Biology: a Review

Genetics and Inheritance

1. What is the definition of a gene? 

A portion of DNA that codes for a protein. 

2. What makes up a gene?

Nitrogenous bases, ATGC. 

3. What is the product of a gene?

A protein that expresses an organism’s characteristics or traits. 

4. What is an allele?

Different versions of a gene due to slight changes in DNA sequencing. 

5. Are there only two possible alleles for each gene? (no! think about all the different colors of hair there are in humans)

No there is not, there can be many different alleles as many people have different characteristics. 

6. Why do diploid individuals have two possible alleles for each gene (think homologous chromosomes)

Because they inherit one copy of each gene from each parent. 

7. What does it mean to be homozygous or heterozygous?

Homozygous: both alleles are the same

Heterozygous: alleles are different

8. What is a genotype? A phenotype?

Genotype: genetic makeup of an individual or gamete, and written in pairs for a diploid organism. 

Phenotype is the physical expression of that genotype. 

9. How are new alleles generated? What kinds of mutations are possible?

New alleles are generated by mutations. Possible mutations are:

Deletion: one nucleotide is removed from the sequence. 

Substitutions: one nucleotide is replaced by another, changing the amino acid encoded. 

Insertions: an extra nucleotide is added to the sequence which alters how it is read. 

10. How does a mutation in the DNA actually make a change in the protein it produces?

Changes the resulting mRNA which encodes for a specific protein. If changed, the produced protein will have a different function. 

11. What is a dominant allele? A recessive?

Dominant: alleles that exert their effects when present. 

Recessive: alleles whose effect is masked if dominant allele is present. “Underdog allele” 

12. Is a dominant allele better than a recessive one?

No, a dominant allele shows up in the phenotype if present while the recessive allele can be masked. 

13. What are the forms of allele interactions? What is the result of phenotypes under these interaction types?

1. Complete dominance: when a single dominant allele determines the phenotype and only the absence of a dominant allows the recessive phenotype to show (Mendel’s pea plant, purple flower is completely dominant over white).
2. Incomplete dominance: neither allele is completely dominant, and the resulting phenotype is a blend of both possible genotypes (in snapdragons, a red flowered plant crossed with a white plant produces a pink plant).  
3. Codominance: both alleles are expressed simultaneously (ABO blood groups, A and B alleles are expressed in AB blood type). 

Some traits are controlled by a single gene, some are controlled by multiple genes (polygenic traits). Some single genes have multiple impacts on phenotype.

14. How do genotypes relate to meiosis? Can you relate the letter of the genotype to a chromosome? Think about how chromosomes are sorted and divided during meiosis and end up in different gametes. These gametes then pair during fertilization to form the zygote (the new diploid individual).

During meiosis, the process that makes gametes, the chromosome pairs are separated so that each gamete gets only one chromosome, therefore one allele for each gene. Genotypes are a combination of alleles as you get one allele from each parent for a gene.

15. Can you explain what Mendel’s laws of inheritance mean?

Explains how traits are passed from parents to offspring. 

1. The law of segregation of alleles: for each trait an individual inherits two alleles, one from each parent. During meiosis, these alleles separate for each gamete carries only one allele for that trait, ensuring the offspring inherits one allele from each parent. 
2. The law of independent assortment: traits are inherited independently from each other. Color of pea seeds is inherited separately from the shape of their seeds. 

16. How are Punnett squares used? 

They are used to determine all of the possible combinations of gametes that can result from the mating of two organisms.

17. Can you draw and complete a punnett square and determine the genotypic and phenotypic ratios of the possible offspring?

Evolution

1. What is the definition of evolution?

Genetic change over time – change in allele frequency in a population over time. 

2. What does allele frequency mean?

How often a specific variant of a gene (an allele) appears in a population. 

3. Do individuals evolve?

No, as an individual’s alleles do not change, only happen in a population (an interbreeding group of organisms of the same species – i.e. Darwin’s Finches) 

4. Does a change in phenotype in a population always mean that a population has evolved?

No it does not, as they can also be caused by environmental factors. 

5. Does evolution provide what an organism needs to survive?

No it does not directly provide what an organism needs, instead, it selects traits that enhance an organism’s ability to survive. 

