College Level Bio - Exam #2 - DNA

What is a nucleic acid? What are the two types of nucleic acids?

A nucleic acid is a biological macromolecule that carries genetic info and instruction for cells. The two types are DNA and RNA

Explain the double-helix structure of DNA.

DNA is a double helix shape that is uniform. Its uniformity only allows for specific base pairings, a purine with a pyrimidine. A purine with a purine is too large, while pyrimidine and a pyrimidine is too small.

Which 4 nitrogenous bases make up DNA? Which are purines and which are pyrimidines?

Adenine and Guanine are purines, which are a double ringed structure. Thymine and Cytosine are pyrimidines, which are a single ringed structure.

Explain the complementary base pairing in DNA

Complementary base pairing means that a purine will always be paired with a pyrimidine, more specifically, A with T and G with C

How are the complementary bases joined in a DNA molecule?

They are held together by hydrogen bonds

Explain what it means that two strands of DNA are complementary.

This means that one strand of DNA already determines the sequence of bases in the second strand, which is why DNA replication is easier, since base pairings can only have one other option.

Explain what semiconservative DNA replication means.

It is essentially the idea that half of a DNA strand (parent strand) is old, while the other half (daughter strand that is synthesized by DNA polymerase) is new.

What are the basic steps of DNA replication?

First, DNA is split by a helicase to become a template for a new strand. A DNA polymerase uses the template strand to duplicate by matching the correct bases to the corresponding base on the parent strand, thus resulting in 2 daughter strands of DNA from one parent DNA molecule

Explain the basics of DNA proofreading and repair.

When the DNA polymerase is matching bases to the bases on the template strand, it has an intrinsic mechanism to check for mistakes and adjust accordingly if a mistake is discovered. If that fails, there are repair mechanisms (enzymes) that do another round to check for mistakes in DNA code.

What is the role of DNA polymerase in DNA replication and DNA proofreading and repair?

DNA polymerase synthesize the nitrogenous bases to attach to the parent strand, and they have an intrinsic mechanism to proofread possible mistakes.

What is a mutation?

A mutation is any change in the DNA sequence that persists after proofreading in DNA replication

What are the sources of most mutations?

DNA replication errors

What is a mutagen?

a physical, chemical, and biological agent that causes a mutation

Explain the three categories of mutagens. Give examples of each category

1. Physical agent: high energy radiation or UV light

2. Chemical agent:

   -Nitrosamines: found in tobacco or smoked fish and meats

   -Aromatic amines and amides: dyes, pesticides, cooked meat

   -Sodium azide: component in many airbag systems

   -Benzene: used in drug production, plastics, synthetic rubbers, dyes, gasoline and cigarette smoke

3. Biological agent: virus implanting DNA into host cells

Do mutations usually have negative or positive consequences?

Yes they can have both. Mutations with negative consequences are often called “deleterious mutations”

Why are mutations important?

They offer more genetic variation, essential for organisms to evolve. Mutations are the sources of new alleles

How are mutations passed from parents to offspring

Mutations in the gametes (germ line cells) are the only ones that are passed from parent to offspring. Somatic cell mutations are NOT passed down

What are the different functions of cell division (for prokaryotes and eukaryotes)?

In prokaryote cells, they reproduce asexually, creating genetically identical offspring. With eukaryotes, they have meiosis that creates genetically diverse offspring during sexual reproduction

Explain the difference between cell division and mitosis

Cell division is a broader term for the entire process of cells splitting into two. Mitosis is specifically the division of a cell’s nucleus

Define the term genome

A genome is the total of an organism’s DNA

Explain the differences in how the genomes of eukaryotes and prokaryotes are organized

Eukaryotes have multiple DNA and chromosomes incased in the nucleus of a cell, while prokaryotes have one double stranded DNA (1 chromosome) in the shape of the ring incased in the nucleoid region of the cell

Explain the concept of ploidy (haploid or diploid). E.g., if an organism is 2n, what does the n stand for? Why is n multiplied by 2?

