Semester 2 Finals

Living Earth

Griffith and Transformation

The transformation experiment showed that bacteria can share genetic material.

A harmless type of bacteria became deadly after it was mixed with dead, harmful bacteria. This happened because something from the dead bacteria—called the "transforming principle"—changed the harmless ones.

The mice were injected with different combinations of harmless and deadly bacteria—some alive, some heat-killed—to see how they affected the mice.

Avery and DNA

Avery’s experiment showed that DNA is the "transforming principle" by proving that only DNA, not proteins, could change harmless bacteria into harmful ones.

Avery mixed parts of dead deadly bacteria with harmless ones and found that only DNA caused the harmless bacteria to become deadly.

The Hershey-Chase Experiment

Avery’s experiment showed that DNA is the "transforming principle" by proving that only DNA, not proteins, could change harmless bacteria into harmful ones.

Avery mixed parts of dead deadly bacteria with harmless ones and found that only DNA caused the harmless bacteria to become deadly.

Structure of virus

Composed of a nucleic acid genome (DNA or RNA) enclosed within a protein coat called a capsid, and some viruses may also have an outer lipid envelope.

Bacteriophages

Is a virus that infect and replicate only in bacterial cells

Bacteriophages are smaller than bacteria.

This virus was used in Hershey and Chase’s experiments which showed that when bacteriophages, which are composed of DNA and protein, infect bacteria, their DNA enters the host bacterial cell, but most of their protein does not

Nucleic Acid-types

Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA).

DNA is the genetic material found in all living organisms, while RNA plays a crucial role in protein synthesis and other cellular processes.

Structure of DNA versus RNA

DNA is double-stranded, forming a double helix, while RNA is usually single-stranded. DNA contains deoxyribose sugar, whereas RNA contains ribose sugar.

Nucleotides versus atp molecule

Nucleotides are the building blocks of DNA and RNA. Each nucleotide has three parts: a sugar, a phosphate group, and a nitrogen base.

ATP (adenosine triphosphate) is a nucleotide that stores and provides energy for cells. It has three phosphate groups and is used as the cell’s energy currency.

Nucleotides differ from ATP in that they consist of a single unit for genetic material, whereas ATP is a multi-part molecule specifically designed for energy transfer.

Purines

Adenine and Guanine (two-carbon nitrogen ring bases)

Pyrimidines

Thymine and Cytosine (one-carbon nitrogen ring bases)

Chargaff’s rules

In any double-stranded DNA, the number of adenine (A) units equals the number of thymine (T) units, and the number of guanine (G) units equals the number of cytosine (C) units.

Rosalind Franklin’s work

Worked as an x-ray crystallographer and took the photograph called “Photo 51” which revealed the double helix of DNA — a discovery that was essential in unlocking the mystery to how life is passed down from generation to generation.

DNA and chromosomes (prokaryotes versus eukaryotes)

Prokaryotes typically have a single, circular chromosome located in the cytoplasm within a region called the nucleoid.

Eukaryotes, on the other hand, have multiple, linear chromosomes housed within a membrane-bound nucleus, and their DNA is tightly packaged with proteins called histones.

Eukaryotic chromosome structure- histones, chromatin, nucleosome

DNA wraps around proteins called histones, forming nucleosomes.

Nucleosomes coil into chromatin, which further folds into chromosomes.

DNA replication steps

1. Topoisomerase unwinds and relieves tension in DNA.

2. Helicase unzips the DNA strands.

3. Primase adds RNA primers to start replication.

4. DNA polymerase builds the new DNA strand.

5. Exonuclease removes RNA primers.

6. Ligase seals gaps between DNA fragments.

Topoisomerase

Enzymes that remove supercoiling at the replication fork by introducing cuts in DNA strands

Helicase

Enzymes that unwind double-stranded nucleic acids (DNA or RNA) into single strands.

Primase

An enzyme that synthesizes short RNA sequences called primers

DNA polymerase

Enzymes that create DNA molecules by assembling nucleotides

Exonuclease

Enzymes that remove nucleotides one by one from the ends (exo) of DNA or RNA

Ligase

An enzyme that catalyzes the joining of two molecules by forming a new chemical bond

Semiconservative replication

Each new DNA molecule has one original strand and one new strand.

What is the central dogma of biology

A theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein.

Structure and types of RNA and their role

mRNA: carries instructions from DNA.

tRNA: brings amino acids to build proteins.

rRNA: part of ribosomes where proteins are made.

Steps of protein synthesis, transcription, and translation, and key enzymes

Transcription: RNA polymerase copies DNA into mRNA.

Translation: Ribosomes read mRNA to make proteins.

