biology 12-17

1. Briefly describe the structure of DNA.

 DNA is a double stranded polymer of nucleotide. It has a sugar and a phosphate on the outside and a nitrogen-containing base pointing toward each other in the middle. Complementary base pairing occurs between the nitrogen bases.(a goes with t and c goes with g)

2. Briefly describe the steps in the process of DNA replication.

 The two DNA strands separate, DNA polymerase creates a new strand by making a copy of one of the old DNA strands, laying  codondown one nucleotide at a time with complementary base pairing.

3. Briefly describe the steps in transcription and translation that produce proteins.

 Transcription is making RNA from a DNA template. Transcription begins when RNA polymerase attaches to a region of DNA called a promoter. A promoter defines the start of transcription, the direction of transcription and the strand to be transcribed.

Translation is making a protein based codon sequence of mRNA. This takes place in the ribosomes. Transfer RNA brings amino acids to ribosomes one at a time and ribosomes bind them into a chain. Translation starts at a start codon and stops at a stop codon.

4. What is the start codon for translation? List the stop codons for translation.

 Stop codons: UAA  UGA  UAG

1. Briefly describe the difference between heterochromatin and euchromatin.

 Heterochromatin is tightly packed and inactive and euchromatin is lightly packed and active.

2. Briefly describe the difference between transcription factors and transcription activators.

 Transcription factors are proteins that help regulate transcription by assisting the binding of RNA polymerase to the promoter. Transcription activators bind to regions of DNA called enhancers, which may be located some distance from the promoter. So overall they are similar in the fact that they are both DNA-binding proteins, and the difference is where they bind.

3. Briefly describe the various ways in which eukaryotes control gene expression.

Transcriptional control: transcription factors help RNA polymerase bind DNA at promoter region more transcription leading to more transcription. Transcription activators bind DNA at enhancor regions and also lead to more transcription. Absence of these factors leads to less transcription

1. Define a clone.

 A clone is an exact copy of a gene, cell, or organism.

2. Briefly describe how a restriction enzyme works, including its function in bacteria.

 Restriction enzyme is made by bacteria to cut up foreign DNA. They cut DNA at the recognition sequence.

3. Briefly describe the steps in the process of DNA fingerprinting, including using PCR to obtain DNA and analyzing STRs.

 DNA fingerprinting uses PCR to make copies of short tandem repeats (STRs) and compare DNA from two different sources to see if they have the same number of repeats.

4. Briefly describe the steps in the procedure for cloning a gene.

Cut chromosomes and plasmid with restriction enzyme. This creates “sticky ends.: Place two pieces of DNA in the same sticky tube and they stick together because of complementary base pairing. Put recombinant plasmid into bacteria. Bacteria makes protein gene code for DNA sequencing which is a procedure used to determine the order of nucleotides in a DNA segment.

1. Define evolution

 Evolution is the change in the gene pool of populations over time.

2. List the components of the Theory of Evolution Through Natural Selection.

 Organisms exhibit variation that can be passed from one generation to the next — that is, they have heritable variation.

Organisms compete for available resources.

Individuals within a population differ in terms of their reproductive success.

Organisms become adapted to conditions as the environment changes.

3. Briefly describe the different types of evidence for Evolution.

Fossils: Show animals that resemble animals of today but are not the exact same. Show animals that resemble extinct animals as well as animals that live today.

Biogeographical evidence: Geography separates continents and you have a different mix of organisms.

Anatomical evidence: Holly’s structures have similar structure due to common ancestor.

Biochemical evidence: Every organism uses DNA, uses the same genetic code, and uses ATP. 

Development biology: Hox genes control development of embryos. There are hox genes in every animal. There are different numbers and types in different animals, but all of them have them.

1. Define the following

   1. Population: A group of organisms of a single species living together in the same geographical area.

   2. Microevolution: The change in allele frequencies in a population over time.

   3. Gene pool: All the alleles of all the genes in all the individuals in a population.

2. Briefly describe the factors that can change allele frequencies in a population.

 No mutation: No new alleles can arise by mutation.

No migration: No new members (and their alleles) can join the population, and no existing members can leave the population.

Large gene pool: The population is very large.

Random mating: Individuals select mates at random; mate choice is not biased by genotypes or phenotypes.

No selection: The process of natural selection does not favor one genotype over another.

3. Briefly describe the modes of natural selection.

 Stabilizing: Favors average over either extreme.

Directional: Favors one extreme over average and other extreme.

Disruptive: Favors either extreme over average.

1. Define biological species.

 Biological species is a group of organisms that successfully reproduce.

2. Briefly describe the reproductive isolation mechanisms that prevent two groups from interbreeding.

 Habitat Isolation: Species at the same locale occupy different habitats

Temporal Isolation: Species reproduce at different times.

