Unit 1 Learning goals
Scientific Reasoning:
1. Describe the basic requirements for a controlled experiment
1. Control group: this group doesn't receive the experimental treatment and serves as a baseline for comparison
2. Experimental group: this group receives the treatment or condition being tested
3. Independent Variable: this is the variable that is manipulated or changed by researchers to observe its effect
4. Dependent Variable: This is the variable that is measured or observed in response to changes in the independent variable.
5. Constants: all other variables that could affect the outcome of the experiment must be kept constant to ensure that any observed changes are due to the manipulation of the independent variable
6. Replication: The experiment should be repeatable and include multiple trials to ensure the reliability and accuracy of results
These components help ensure that the results of the experiment are valid and that conclusions drawn from the data are based on the effects of the independent variable alone.
2. Distinguish between science and pseudoscience
Pseudoscience: an explanation that can not be falsified
Science- convinces by appeal to evidence by argument board on logic
3. Explain the process and reasoning behind “falsification”
Empirical falsification
Scientific experiments need to rule out wrong hypotheses
This is done by a process of elimination and not just repeated verification
1. Pose competing hypotheses to potentially explain an observation
2. Predict what will happen if you test each hypothesis
3. Design rigorous experiments to test each hypothesis and analyze the results
4. Decide whether results support or refute each hypothesis this process continues until one hypothesis is the last hypothesis standing.
Life and chemistry:
4. Describe the properties of carbon that make it well-suited to be a chemical building block of life
Small size (radius) and unique electron configuration (molecular glue)
Can make 4 bonds
Small bonds help it make stable bonds
Bonds with other key elements: Hydrogen, Oxygen, Nitrogen, Phosphorus
It can bond with itself to make carbon backbones
5. Define polar and nonpolar molecules, and explain the hydrophobic effect
Polar- there is an unequal sharing of electrons ( sugars are polar and water-soluble or Hydrophilic)
Nonpolar- equal sharing of electrons( grease is nonpolar and not water-soluble or hydrophobic)
Hydrophobic effect- drives self-organization of membranes and protein folding- proteins have evolved to contain hydrophobic cores
nonpolar substances aggregate in aqueous solution and exclude water molecules, nonpolar substances disrupt hydrogen bonds between water.
6. Describe how polymerization creates diversity and allows the storage of information in biology
Individual molecules assemble into long chains
Harnessing chemistry to efficiently evolve (Monomer + Monomer= polymer)/ Monomers are linked together by covalent bonds
Life and evolution:
7. Explain how the concept of homology is integral to the study of biology and medicine
Homologous traits are shared characteristics inherited from a common ancestor
Because all life shares a common ancestry so should the parts of life
1. Classify features
2. Classify similar in similar positions (structures)
3. Link features to tree of evolutionary relationships
8. Explain how homology exists at multiple levels
Homology is similar due to common descents
There are a level of homology
Parts of animals and plants
Parts of cells, molecular structures, genes and proteins, nucleotides and amino acid position with genes and proteins
Unit 2 Learning goals
DNA and the Central Dogma:
1. Describe the structure of a DNA molecule, and explain how it guides DNA replication and allows DNA to store information.
Discovered that DNA was a polymer mode from building blocks called nucleotides consisting of a deoxyribose sugar, a phosphate group, and one of the 4 nitrogen bases
Adenine (A), Thymine (T), Guanine (G), and Cytosine ©
DNA was a now-known biological molecule but of unknown function
it's a double-helix structure
2. List the basic reactions in the Central Dogma, and name the enzymes that carry out each one.
DNA replication self-replicating genetic material encodes the blueprint capable of variation DNA polymerase
Transcription RNA converts the information from the DNA into proteins RNA polymerase
translation Proteins are catalysts and workhorses' ribosome
3. Describe the molecular interaction that allows transcription to copy information from DNA to RNA.
transcription involves RNA polymerase binding the DNA promoter, unwinding the DNA, and synthesizing RNA through complementary base pairing between DNA and RNA nucleotides using a DNA template to make mRNA
4. Describe how promoters and transcription factors control gene expression.
Gene expression is patterned during development
Each color indicates the pattern of a different master transcription factor
The transcription factors are the underlying rules that make the body pattern gene expression drive cell “fate”
5. Explain how gene regulation can generate different cell types.
Transcription factors regulate many genes at once
Sets of genes are often controlled together because a cell wants to make all the parts That will be needed for a particular task at the same time
Gene expression drives “fate”
6 .Use a codon table to translate an mRNA sequence into its corresponding protein sequence.
