Biology Exam 1

What are the 5 characteristics of life?

Cells, replication, adaption, regulation, metabolism/energy

What is the scientific method?

Observation, question, hypothesis, prediction and then an experiment to test hypothesis. A theory is an explanation for a specific phenomenon.

What are 3 types of reasoning?

Inductive (specific observations to general rule), deductive (general rule to specific observations), abductive (the most obvious explanation is usually the right one)

How to test a hypothesis?

Use a negative control to establish a baseline amount of signal (reference) which should not give a positive signal. Positive control which validates detection system which should produce a positive signal.

What is the scale of life?

An atom is 10 times smaller than a molecule which is 10 times smaller than organelles which are 10 times smaller than cells. A micrometer is a millionth of a meter. A nanometer is a billionth of a meter

Radiometric dating

Elements have patterns of decay. The half life measures how much of an element is left in a structure to measure how old it is

What are the 3 biggest questions about life throughout history?

Where did life come from? How are different species related or not? What’s the basic unit of life?

What are the theories on how life arose?

Spontaneous generation, primordial soup/chemical evolution.

What are the 2 ways life could’ve begun in the universe?

Exogenesis (life came from somewhere else in the universe and spread to Earth). Abiogensis (non-living matter created life).

Cell theory

Organisms are made of cells and all cells come from pre-existing cells.

The first cells had 2 traits

Organic chemicals with characteristics of life and cell membranes

What are the different abiogenesis theories on where life came from?

Lipid world hypothesis, RNA world hypothesis, RNA-Peptide world, panspermia.

Intense climatic shifts in Earth’s history

Cosmic bombardment, tectonic shifts, snowball earth, oxygen catastrophe, stomatolites, cambrian explosion

How old is the planet and when did life first appear?

4.5 billion years old. Life appeared 3.7 billion years ago

Lamarck’s discoveries

Organisms evolve by acquiring traits and passing them to offspring.

Darwin and Wallace’s discoveries

Life evolved from a common ancestor. Creatures of the same species can mate to achieve various characteristics which can be passed down

What are the 2 claims of evolution?

Universal common descent (every living organism alive today is descended from a common ancestor). Descent with modification (species change over time; natural selection, mutation, genetic drift, migration, recombination)

Natural selection

Variants exist but environment determines what survives or doesn’t. There’s no external force ‘doing’ natural selection. Heritable variations increase or decrease organism’s ability to reproduce. Variation is created by mutations which are selected in reproduction and increase likelihood of successful reproduction are passed on to future generations

How long does evolution take (micro vs macro)?

Small observable changes in genotypes/phenotypes within population’s gene pool vs. the sum of microevolution when new species arise over a long period of time

What’s the evidence for common ancestry?

Fossil record, radiometric dating, biogeography, homology (similarities in gene sequences of amino acids and bone structure of species alive today)

What’s the evidence for descent with modification?

Mutation, genetic drift (pure chance can have an outsized impact on small sample sizes)

What are macromolecules?

The building blocks of life. Chemistry and function have an intimate relationship. Lipids, carbohydrates, proteins and nucleic acids.

Structure and function of lipids:

Polymers of fatty acids + glycerol (monomers). Lipids contribute to membrane structure and provide energy

Structure and function of carbohydrates:

Polymers of monosaccharides (6 carbon + 12 hydrogen + 6 oxygen) bound by glycosidic bonds. Function of carbs is storing energy and contributing to cel structure

Structure and function of protiens:

Polymers of amino acids (carbon atom + H + COOH + NH2 amino group + r-group) joined by peptide bonds. Proteins contribute to cell structure, catalyze reactions, transport nutrients and provide energy.

Naming conventions of macros:

Monomer, dimer, trimer, tetramer, pentamer. Denotes the number of parts (1-5) of a component of a polymer

Why aren’t nucleic acids on nutrition labels?

They’re not energy-storing molecules.

Where is energy stored in molecules? How is it released?

It’s stored in the bonds of molecules and cells access it using enzymes to break the bonds.