Behavioral Isolation: Courtship behaviors make them unattracted to each other.

Mechanical Isolation: Genitals don’t match up.

Gamete Isolation: Sperm cannot fertilize the egg.

Zygote mortality: Zygote does not survive.

Hybrid Sterility: Offspring is sterile.

F2 Fitness: Second generation does not survive or is sterile.

3. Define the following:

   1. Speciation: The splitting of one species into two or more species

   2. Allopatric speciation: Populations separated by geographic barrier. They evolve into separate species.

   3. Sympatric speciation: Populations not separated by geographic barrier. Can lead to speciation in plants.

   4. Adaptive radiation: One species gives rise to several new species when introduced to a new environment.

Start codon: AUG(methionine)

Structure of DNA DNA (deoxyribonucleic acid) is a double-stranded polymer made up of nucleotides, which are the building blocks of this genetic material. Each nucleotide consists of three components: a phosphate group, a five-carbon sugar (deoxyribose), and a nitrogen-containing base (adenine, thymine, cytosine, or guanine). The two strands of DNA are oriented in an antiparallel manner, with the sugar and phosphate forming the backbone of each strand. In the center, nitrogenous bases pair specifically through hydrogen bonds, following the complementary base pairing rules: adenine (A) pairs with thymine (T) and cytosine (C) pairs with guanine (G). This double helix structure was first described by James Watson and Francis Crick in 1953 and is fundamental to the replication and expression of genetic information.

DNA Replication DNA replication is a precise process that occurs before a cell divides, ensuring that each new cell receives an identical copy of the DNA. The process begins with the unwinding of the double helix by the enzyme helicase, which separates the two strands. Single-strand binding proteins then stabilize the unwound strands to prevent re-annealing. Next, the enzyme DNA polymerase synthesizes a new complementary strand by adding nucleotides one at a time, using one of the original strands as a template. This process occurs in the 5' to 3' direction, and RNA primers are required to initiate synthesis. The result is two identical DNA molecules, each consisting of one old strand and one newly synthesized strand, a method known as semiconservative replication.

Transcription and Translation Transcription is the first step in gene expression, where RNA is synthesized from a DNA template. It begins when RNA polymerase binds to a specific region on the DNA called the promoter, which marks the start of the gene to be transcribed. The DNA unwinds, and RNA polymerase reads the DNA template strand, synthesizing a single strand of messenger RNA (mRNA) by adding complementary ribonucleotides. This process modifies the initial mRNA transcript through capping, polyadenylation, and splicing to produce a mature mRNA molecule that exits the nucleus.

Translation occurs in the ribosomes, where the mRNA is read in codons, each consisting of three nucleotides. Transfer RNA (tRNA) molecules transport specific amino acids to the ribosome, matching their anticodon with the corresponding codon on the mRNA. This process begins at the start codon (AUG, which codes for methionine) and concludes at one of the three stop codons (UAA, UGA, UAG). As the ribosome moves along the mRNA, it facilitates the formation of peptide bonds between amino acids, creating a polypeptide chain that folds into a functional protein.

Heterochromatin vs. Euchromatin Heterochromatin and euchromatin represent two types of chromatin in the nucleus. Heterochromatin is densely packed and transcriptionally inactive, often found at the nuclear periphery. Its structure is essential for maintaining chromosome stability and regulating gene expression. In contrast, euchromatin is loosely packed and transcriptionally active, allowing genes to be expressed more readily. The dynamic balance between these two forms of chromatin is crucial for proper gene regulation and cellular function.

Transcription Factors vs. Transcription Activators Transcription factors are a broad category of proteins that facilitate or inhibit the transcription of specific genes by binding to nearby DNA. They are essential for the recruitment of RNA polymerase to the promoter region, where transcription initiates. In contrast, transcription activators are a subset of transcription factors that specifically enhance gene transcription by binding to enhancer regions, which can be located far from the promoter. Together, these proteins play a vital role in the intricate regulation of gene expression in eukaryotic cells.

Eukaryotic Gene Expression Control Eukaryotes utilize multiple layers of control to manage gene expression, including transcriptional control via transcription factors and activators, as well as post-transcriptional regulation such as mRNA splicing, editing, and degradation. Additionally, epigenetic modifications, including DNA methylation and histone modification, can influence gene expression without altering the underlying DNA sequence, providing another layer of regulation in response to environmental signals.

Definition of a Clone A clone is defined as a genetically identical copy of a gene, cell, or organism. Cloning techniques can be applied in various fields, including biotechnology and medicine, for purposes such as therapeutic cloning and the production of genetically modified organisms.

