendency to change to a more stable state. Unstable systems (higher G) tend to change in such a way that they become more stable (lower G).
shared ancestral vs derived character
ancestral - a character that originated in an ancestor of the taxon (any unit used in the science of biological classification) derived - an evolutionary novelty unique to a clade (a branch that includes a single common ancestor and all of its descendants)
enzymes
biological catalyst - increases speed of a chemical reaction w/o being consumed enzymes lower activation energy
how do enzymes speed up metabolic reactions
by lowering the activation energy
exergonic vs endergonic reactions
exergonic - energy is released, spontaneous endergonic - energy is required (it absorbs energy from its surroundings bc this kind of energy stores free energy in molecules), non spontaneous ATP links exergonic and endergonic reactions
what are the first two laws of thermodynamics and explain how they relate to biological systems
first law of thermodynamics - energy cannot be created nor destroyed but can be transferred and changed in form (conservation of energy) second law - when energy is transferred, there will be less energy available at the end of the transfer process than at the beginning. Due to entropy, which is the measure of disorder in a closed system, all of the available energy will not be useful to the organism. organisms that follow laws of thermodynamics are open systems and they use energy from surroundings to do work
Describe the possible structure of the tree of all life.
made up of bacteria, archea, and eukaryota
Describe how regulation of enzyme activity helps control metabolism
metabolism is the sum of all the chemical reactions that take place in an organism that includes catabolism (break down complex molecules in to simpler molecules while harvesting their energy and storing it usually as ATP, exergonic) and anabolism (build more complex molecules from simpler molecules) the energy acquired through catabolic processes is used to drive anabolic processes enzymes speed up metabolic reactions by lowering energy barriers
Give examples of beneficial and harmful effects that prokaryotes have on humans.
mutualistic bacteria - ? Pathogenic bacteria - cause abt half of all human diseases (i.e. lyme disease, ecoli) antibiotics - saved many lives and reduced the incidence of disease caused by pathogenic bacteria
Identify major phylogenetic groups of prokaryotes
proteobacteria, chlamydias, spirochetes, cyanobacteria, and gram-positive bacteria.
Identify and describe the closest eukaryotic relatives of fungi and animals.
protists - is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus.
identify different types of mutations and how they can affect protein structure and function
substitutions - replacement of one nucleotide and its partner with another pair of nucleotides Some substitutions have no effect on the encoded protein, owing to the redundancy of the genetic code. insertions deletions frameshift mutation - MOST IMPACTFUL occurs whenever the number of nucleotides inserted or deleted is not a multiple of three. All nucleotides downstream of the deletion or insertion will be improperly grouped into codons; the result will be extensive missense mutations, usually ending sooner or later in a nonsense mutation that leads to premature termination. Unless the frameshift is very near the end of the gene, the protein is almost certain to be nonfunctional
Give examples of ecological roles played by protists.
symbiotic protists - protists that live with other larger organisms in a mutually beneficial relationship (i.e. coral reefs diversity ultimately depends on corals and on the mutualistic protist that nourish them) photosynthetic protists - important producers, organisms that use energy from light to convert to organic compounds. (i.e. when fertilizer is applied to a field, some of the fertilizer may be washed by rainfall into a river that drains into a lake or ocean. When people add nutrients to aquatic communities in this or other ways, the abundance of photosynthetic protists can increase spectacularly. Such increases can have major ecological consequences, including the formation of large "dead zones" in marine ecosystems) Some bacteria produce antibiotics Some bacteria used to produce food items Like cheeses and other fermented products Some bacteria used to produce insulin and other hormone treatments
genome
the haploid set of chromosomes in a gamete or microorganism, or in each cell of a multicellular organism. all of the genetic material in an organism
Describe evidence that helped us understand the process of gene expression, and describe the process.
the process by which DNA directs protein synthesis includes transcription and translation Gene expression is the process by which information encoded in a gene leads to the production of a protein. The gene expression measure at any given time is indicative of the state of the system at that time. When a gene is expressed, it allows the cell to take part in a certain function or mechanism.
Free Energy-
○ (of a living system) energy that can do work when temperature and pressure are uniform ○ Change in free energy is represented as ΔG ○ ΔG=ΔH-TΔS ■ [change in energy equals change in total energy minus temperature times changed in enthalpy] ○ A measure of a system's instability, its tendency to change to a more stable state ■ During spontaneous change, free energy decreases and stability increases
Cellular Respiration Stages-
○ 1. Glycolysis- breaks down glucose into two molecules of pyruvate ○ 2. Citric Acid Cycle- completes the breakdown of glucose ○ 3. Oxidative Phosphorylation- accounts for most of ATP synthesis
Photosynthesis Logistics
○ 1. Mesophyll- the interior tissue of the leaf where chloroplasts are mainly formed ○ 2. Stomata- microscopic pores in the leaf through which CO2 enters and O2 exits ○ 3. Stroma- a dense fluid surrounded by an envelope of two membranes of a chloroplast ○ 4. Thylakoid- connected sacs in the chloroplast that compose a third membrane system ○ 5. Chlorophyll- pigment that gives leaves their green color (in the thylakoid membranes)
Enzyme Function
○ Catalysis- enzymes or other catalysts speed up specific reactions by lowering the activation energy barrier ○ Substrate- the reactant that an enzyme acts on ■ When an enzyme binds to a substrate, the enzyme-substrate complex is formed, and substrate is converted to product