6. What is a habitat? A niche?

Habitat: The type of natural environment that a species lives in. Made up of both abiotic (physical features, landscape, temp, rainfall) and biotic (biological features, prey, predators, competitors) factors.

Niche: how a species utilizes the space – the role they play in a habitat, including location and resources used.  

7. What happens when two species occupy the same niche?

They compete for the same resources which will lead to one outcompeting the other and eliminating the competition. However, it could also be possible that each species evolves different strategies to use the same resources. 

8. What does fitness mean in regards to evolution?

An organism that has successful traits that allow them to gather resources better than others. This allows them to survive and pass those traits on to the next generation…how well an organism is able to reproduce. 

9. Does evolution provide new alleles? What does?

Evolution doesn’t necessarily provide new alleles. Instead, mutation is the primary contributor to new allele formations. 

Selection

1. Natural selection is a force for?

Adaptive change (modifications in an organism) in populations. 

2. Natural selection provides a major driving force for evolution, can you explain what each facet of natural selection means?

1. There is variation in the population: individuals within a species have different traits (physical, behavioral, or physiological) and these arise from genetic differences caused by mutations. 
2. That variation is heritable: variation/traits can be passed down from parent to offspring. 
3. There is overproduction of offspring: more species produce more offspring than can survive to maturity. This creates competition for limited resources like food, shelter, and mates. 
4. There is differential survival of offspring: due to this overproduction of offspring, only some individuals will survive and reproduce. Those with traits that give them a better chance at survival will reproduce, leading to a gradual change in alleles/traits over time. 

3. What does “survival of the fittest” mean? What is evolutionary fitness?

Organisms with traits better suited to their environment are more likely to survive and reproduce. 

4. Explain how natural selection determines who survives to reproduce and who does not.

Natural selection favors individuals with traits that enhance their ability to thrive and reproduce in a specific environment. These traits are then passed onto offspring. 

5. What are factors in the environment, abiotic/biotic, that produce selective pressure on organisms

Abiotic: changes in the environment – temperatures, water availability, sunlight. 

Biotic: available food, surrounding competitors, potential predators or pathogens. 

6. Can you explain what genetic/phenotypic variation means in a population?

Genetic variation: changes in DNA/alleles among individuals

Phenotypic variation: physical result of genetic differences, and can be advantageous or disadvantageous depending on environment or situation. 

7. Can you explain the different types of selection and their impacts?

1. Directional selection: selection favors one extreme of a trait, moving the average trait in one direction. If faster cheetahs catch more food and survive better, then over time, cheetahs in the population will become faster. 
2. Stabilizing selection: favoring the middle or average trait, selecting against the extremes, making the population uniform and decreasing variation around the average. Human babies with average birth weights survive more than very small or very large babies. 
3. Disruptive selection: Favors both extremes, but not the average. So the population splits, forming two new groups over time.  In a place where both black and white rabbits hide well (shadows and snow), but gray rabbits stand out, the black and white rabbits survive better. 

8. Why do some extreme phenotypes persist in a population even if they might get an organism killed?

Sexual selection: traits are favored because they help an individual attract mates, even if they don’t help with survival. Leading to flashy, exaggerated traits, especially in males, and can cause sexual dimorphism – differences between male and females. A peacock’s bright feathers make it more visible to predators, but females prefer colorful males, so those males reproduce more.

9. Can you explain how the other forces that drive evolution work?
10. Genetic drift – random events result in non-adaptive change in populations – most effective in small populations

• What does it mean to “fix” or “lose” an allele in a population? 

Lost allele: The complete disappearance of an allele from a population. 

Fixed allele: everyone in the population has the same allele as its the only version left. 

• Bottlenecks: when a large population is suddenly reduced in size due to natural disaster, disease, hunting, etc. New population has reduced genetic variation and there’s different allele frequencies. 

• Founder effect: when a small group of individuals breaks off from a larger population to start a new population in a new place. Lower genetic diversity going forward. 

• Why does the size of a population matter in relation to genetic drift?

Smaller populations feel the change more profoundly than larger populations. 