Prokaryotic cells vs. Eukaryotic cells

No nucleus, internal membranes or major organelles vs. membrane-bound DNA in nucleus, multiple organelles and different structured macros.

Centrifugation

Separates cell components based on size and density: larger components experience greatest centrifugal force, smaller components stay suspended above.

What’s involved in chemical interactions

The valence electron shell is involved in reactions.

Covalent bonds

Electrons are shared. Either equally (nonpolar) or inequally (polar).

What determines whether a covalent bond is polar or nonpolar?

If different elements have different electronegativities (tendency of atoms to attract electrons). A large difference in electronegativity between elements makes it polar, no difference or little difference=nonpolar.

Ionic bond

Atoms gain or lose electrons (ionization) with an electronegativity greater than 1.6.

How does hydrogen bond?

H atoms with one unpaired electron share their electrons. Hydrogen bonds are non-covalent (nonchemical) molecular interactions. It’s weak attraction between partially charged H atom and a partially negative-charged atom.

How do hydrogen bonds form between water molecules?

H+ bonds to O-

Van der Waals interactions

Identical atoms are brought close enough together to bond and force each other to conform to one another so + and - face each other. Ex: water surface tension is caused by water’s polar structure

Lipids are…

Large organic (has carbon), nonpolar, hydrophobic molecules which are insoluble in water.

Types of lipids

Fats (triglycerides), phospholipids, steroids

Fats (triglycerides)

Nonpolar lipids composed of glycerol (carboxyl + water) and 3 fatty acids. Fats store energy, insulate and cushion against toxic compounds and help with membrane structure.

Saturated vs unsatuated fats

Saturated fats stay solid at room temperature and have single-bonded hydrocarbon chains, unsaturated fats are liquid and have one or more double bonded hydrocarbon chains.

Phospholipids

Phosphate group + another functional group + glycerol (carboxyl and water) and 2 fatty acids (carboxylic acid and a chain). Phospholipids are amphipathic (have a polar hydrophilic head, nonpolar, hydrophobic tails) which form the structure of the cell membrane

Steroids

4-ring structure which forms the polar (hydrophilic) and nonpolar (hydrophobic) regions + other stuff. Steroids facilitate cell communication and membrane structure

Ring structure (cyclic compound)

A series of atoms in a compound connected to form a ring.

Double vs single bonds in fatty acids

Single bonds allow things to move freely (C–C) vs. double bonds (C=C) which makes it harder for things to move, but also produces kinks in the fatty acid chain.

Hydrophobic effect in phospholipid bilayer

Cell membrane is created by a bilayer when hydrophobic tails interact with each other and hydrophilic heads interact with water. Usually bilayer is fluid and moves laterally.

How do atoms and molecules get through the phospholipid bilayer?

Membranes are selectively permeable so hydrophobic molecules pass through most easily because the core of the bilayer is also nonpolar/hydrophobic. Small enough molecules can get through the bilayer, but large, uncharged polar molecules can’t and ions cannot because they’re charged.

How does fatty acid saturation and fatty acid chain length affect membrane permeability?

Saturation makes a bilayer stronger and less permeable whereas unsaturation (double bonds) creates kinks that make it more permeable. The longer a fatty acid chain is, the higher the melting point which means it’s solid at room temperature and therefore less permeable.

How does cholesterol affect membrane permeability?

Cholesterol bonds to various parts of phospholipid bilayer to either stiffen or loosen the membrane. The amount of cholesterol in a membrane changes its permeability (more cholesterol=less permeable)

What is the fluid mosaic model?

Describes the plasma cell membrane structure as a mosaic of phospholipids, cholesterol, proteins and carbs. Explains the role of proteins in membrane structure and cell signaling

What are the different kinds of movement of things through membrane called?

Diffusion, movement of chemicals and molecules which can be passive (including facilitated, when protein channels allow ions through the bilayer) or active (ions are needed in the cell). Osmosis, when water moves from areas of high concentration to low concentration.

