Exam 1 Review

methyl group

-CH3 Compound name: methylated compound Affects gene expression as well as the shape and function of sex hormones.

carboxyl group

-COOH (C double bonded to O and single to -OH) Acts as an acid (carboxylic acid or organic acid). Can donate an hydrogen ion.

hydroxyl group

-OH A functional group consisting of a hydrogen atom joined to an oxygen atom by a polar covalent bond. Molecules possessing this group are soluble in water and are called alcohols.

phosphate group

-OPO3^2- (PO4^2-) Compound name: organic phosphate Releases energy and gives negative charges. Allows molecule to react with water. Is an important signaling molecule.

sulfhydryl group

-SH Compound name: Thiol Can form cross links with each other to help stabilize protein structure.

List the four emergent properties of water and explain how each come about.

1. Cohesion (adhesion) - cohesion is the ability of water molecules to pull themselves together via hydrogen bonds. Responsible for water tension. 2. High specific heat - makes water a climate moderator. Due to hydrogen bonds, water has an unusually high specific heat (to raise or lower 1g of a substance by 1 degree C) 3. Solid is less dense than liquid form allowing ice to float. the molecules of water when frozen are more spread out and defined than the typical 'chaos' of liquid water. 4. Universal solvent - thanks to the polarity of water molecules it is capable of dissolving most ionic compounds.

Describe four examples of structural isomers.

1. Length - a hydrocarbon chain isomer may contain an extra or one less carbon (and its accompanying hydrogens). 2. Branching - when a carbon breaks the linear structure of the chain and 'branches' out. 3. Double Bonds - when carbons double bond to each other eliminating the availability of two additional hydrogen with each double bond. 4. Rings - hydrocarbons sometimes form rings for the sake of structural stability and can have many variations including double bonds as well.

carbonyl group

>C=O A chemical group present in aldehydes and ketones and consisting of a carbon atom double-bonded to an oxygen atom.

Condensation vs. Hydrolysis

A condensation reaction (aka dehydration) is the ejection of a water molecule to combine two molecules. Hydrolysis is the addition of a water molecule to break down a molecule.

Identify a glycosidic linkage and describe how it is formed.

A glycosidic linkage forms when two sugars are joined together by condensation.

Understand a history tree and what the dead ends signify.

A history tree shows how similar species are to one another based off common ancestors, anatomy, and DNA. A dead end signifies extinction of the species.

Monosaccharide vs disaccharide

A monosaccharide is simply a singular sugar where as a disaccharide is consists of two monosaccharides joined together.

saturated vs unsaturated fats, describe unique emergent properties of the two as consequence.

A saturated fat, typically found in animals, is an unhealthier fat that is solid at room temperature and shows direct correlation with increased heart failure. An unsaturated fat, typically made of vegetable fat and found in animals, contains double bonds that leads to kinks its shape. They are liquid at room temperature and typically much healthier than saturated fats. Trans fats - unsaturated fats turned into saturated to make for better marketing and utility. Peanut butter example - normal pb is liquid at room temp but was made into a trans fat so that it would be solid and easier to spread.

Describe the basic structure of an amino acid. Explain how amino acids may be grouped, according to the physical and chemical properties of the side chains (R groups).

An amino acid is comprised of an amino group and a carboxyl group bonded to a central carbon which is combined to a side chain (R) and Hydrogen

Explain why a biologist is interested in the atomic structure of an atom.

An atoms function all relies on its structure, just a slight change in structure can lead a molecule to have a completely different array of properties and functions.

Define isomer. Describe three types of isomers.

An isomer is a variation of structure from a molecule that consists of the same amount of atoms.

What is an isotope and how does it relate to fossil age records? What are some isotopes used.

An isotope is an unstable atom of an element that decays overtime, meaning the decay curve can be used to determine how old a fossil is. U235 Rb87 K40 C14

Describe the historical context of evolutionary theory. Be able to trace the early thoughts of Western culture up to and including natural theology.

Aristotle was the greatest early influence in Western society, suggesting that animals were permanent and had a place on a ladder of increasing complexity (scala naturae). Linneaeus developed the binomial format for naming species in the 1750's. He used a nesting system to classify species who were similar (i.e. genus) Cuvier proposes the theory of catastrophism in 1769, the idea that there are catastrophes that wipe out species and new ones arise that are similar to them, but not evolved from. Hutten proposes the theory of gradualism in 1790 stating that over long periods of time, small changes will gradually occur. A few years later 1798, Malthus publishes his "Essay on the Principle of Population," basically stating that populations are growing too fast for how little the production of food is happening, insinuating that life will run out of food at some point. Natural Theology, published by William Paley in 1802 (7 years before Darwin was born), suggested that life needed a skilled designer who could only be God.