2. Gene flow: the movement of alleles from one population to another. 

• Does migration impact genetic variation?

Yes, by moving individuals and their genetic material between populations, it can introduce new alleles, alter frequencies, and reduce genetic differences between populations. 

• How are the two populations changed as a result of individuals moving from one to another?

When individuals move from one population to another they bring their alleles with them.

• Do differences in the population decrease as migration increases?

Yes, the more individuals move the more similar their gene pools become. 

• What will influence the rate of gene flow?

Distance, barriers (mountains, rivers, human-made structures), mobility (how well they travel), mating behavior, human activity (habitat destruction or moving species). 

3. Mutation

• Is this a good thing, bad thing, neutral?

Good because it generates diversity, which allows for evolution to occur. This is how new alleles are added to a population!

Species/Speciation/Extinction

1. Define a species using the biological species concept.

Individuals are members of the same species if, 

1. They can interbreed in nature: mate with each other naturally. 
2. They can produce viable and fertile offspring: healthy babies that can grow up and have their own.
3. They cannot produce viable and fertile offspring with members of other species: if they try to mate with different species, it doesn’t work – no baby or infertile baby. 

2. The impact of reproductive isolation on a population:

Drives the evolution of new species as they can no longer mate and produce fertile offspring with each other. It stops the gene flow between groups of organisms – causing them to evolve separately – leads to differences over time as each group adapts to its own environment or mutations – which leads to speciation (two separate species). 

3. Define and provide examples of prezygotic and postzygotic barriers to reproduction

• Those things that can prevent reproduction between two populations before mating and after mating

Prezygotic barriers: 

1. Geographical isolation: breed in different habitats
2. Temporal isolation: breed at different times 
3. Behavioral isolation: courtship displays differ
4. Mechanical isolation: incompatible sexual organs
5. Gametic barrier: incompatible egg & sperm

Postzygotic barriers: 

1. Hybrid Viability: offspring do not develop normally and die as embryos. 
2. Hybrid Sterility: offspring mature but are sterile as adults. 

4. How evolution impacts speciation – discuss how two populations that are separated from one another build up changes to their genetics in different ways and eventually form two species. 

Evolution drives speciation by causing genetic changes in population that become separated from one another. When two groups of the same species are isolated–whether by geography, behavior, or timing–they stop exchanging genes. Without gene flow, each population begins to evolve independently. Natural selection may favor genetic drift and also cause unique changes in their DNA over time. As these genetic differences build up, the two groups become more and more distinct. Eventually, they become so different that they can no longer interbreed and produce fertile offspring, even if they come back into contact. At that point, they are considered separate species–this is the process of speciation. 

5. Be able to discuss how sexual selection and habitat differentiation can allow speciation when two populations are still inhabiting the same spaces. 

In sexual selection, individuals choose mates based on specific traits which can lead to certain traits becoming more common in one group rather than the other. Over time, if individuals prefer mates with certain features, this can reduce mating between groups with different preferences, eventually leading to reproductive isolation. 

In habitat differentiation if certain individuals start using different parts of the environment then they can become ecologically separated and over time, genetic differences build up.  

6. Discuss how disruptive selection can lead to speciation. 

Because disruptive selection favors individuals at both ends of the extreme of a trait, then individuals with average traits will have lower survival/reproduction rates, while individuals with the extreme trait will do better. Over time this will lead to two distinct groups, each adapted to different conditions or niches. 

7. Define extinction.

When all members of a species have died. 

8. What natural forces cause extinctions?

Plate tectonic movements, Geologic activity, climate shifts. 

9. How are humans responsible for extinction?

causing habitat loss and fragmentation, creating pollution, introducing non native species, overharvesting, indirectly affecting climate shifts. 

Adaptation

1. Define adaptation by discussing how organisms are shaped by evolution to be “fit” or adapted to their particular environment

Adaptation is the process by which organisms become better suited to their environment through evolution. Traits that help them survive and reproduce become more common over generations, making the species more “fit” for its surroundings. 

2. Be able to provide some examples of the factors that are selective pressures that can change a population.

Predators (favoring better camouflage or speed)

climate (favoring heat or cold tolerance)

availability of food (favoring certain feeding traits)

diseases or parasites (favoring immune strength)

competition for mates (leading to traits favored by sexual selection).  