Function of Restriction Enzymes Restriction enzymes, produced by bacteria, are biological tools that cut DNA at specific recognition sequences. These enzymes defend against foreign DNA such as viruses by cleaving it, but they are also utilized in molecular biology for cloning and genetic engineering, allowing scientists to manipulate DNA fragments with precision.

Steps in DNA Fingerprinting DNA fingerprinting is a forensic technique used to identify individuals based on their unique DNA profiles. The process typically begins with the extraction of DNA from a sample, followed by the amplification of specific regions through polymerase chain reaction (PCR). Short tandem repeats (STRs) are then analyzed; these are repeating sequences of DNA that vary in number among individuals. By comparing the STR patterns from different individuals, scientists can determine genetic similarities and differences, aiding in identification and paternity testing.

Cloning a Gene The procedure for cloning a gene involves several steps: First, restriction enzymes are used to cut the DNA of interest and a plasmid vector to create complementary “sticky ends.” The gene of interest is then ligated into the plasmid, forming recombinant DNA. This recombinant plasmid is introduced into bacterial cells, which replicate the plasmid during cell division and express the gene, resulting in the production of the corresponding protein. The success of gene cloning is monitored through molecular analysis methods.

Definition of Evolution Evolution refers to the change in the gene pool of populations over time, driven by mechanisms such as natural selection, mutation, gene flow, and genetic drift. This process accounts for the diversity of life on Earth and the adaptation of organisms to their environments over generations.

Theory of Evolution Through Natural Selection The Theory of Evolution Through Natural Selection is framed by several key components:

• Variation: Organisms exhibit heritable variation that can be passed down to offspring.

• Competition: Individuals compete for limited resources necessary for survival and reproduction.

• Reproductive Success: Some individuals reproduce more successfully than others based on advantageous traits.

• Adaptation: As environments change, populations adapt, leading to evolutionary changes over time.

Evidence for Evolution Different types of evidence support the theory of evolution, including:

• Fossils: Provide historical records of life forms, showing transitions and common ancestors.

• Biogeography: The geographical distribution of species illustrates how populations adapt to different environments.

• Anatomical Evidence: Homologous structures indicate evolutionary relationships among different species.

• Biochemical Evidence: Conservation of DNA, RNA, and ATP across diverse life forms points to a common ancestry.

• Developmental Biology: Similar genes (such as Hox genes) that control embryonic development in various species suggest shared evolutionary paths.

Definitions in Population Genetics

• Population: A group of organisms of the same species living in the same area, capable of interbreeding.

• Microevolution: Small-scale evolutionary changes within a population, often measured by changes in allele frequencies over time.

• Gene Pool: The total collection of alleles in a population at any given time.

Factors Influencing Allele Frequencies Allele frequencies in a population can change due to several factors, including:

• Mutation: The introduction of new alleles through genetic changes.

• Migration: The movement of individuals into or out of a population, altering allele composition.

• Population Size: Small populations are more susceptible to genetic drift, impacting allele frequencies.

• Mating Patterns: Non-random mating can affect the distribution of genotypes.

• Natural Selection: Differential survival and reproduction based on advantageous traits leads to changes in allele frequencies.

Modes of Natural Selection Natural selection operates through different modes:

• Stabilizing Selection: Favors average phenotypes, reducing extremes.

• Directional Selection: Favors one extreme phenotype over others, leading to shifts in trait distribution.

• Disruptive Selection: Favors extreme phenotypes at both ends, potentially leading to speciation.

Definition of Biological Species A biological species is defined as a group of organisms that can interbreed and produce viable, fertile offspring, thereby sharing a common gene pool.

Reproductive Isolation Mechanisms Reproductive isolation prevents different species from interbreeding and includes:

• Habitat Isolation: Species inhabit different environments within the same area.

• Temporal Isolation: Species breed at different times.

• Behavioral Isolation: Unique courtship behaviors prevent mating.

• Mechanical Isolation: Incompatible reproductive structures prevent mating.

• Gamete Isolation: Sperm and egg cannot fertilize.

• Zygote Mortality: Hybrid zygote does not develop properly.

• Hybrid Sterility: Offspring produced are sterile (e.g., mules).

• F2 Fitness: Hybrid offspring have reduced survival or fertility in the next generation.

Definitions of Speciation

• Speciation: The evolutionary process by which populations evolve to become distinct species.

• Allopatric Speciation: Occurs when populations are separated by geographical barriers leading to reproductive isolation.

• Sympatric Speciation: Occurs without geographical separation, often through mechanisms like polyploidy in plants.

• Adaptive Radiation: Rapid evolution of diverse species from a common ancestor when introduced to new environments.