BIOL 202 Exam 1

The human genome has about ____________ protein-coding genes. This DNA sequence only accounts for ____________ of the entire human genome.

- 20,000 - 1-2%

If you could build a protein with 10 amino acids, and any amino acid could be at each position, how many variations are possible?

- 20^n - There are 20 different amino acids commonly found in proteins and if we could build a protein with 10 amino acids, there would be 20^10 variations.

Together LINEs and SINEs make up what percent of the DNA of the human genome?

- 34% (13% SINEs and 21% LINEs)

What is bioinformatics?

- A field that focuses on the design and use of software and computational methods for the storage, analysis, and management of biological information such as nucleotide or amino acid sequences.

What is mitosis?

- A form of cell division producing two progeny cells identical genetically to the parental cell. - The production of two cells from one, each having the same chromosome complement as the parent cell. - Occurs in autosomal cells, not gametes.

What are model organisms? What are some examples?

- A model organism is a species that has been widely studied, usually because it is easy to maintain and breed in a laboratory setting and has particular experimental advantages. - Drosophila melanogaster (fruit fly) - Bacillus subtilis (bacteria) - Caenorhabditis elegans (roundworm) - Arabidopsis thaliana (flowering plant) - Mus musculus (house mouse)

What happens to the structure of hemoglobin (protein) when the β-globin gene has a mutation that changes a codon from GAG to GUG? Thus, a person with the genotype with two copies of the GUG allele will have what phenotype?

- A single nucleotide change in the DNA encoding β-globin (CTC --> CAC) leads to an altered mRNA codon (GAG --> GUG) and the insertion of a different amino acid (Glutamic Acid --> Valine), producing the altered version of the β-globin protein that is responsible for sickle-cell anemia.

What is genomics?

- A subdiscipline of genetics created by the union of classical and molecular biology with the goal of sequencing and understanding genes, gene interaction, genetic elements, as well as the structure and evolution of genomes. - The study of genomes; studies the structure, function, and evolution of genes and genomes.

What is a codon?

- A triplet of mRNA nucleotides (bases) that specifies a particular amino acid or a start or stop signal in the genetic code.

What does the phrase, "The process of science is not predetermined," mean?

- Any point in the process leads to many possible next steps, and where that next step leads could be a surprise.

Genetic information is encoded by the sequence of...?

- Bases (ACTG)

What is the centromere and what does the DNA sequence look like at the centromere?

- Centromere: The specialized heterochromatic chromosomal region at which sister chromatids remain attached after replication, and the site to which spindle fibers attach to the chromosome during cell division. The location of the centromere determines the shape of the chromosome during the anaphase portion of cell division. Also known as the primary constriction. - At the centromere, the DNA is composed of repetitive sequences. - The separation of homologs during meiosis and mitosis depends on the centromere. - The centromere is the heterochromatic (important for cell movement during cell division) chromosomal region at which sister chromatids remain attached after replication and the site at which spindle fibers attach to the chromosome during cell division. - DNA sequence is repetitive!!

Do chloroplasts occur in both prokaryotes and eukaryotes? Do they contain DNA? The same DNA as the cell nucleus?

- Chloroplasts are found in plants, algae, and some protozoans, are associated with photosynthesis. - Chloroplasts are found in only eukaryotes and contain their own distinct form of DNA.

Define the word chromatin and contrast it to the word chromosome.

- Chromatin: The complex of DNA, RNA, histones, and nonhistone proteins that make up UNCOILED chromosomes, characteristic of the eukaryotic interphase nucleus. - Nucleosomes --> Chromatin --> Chromatid (Chromosome)

Which is bigger a gene or a chromosome?

- Chromosome

What are homologous chromosomes?

- Chromosomes that synapse or pair during meiosis and that are identical with respect to their genetic loci and centromere placement.

What is the first order of chromatin packaging?

- Coiling around nucleosomes.

Fill in the blanks: __________ stores the genetic information and serves as the template for its own reproduction (__________) and for the production of __________ copies (__________). These copies carry the genetic information to be used for the synthesis of __________ (__________).

- DNA - Replication - RNA - Transcription - Proteins - Translation

What are some characteristics of bacterial chromosomes?

- DNA (double-stranded) - Circular

Which of these characteristics describes eukaryotic chromosomes?

- DNA (single- or double-stranded) - Linear

What are some characteristics of viral chromosomes?

- DNA (single- or double-stranded) - RNA (single- or double-stranded) - Circular - Linear

What is transcription?

- DNA --> RNA - Transfer of genetic information from DNA by the synthesis of a complementary RNA molecule using one strand of the DNA as a template; mRNA is produced.

What is the central dogma of molecular genetics?