3. Discuss how adaptations can make changes to the physical body, behavior, and physiology/biochemistry of an organism and have examples ready. 

All to improve survival or reproduction in one’s environment. 

Physical: changes in body structure – long neck of a giraffe for reaching high leaves. 

Behavioral: changes in action or habitats – desert animals are more active in the morning and evening due to intense heat during the day. 

Physiological/biochemical: internal body functions and changes to survive harsh environments – hummingbirds enter torpor at night, or long-term torpor such as hibernation for bears. 

4. Remember that adaptation is a result of natural selection, those individuals with the traits or alleles that allow them to survive – are the ones that reproduce while others die off

• NO ADAPTATIONS ARE BECAUSE AN ORGANISM NEEDS SOMETHING

5. Be able to describe the process of how a population changes over time to incorporate a new body plan, behavior, physiology into the entire population. 

Natural selection is the process by which a population changes over time. It starts when a random mutation causes a new trait, like a change in body shape, behavior, or physiology, that gives some individuals an advantage over others. These individuals are more likely to pass on their trait to the next generation. Over time these traits that allow organisms to survive and reproduce become more widespread and fixed. 

6. Know the difference between adaptation and acclimation

Adaptation is long-term genetic change in a population over generations

Acclimation is a short-term, reversible response by an individual to environmental changes. 

7. Be able to explain the concept of an ecological niche – how an organism fills a very specific role in the environment. 

An ecological niche is when an organism fills a specific role in the environment, including how it gets food, interacts with other species and survives in its habitat. It’s an organism’s “job” in the ecosystem, shaped by its behavior, diet and physical needs. 

8. HOW DID WE END UP WITH SO MANY DIFFERENT KINDS OF BEARS!?

Evolution and adaptation. Millions of years ago bears had a common ancestor, but as the early bears spread across different parts of the world, they encountered different environments that required them to adapt to survive. 

Populations

1. What is a population?

An interbreeding group of organisms of the same species occupying the same location.

2. 1) Discuss how populations change in number over time, how individuals are added and removed, what may drive organisms into or out of a population? 2) Define carrying capacity and be able to describe how it limits population growth

1. Population change in number either by adding individuals through birth or immigration, or removing individuals by death or emigration. A major driver of these changes is access to resources, including food, water, shelter, and mates. A smaller population may have more abundant resources allowing for exponential growth of a population, while larger populations lack access to resources and experience a decline in population. 
2. While this may seem great for the small population, the environment still has a carrying capacity. A carrying capacity is the maximum abundance of a species population that a habitat or ecosystem has the resources to support. This can limit the growth of a population because once a habitat or ecosystem reaches this carrying capacity, resources become scarce. 

3. How do available resources impact a population? When resources become limited, what are the effects?

Impacts a population because they determine how many individuals can survive and reproduce in an environment. As a population increases in size, it can become density-dependent, meaning that factors like competition for resources, disease spread, and predation become more significant and can slow down the growth rate or reduce population size. When resources become limited it can increase:

• Competition: individuals compete for more food, shelter, and mates. 
• Territoriality: animals become more aggressive in defending their territories to ensure access to limited resources. 
• Reproduction: reduce the ability of individuals to reproduce as energy is diverted towards survival rather than mating. 
• Predation: in a crowded population with less resources, predators may have an easier time finding and capturing prey. 
• Disease: overcrowding – increases the likelihood of disease transmission among individuals. 

Life Histories

1. Be able to define fitness in terms of reproductive success

Fitness in terms of reproductive success refers to an organism’s ability to survive, reproduce and pass its genes to the next generation. The more offspring an organism produces that survives to reproduce themselves, the higher its fitness. 

2. Recall the allocation of consumed energy

C = P + R + (U + F)

Consumption = production + respiration (metabolism) + (U+F) – waste – urea & feces. 

