Biology Lab Final Study

CSE Journal citation

uthor(s). Date. Article title. Journal title. Volume(issue):location.

for example: Mazan MR, Hoffman AM. 2001. Effects of aerosolized albuterol on physiologic responses to exercise in standardbreds. Am J Vet Res. 62(11):1812–1817.

Parenthetical Citation CSE

(Author(s) Year).

• if 3-10 authors: (Smart et al. 2003)

• if 2 authors: (Mazan and Hoffman 2001)

DNA

genetic blueprint for all living organisms

• some viruses have only RNA, not DNA.

is a virus a living organism?

not generally considered to be living organisms, since they do not have all of the characteristics of life

components of DNA

• A five-carbon deoxyribose sugar, whose carbons are numbered 1′ to 5′.

  • the prime (′) symbol is used to differentiate the carbon in carbon atoms in deoxyribose from nitrogenous base

• one of four nitrogenous bases covalently bound to carbon 1’ of deoxyribose

• at least one phosphate groups covalently bound to carbon 5’ of deoxyribose (can be as many as 3 phosphate groups)

Types of nitrogenus bases

1. Adenine

2. Thymine

3. Cytosine

4. Guanine

what is pyrimidine and purine?

A and G = purine

C and T = Pyrimidine

Histones

positively charged protein which Dna wraps around to condense 2m of DNA into 5 nanometers .

• name for eukaryotes

Chromatin

DNA in a highly condensed structure

What do we take advantage of to extract DNA for genetic analysis

• cell membranes are made of lipids that can be disrupted by detergents

• DNA interacting preteens have positive charges that can be neutralized by negatively-charged ions from salts

• DNA has a negatively charged backbone that can attract specific dyes

• double stranded DNA had 2 antiparrallel strands making it a polar molecule

how is DNA extracted

• detergent lyses cell membranes and denatures proteins

• salt (NaCl) helps separate DNA from histones through positive electrostatic interactions with the negatively charged DNA.

  • negatively charged chloride ions from favourable electrostatic interactions with positively charged histones.

• In prescient of sodium DNA remains highly soluble in water since water and DNA are polar molecules.

• To precipitate DNA, isopropanol is added to reduce solvent polarity, allowing long DNA strands to wind around glass rod for collection.

Why are we using DNa as source of DNA

• Strawberries, like many crop plants, have been bred to have multiple copies of each chromosome also known as polyploidy

• policy of commercial strains of strawberries:

  • octoploid and contain eight copies of each chromosome

  • larger amount of DNA gives us more DNA to extract and helps strawberries grow larger and taste sweeter

How can we tell that what we have extracted from the cells is really DNA?

• DNA is invisible to naked eye.

• specific dyes bind strongly to the negatively charged phosphates and hydrophobic bases of DNA.

what dye did we use and how does it work

• fluorescent dye called SYBR Gold® (Invitrogen™)

• gives off bright yellow-gold light when bound to DNA and exposed to blue light

• dye interacts with both the negatively charged backbone and the closely stacked bases found in double-stranded DNA

• single-stranded DNA does not bind strongly to the
  dye because the bases are not stacked tightly in this form of DNA

Sodium Hydroxide

a strong base that removes some of the protons in the nitrogenous bases of DNA, thus disrupting the hydrogen bonding needed to stabilize the structure of double-stranded DNA

Confirming DNA property from dye and fluorescence

visually estimating the amount of fluorescent light given off when the dye is added to either water, DNA, or DNA denatured by the addition of a small amount of sodium hydroxide.

mutations

• permanent changes to the genetic information of a cell

• generally occur at a fairly low rate in most organisms

• occur by many different mechanisms, one of which is exposure
  of cells to ionizing radiation, such as ultraviolet light from the sun or artificial sources (e.g., fluorescent and halogen lights).