- DNA --> RNA --> Protein

How is DNA transmissioned?

- DNA is transmissioned through mitosis (eukaryotes) and binary fission (prokaryotes).

Why was Darwin's theory of natural selection open to criticism when he published it?

- Darwin lacked an understanding of the genetic basis of variation and inheritance, a gap that left his theory open to reasonable criticism well into the twentieth century. - Variation and inheritance is key here.

What is meant by benefits and outcomes in the model?

- Develop technology - Address societal issues - Build knowledge - Inform policy - Satisfy curiosity - Solve everyday problems - The process of science is Intertwined with society

What are alleles?

- Different sequences/versions of the same gene

Draw a bar graph comparing the telomere length of white blood cells in newborns, adults, and the elderly.

- Each time a cell divides, it loses 30-200 base pairs from the ends of its telomeres. - Newborns = 8000 - Adults = 3000 - Elderly = 1500

What is the major difference between regions of DNA of a chromosome that are identified as heterochromatin vs. euchromatin? Where in the genome would you find heterochromatin?

- Euchromatin: Chromatin or chromosomal regions that are lightly staining and relatively uncoiled during the interphase portion of the cell cycle. Euchromatic regions contain most of the structural genes. - Heterochromatin: The heavily staining, late-replicating regions of chromosomes that are prematurely condensed in interphase. - Euchromatin = Uncoiled (Loose) - Heterochromatin = Condensed (Tight) - Heterochromatin regions are genetically inactive.

What makes a eukaryotic cell different from a prokaryotic cell?

- Eukaryotes: Organisms having true nuclei and membraneous organelles and whose cells divide by mitosis and meiosis. - Prokaryotes: Organisms lacking a nuclear membrane, true chromosomes, and membraneous organelles. - Prokaryotes do not have a nucleus or organelles. - Prokaryotes do have DNA (nucleoid)

Where is DNA stored?

- Eukaryotic nucleus

True or False: The majority of repetitive DNA in the genome contains genes.

- FALSE - The majority of repetitive sequences are non-genic.

True or False: The length of a species' telomeres predicts the lifespan of that species.

- FALSE - While telomere shortening has been linked to aging, it is not yet known whether shorter telomeres are just as sign of aging or contribute to it.

What kinds of things are done in community analysis and feedback?

- Feedback and peer review - Replication - Discussion with colleagues - Publication - Coming up with new questions/ideas - Theory building

What kinds of things are done in testing ideas?

- Gathering data (hypothesis, results/observations) - Interpreting data (supportive, opposing, inspiring, revising the hypothesis)

What is a genotype?

- Genetic makeup of an organism - Examples: BB, Bb, or bb

What base corresponds with cytosine in DNA?

- Guanine

What is the difference between heterochromatin and euchromatin?

- Heterochromatin = Condensed and few expressed genes - Euchromatin = Loose and many expressed genes

What is proteomics?

- Identifies the set of proteins present in a cell under a given set of conditions and studies their functions and interactions.

What kinds of things are done in exploration and discovery?

- Making observations - Asking questions - Finding inspiration - Exploring the literature - Sharing data and ideas

Do mitochondria occur in both prokaryotes and eukaryotes? Do they contain DNA? The same DNA as the cell nucleus?

- Mitochondria are found in most eukaryotes, including both animal and plant cells, are are the sites of the oxidative phases of cell respiration. - Mitochondria does contain DNA in a form distinct from that found in the nucleus.

What is the difference between mitosis and meiosis?

- Mitosis occurs in somatic cells, while meiosis occurs in germ cells. - Mitosis produces 2 diploid daughter cells (identical), while meiosis produces 4 haploid daughter cells. - Mitosis daughter cells have the same number of chromosomes as parental cell, while meiosis daughter cells have half of the chromosomes as parental cell.

Eukaryotic cells contain DNA in the mitochondria and chloroplasts (in addition to the nucleus). Is the organization of DNA in these organelles more similar to bacterial or eukaryotic chromosomes? Why?

- More like bacterial chromosomes!! - Mitochondrial DNA exists as a double-stranded, closed circle that is free of the chromosomal proteins characteristic of chromosomal DNA. - Chloroplast DNA shares many similarities to DNA found in bacterial cells. It is circular and double-stranded, and it is free of the associated proteins characteristic of eukaryotic DNA.

How do variations in gene sequences (alleles) arise in a population?

- Mutations

Does most repetitive DNA, such as telomeres, VNTRs, and SINEs, code for proteins?

- NO

Was Mendel's work immediately accepted by the science community?