3. What is the energy available for growth/survival or reproduction of an organism? Be ready with an example of these tradeoffs that we have discussed

The production value (P) is the energy available for the growth/survival of the organism OR reproduction. More energy used for producing offspring can decrease organism size or survival, etc. In female deer there is a reproductive trade-off between having offspring and long-term survival. A graph from class showed that reproductive females had a higher mortality rate as they aged, likely because pregnancy, nursing, and protecting young used up more energy and exposed them to risk. While the non-reproductive females  showed lower mortality rates until they reached an old age, since they didn’t expand energy raising and taking care of young, highlighting the investment of energy in reproduction can reduce an individual’s chance of survival. 

Communities

1. What is community structure? 

The ways animal and plant species living together in a shared habitat interact with one another directly and indirectly. 

2. Why is diversity of organisms in a community important?

Because they contribute to the overall health and stability of an environment. 

3. Be able to define the niche of an organism and explain how a species fits this role. 

Niche of an organism is the role it plays in the ecosystem. In a community structure, this maintains balance, like bees pollinating flowers while feeding on nectar. 

Fundamental niche – full range of environmental conditions and resources a species could potentially occupy and use. 

Realized niche: part of the fundamental niche a species actually occupies and uses. 

4. Explain how small differences between species allow them to access different parts of the environment they live in.

Like Darwin, finches, differences between species–beak size–allow them to use different resources or parts of the environment, reducing competition. Larger beaks can eat larger nuts while smaller beaks eat smaller nuts.

5. Be able to define and provide examples of how competition between species results in competitive exclusion

Competitive exclusion is when species compete to occupy the same ecological niches. This occurs with two species of Paramecium. When separate, both species thrives, however when grown together one always outcompeted the other, eliminating the second species. 

6. Be able to define all of the types of interactions that we discussed in class, explain the effect on each species, and examples of how they work: in addition to the terms and factors within each as shown below. 
7. Competition (-/-)

Intraspecific competition, Interspecific competition: 

Intra = competition within a species, Inter = competition between species. 

Competitive exclusion: when two species occupy the same ecological niche cannot stably coexist. 

Resource partitioning: when species share the same habitat and have similar resource needs access resources in slightly different ways – reduces likelihood of direct competition between species. 

2. Predation (+predator/-prey)

Specialists and generalists, pros and cons:

Specialists: use a narrow range of food resources. While specialized food adaptations make efficiency high, there are no alternatives to target prey. 

Generalists: use a broad range of rood resources. While individuals can target food as it fluctuates and a preferred food item can be used while abundant, lower energy foods might be ignored until abundances become low and ultimately feeding efficiency is low. 

How predation impacts population dynamics between predator and prey: When prey population increases, predators have more food so their numbers also increase. But as they rise and eat prey–lowering their numbers–predator numbers also lower. 

Predator and prey co-evolution: can result in “evolutionary arms race” – continuous cycles of adaptations and counter-adaptions between predator and prey. As predators evolve more effective hunting strategies, prey species concurrently develop enhanced defensive mechanisms. 

Traits that predators and prey each possesses:

Predator: claws, teeth, stingers, poisons. 

Prey defense mechanisms:

1. Behavioral: self defense, hiding, fleeing, forming schools, alarm calls
2. Morphological: cryptic coloration (camouflage), aposematic coloration (bright warning colors), mimicry (mimicking appearance of another – batesian mimicry (harmless species mimic appearance of harmful), mullerian mimicry (two or more unpalatable or harmful species mimic the appearance of one another. 

Herbivory:

Impacts on plants/environment 

Plant responses to herbivores:

1. Resistance: the ability of a plant to avoid being eaten. 

Morphological – spikes, needles, tough bark

Chemical – nicotine, caffeine, pine resins

2. Tolerance: the ability to minimize reduction in fitness due to herbivory. 

Growth/reproduction increase to reduce impacts from herbivores in the future

3. Mutualism (+/+): interspecific interaction in which both species benefit. 

Facultative vs obligate mutualists: interaction is not crucial for survival vs. interaction is crucial for survival. 

4. Commensalism (+/0): interaction in which one species benefits and the other is neither helped nor harmed 
5. Parasitism (+/-): one organism derives nourishment from another organism which is harmed in the process. 

Endoparasite – lives within the body of their host

Ectoparasite – parasites that live on the external surface. 