RNA editing

Introns (non-coding parts) are removed.

Exons (coding parts) are joined together.

Codon

3 bases on mRNA.

Anticodon

matching 3 bases on tRNA.

HOW DOES RNA POLYMERASE KNOW WHERE TO START or to STOP

It binds to specific promoter sequences to start and terminator sequences to stop.

Mutation

A change in DNA sequence.

Gene mutation

Changes in a single gene.

Chromosome mutations

Changes in whole chromosomes.

How do mutations appear?

Mistakes during DNA replication or from environmental factors like radiation.

Silent mutations

Mutations that don’t change the protein.

Are all mutations harmful? Significance of mutations

No, some are harmless or even beneficial. Helps with evolution and natural selection.

Why might farmers induce mutations in their crops?

To create new crop traits like disease resistance or better yield.

Missense mutation:

One base changes, and it does change the amino acid.

Can change how the protein works.

Example: sickle cell anemia.

Nonsense mutation:

A base change causes a stop codon too early.

Makes the protein too short and usually nonfunctional.

Frameshift Mutations:

Caused by insertion (adding a base) or deletion (removing a base).

Since codons are read in 3s, adding or removing a base shifts everything, changing many amino acids after that point.

Usually causes a big change in the protein or makes it nonfunctional.

Theory of Evolution:

The idea that species change over time through natural processes like natural selection.

Fossils:

Preserved remains of ancient organisms; they show how species have changed over time.

Descent with Modification:

Living species are descended from common ancestors, but with changes (modifications) over generations.

Gene Pool:

All the genes (and their different versions) in a population.

Relative Frequency:

How often a certain allele (gene version) appears in a population compared to other alleles.

Fitness:

An organism’s ability to survive and reproduce in its environment.

More fit = more likely to pass on genes.

Single-Gene Trait:

A trait controlled by one gene, often showing only a few distinct outcomes (like widow's peak or not).

Polygenic Trait:

Controlled by many genes, creating a wide range of variations (like height or skin color).

Gradualism:

Evolution happens slowly over long periods of time with small changes.

Catastrophism:

Sudden disasters (like volcanoes or floods) cause big changes and can lead to fast evolution or extinctions.

Developmental Genes:

Control how an organism’s body forms during development (like where arms, legs, eyes go).

Body Plans:

The general layout of an organism’s body (like head-tail, back-belly, symmetry).

Hox Genes:

A special group of developmental genes that control the basic body structure in many animals.

Example: they help decide where the head, legs, or wings go.

Who is Charles Darwin, and what did he do?

A naturalist who developed the theory of evolution by natural selection.

He traveled on the HMS Beagle, studied plants and animals (especially in the Galápagos Islands), and wrote On the Origin of Species.

Compare and contrast Darwin and Lamarck’s theories.

Darwin	Lamarck
Evolution happens through natural selection.	Evolution happens through use and disuse.
Traits that help survival get passed on.	Traits are gained during life and passed on (not true).
Example: Giraffes with longer necks survive and reproduce.	Example: Giraffes stretch their necks and pass that on.
Based on variation and genetics.	Based on need and effort.

Thomas Malthus:

Populations grow faster than resources; leads to competition → only the fittest survive.

Alfred Wallace:

Developed a similar theory of evolution; pushed Darwin to publish his own ideas.

Charles Lyell:

Earth changes slowly over time → gave Darwin the idea that evolution also takes time.

Who influenced Darwin?

Thomas Malthus, Alfred Wallace, Charles Lyell

What ideas shaped Darwin’s thinking?

Earth is very old and changes gradually.

There is variation in traits among individuals.

More offspring are born than can survive.

Traits that help survival and reproduction become more common over time.

What is artificial selection, and humans’ role in it?

Humans choose which organisms reproduce based on desired traits.

Example: breeding dogs, cows, or crops.

It’s like natural selection, but humans are selecting instead of nature.

Evolution by natural selection

Organisms with traits that help them survive and reproduce pass those traits on.

Over time, those traits become more common in the population.

How & why are traits passed on from generation to generation?

Traits are passed through genes (DNA).

Traits that improve survival or reproduction are more likely to be inherited.

What type of evidence (that is available today) did Darwin lack that helped support his theory?

DNA and how traits were inherited.

Mutations as a source of variation.

Molecular evidence (like comparing DNA sequences).

Evolution involves change…describe what and how things change.

Over many generations, gene frequencies in a population change.

This can lead to new traits, new species, and extinction of others.

Explain why this statement is not accurate: “The light-peppered moths needed to adapt to the dark trees after the industrial revolution, so they decided to change their color to survive.”