- NO!! - Published a paper showing how traits were passed from generation to generation in pea plants and offered a general model of how traits are inherited. - Work was little known until it was partially duplicated and brought to light by Correns, de Vries, and Tschermak around 1900.

What is a nucleoid and how does it compare to a nucleus?

- Nucleoid: The DNA-containing region within the cytoplasm in bacterial cells.

What is the difference between a nucleus and a nucleolus?

- Nucleus: The membrane-bound cytoplasmic organelle of eukaryotic cells that contains the chromosomes and nucleolus. - Nucleolus: The nuclear site of ribosome biosynthesis and assembly; associated with or formed in association with the DNA comprising the nucleolar organizer region (NOR), where RNA is synthesized.

What is the second order of chromatin packaging?

- Occurs when nucleosomes coil together to form a solenoid fiber that is 30 nm in diameter.

What is a haploid?

- One set of chromosomes (n) - The number of homologous chromosome pairs characteristic of an organism or species. - Humans have a haploid number of 23

How is eukaryotic chromatin organized?

- Organized into repeating units called nucleosomes - Composed of 200 base pairs of DNA, an octamer of four types of histones, plus one linker histone. - Two tetramers of histone proteins make up the nucleosome core. - DNA + Histones = Nucleosome - Nucleosomes --> Chromatin --> Chromatid (Chromosome)

What is a phenotype?

- Physical appearance/characteristics - Examples: Blonde hair, black hair, or brown hair

What are some lifestyle changes that increase telomere length?

- Plant-based diet - Moderate exercise - Stress reduction - Group support

A substantial amount of protein is associated with DNA in eukaryotes. What are these proteins and what are their function?

- Positively charges histones and less positively charged nonhistones. - Histones: Positively charges proteins complexed with DNA in the nucleus. They are rich in the basic amino acids arginine and lysine and function in coiling DNA to form nucleosomes. - DNA + Histones = Nucleosome - Histones play an important structural role in packaging DNA into the nucleosomes that make up chromatin.

What does the phrase, "The process of science is iterative," mean?

- Science circles back on itself so that useful ideas are built upon and used to learn even more about the natural world. This often means that successive investigations of a topic lead back to the same question, but at deeper and deeper levels.

LINES and SINES are longer sequences and they do not repeat in tandem. Why are they called repetitive?

- Short Interspersed Elements (SINEs) are found up to 500,000 times in the human genome. - Long Interspersed Elements (LINEs) are found up to 850,000 times in the human genome.

If the sequence was much shorter, such as GA and repeated 50 times in tandem, this would be known as a _____________?

- Short Tandem Repeat (STRs)

True or False: Telomeres are ONLY found in eukaryotic cells.

- TRUE

True or False: The majority of repetitive DNA sequences in the genome have no known function.

- TRUE

How does telomerase work?

- Telomerase counteracts telomere shortening by adding bases to the ends of telomeres.

What is telomerase and what cells express this protein?

- Telomerase is an enzyme that adds bases to the ends of telomeres. - In young cells, telomerase keeps telomeres from wearing down too much. But as cells divide repeatedly, there is not enough telomerase, so the telomeres grow shorter and the cells age. - Telomerase remains active in sperm and eggs, which are passed from one generation to the next.

What are the regions of heterochromatin? What are there functions?

- Telomere and centromere - Telomere: Maintains chromosome structure during DNA replication. - Centromere: Facilitates chromosome movement during cell division.

What is the purpose of telomeres?

- Telomeres allow cells to divide without losing genes.

What are the two examples of satellite DNA?

- Telomeres and Centromeres

Where are telomeres located on a chromosome? How many telomeres are there on each chromosome?

- Telomeres are located at the ends of chromosomes to protect genetic data, make it possible for cells to divide, and hold some secrets to how we age and get cancer. - Telomeres are sequences of DNA - Each chromosome has 4 telomeres (2 per chromatid)

What does the DNA sequence look like at a telomere?

- Telomeres are made of repeating sequences of TTAGGG on one strand paired with AATCCC on the other strand. - One section of telomere is a "repeat" made of six "base pairs."

How are telomeres an example of repetitive DNA?

- Telomeres are repeating sequences of DNA that allow cells to divide without losing genes.

When does a telomere shorten? What is the consequence of a shortening telomere?

- Telomeres shorten every time the cell divides and its DNA replicates. - When telomeres get too short, they can no longer divide and they become inactive and die. - The shortening of telomeres has been associated with aging, cancer, and death.

Draw the diagram of the real process of science. What idea is in the center? What are the three circulating ideas surrounding the central idea? Why do the arrows go in both directions?

- Testing Ideas - Exploration and Discovery - Community Analysis and Feedback - Benefits and Outcomes - The arrows go in both directions because the process of science is iterative, meaning science circles back on itself so that useful ideas are built upon and used to learn even more about the natural world.