Electrochemical gradient

The gradient of electrochemical potential usually for an ion that can move across a membrane. The gradient is chemical (difference in solute concentration across a membrane) and electrical (difference in charge across a membrane)

Carbohydrates are composed of…

Monosaccharides: chain of carbons, hydroxyl group (–OH), carbonyl group (C=O) which are bonded by glycosidic links

Carbohydrates have isomers:

Each of 2 or more compounds with the same formula but a different arrangement of atoms in the molecule and different properties. Ex: glucose and fructose have same formula (C6H12O6) but different properties and function and arrangement. Usually, isomers differ at chiral carbons and there’s variation of the configuration of –OH/hydroxyl group

What are the 5 classifications of isomerism?

1. D and L form, when OH group is to the right of primary carbon vs to the left. 2. alpha and beta anomers (H and OH groups change position around the carbon) 3. Epimers (isomers formed by interchange between OH and H on carbon atoms) 4. pyranose and furanose ring structures (sugars forming 6-membered rings are pyranose, sugars forming 5-membered rings are furanose) 5. aldose-ketose (if there’s a free H on carbon 1 it’s aldose, if there’s a CH2OH group it’s ketose)

Chiral carbon

A carbon atom attached to four different types of atoms or groups of atoms

How do carbohydrates function as cell identifiers?

Simple carbohydrates attached to red blood cells determine ABO blood type because they’re named after the antigens (simple chains of sugar) found on the surface of red blood cells which can either be O, A or B.

Carbohydrate antigens on the surface of red blood cells:

O (chain of glucose+galactose+n-acetylglucosamine+ galactose+fucose). A (chain of glucose+galactose+n-acetyl+galactose+n-acetylgalactoseamine+fucose) and B (chain of glucose+galactose+n-acetylucos+galactose+galactose+fucose)

Oligosaccharides

Saccharide polymer made of a small number of monosaccharides which can perform cell recognition and adhesion. Usually linked to lipids or compatible amino acid r-groups in proteins via N or O-glycosidic bonds.

Glycosidic bond

Type of ether (R–O–R) bond joining carb molecules to another group, either carbs or other. (Ex: H–OH bonds to HO & CH3–> H–O–CH3 + H2O)

Glycolipids

Lipids with a carbohydrates attached via a glycosidic (covalent) bond whose function is maintaining stability of the cell membrane. Lipid tails are hydrophobic, sugar chain is hydrophilic

What are ligands?

Molecules that bind to another (larger) molecule.

What other functions can complex carbohydrates serve?

Complex carbohydrates are responsible for identifying pathogens from the cell membrane then signaling to the membrane receptor to signal the inside of the cell to initiate an immune response.

Which bonds store more potential energy?

Nonpolar bonds store more energy than polar bonds because the electrons, shared equally, overlap more and thus more energy is needed to break them. Carbon-hydrogen bonds store potential energy in covalent energy

Why does changing 2 amino acids in hemoglobin cause sick cell anemia?

Because changing glutamate for valine is a nonconservative sub so the hemoglobin assembles into long fibers which distort the shape of red blood cells into crescents and causes red blood cell to die.

Why do hydrogen bonds form best with hydrophilic substances?

Because hydrophilic substances tend to be polar solutes which have partial positive and negative charges to bond with.

What happens when water comes into contact with nonpolar molecules?

The water molecules bond with each other because they can’t bond with hydrophobic molecules. The hydrophobic molecules, if they’re close enough together, can attract on the basis of respective, weak electrical attractions.

Cohesion

Attraction between like-molecules. Example: water forming hydrogen bonds

Adhesion

Attraction between different molecules. Example: water on a solid surface

How many water molecules are in 1 mole of water?

6×10²3

What are proteins?

Polymers of amino acids (monomers) which are linked by peptide bonds between the carboxyl (COOH) of one amino acid and the amino (NH2) of another

Composition of amino acids

Central carbon, hydrogen, amino group (NH2), carboxyl (COOH) and an r-group/sidechain which distinguishes different amino acids from each other

What happens to an amino acid if acid or a base is added?

If a base or acid is added, the amino acid will ionize (gain a charge). If a base is added, the hydrogen concentration is lowered so COOH loses an H and the amino acid is negatively charged. If acid is added, an H is added to the NH2 and becomes NH3, positively charged.

What does it mean if the sidechain/r-group is polar vs nonpolar?

If the sidechain is polar and charged it’s hydrophilic. If the sidechain is nonpolar and uncharged (or negative) then it’s hydrophobic

What is a peptide bond?

Covalent bond between the C1 of one alpha-amino acid and the N2 of another alpha-amino acid along the peptide chain.

What are alpha and beta amino acids?

Alpha and beta amino acids are two forms of amino acids which difer based on where their carboxylic and amine groups are attached (either to the same central carbon (C1) or to secondary carbons).

Oligopeptide

Chain of less than 50 amino acids

Polypeptide

Chain of 50+ amino acids

Different types of protein

Collagen, TATA box-binding protein, porins, chymotrypsin

Collagen

Protein that provides structural support for cells or tissue

TATA box-binding protein

Protein shaped like a saddle which binds DNA to regulate gene activity

Porin

Protein shaped like a doughnut which creates a channel for certain hydrophilic molecules to pass through the cell membrane

Chymotrypsin

Globular (spherical) protein which binds and breaks the peptide bonds of other proteins

What are the 4 levels of protein structure?

Primary, secondary, tertiary, quaternary

Primary protein structure

The unique sequence of amino acids in each protein of a polypeptide which determines it’s properties and function

Secondary protein structure

Formation of structures via protein folding into either alpha helices or beta pleated sheets in a polypeptide. Generated partially by the interactions between functional groups in peptide bonds of protein.

What interactions take place within protein at the secondary level?

Hydrogen-oxygen bonds between carbonyl (C=O) and amino (N-H) groups of different amino acids.

What determines if a protein folds or pleats at the secondary level?

Hydrogen bonds, which form between residues (left over after water is removed from multiple amino acids), change the structure of the peptide backbone to either be an alpha helix or a beta-pleated sheet

Tertiary protein structure

Protein’s overall 3D shape of a polypeptide which is a result of interactions/bonds between amino acid residues from the secondary structure (the structure of the backbone).

What’s involved in the bonds in the tertiary structure of protein?

Bonds are either between two r-groups or between r-group and the peptide backbone

What kinds of interactions take place within protein at the tertiary level?

Hydrogen bonds, hydrophobic interactions, Van der Waals interactions, covalent bonds (between cysteine r-groups), disulfide bonds (either within the polypeptide or between 2 polypeptides), ionic bonding (only between groups with opposing charges)

Quaternary structure of protein

Proteins with multiple polypeptides (each is a subunit). The shape of which is determined by the combinations of the polypeptides

What are the different proteins called at the quaternary level (based on number of subunits)?

Dimers (proteins with 2 polypeptides), tetramers (proteins with 4 polypeptides), macromolecular machines

Why is protein folding important to protein’s function?

Denatured/unfolded protein cannot function properly. Protein shape must take a native, active form in order to function

What is the most important structure level of protein for its functioning?

Primary. The sequence of amino acids determines the secondary, tertiary and quaternary structures which determines whether or not a protein will be active

What causes denaturing?

Temperature (high), agents like urea which breaks the bonds that must form to structure protein.

Molecular chaperones

Special proteins specifically for aiding proper protein folding or re-folding in cases where a protein has been denatured or is scrambled (must be unfolded and then refolded properly).

Prions

Infectious, disease-causing particles with the same primary structure as a normal protein but different secondary shape. Prions spread disease by binding to normal proteins and turning them, leading to cell death

What are the functions of protein?

Catalysis, structure, movement, signaling, transport, cell defense

What does it mean for an amino acid to be protonated vs deprotonated?

Protonated means the amino acid got a H+, deprotonated means amino acid lost an H+ (fewer protons)