Ploidy is the number of chromosomes an organism has in one complete set, represented by n

-Haploid: one chromosome in 1 complete set, n

-Diploid: two chromosones in 1 complete set, 2n

Explain the basic characteristics of the human genome: the number of chromosomes, cells that are diploid, cells that are haploid (you do not need to know the number of bases in the genome)

Human cells are diploid, having 23 sets of chromosomes, 46 chromosomes in total. Gametes are the only human cells that are haploid, having only 23 chromosomes in total, 1 in each complete set.

What are homologous chromosomes?

They are matching pairs of chromosomes, one inherited from each parent, that have the same genes in the same order, though they may have different versions (alleles) of those genes.

What is a gene? Explain the difference between genes and allele

A gene is a section of DNA in a specific area that codes for a specific product. Alleles are different variations of a gene.

What is the cell cycle? Which steps of the cell cycle take place in interphase and which take place in the mitotic phase?

The cell cycle is a series of events that take place during a cell’s life, before and after the divide.

Interphase is when the cell grows and duplicates its DNA, while the mitotic phase is when the cell splits into 2 daughter cells

Explain what happens in the two parts of the mitotic phase?

First there is mitosis, which is division of the nucleus, then there is cytokinesis which is division of the cytoplasm

Explain what happens in the 4 main phases of mitosis: prophase, metaphase, anaphase, & telophase (as described in lecture)

• Prophase: chromatin condenses into chromosomes, the nuclear envelope begins to disappear as the spindle fibers begin to appear from centrosomes and move to the opposite poles of the cell

• Metaphase: the chromosomes begin line up along the metaphase plate of the cell, with each sister chromatid of the duplicated chromosome attached to the spindle fiber of the opposite pole

• Anaphase: the chromosomes are split apart from their centromere and to opposite sides of the cell

• Telophase: the sister chromatids are fully separated as the nuclear envelope begins to reform

Explain what happens in cytokinesis and how the process differs in animals & plants.

With cytokinesis, the cytoplasm is divided to fully form 2 daughter cells after the DNA and nucleus has been divided in mitosis.

In animals, the cleavage burrow forms to separate the daughter cells

In plants, a cell plate forms to separate the daughter cells

Explain the following terms related to the cell cycle and cell division: sister chromatids, centromere, spindle fibers, cleavage furrow, cell plate.

• sister chromatids: attached together by a centromere to be split apart during cell division

• centromere: holds the sister chromatids together

• spindle fibers: pull apart sister chromatids during anaphase

• cleavage furrow: occurs during cytokinesis of an animal cell, helps divide the cell fully into 2 daughter cells

• cell plate: occurs during cytokinesis of a plant cell, helps divide the cell fully into 2 daughter cells

Explain how the cell cycle is regulated. What happens if the regulation of the cell cycle does not function correctly?

Throughout the cell cycle and cell division there are checkpoints to ensure everything is going smoothly, and if it isn’t, the cell can thus be stopped from dividing.

If the regulation fails, cancer can occur because if a faulty cell divides, the most likely deleterious mutations will persist in its daughter cells.

In which types of organisms does binary fission occur?

Prokaryotes

Explain the basic sequence of events in binary fission

1. The single ring shaped chromosome is duplicated

2. A cleavage furrow is formed and 2 daughter cells separate

What is asexual reproduction?

The production of offspring without a mate

What are the advantages of asexual reproduction? In which contexts is asexual reproduction advantageous or adaptive?

Advantages would be that there is no need for a mate, asexual reproduction occurs faster and more offspring are produced. Also, offspring inherit 100% of the parent’s DNA

It is good when the environment is stable and there is mate scarcity

What are the disadvantages of asexual reproduction?

There is a lack of genetic variation, no diversity !!

Explain the basic steps of sexual reproduction

In sexual reproduction, a mate is needed, then the gametes of both parents fuse together in the process of fertilization, which creates a zygote, which grows into an embryo

What are the disadvantages of sexual reproduction (in comparison to asexual reproduction)?

it takes longer, produces less offspring, a mate is needed, and offspring only inherits 50% of parent’s DNA

What are the advantages of sexual reproduction (in comparison to asexual reproduction)?

it allows for genetic variation

Explain Van Valen’s Red Queen Hypothesis and how it outlines the benefits of sexual reproduction. Support your explanation with an actual example from nature.

The Red Queen Hypothesis is the idea that without genetic variation, a population cannot evolve, so species evolve in an arms race. Genetic variation offers the chance that offspring could gain a useful trait in changing environments that help them survive better.

For example, the aquatic garter snake had evolved resistance to tetrodotoxin, a neurotoxin produced by the California newt. So as they evolve, the newt gets more poisonous as the garter snake gains more resistance.

Know the function and the ploidy of the following cell types involved in sexual reproduction: gamete, sperm, egg, zygote. Make sure you know how each of these is formed/produced.

In gametes, the egg and sperm, they are haploid so that when they fuse their nuclei together they create a diploid zygote.

-gametes are created through meiosis

When do transitions in ploidy take place in sexual reproduction (i.e., 2n to n & n to 2n)?

In sexual reproduction, first a diploid cell goes through meiosis to produce 4 haploid daughter cells, then in fertilization, haploid gametes meet together to create a diploid zygote

What are somatic cells? Where are somatic cells located in the body? How are somatic cells duplicated?

Somatic cells are cells not responsible for reproduction, dividing through mitosis and located essentially everywhere in the body.

Define the term meiosis

Meiosis is the formation of gametes, creating genetically unique haploid cells

Contrast how mitosis and meiosis affect ploidy. I.e., compare the ploidy of the parent cell to the daughter cells for each process

Mitosis does not affect ploidy whatsoever, while meiosis decreases it from 2n to n

Which cells in the body undergo meiosis?

germ line cells (gametes)

What is the product of meiosis?

4 haploid daughter cells, creating gametes

How does meiosis produce genetic variation? What are the main sources of genetic variation in sexual reproduction (including meiosis)?

Through crossing over and independent assortment of chromosomes during prophase and metaphase 1

Also, the fusion of any sperm cell with any egg cell (random fertilization) further increases genetic diversity in the offspring

Describe the process of crossing over (genetic recombination) in Prophase 1

In crossing over, homologous pairs of chromosomes, one from mom and the other from dad “switch genetic material”. They switch the same genes, but it can change alleles.

Explain the way in which pairs of duplicated homologous chromosomes line up at the metaphase plate in Metaphase 1 Why is this process so important in meiosis?

In independent assortment, homologous chromosomes line up randomly @ the cell’s metaphase plate, with 2^n possibilities, which is important because this ensures proper chromosome distribution and more genetic diversity.

Explain how anaphase I in meiosis is different from anaphase in mitosis with respect to how pairs of homologous chromosomes line up on the metaphase plate in metaphase/metaphase I

Anaphase 1 in meiosis splits apart pairs of homologous chromosomes, still having duplicated chromosomes while anaphase in mitosis splits apart sister chromatids.

In metaphase 1 of meiosis, the homologous pairs line up together while in mitosis they line up individually

What is produced in cytokinesis at the conclusion of meiosis I? What happens to these products next?

at the end of Meiosis 1, 2 haploid daughter cells with duplicated chromosomes form. Next the cells go into meiosis 2, which is essentially just like mitosis

Compare meiosis & mitosis. How are the two processes similar? How are they different? Is meiosis I or meiosis II more similar to mitosis

Meiosis and Mitosis are both forms of cell division, where the cell has duplicated chromosomes that need to be split apart. Though in Mitosis, the homologous pairs of chromosomes act independently, unlike the homologous pairs in meiosis which interact in crossing over and independent assortment.

Meiosis 2 is similar to Mitosis

How does independent assortment of chromosomes occur in meiosis? What effect does this have on genetic variation in the gametes?

It occurs when the chromosomes randomly line up to get assorted away from their homologous pair, increases genetic variation

What is fertilization? What is the product of fertilization? How does fertilization affect genetic variation in the offspring?