6. Amensalism (-/0): one species is harmed and the other species is neither helped nor harmed. 
7. Altruism (-/+): an interaction in which one organism decreases their own fitness to increase the fitness of another. They do this to help their own species survive and live. 

DNA

1. What is the function of DNA? Why does it need to be replicated before cell division?

DNA stores and transmits genetic information, acting as a blueprint for synthesis of proteins. Needs to be replicated to ensure that each new daughter cell receives an exact copy of the genetic material. 

2. What is a gene?

Small region of a chromosome that contains DNA that encodes a specific protein. 

3. Can you explain the process of transcription? Initiation, elongation, termination.

Initiation: Enzyme RNA Polymerase finds the promoter (specific gene region for a protein), binds to it, melts the DNA (breaking apart base pairs) and then reads template strand. 

Elongation: RNA polymerase moves along the genes in 5’to 3’ direction, recognizing base paris in template strand, and matches them up, building the molecule. 

Termination:  RNA polymerase reaches the end of the gene called the terminator, separates from DNA and mRNA drops off. 

4. Where is transcription happening in the cell?

Nucleus. 

5. How does RNA polymerase find the start of the gene?

By finding the promoter. 

6. What is the difference between the template strand and the non-template strand?

Template strand is a DNA strand that is used as the template for RNA synthesis. Non-Template strand is the complementary strand that has the same sequence as the resulting RNA, minus T for U.  

7. What is complementary base pairing? How is it used by RNA polymerase to make the mRNA strand?

Specific pairing of nitrogenous bases through hydrogen bonds. RNA polymerase matches the sequence of the template DNA strand with complementary RNA nucleotides. 

8. Can you explain the process of translation?

Translation takes the amino acid sequence and produces the proteins the sequence codes for. 

9. Where is it happening in the cell?

Ribosomes. 

10. What is a codon? What does a codon code for?

Codon is a set of three nucleotides of mRNA that encodes one amino acid 

Anticodon is a three nucleotide sequence in tRNA that is complementary to mRNA codon, building the amino acids. 

11. What is tRNA? What is on one end and what is on the other?

Transfer RNA: connector molecules that carry each amino acid to the correct spot along the mRNA molecule, recognizing and translating what the mRNA is calling for. Has an anticodon at 5’ end and the resulting specific amino acid at the 3’ end. 

12. Can you describe the process of translation as it continues from initiation, elongation, termination?

 Initiation: starting codon of the mRNA calls the small ribosomal subunit to bind to the start, where tRNA will arrive with the first amino acid nucleotide. This brings in the large ribosomal subunit that encloses the entire process. 

Elongation: more tRNA arrives with following amino acids, matching the codons of the mRNA, moving linearly down the line from 5 end to 3 end and are joined together in a peptide bond as more amino acids arrive. 

Termination: the ribosome will reach the stop codon at the end of the mRNA and a protein called the release factor binds to the stop codon. Since no more are being created the polypeptide will detach front the mRNA and fold into a functional protein. 

13. Can you explain why the order of the nucleotides in the mRNA is important to the protein it codes for?

It dictats the sequence of amino acids in the proteins, which then determine the proteins structure and function. mRNA is created to code for specific proteins your body is in need of so it is important those codes are right. 

Respiration

1. What is the general chemical formula for respiration? What are the reactants and what are the products?

C6H12O6 + 6O2 —> 6CO2 +6H2O + ATP

Reactants: C6H12O6 + 6O

Products:  6CO2 +6H2O +ATP

2. Can you outline the general process of the following by mentioning the starting and  ending materials, energy consumed or generated, and overall function?

I. Glycolysis: Metabolic pathway that converts glucose into pyruvate, generating electron carriers and energy. Starts with 6 carbon glucose, burning two ATP to form 3 carbon molecules. High energy electrons are then pulled from 3 carbon molecules by two NAD+ to form two NADH. Two ADP molecules are then converted into two ATP molecules. Two 3 carbon molecules of Pyruvate are left, which will be used in the Kreb cycle. Ending products are 2 ATP, 2 NADH, 2 Pyruvate. 

II. Kreb’s cycle: Generate energy in the form of high-electron carriers like NADH and FADH2, used in ETC to produce ATP. Starts with two 3-carbon molecule pyruvate and undergoes 7 chemical reformations, before starting the cycle over again. Three phases of the cycle: Preparation, Oxidation, and Regeneration. Ending products are 2 ATP, 2 FADH2 8 NADH, 6 CO2. 

• Phase one: The carbon-carbon bonds are broken, losing electrons to NAD+ to create NADH, releasing CO2, and leaving a 2 carbon molecule CoA behind. The ending product of oxaloacetate (5C) combines with CoA (2C) molecule to form a Citrate (6C). Phase two: citrate is then chemically rearranged into isocitrate, NAD+ is added to break c-c bond, releasing CO2 in the process and creating NADH. Now a 5C molecule goes through the process again, losing electrons and carbon to CO2. ADP joins to create ATP. A 4C molecule is left. Two chemical reactions take place, one with FAD – FADH2, and then another NAD+ – NADH. Left product is oxaloacetate which is used to combine with a CoA to begin the process over again. 

III. Electron transport chain: transfer energy from electron carriers to eventually generate more ATP molecules. NADH and FADH2 are oxidized to release electrons by protein complexes. Electrons will then gather to a central pool in the UQ, which shuttles electrons between hydrogen ion pumps. Hydrogen ions are gathered by complexes and pushed through protein complexes into the intermembrane, using energy from high energy electrons. NADH and FADH2 will return to NAD+ and FAD which can then return to grab more electrons. The higher concentration gradients of H+ ions in the intermembrane are then used in ATP Synthase enzymes to generate ATP, as they push them to their lower gradient in the mitochondrial matrix. Ending results are 28 ATP molecules. 

3. What are cells doing with the energy they produce? Where are they getting the carbon skeletons to build other molecules? What other molecules can be made with carbon skeletons?

Energy produced is used to complete and perform all other biochemical processes. 

Carbon skeletons are taken from the Kreb Cycle as carbon atoms are rearranged and used in different ways. These breakdowns of carbon compounds can produce intermediates which can then be repurposed into other important biomolecules for various metabolic needs. Such as, Hexose (6C molecule) used in cellulose, Pentose (5C molecule) used to form nucleotides, ATP and electron carriers, or various 3C and 4C molecules which are used to generate amino acids, lipids, and nitrogen carriers. 

4. When energy is released from breaking carbon-carbon bonds, in what forms do cells capture that energy?

NADH 

5. Is glucose the only molecule that can be broken down for energy in cellular respiration? Where in the process do fats/fatty acids or protein/amino acids come in to be broken down?

No it is not the only molecule that can be broken down. Lipids and Proteins can be converted into molecules that can be integrated into metabolic pathways as in the Krebs cycle, carbon compounds can leave to build biomolecules necessary for cell function, and new compounds must take their places. Lipids and Proteins can be broken down into fatty acids and amino acids which then are processed to produced CoA, essential molecule enters the Krebs cycle. 

Photosynthesis – Light reactions and carbon reactions

1. What is the general chemical formula for photosynthesis? What are the reactants and what are the products?

6CO2 +6H2O → sunlight → C6H12O6 + 6O2

Reactants: 6CO2 +6H2O

Products: C6H12O6 + 6O2

2. In the light reactions: What does the plant do with all of the energy generated from the light reactions?

Used to power the synthesis of glucose. 

Calvin Cycle

1. After a few turns of the calvin cycle there are a number of 3-carbon sugars produced. Two are used to form 6-carbon glucose, what happens to the other 3 carbon sugars?

It takes 3 turns for one 3-carbon sugar molecule G3P. The other3 carbon sugars are used to regenerate RuBP. 

2. Why must the 5-carbon RuBP be remade at the end of the cycle?

Because it is the primary CO2 acceptor, making it necessary to start a new cycle and produce glucose. 

3. Why do plants turn ATP and high energy electron carriers into C-C bonds in to form of glucose? Why not just use the ATP generated from the light reactions all the time?

Because these energy molecules act as the fuel needed to build carbohydrates which store energy in a usable form for growth and development.