Define atomic number, mass number, and isotopes.

Atomic number - Number of protons Mass number - sum of protons and neutrons Atomic Mass - weighted, relative mass based of isotope abundances and weights. Isotope - an atom with a differing number of neutrons than that of the accepted atom

Explain the key to an atom's chemical characteristics.

Atoms chemical characteristics come from their amount of valence electrons. This dictates how reactive they are, how many other atoms can react to it as well as which atoms can react to it.

Describe antibiotic resistance and pesticide resistance and how they come about.

Bacteria and pests are treated with antibiotics and pesticides to wipe them off. However, some of these organisms are randomly born with a gene that allows them to survive these treatments. This leads to them repopulating and forming offspring with this gene until it has spread to the majority of the population and are resistant to treatments.

Explain the function of chaperonins and the importance of protein folding.

Chaperonins are containers that aid the process of protein folding by keeping the chains inside until finished. Folding is important because if done wrong then the entire protein can cause severe issues for the body.

Describe a specific compound and explain the emergent property found.

Chlorine is typically a poisonous gas, but when combined with sodium it becomes nontoxic and edible.

Explain the differences between covalent, ionic, hydrogen bonds, and Van der Waals forces.

Covalent Bond - the sharing of electrons between two molecules that occurs between two nonmetals. Ionic Bond - the transferring of an electron from a metal to a nonmetal. Hydrogen bonds - the covalent bonding that occurs between water molecules as well as other polar, electronegative atoms due to the polarity of the atoms in the molecule. Typically weak bonds that are constantly breaking and reforming. Van der Waals forces - occurrences in which electrons are transiently distributed to give fleeting moments of polarity to cause temporary bondings with other atoms.

Be able to explain the argument for descent with modification and natural selection.

D.W.M - believed that there was one common ancestor that all organisms came from. The farther away from the common ancestor, the more changes the organism has. The closer the organisms the more similar to one another. Natural selection - theory that species continue to populate and flourish due to their accumulation of desirable traits in their environment. Organisms that are more suited for their habitat produce many offspring. Favorable traits accumulate over time.

Explain how the principle of gradualism and Charles Lyell's theory of uniformitarianism influenced Darwin's ideas about evolution.

Darwin thought that if their theories meant that this change can occur to Earth, small changes over large periods of time, then the same could happen to animals.

Define denaturation and explain how proteins may be denatured

Denaturation is when a protein loses its shape and therefore its function. This can occur when there are drastic changes in pH and temperature, or even errors in folding.

Explain Darwin's two major points from "The Origin of the Species."

Descent with modification - the theory that species descended from a common ancestor and acquired small adaptations throughout generations. Natural selection - theory that species continue to populate and flourish due to their accumulation of desirable traits in their environment.

Structure and function of polysaccharides

Exs. Starch (plants), Glycogen (animal), Cellulose (plant, beta glucose) Polysaccharides are long chains of combined sugars that are used to store energy and provide stability.

Describe the unique properties, building-block molecules, and biological importance of the three important groups of lipids: fats, phospholipids, steroids.

Fats are made from fatty acid tails attached to glycerol by ester linkages (formed by dehydration). Fats are good storage unit of energy. Phospholipids are made of a hydrophilic, glycerol head and hydrophobic fatty acid tails. They are great for structure (phospholipid bilayers). Steroids - are good for regulation and cell ID. Cholesterol is the most common steroid and is where many hormones are synthesized from.

Describe the various examples used as evidence for evolution and natural selection.

Finches, Andes mountains fossils. bio geography, pesticides and antibiotics, anatomy of organisms, dna, radiometric dating

Identify a peptide bond and explain how it is formed.

Formed by dehydration between amino acids.

How has the fossil record been used for evidence of evolution.

Fossils show that organisms who appear similar but have different characteristics come from different time periods suggesting ancestry and evolution. Fossils found closer to the surface being newer, deeper older. Fossils show chronological appearance of vertebrates in sequence with fish than amphibians. (relative dating)

Explain how functional groups add to the distinctive properties of organic molecules. Give a specific molecular example.

Functional groups are the components of organic molecules that are most commonly involved in chemical reactions. The number of and arrangement of these groups is what gives them unique properties. For example, the addition of a hydroxide group to a hormone molecule turns it into estrogen rather than testosterone, giving the bearer more feminine characteristics as well as functions.

Distinguish between the glycosidic linkages found in starch and cellulose and describe why the differences are biologically important.