Fertilization is when sperm and egg fuse, this plays into random fertilization, where the fusion of any sperm cell with any egg cell further increases genetic diversity in the offspring. It creates a genetically diverse zygote

Define the following terms: genetics, heredity, wild type.

Genetics is the science of heredity, heredity is the transmission of traits from one generation to another. Wild type is individuals with traits most commonly found in nature.

What were the advantages of using pea plants in Mendel’s experiments?

the pea plants had several easy to observe traits that showed discontinuous variation (not affected by the environment), inherited from one single gene

What is the difference between continuous & discontinuous variation?

• continuous variation are traits that are affected by the environment, ex: skin color. They are often reversible and are polygenetic, meaning many genes are involved in coding for a trait, the effects are often additive.

• discontinuous traits are not affected by the environment and are inherited through one single gene, 2 or fewer distinct outcomes are possible and they are not effected by the inheritance of other genes. ex: blood type, eye color

Define phenotype

Phenotypes are the observable traits expressed by an organism

In which context does environment (and not just genotype) affect an organism’s phenotype? What are some actual examples of this?

In continuous traits this occurs, such as an orgranism’s skin color, which can be affected by lifestyle choices and areas of living.

Define phenotypic plasticity. What is the difference between reversible phenotypic plasticity and irreversible phenotypic plasticity? Give examples of each.

it is the ability of a genotype to express different phenotypes in different environments

• reversible: traits that can be changed once again, ex: skin tanning

• irreversible: traits that cannot be changed once again, ex: fetal alcohol syndrome

What are ‘true breeding’ lines?

self-fertilized (inbred) lines — always produce offspring that look like parents, always produce offspring with the same traits over multiple generations.

What does the term hybridization mean with respect to Mendel’s experiments?

Hybridization is the mating between 2 distinct organisms

What do the variables P, F1, & F2 represent?

P: parental generation, F1: 1st filial generation, F2: 2nd filial generation

Describe Mendel’s monohybrid cross. Diagram a monohybrid cross using a Punnett Square.

Mendel’s monohybrid cross is when he bred 2 pea plants with 1 different trait from the other

How does a monohybrid cross leads to a 3:1 phenotype ratio and a 1:2:1 genotype ratio?

It can lead to a 3:1 phenotype because in the p generation, a PP x pp breed will yield all heterozygous offspring. Then in the F1 generation, Pp x Pp will yield 4 options, 3 of which present purple flowers, and one of which presents white, creating a 3:1 phenotype ratio

Then with 1:2:1 genotype, the F2 generation will have the genotype PP, Pp, Pp, and pp, 2 heterozygotes, 1 recessive homozygote, and 1 dom homozygote

What are the differences between between dominant and recessive traits? What are the differences between between dominant and recessive alleles

-Dom traits have at least 1 dom allele to mask the recessive trait.

-Dom alleles are represented by an uppercase letter, recessive are represented by a lowercase letter

What is meant by the terms dominant phenotype and recessive phenotype?

A dominant phenotype is observable when at least 1 dom allele is present, and a recessive phentoype is observable when both alleles are recessive

What is the difference between a homozygote and a heterozygote?

• homo: same alleles in genotype (BB, bb)

• hetero: different alleles in genotype (Bb)

Give examples of human traits that show a dominant/recessive pattern of inheritance.

Widows peak, detached or attached earlobes

What is a test cross? Why is it useful?

Test cross is breeding a unknown genotype of an organism with a recessive homozygote to determine unknown genotype of the organism, since it is hard to determine the genotype of a dominant presenting phenotype.

Briefly explain Mendel’s 3 laws (use the table in the lecture slides)

• Law of Dominance: the dominant alleles always mask the recessive alleles

• Law of segregation: in the formation of gametes, 2 alleles for a trait (one from each parent) separate into 2 different gametes so each one has one allele

• Law of independent assortment: the inheritance of one allele has no effect on the inheritance of another because the alleles of different traits assort independently. Different genes on different chromosomes are inherited independently of one another.

Explain how Mendel’s law of independent assortment is connected to meiosis

It is connected to Meiosis with metaphase 1, when chromosome pairs assort independently to create different combos of traits to help create genetic variation

What is incomplete dominance? Be able to predict outcomes of crosses between parents with traits (i.e., alleles) that show incomplete dominance

Occurs in heterozygotes, when the dominant and recessive traits mix together (ex: red RR x white rr = pink Rr)

What is codominance? Be able to predict outcomes of crosses between parents with traits (i.e., alleles) that show codominance

When both dom and recess traits show up together (ex: red RR x white rr = red and white Rr)

What is the basic sequence of events in protein synthesis?

transcription, rNA processing, and translation

State the Central Dogma of molecular biology

Describes the flow of genetic information in cells, stating that DNA codes for RNA, which in turn codes for proteins. DNA is read or ‘transcribed’ into an mRNA, mRNA provides code to form a protein through translation. Info travels one way

Describe the differences between DNA & RNA

DNA is double helixed and has the base thymine, while RNA is single helixed with the base Uracil

In which part of the cell does transcription take place?

occurs in the nucleus

List the sequence of events in transcription. What happens during initiation, elongation, & termination?

1. Initiation: RNA polymerase binds to a promoter (short nucleotide sequence that precedes gene on the DNA and promotes the start of transcription)

2. Elongation: mRNA molecule grows as more nucleotides are added, the new RNA molecule is a separate molecule from DNA template

3. Termination: RNA polymerase reaches terminator signal, nucleotide sequence that signals the end of the DNA to be transcribed, and the RNA polymerase detaches from DNA.

What is the importance of the following structures in transcription: RNA polymerase, promoter, mRNA transcript

• RNA polymerase: synthesizes the RNA nucleotide sequences and reads the DNA to make sure the mRNA sequence matches

• promoter: marks the start of the DNA sequence for the RNA polymerase

• mRNA transcript: the final product of transcription and provides directions to synthesize proteins

What is the function of messenger RNA (mRNA)?

mRNA leaves the nucleus after being created to provide directions for the synthesis of proteins

What happens to mRNA before it can be exported from the nucleus

RNA gets processed before it can leave, it is called RNA splicing

What are exons and introns?

• exons: protein coding nucleotide sequence of a gene (expressed portion of a gene)

• introns: non-coding nucleotide sequences between exons (non-expressed portion of gene)

What is RNA splicing? What would happen if RNA did not undergo splicing?

Introns are removed from mRNA through RNA splicing, they must be because if not the protein will be defective

What is alternative splicing?

in the presence on introns, alternative RNA splicing occurs. Particular exons may be included or excluded from final mRNA produced from gene, allowing for a single gene to code for multiple proteins

In which part of the cell does translation take place? Which cellular structure is involved?

It takes place in the cytoplasm, on ribosomes.

What is the sequence of events in translation?

specific tRNAs bind to the sequences on the mRNA template and add corresponding amino acid to polypeptide chain

Explain the Triplet Code and codons

• Triplet code: mRNA is read as a series of codons

• codons: 3 nucleotide sequence that specifies a specific amino acid

What is a start codon? What is a stop codon

• Start codons code for methionine and tell the tRNA to start binding to the mRNA to start producing the amino acid chain

• Stop codons tell the tRNA to stop the amino acid chain and release the completed polypeptide chain

What is the importance of amino acids in the process of protein synthesis?

they are the fundamental building blocks of proteins, acting as the monomers that link up polypeptide chains that fold into functional proteins

What are some of the functions of proteins?

they make up hormones, enzymes, structure, important for transportation, storage, defense, receptors, and contractile

What is the function of transfer RNA (tRNA)

tRNA recognize and translate mRNA codons and bring the required amino acids

What is the importance of the two ‘ends’ of a tRNA? How does each end function?

• amino acid attachment end: where the tRNA attaches to a specific amino acid

• anticodon end: 3-nucleotide sequence complementary to mRNA codon

Explain how gene expression leads to cell differentiation

each cell of an organism has the same DNA (same genes) but are different because of gene expression, the process of turning on a gene to produce RNA and a protein. All cells control which genes are expressed, when they are expressed, and how much they are expressed.