UAU-GGA-AAU= Tyr-Gly-Asn
7. Explain why there are three possible reading frames for an mRNA and how the cell knows which one to use.
Some codons don't code for any amino acids and instead act as signposts that communicate where the ribosome should start or stop reading the mRNA. There are 3 cells that ensure that the mRNA is read in precisely the same way every time. For example, if we have GAUGCC, we can either start with codons: GAU, AUG, or UGC (Three frames right there). But the cell KNOWS that it must start with its start codon, which is AUG for mRNA, or ATG in DNA. The ribosome will scan the RNA until it finds its start codon and will keep going until it finds its stop codon.
8. Define a mutation, and describe where mutations come from.
Mutations are random changes in a DNA sequence
DNA replication errors: about 1 copying mistake per 100,000 base pairs= 100-200 typos per generation
Environmental damage: chemical and UV light
Mutations are not necessarily a bad thing, mutations generate variation randomly, so it's neither good nor bad just different
Selection pressure affects whether they are retained
Mutations must occur in the germ line to be transmitted to progeny
9. Explain how different types of mutations in genes affect the corresponding proteins, and distinguish between types of mutations likely to have small versus big effects.
Silent: a sequence is changing but the output is the same, the amino acids are still the same
Missense: just changing one amino acid the rest of the protein will be fine will have a very small effect
Nonsense: goes into premature stop codon
Frameshift: the protein completely shifts and won't be the same anymore. This would happen with the deletion of two bases. If you delete three bases the reading actually goes back to normal and the proteins remain the same
Frameshift and nonsense have the biggest impact
10. Describe what CRISPR (or CRISPR-Cas9) is, and how it can be used to “edit” DNA.
It is found in bacteria (like a molecular photo album) CRISPR is a record of past viral infections (this is used to defend against future infections)
Cas9 is an enzyme Cas9, cuts DNA into two pieces
It's driven by nucleotide base pairing, they intervene and cut the DNA to disable the virus
Viruses:
11. Explain why most viruses are specific for a particular host species, but sometimes they can “jump” from one species to another.
The viruses have specific surface proteins that need to be able to bind to other reciprocating cell surface proteins.
They can jump from one species to another because of homology we share similar enough protein structure with other species that it can jump from one organism to another.
12. Explain what the purpose of the mRNA in the vaccines for COVID-19 is.
teach cells how to make a protein that triggers an immune response if someone gets infected.
13. Describe how drugs can target different aspects of the viral life cycle, and distinguish between candidate drug targets that are virus-specific and those that are also important for cellular function.
Drugs can target specific processes in the RNA process or DNA process to help kill the virus off.
there are genes that are specific to the virus, meaning there are proteins also specific for the virus so the purpose of the drugs is to focus on those proteins/genes and get rid of them, the drugs don't target your own cells/proteins in your immune system
Unit 3 Learning Goals
Genotype to Phenotype:
1. Explain the concept of genes.
A gene is most often a “recipe” for a protein
A gene is a piece of DNA that encodes one protein
Genes are expressed by the combined processes of transcription and translation
2. Distinguish between genotype and phenotype.
A gene is most often a “recipe” for a protein
A gene is a piece of DNA that encodes one protein
Genes are expressed by the combined processes pf transcription and translation
3. Define “allele” and distinguish between a gene and an allele.
alleles= versions of genes
Alleles may differ because of mutations that happened in the past
Inherit one allele from each parent
Different alleles (versions) are abbreviated as capital or lowercase (T/t)
allele= type of color
gene= eye color
4. Describe an example of a monogenic trait and describe the inheritance pattern for dominant and recessive alleles.
A trait associated with a single gene (single protein) like albinism, or blood type.- For example, we can use Mendel's experiment with the pea plants. If the parents have say Bb and bb as their genotypes, we can see that one of the parents has a recessive genotype and one has a dominant genotype. Based on the Punnett square, the possible offspring will be two with the dominant trait and two with the recessive trait.