How does UV cause mutations

• radiation can ionize water molecules to form free radicals, which
  in turn react with the nitrogenous bases of DNA to change their chemical structure, altering their ability to form specific base pairs with other base

Etc about UV

• Some exposure to UV radiation is normal, and organisms have evolved mechanisms to deal with the amount of free radicals generated by a limited degree of radiation exposure

• high amounts of exposure cause more generation of free radicals than cells can control

• when too much free radical image occurs then DNA damage is more likely to become a mutation, damaging health of cells

3 types of exposure to UV

1. Sunscreen

2. Foil

3. No foil

Bar chart

compare category or groups

Line graph

• represent trends overtime or relationships between variables

• plot points on a graph and connect them with lines making it easier to see change in value over time or discrete intervals

• useful in tracking changes over time or identifying patterns or correlations

Scatter plot

• display individual data pouts as dots on a graph with one variable plotted on the x axis and another on the y axis

• used to visualize relationships b/w 2 variables and identify patterns or correlation between the,.

• useful in identifying outliers, clusters, or trends

• benefit from addition of a trend line

Box plots

• concise summary for distribution of data set

• highlight key stats amusers like median, quartiles, and range

• effective for comparing spread and central tendency of multiple groups or categories within a data set

• care good at seeing sim and diff between multiple groups or categories

Regarding the wild-type strain data set alone, describe the results from this
experiment. What conclusion can you draw with respect to your null hypothesis that sunscreen will have no protective benefit from UV radiation on yeast survival?

wild-type strain:

• The plates with the highest UV exposure/ saran-wrapped plates, yielded the lowest average number of colonies

• The sunscreen-protected plates yielded a higher average number of colonies

• results reject the null-hypothesis that sunscreen will have no protective benefit for yeast survival.

Regarding the light-sensitive mutant strain data set alone, describe the results from this experiment. What conclusion can you draw with respect to your null hypothesis that sunscreen will have no protective benefit from UV radiation on yeast survival?

mutant strain

• plates with the highest UV exposure/ saran-wrapped plates, yielded the lowest average number of colonies

• The sunscreen-protected plates yielded a higher average number of colonies

• results reject the null-hypothesis that sunscreen will have no protective benefit for yeast survival.

Compare the data between the wild-type yeast strain and the light-sensitive mutant strain and describe the results in your own words. Based on this data, what conclusions can you draw with regard to your second null hypothesis that there will be no difference between yeast strains in response to similar UV-blocking conditions?

• mutant strain is not as efficient in its ability to resist/ survive damage caused by UV radiation causing cellular death compared to the wild-type strain (especially in "None" and SPF 15 groups)

• reject their null hypothesis that wild-type and mutant strains will show no difference in response to similar UV-blocking conditions

What is the biological significance of your experimental results? Your response should be concise and touch on each exposure condition and yeast strain, and the functionality of DNA repair pathways. How do your results compare with literature on this topic? (Refer to the paper posted in Lab 4 folder: Alhamdy and Alsowayan, 2020)

• Results suggest that any level of blocking (SPF 15, 50, or foil) is equally protective for wild- type cells, but light-sensitive mutant yeast only remain viable when UV is completely blocked by foil or SPF 50 sunscreen.

• DNA repair is much more functional in sunscreen exposures of wild-type cells compared with mutants as observed with higher survival of wild-type
  

  Lit comparison:
  • Regular sunscreens use was shown to reduce the effect of UV exposure with similar results to ours (e.g. Alhamdy and Alsowayan, 2020)

The data presented in the graph is a compilation of data from all groups across all 33 lab sections. Compared with your own graph that you submitted, why are the SEM error bars smaller in this graph in Figure 1 above? What information can you infer from the error bars when trying to determine meaningful differences between samples? Give an example from the graph in Figure 1

• Fewer samples in student graphs will result in larger SEM bars (OR more samples in compiled graph will give smaller SEM bars

• Generally if error bars overlap with each other, there is no meaningful difference (and vice versa).