Moths can’t decide to change.

Random mutations caused darker moths to appear.

In the new environment, darker moths survived better, so they became more common over time.

What is a common ancestor?

A species from the past that two or more species evolved from.

Example: Humans and chimps share a common ancestor.

What is natural selection? What MUST be present for natural selection to occur?

The process where organisms with favorable traits survive and reproduce more successfully.

What are the different pieces of evidence of evolution, and how do they serve as evidence of evolution?

Fossils

Comparative Anatomy (homologous, analogous, vestigial structures)

DNA & Molecular Evidence

Embryology

Hox Genes

Geographical Distribution (Biogeography)

What evidence do fossils provide for evolution?

Fossils show how species have changed over time.

They reveal transitional forms (like the shift from fish to amphibians).

Fossils are arranged by age in rock layers, showing gradual changes.

Homologous structures

Same structure, different function.

Shows common ancestry.

Examples:

• Human arm & bat wing

• Whale flipper & cat leg

Analogous structures

Same function, different structure.

Shows convergent evolution, not common ancestry.

Examples:

• Bird wing & insect wing

• Dolphin fin & shark fin

Vestigial organs.

Body parts that no longer serve a purpose but were useful in ancestors.

Shows evolutionary change over time.

Examples:

• Human appendix

• Pelvic bones in whales

What do homologous structures show about two organisms?

They suggest that two organisms share a common ancestor, even if they’ve evolved to live in different environments.

What is the most effective way to prove that two organisms are related? How do we compare two organisms’ DNA, and what does it mean if their DNA is similar?

The more similar the DNA, the more closely related the species are.

Example: Humans and chimps share about 98–99% of DNA.

Explain how studying DNA sequences (genes) helps scientists to determine which species are closely related

Scientists look at gene sequences and mutations.

If two species have similar genes or genetic codes, it means they likely evolved from a common ancestor.

The fewer differences, the more recent the split between the species.

Embryological evidence

Early-stage embryos of different animals look very similar.

Suggests they share developmental genes and a common ancestor.

Example:

• Fish, humans, and chickens all have gill slits and tails early on

Hox genes as evidence

Hox genes control the body layout (head, tail, limbs).

Found in almost all animals = shows common ancestry.

Small changes in Hox genes can cause big evolutionary changes in body structure.

Geographical distribution

Species living in similar environments may evolve similar traits (convergent evolution).

Island species often resemble nearby mainland species, showing common ancestry + isolation = evolution.

• Example: Darwin’s finches on the Galápagos Islands evolved from one ancestor but adapted to different niches.

Variation

Differences within a species (like hair color in humans).

Diversity

Differences between species or in an ecosystem (like birds, insects, and plants living in one forest).

How variation arises:

Through mutations, genetic recombination (during meiosis), and sexual reproduction.

Genetic drift

Random changes in allele frequencies, more likely in small populations (e.g., natural disaster wipes out part of a population).

Gene flow

Alleles move from one population to another through migration, increasing genetic variation.

Single-Gene Traits:

One gene = two phenotypes

• Example: black vs. white fur

Polygenic Traits:

Many genes = range of phenotypes (like height)

Directional

Favors one extreme (e.g., longer beaks)

Stabilizing

Favors the average (e.g., medium birth weight)

Disruptive

Favors both extremes (e.g., light and dark fur, but not medium)

Microevolution (small changes in a population):

Natural selection

Genetic drift

Gene flow

Mutation

Macroevolution (big changes over long time):

Mass extinction

Adaptive radiation

Speciation

Evolution versus genetic equilibrium

Evolution = allele frequencies change over time

Genetic Equilibrium = allele frequencies stay the same (no evolution)

Described by the Hardy-Weinberg principle

Five conditions to maintain genetic equilibrium

1. Large population

2. No mutations

3. Random mating

4. No migration (gene flow)

5. No natural selection

Process of speciation: isolating mechanisms

One species splits into two

Reproductive isolation must happen

Reproductive isolation can occur due to:

Behavioral isolation, geographic isolation, and temporal isolation

How did speciation happen in Darwin’s finches (what pattern of evolution)

Example of adaptive radiation

Evolved differently based on food sources and isolation

What is a cladogram, and how can we use it to determine common ancestry? How to draw and interpret a cladogram

A diagram that shows evolutionary relationships

Closer branches = more recent common ancestor

Use shared traits to build it

Describe the fossil record

Show organisms changed over time

Relative dating

Position in rock layers

Absolute dating

Radioactive isotopes for exact age

How do fossils form

When an organism dies and is quickly buried by sediment, usually mud or sand, in a watery environment.