Glycosidic linkages in starch occur between alpha glucose which leads to bends and turns in the chain making for weaker and easier to break bonds for easy energy access. In cellulose, the bonds are more rigid and straight amongst beta glucose leading to form indestructible fiber and provide support to plants. (used in chitin to form exoskeletons and suture.)

Explain what a half-life is and how to interpret a radioactive isotope decay curve.

Half-life is a 'daughter isotope' or 50% of the original isotope. There are multiple half lives until the isotope is virtually finished decaying. The decay curve on a graph represents how much of the isotope is left and where the half lives are located along the x axis.

Using hemoglobin as an example, describe quaternary protein structure.

Hemoglobin has four subunits, each containing a Heme group that has an iron group within it. Each iron group can carry an oxygen molecule, therefore hemoglobin is capable of carrying up to 4 oxygen molecules at a time.

Describe how Darwin used his observations from the voyage of the HMS Beagle to formulate and support his theory of evolution.

His most known is the use of Finches in a family tree. By studying these finches he was able to support his hypothesis by showing how the beaks of finches were best suited to their diets. This meaning that depending on where the common ancestor finch found itself, it would adapt to available diets by changing the form of its beak to make eating easier. (Galapagos islands)

Explain why inert elements are so stable.

Inert elements, a.k.a the noble gases, have a full valence shell of 8 electrons. They are already stable and do not search to gain or lose any electrons as it would throw off their balance.

Why is the valence shell important?

It determines many of an atoms chemical properties.

Explain why carbon is able to form such diverse molecules.

It has 4 valence electrons meaning that it can bond with up to four other atoms.

Explain differences between Darwin and Lamarck's theories.

Lamarck believed in use and disuse, that if an organism used a feature it would improve on it and rid of it if not. He believed this to happen throughout an organisms lifetime. (Epigenetics) Darwin theorized that organisms are born randomly with specifics traits and characteristics rather than forming these adaptations in their lifetime.

Describe what distinguishes lipids from other macromolecules.

Lipids are distinguishable because they do not interact with water, which is why they are grouped together. they are not true polymers.

Explain how an essay by the Rev. Thomas Malthus influenced Charles Darwin.

Malthus's work made Darwin consider why species become overpopulated. This led him to study and eventually lead him to theorize natural selection.

Explain a possible origin of organic molecules. Describe any evidence for this idea.

Miller and Urey conducted an experiment that mimicked the conditions of a volcanic eruption. Upon analyzing the inorganic sample used, it was found that amino acids had been formed.

Describe, with a specific example, how molecular structure affects function.

Natural endorphin and engineered morphine have the same signaling/'key' molecule that both fit into endorphin receptors. By modifying the morphine molecule it tricks the body into accepting the morphine to help ease pain.

Explain how natural selection results in evolutionary change with the aid of contemporary examples.

Natural selection leads to organisms with favorable traits to keep passing on these traits to offspring and creating organisms much better suited to their environment. These traits are improved upon leading to evolutionary change. 1. Due to global warming, typically colder climate inhabiting animals such as owls are becoming better suited to warmer climates. 2. Green Anole Lizards adapted larger toe pads and scales to be able to climb higher branches and avoid competition with Brown Anole Lizards.

What are emergent properties?

New properties that arise with each step upward in the hierarchy of life, owing to the arrangement and interactions of parts as complexity increases.

Explain the abiotic synthesis theory of Oparin and Haldane and explain the Miller and Urey experiment that examined the theory.

Oparin and Haldane came up with the primordial soup theory, suggesting that the first life existed in a set of seemingly unsuitable conditions on earth 4 billion years ago. Miller and Urey simulated these conditions and caused a reaction that simulated being near a volcano in their experiment. When viewing the primordial soup sample, they were able to identify amino acids, the building blocks of organic life.

Describe the properties of life

Order, Evolutionary Adaptation, Response to Environment, Reproduction, Growth and Development, Energy Processing, Regulation.

Explain the five unifying themes of biology

Organization -new properties emerge at successive levels of biological organization (emergent properties, structure and function, the cell is the basic unit of life) Information -life processes involve expression and transmission of genetic information (DNA, genomics) Energy and matter - life requires transfer and transformation of energy and matter (consumers & producers) Interactions - important in biological systems (internal- feedback; external-detect environment) Evolution & natural selection -core that accounts for unity and diversity.

Polymers vs. Monomers

Polymer means many monomers. Sometimes polymers are also known as macromolecules or large-sized molecules. Usually, polymers are organic (but not necessarily). A monomer is a molecule that is able to bond in long chains.

How does radiometric dating work?