5. Explain how we can test if a trait has a genetic basis.
Genetics- some suggestions of inheritance (heritability)
Increased probability in families
Increased prevalence in maternal over parental relatives
Twin studies indicate 30-40% explained by genetics
At least one region on the x chromosome implicated
6 . Explain how the environment may influence the phenotype.
phenotype=genotype+environment+interactions (height) environment affects because of diet- varied height both genotype and environment may contribute many small factors
7 . Define a “SNP” and describe how SNPs relate to mutations.
Single nucleotide polymorphism (e.g., mutation)
-SNPs: correspond to missense mutations causing amino acid change on the protein level. -Mutations can have different effects on protein function (from no effect to complete disruption of its function)
8. Describe how SNPs in both promoters and in the coding regions of genes can affect phenotypes.
SNP in the promoter of KITLG affects hair color
SNP in the coding region of the PTC receptor affects bitter-tasting
Cell Structure and Function:
9. Describe the role of ATP as a currency for energy in the cell, including how it is produced and how it is used.
ATP=cell currency of energy
ATP can be used as energy wherever and wherever the cell needs it
sugars-> chemical reactions in mitochondria-> ATP
Mitochondria generates ATP, this is a multi-step process that requires O2 (oxygen) and it uses chemical energy from sugars to make ATP
Mitochondria are specialized for: Aerobic (using O2) ATP production
ATP serves as the energy currency of the cell produced mainly through cellular respiration and photosynthesis and is used to drive various cellular processes by releasing energy upon hydrolysis
Humans use ATP since we use it for various biological functions such as muscle contractions, nerve impulse transmission, protein synthesis, etc. We use 50 to 75kg or 110lb to 165 lbs per day of ATP
Key points: coupling of chemical reactions allows the transfer of energy
compartments make the transfer process more efficient
ATP serves as a chemical currency for energy
10. Explain the roles of pancreatic beta cells, insulin, and insulin receptors in the regulation of uses glucose uptake in Type 1 and Type 2 Diabetes.
Pancreatic beta cells: secrete insulin
Insulin: signal cells should eat glucose
Glucose: sugar=eneregy source
Insulin receptors: regulation of glucose metabolism/other cellular processes
Type one diabetes: defect in sending the signal(insulin is not secreted by pancreas/cells don't take up glucose
Type two diabetes: A defect in receiving the signal/insulin is present, but the cells don't detect it and don't respond(cells don't take up glucose)
11. Explain how insulin for treating diabetes patients can be produced in bacteria.
Human insulin is produced in bacteria, through genetic engineering
There is a gene for human insulin
That gene can be copied and inserted into bacteria
Bacteria turn on the gene and produce human insulin
12. Distinguish between infection and inflammation.
Infection: infection is the invasion and growth of a pathogen inside the body
Inflammation is the body's response to fight the infection, send immune cells, and protect itself
inflammation: increases fluid from blood vessels such as swelling, heat, pain, and immune cells swarm to the site
13. Describe how “clonal selection” helps the body defend itself against pathogens it hasn’t seen before.
Colonel Selection: during a response to infection, B and T cells that find a target for their receptors get activated and multiply( an army of clones)
It creates a memory of the invader
They are now primed to respond
14. Explain in one sentence the goal of a vaccine in terms of B and T cells.
Contains a piece of target virus/pathogen that generates the immune response from B and T cells, and generates a memory of the invader
Cell Reproduction and Cancer:
15. Define “oncogene” and “tumor suppressor”, and distinguish between them.
Tumor suppression: tumor suppressor genes act in normal cells to prevent cancer. Loss of function of a tumor suppressor can lead to cancer
Oncogenes: Proto-oncogenes normally act to promote cell growth, but they are regulated. Oncogenes are mutated proto-oncogenes that promote cancer because of excessive or unregulated activity
16. Describe how genetics and environment can both contribute to cancer risk.
Cancers: are caused by mutations, though most cases of cancer are not explained by genetics
Environment: smoking, UV light, HPV, Chemicals
17. Explain how mutations underlie cancer.
Mutations cause cancer-uncontrolled proliferation is caused by mutations
18. Describe how growth factors regulate the cell cycle, and how this process can be misregulated in cancer.
secrete signals that tell cells to grow and divide
misregulated in cancer= there is an excess of growth factor or growth of signal that cells to divide and/or loss of the checkpoint that tell cell to divide.
19. List three reasons why cancer is hard to treat.
Specificity: cancer cells are very similar to our normal cells(it's hard to make a drug that just kills cancer cells)
Know your enemy: every patient's cancer is different
Resistance: A high mutation rate promotes the evolution of drug resistance
20. Explain why chemotherapy often causes severe side effects.
blocks cell division and pulls chromosomes apart.
breaks DNA, vulnerable
kills immune cells
21. Explain how drug resistance occurs during chemotherapy, and describe how the problem of drug resistance is similar to the treatment of cancer and viruses such as HIV.
higher mutation rate
resistant mutant arise and survive
similar to hIV b/c the virus can be invisible to drugs an keep mutation everytime and keep infecting
22. Describe the basic idea of cancer immunotherapy.
The immune system can fight cancer
The cancers we see are good at avoiding the immune system
Cancer immunotherapies are designed to target and unleash the immune system against the cancer
There are three types of cancer immunotherapy: Her2 which has Herceptin: which is an antibody that explicitly targets Her2 (people with cancer that have amplified Her2) Cytotoxic T cells: their job is to kill cells that can no longer be trusted(T cells with engineered receptors to target cancer cells
T cells kill bad cells, but not good cells, PD-1 is an immune checkpoint to helps protect normal cells(cancer cells are good at the secret handshake)
Immune checkpoint inhibitors get rid of the secret handshake, and antibodies against PD-1 are immune checkpoint inhibitors
Unit 4 Learning goals (text and lecture)
Stem Cells and Development:
1. Explain whether the genotype or gene expression differs between different cell types within an individual.
Regulation of gene expression makes cells different
A combination of transcription factors can generate different cell types during the development
Gene expression drives cell fate
transcription factors are what cause these patterns or fates
Different cell types express different genes
2. Distinguish between the capabilities and roles of embryonic stem cells and more specialized adult stem cells.
Embryonic stem cells come from embryos and are capable of making any cell type in the body
On the other hand, adult stem cells or somatic stem cells maintain function by replacing and replenishing damaged cells in tissue
Adult stem cells are also very rare and reside in specialized places of niches
3. Describe the concept of stem cell therapy, and explain why stem cell therapies may not always work.
- The idea behind stem cell therapy is that if you inject stem cells into the right place, they will replace missing or defective cells.
- Stem cell therapies may not always work because they are not magic. Just because stem cells have the potential to make important cell types does not mean they always do/can.
4. Distinguish between examples of science and pseudoscience in stem cell therapies.
- Science: "Real" clinical trials to test promising treatment strategies supported by research (participants pay nothing)
- Pseudoscience: Pay-to-Participate "clinical trials" run by for-profit stem cell clinics
The brain and the senses:
5. Define and contrast the two main modes of information transmission in the brain: conduction and neurotransmission.
Conduction: within a neuron moves signals over long distances using an electronic signal or “action potential”
Action potential takes place during conduction and requires ion transport. In addition, an action potential is sort of like a traveling wave and triggers neurotransmitters release, which are chemicals. There are many neurotransmitters, for example, endorphins are euphoria neurotransmitters, GABA is a calming neurotransmitter and glutamate is a memory neurotransmitter.
Neurotransmission: between neurons at synapsis using chemical signals or neurotransmitters
The process in which one neuron sends a chemical signal to another neuron. Neurotransmitters are secreted and occur in synapse
6. Distinguish between the dendrites, cell body, and axon of a neuron.
- Neurons physically connect to communicate.
- The dendrite is a short branched extension of the neuron cell body, along which impulses received from other cells at the synapses are transmitted to the cell body.
- The axon is the long threadlike part of a neuron along which impulses are conducted from the cell body to other cells.
7. Define a synapse.
- A synapse is the area between two nerve cells, which consists of a minute gap across which impulses pass by diffusion of a neurotransmitter.
- Neurotransmission occurs here.
8. Discuss how drugs can interfere with communication between cells of the brain or nervous system.
- Drugs can affect the brain by interfering with the way neurons normally send, receive, and process information.
- Drugs can alter neurotransmission because their chemical structure mimics that of a natural neurotransmitter.
- Enhancers block termination ex. cocaine and ecstasy (increase serotonin)
- ex. MDMA inhibits the reuptake of serotonin at synapses, amplifying and extending its activity
- Blockers ex. alcohol: blocks signals serotonin receptors
9. How many inputs and outputs do neurons typically have?
100 billion neurons
Neurons can have more than 1,000 dendrites, and up to 1,000 different branches of their axonss
There are 50 known neurotransmitters
There can be multiple receptor types for each of the neurotransmitters
A conservative estimate of the number of interactions is 225x10^15= 225 million billion
10. Describe how connections in the brain can change during development and learning.
- Synapses strengthen
- Plasticity/dynamic. Changes to adapt and can change connections between neurons
Strentheing: synapses that are used get stronger
Synaptic pruning: removing synapses (removes the synapse that dont get used)
11. Describe how a memory could be stored by cells in the brain. (Does a single neuron store a memory?)
Memories exist in the brain
The brain contains neurons that can activate or fire
Neurons can activate or inhibit other neurons
A single neuron doesnt store a memory why?
We see that when we have an initial experience-> many neurons are activated
If we have the same experience-> many of the same neurons are aacttive
If we have a Pavlov like stimulus-> many of the same neurons are aactive
Which leads to the hypothesis: that this opattenr of neuron activatopn stores memory
Engram= patterns of cells that fire together which is associated with a memory
12. List the different tastes that we know about and explain how they relate to our dietary needs.
Sweet=sugar for energy
Sour= not clear
Salty= water regulation
Bitter(?)
Umami= protein which we need for lipids
Itt can help us to know if something is off like spoiled or if its too saulty and things like that. This also tells us that we have the highest bitter receptors
Food and digestion:
13. Describe how Ozempic and Wegovy affect the body, including appetite.
14. Contrast catabolism and anabolism. Be able to describe examples of each.
- Catabolism is energy-yielding metabolism that is the process of breaking down chemical fuels such as glucose to make ATP (or energy). Ex: adrenaline.
- Anabolism is biosynthetic metabolism which is the process of building large molecules by using energy or ATP.
- Anabolism uses a few basic raw materials to produce a wide variety of products, such as peptides, proteins, polysaccharides, lipids, and nucleic acids.
15. What is lactose intolerance? Describe and contrast how lactose is metabolized in the body of a lactose-tolerant versus lactose-intolerant person.
- Lactose intolerance results from an inability to digest or break down lactose, which isn't able to be absorbed.
- Lactase enzyme isn't present and can't break down lactose
- Some people are lactose tolerant because their bodies still make the lactase enzyme
- Determined by gene expression
- If a person is lactose intolerant, it means that their gut microbiome is digesting the lactose instead. As a result, the gut microbiome will produce gas.
16. Define “vitamin” and describe how vitamin A is used in the body.
A vitamin is any specific group of ORGANIC compounds that are essential in small quantities. Necessary for growth, metabolism, development, and body function. Deficiencies can produce disorders.
Vitamin A is a cofactor for opsin light receptors in the eye (it's bound to the opsin protein which is the molecule that allows humans to absorb light). Vit A regulates gene transcription during development & acts as a hormone by binding and activating transcription factors.
17. Describe how cancer cells make ATP, how it is different from how most cells of our body do it, and why we think cancer cells use this alternate mode of metabolism.
Cancer cells rely on glucosis, cancer cells do not do respiration
- Cancer cells need building blocks to grow/divide, greedy for fast energy like glucosis
18. Describe what “probiotics” are, and how they are thought to be useful.
- Probiotics consist of yeast or bacteria, especially lactic acid bacteria. Ex: yogurt
- The most common probiotics are lactobacillus and bifidobacterium, and these common probiotics form a healthy, normal intestinal microbiome
- Probiotics can be used to replenish food bacteria you may lose in your body, balance out bad bacteria
19. Describe how “environmental” factors such as diet and medication can affect your gut microbiome.
- The presence of antibiotics, stress, and parasites disrupt the microbial population of our gut.
- For example, antibiotics kill bad and good bacteria so then our body needs to replenish the good bacteria.
- We can fix a "bad gut" by eating food with probiotics or if necessary, having a fecal transplant or taking "poop in a pill".
Natural selection and antibiotics:
20. Define an antibiotic.
Antibiotic= drugs that kill bacteria, that target bacteria-specific structures(cell wall) or bacteria-specific versions of essential components(ribosome)
21. Define antibiotic resistance.
- The ability of bacteria to resist the effects of antibiotics.
- Antibiotic resistance can occur when the drug is pumped out, there is a mutation in the target protein, the drug is modified or the drug is inactivated.
- We can become resistant because antibiotics are made naturally by bacteria to kill other bacteria. Because bacteria can rapidly reproduce and have extremely large populations, the current variation may contain some members with antibiotic-resistant genes.
- In addition, bacteria cells can acquire resistant genes through conjugation (aka horizontal gene transfer), therefore, these resistant genes can spread, even to different species of bacteria.
22. Describe how antibiotic resistance in microbes is analogous to antiviral drugs and chemotherapy for cancer.23. Explain how antibiotic resistance is different from resistance to cancer chemotherapies in terms of long-term (decades) challenges of overcoming resistance.
Bacteria are resistant
- Why is the problem of antibiotic resistance different from the problem of resistance in treating cancer?
- Once resistant bacteria emerge, they can be selected for and become dominant in the population
Unit 5 Learning Goals
1. Define a genetically modified organism (GMO).
An organism whose genetic makeup DNA sequence has been altered by humans for a specific purpose
2. Compare and contrast selective breeding and the making of GMOs.
Selective breeding Animals or plants with desired traits are chosen and traits are passed on to new offspring with breeding. Traits are from variants within the same species. All other genetic factors of the chosen individuals are also passed on.
Genetic engineering traits of an organism are changed by direct modification of the organism’s DNA modifying a gene or introducing a new gene, the traits can be from the same or different species.
GMO- is artificial selection in which genes from the DNA of a species are forced into the genes of an unrelated plant or animal
3. Describe how selective breeding works, and how other unselected traits often get enriched during the process.
Selective breeding also known as artificial selection is a process used by humans to develop new organisms with desirable characteristics. Breeders select two parents that have beneficial phenotypic traits to reproduce, yield offspring with those traits
4. Explain how the greenhouse effect works.
Absorbed radiation the earth absorbs radiation from the sun's
reflected radiation, greenhouse gases absorb some outgoing radiation
greenhouse gasses, and greenhouse gases emit absorbed radiation that warms the earth and its atmosphere
5. Describe how carbon fixation occurs during photosynthesis (where does the carbon come from? Where does the energy come from?)
Carbon fixation in photosynthesis, plants use energy from the sun via chlorophyll molecules to turn carbon dioxide gas from the atmosphere into carbohydrates like glucose
Carbon combustion in aerobic respiration plants and animals break carbohydrates down into carbon dioxide and water and use the energy released to fuel biological activities such as growth, movement, etc.
6. Define a reservoir of carbon, and describe how some reservoirs exchange carbon rapidly with each other (what is an example?) and other reservoirs are essentially isolated (example?).
Carbon Reservoirs: significant amounts of carbon stored in a particular place, form, or state (may also be referred to as Carbon pool)
carbon moves between reservoirs which are dynamic and link together
carbon reservoirs have different sizes, origins, and flux or residence times
ex. Atmospheric CO2, fossil fuels, carbon in plants, and carbon dissolved in the deep ocean
7 . Explain the Suess Effect: how has the measurement of carbon isotopes in the atmosphere provided evidence that the increase in greenhouse gas levels is due to human activity?
The Suess effect is how we know that C02 levels are rising in the atmosphere from human activities. This comes from carbon isotopes such as isotope 14 carbon which comes from the atmosphere and has a stable ratio of c14 to c12.
c12=6 protons and 6 neutrons (lighter)
c13= 6 protons and 7 neutrons
c14 = 6 protons and 8 neutrons (heavier)
Carbon 14 is created in the atmosphere by cosmic radiation-> carbon 14 enters the carbon cycle-> carbon 14 disappears through radioactive decay
High ratio of c14 we see that carbon came from fluctuations between life on the surface and atmospheric gases
A low ratio of c14 means that carbon comes from isolated reservoirs like fossil fuel
Carbon from fossil fuels is returned to the atmosphere through combustion is depleted in c13 and c14 as compared to atmospheric carbon dioxide
Burning fossil fuels dilutes the overall c14 in the atmosphere/this tracks with industrialization