What does the cell theory state?

- The cell theory states that all organisms are made of cells and that all cells come from pre-existing cells. - Proposed by Matthias Schleiden and Theodor Schwann

What does the homunculus tell us about how scientists once incorrectly thought about reproduction? What was this belief called?

- The homunculus depicted is a sperm containing a miniature adult, perfect in proportion and fully formed. - Preformationism: Scientists once believed that development was the result of the assembly of structures already present in the egg. - Epigenesis: Holds that an organism arises through the sequential appearance and development of new structures.

What is meiosis?

- The process of cell division in gametogenesis or sporogenesis during which the diploid number of chromosomes is reduced to the haploid number.

If telomere shortening could be stopped in an individual, what might be the result?

- The risk of cancer may increase, but we may also be able to mass-produce cells for transplantation and help test new drugs and gene therapies. - Cancer cells produce more telomerase in order to keep dividing.

What base corresponds with adenine in DNA?

- Thymine

What process leads to the development of mRNA?

- Transcription - DNA is used to make mRNA via transcription.

When a gene from a bacterium is inserted into a corn plant, we would call this corn plant a ______ organism. Why is this done with some crops?

- Transgenic organism - Advantageous because of traits such as resistance to herbicides, insects, and nutritional enhancements.

What process leads to the development of proteins?

- Translation - Codons from the mRNA are used to string amino acids into protein via translation.

How many copies of genes are there in a diploid organism?

- Two copies

What is a diploid?

- Two sets of chromosomes (2n) - The condition when cells contain homologous pairs of each chromosome, one derived from the paternal parent and one from the maternal parent. - Humans have a diploid number of 46

What base corresponds with adenine in RNA?

- Uracil

A sequence such as TATAGCGTAGCTAGCT repeated in tandem (next to each other) 75 times is an example of a _____________?

- Variable Number Tandem Repeats (VNTRs) - DOES NOT CODE FOR PROTEIN!!!!!!!

What is a virus? Is it alive?

- Virus: Tiny infectious particles consisting of RNA or DNA surrounded by protein. Viruses can reproduce only by injecting their genetic material into the cells of living creatures. - Although scientists frequently refer to viruses as alive or dead, no virus is truly alive. It must hijack the cellular machinery of a living cell in order to survive.

What is the problem with DNA that is bound to histones and compacted? When might chromatin need to be remodeled and why?

- When the chromatin fiber is complexed with histones and folded into compaction, it makes the DNA inaccessible to interaction with important nonhistone proteins, such as proteins that function in enzymatic and regulatory roles during the process of replication and gene expression. - Chromatin Remodeling: A process in which the structure of chromatin is altered by a protein complex, resulting in changes in the transcriptional state of genes in the altered region. - Chromatin's structure must be changed so that it can accommodate the protein-DNA interactions; the dynamic forms in which chromatin exists are vitally important to the way that all genetic processes involving DNA are executed.

Is bacterial DNA compacted tightly around histones, like in eukaryotic cells?

- YES

What is translation?

- mRNA --> Protein - The synthesis of proteins under the direction of mRNA

Complete this sentence: The chromosome theory of inheritance explains how...

-... heredity and development were dependent on genetic information residing in genes contained in chromosomes, which are then contributed to each individual by gametes. -... genetic information is transmitted from generation to generation.

What are the three processes of information?

1. Storage 2. Transmission (from one source to another) 3. Flow (how is it used?)

What are the four reasons why the simplified, linear model for the process of science is wrong? What is true in reality?

1. The simplified, linear scientific method implies that scientific studies follow an unvarying, linear recipe. But in reality, in their work, scientists engage in many different activities in many different sequences. Scientific investigations often involve repeating the same steps many times to account for new information and ideas. 2. The simplified, linear scientific method implies that science is done by individual scientists working through these steps in isolation. But in reality, science depends on interactions within the scientific community. Different parts of the process of science may be carried out by different people at different times. 3. The simplified, linear scientific method implies that science has little room for creativity. But in reality, the process of science is exciting, dynamic, and unpredictable. Science relies on creative people thinking outside the box. 4. The simplified, linear scientific method implies that science concludes. But in reality, scientific conclusions are always revisable if warranted by the evidence. Scientific investigations are often ongoing, raising new questions even as old ones are answered.

What are the five common themes in the study of living systems?

1. Transformations of Energy and Matter (O2 and CO2 Exchange; Lactose Function) 2. Structure Fits Function 3. Balance within Systems 4. Information Pathways (DNA --> RNA --> Proteins) 5. Evolution