Post 1950's - lead to absolute dating. Exact date can be told. By knowing the half lives of isotopes and comparing this to the isotopes found in the fossils of organisms, exact dates can be determined from when the organism died.

Explain the key events in the timeline of life evolving.

Prokaryotes existed first. They began to use photosynthesis. Single celled eukaryotes exist. Multicellular eukaryotes exist Animals are formed (Paleozoic(colonization of land), Mesozoic, Cenozoic) Humans

Explain what determines protein conformation and why it is important. Define primary structure and describe how it may be deduced in the laboratory. Describe the two types of secondary protein structure. Explain the role of hydrogen bonds in maintaining the structure. Explain the quaternary protein structure.

Protein conformation is determined by a proteins ability to recognize and bond with another protein and is important because without this ability a protein can bond to or not bond to other proteins leading to denaturation or issues with the chain. Primary structure is a nonfunctional, specific sequence of amino acids that gives rise to secondary structure. Can be deduced by reading the gene expressed with the chain off the mRNA. The two types include a pleated sheet form which stabilized with other sheets via H bonds. Then there is the helix shape. Tertiary structure is when the chain begins to fold in on itself and form bridges and many other forms of bonds with itself to stabilize and give rise to a functioning protein with 3-D structure. (ribbon) Quaternary Structure - Where subunit tertiaries come together to form complex bundles of proteins forming units such as hemoglobin.

Describe characteristics that distinguish proteins from the other major classes of macromolecules and explain the biologically important functions of this group.

Proteins are important because they have a much wider array of function than other macromolecules including enzymatic proteins, defensive, storage, transport, hormonal, receptor, contractile and motor, and structural proteins. Proteins are vital because they account for many of the properties and functions of the body. A single misplaced monomer (amino acid) can cause diseases in the body that can prove fatal (i.e. sickle cell disease).

Describe the ethical concerns scientists need to consider and have some specific examples of how ethical concerns are safeguarded

Scientist need to consider if what they are testing and how is a threat to the health and well being of test subjects, most likely the case in animals. Now experiments are sent to committees that will take into consideration the ethicality and importance of the study to determine whether or not it will be conducted (i.e. Institutional Animal Care and Use Committee)

What does "structure and function are related" mean?

Structure compliments function. For example, a hummingbird is able to rotate its wings around its shoulder (this being the structure), allowing it to basically float and move in all directions (function).

Explain the pH scale.

The PH scale is a scale of values from 0 to 14, used to measure the concentration of h+ ions in a solution. A PH of 0 to 7 is acidic, a PH of 7 is neutral, and a pH of 7 to 14 is basic.

Explain how biogeography influenced Darwin and know examples used as proof of evolution.

The common ancestor located on Pangaea faced many different changes as continental drift occurred and land masses moved to different parts of the Earth, they had to adapt to those environments. Andes mountains, ocean fossils.

How do different half-lives of elements affect their use in fossil records.

The larger the isotope the longer it takes to decay, meaning that half lives are not the same between elements. The number half life also indicates the stage, the second half life means the isotope is at 25% mass not gone.

Explain how Cuvier and his followers used the concept of catastrophism to oppose the theory of evolution.

They believed that every once in a while there was a catastrophy that wiped out species and that new ones who were similar but now evolved from them replaced them. This was to argue fossils.

Describe the types of items you would use to judge the validity of a scientific study

Was there a testable hypothesis? Was there a fitting sample size? Was there a control group and a test group?

Explain the process of water dissociation.

Water dissociation is a rare process in which a hydrogen from a water becomes detached from a molecule and attaches to the molecule previously bonded to it. This leads to reactive hydronium and hydroxide ions.

Explain weak interactions and disulfide bridges contribute to tertiary protein structure.

Weak interactions as well as strong interactions occur between side chains of amino acids who can be hundreds of monomers away so that the chain begins to fold itself and keep a strong and specific structure that leads to different functions.

Explain the movement of electrons from one shell (orbital) to another.

When electrons gain energy the move to the outer orbitals of the atoms, when they lose energy they fall to the orbitals closer to the nucleus.

Define reductionism

a strategy in biology of reducing complex systems to simpler components that are more manageable to study

Describe the levels of biological organization

biosphere, ecosystem, community, population, organism, organ system, organ, tissue, cell, organelle, molecule, atom

4 major classes of macromolecules

carbohydrates, lipids, proteins, nucleic acids

Define Biology

the scientific study of life

Define organic chemistry.

the study of most carbon-containing compounds.

amino group

—NH2 a functional group composed of nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. Can act as a base in solution, accepting a hydrogen ion and acquiring a charge of +1. Compound is referred to as an Amine