• Can look at error bars between WT "none" vs WT Foil/sunscreens, or WT SPF15 vs Mut SPF15 (for differences) (1 for any example that works)

mitosis

divides genetic material equally between two daughter cells, giving each daughter cell the same genetic material as the mother cell

meiosis

divides genetic material among four daughter cells (gametes in animals and spores in plants or fungi), each of which contains half of the genetic material of
original germ cell

Mitosis Phases

Mitosis

• one copy of each chromosome is given to each daughter cell, thus providing each daughter cell with a full complement of genetic material identical to that found in mother cell

• occurs in all eukaryotic organisms. The process happens in stages that must be carried out very precisely, because mistakes would be catastrophic for daughter cells.

What happens when there is an error in mitosis

• a daughter cell is given an incomplete complement of chromosomes or an excess copy of one or more chromosomes the daughter cells usually nonviable and will die.

• extremely rare cases where such cells with defective complements of chromosomes somehow survive, such cells may behave in an abnormal fashion that may sometimes lead to disease states
  such as cancer.

Meiosis

Meiosis is the process by which a germ cell divides its full genetic complement among four daughter cells, reducing its diploid chromosome set to haploid.

Purpose of Meiosis

Meiosis ensures genetic diversity by creating unique haploid cells, which combine during sexual reproduction to form a diploid zygote.

Meiosis in Animals

In animals, including humans, meiosis produces haploid gametes (sperm and egg cells) necessary for sexual reproduction.

Meiosis in Other Organisms

Meiosis doesn’t always produce gametes. In plants and fungi, it results in haploid spores instead.

Haploid cell

only one cope of each chromosome

diploid cell

• 2 copies of each chromosome

• one copy of maternal and other is paternal

Homologous pair

• also known as homologous chromosome or homologues

chromes set (n)

• one representative chromosome from each of the pairs of homologous chromosomes in a diploid species.

• diploid cells are 2n

Acrocentric vs metacentric

• used to describe structure of chromosomes

• metacentric = has arms on either side of centromere equal in length

• acrocentric = chromosome has one arm longer than other on one side of centromere than other side

Meiosis and diploid cells

Meiotic process and its functions

• reduce diploid to haploid through segregation of alleles

• through cross over and random movement of non homologous chromosomes producing new combo of genes or genotypes.

Etc about meiotic process

• frequency of recombination in large sample of meiotic cells can by studied by recombinational analysis in Drosophila melanogaster, corn and other diploid organisms that are used as genetic tools.

genes

specific sequences of DNA that most often encode a protein whose expression
results in a specific phenotype

alleles

different DNA sequences of a gene

genotype

specific combination of alleles in an organism

genotype nomenclature

represents alleles of genes on different chromosomes. Alleles on homologous chromosomes are separated by a slash ( / ), while different genes are separated by a semicolon ( ; ).

Example of Genotype Representation

A male heterozygous for genes A and B is written as A/a; B/b; X/Y, where:

• A/a and B/b show heterozygosity for genes A and B.

• X/Y represents the sex chromosomes in males.

Role of Statistics in Research

Statistical tests help determine whether observed differences in data are meaningful or due to chance, aiding in hypothesis evaluation.

The Null Hypothesis

In statistical tests, the null hypothesis (H₀) assumes no significant difference between groups. A test determines whether to reject or fail to reject H₀.

The t-Test

t-test compares the means of two groups to assess statistical significance. A larger t-value increases the likelihood of a significant difference.

Interpreting the t-Test

calculated t-value is compared to a t-table based on degrees of freedom and p-value. If it meets or exceeds the critical t-value, the difference is statistically significant.

Understanding p-Value

p-value of 5% (p = 0.05) means that if the null hypothesis were true, we would observe a t-value this extreme in less than 5% of cases by chance.

Limitations of the t-Test

t-test can only compare two groups. Using multiple t-tests for more than two groups increases error risk—ANOVAshould be used instead.

Interpreting Non-Significant Results

If calculated t-value is smaller than the critical value, it doesn’t prove there’s no difference—just that the data failed to show a significant difference. A larger sample size may reveal one.

Statistical vs. Biological Significance

A statistically significant result does not always mean a biologically meaningful difference. Always consider real-world relevance before drawing conclusions.

t-test is based on mean and SEM for each of the two groups that you are comparing: