Bio 172 Exam 1 University of Michigan

Properties of Life

1) Order
2) Energy Utilization
3) Regulation or Homeostasis
4) Response to Environment
5) Reproduction
6) Evolution and Adaption
7) Growth and Development

What are peroxisomes?

• associated with processes that metabolize hydrogen peroxide and alcohols

• break down long chain fatty acids

What is a cell’s nucleus?

• where the cell’s chromosomes can be found

• large and highly organized

• surrounded by double-membrane nuclear envelope

• stores and processes information, where DNA is read and converted to RNA by transcription

• molecules must be transported in and out of the nucleus

What is the cytoplasm?

• everything inside the cell (except nucleus)

• cytosol is the fluid portion of cytoplasm

What is the difference between prokaryotic cells and eukaryotic cells?

• Prokaryotes lack nuclear membrane and organelles

• prokaryotes are usually much smaller and have a fast generation time

What are extracellular structures in prokaryotes?

• polysaccharide and protein networks like capsule

  • for protection

• pili and curli

  • adherence

• flagella

  • for motility

What is light microscopy?

-views of live cells and processes in motion

-in the micrometer range

-can utilize fluorescence to better visualize cells

What is electron microscopy?

pro- resolution is excellent

con- most of the time, what you’re viewing is no longer alive

scanning electron microscopy

• specimen coated with thin film, electron beam scans back and forth across sample. Only allows for surface visualization

transmission electron microscopy

• cells need to be thinly sectioned to obtain an image

Where can ribosomes be found in a eukaryotic cell?

• in the cytoplasm

  • proteins destined for organelles, cytosol

• rough ER

  • proteins that will stay in the endomembrane system, or exported/secreted from the cell

• mitochondria and chloroplasts

How can polar solutes cross the lipid bilayer?

• with transport proteins that form channels (pores) or a shuttle system (carriers)

• these proteins are specific for their cargo

How does membrane permeability affect molecule movement?

• small nonpolar molecules such as O2, CO2, N2 very easily pass through the membrane

• small uncharged polar molecules like H2O and glycerol pass through easily

• large, uncharged polar molecules have low permeability (glucose, sucrose)

• ions have very low permeability (Cl-, K+, Na+)

How can proteins be integrated into a lipid bilayer?

-amphipathically, they will have one nonpolar, hydrophobic layer and one polar, hydrophilic layer

How do membranes vary in composition?

• from one species to another

• from on organelle to another

• phospholipids are different on each side of the bilayer

• proteins are different on sides of the bilayer

How do membranes maintain fluidity?

-phospholipids drift within one side of the bilayer

-fluidity and permeability is enhanced by unsaturated fatty acids tails

-cholesterol stabilizes the membrane and is hydrophobic

How are phospholipids organized?

• in lipid bilayers

• hydrophobic parts will find each other and will NOT be exposed to water

• hydrophilic parts will find each other and water

How are biological membranes made?

a fat minus one hydrocarbon chain and plus a polar group

What are triglycerides?

fats, or triacylglycerol (interchangeable names)

• glycerol linked to three fatty acids

What is synthesis?

a condensation or dehydration reaction

How do fatty acids link together?

with glycerol

• there is an ester linkage between glycerol and a fatty acid

• bond to form membranes

What determines the fluidity of fatty acids?

the abundance of double bonds

• saturated fats have fewer double bonds and more hydrogen, making them solid at room temperature

• unsaturated fats have more double bonds and fewer hydrogens, making them liquid or oil at room temperature

How are polysaccharides used?

• fuel storage (usually alpha links)

  • starch (plants)

  • glycogen (animals)

• structural (usually beta links — VERY stable)

  • chitin (arthropod exoskeleton)

  • cellulose (plant cell wall and bacterial extracellular matrix)

  • peptidoglycan (bacterial cell wall)

Where does chemical energy come from?

• from electrons moving from a high energy state to a lower energy state

What are attributes of lower free/potential energy?

-more stable

-less concentrated

-less ordered (more entropy)

-less work capacity

What changes in a proteins’ environment affects hydrogen bonds the most?

pH!, more hydrogens/protons in the environment affect the ability for hydrogens to form these bond

What changes in a proteins’ environment affects ionic bond the most?

salts/ions!! affect ionic bonds the most

What changes in a proteins’ environment affects covalent bonds the most?

temperature! affects covalent bonds the most

• hydrogen bonds and ionic bonds are not affected as easily

How are nucleotides or ‘strands’ attached?

with phosphodiester bonds

How is a sugar-phosphate backbone of a nucleic acid able to bond to other s-p groups?

• the strand has polarity on each end

  • 5’ phosphate end

  • 3’ hydroxyl end

How do RNA and DNA nucleotides differ?

they differ at the 2’ carbon

RNA nucleotide/ribonucleotide- composed of phosphate group, and ribose sugar (and base), **always has a hydroxyl at the 2’ carbon

DNA nucleotide/deoxyribonucleotide- contains either a ribose or deoxyribose sugar, a base, and a phosphate group, **always has a hydrogen at 2’ carbon

What is the difference between pyrimidines and purines?

pyrimidines- a singular ring

purines- double rings, larger than pyrimidines

What is ribose?

• a sugar group of nucleotides

What are the monomers and polymers of carbohydrates?

monosaccharides and polysaccharides

How does a catalyst/enzyme affect a reaction?

• does not change amount of energy released (deltaG)

• does not change equilibrium constant (Keq)

• lowers the activation energy (Ea)

• increases the rate of the reaction

the enzyme or catalyst is not changed by the reaction

Explain binding between a substrate and enzyme.

• substrates bind through interactions between the enzyme’s R-groups and the substrate, substrate specificity

• binding destabilizes chemical bonds in substrate, this lowers the activation energy and reaction will go faster

• folded enzymes brings specific amino acids together to form active sites

need to be polar/nonpolar to attach

What are typical properties of enzyme catalysts?

-they are proteins that are substrate-specific

-contains an active site that a substrate will bind to

When do enzymes catalyze reactions?

enzymes only catalyze reactions where deltaG is negative and the reactants have more energy than products

• 2 or more reactions may need to be coupled so overall delta G is negative and the reactions are spontaneous

Explain ATP and its usage.

ATP is a high free energy molecule and is therefore less stable, more concentrated, more ordered, and has greater work capacity

• has high potential energy from the three phosphate groups that are crowded and negatively charged

• energy is released when ATP is hydrolyzed (hydrolysis is exergonic and releases energy for work)

What is activation energy?

the amount of energy required for reactants to reach the transition state

this can be overcome by heat or a catalyst

____ in free energy determines chemical reaction characteristics

“change”

What are energy-releasing reactions?

-exergonic (work)

• reactants have MORE energy than products, deltaG is < 0

-exothermic (heat)

these reactions are spontaneous

What are energy-consuming reactions?

-endergonic (work)

• reactants have less energy than products, delta G is > 0

-endothermic (heat)

these reactions are NON-spontaneous

What is potential or free energy?

• energy “stored” in an object

  • (stored in cells by electron’s chemical bonds)

Where do electrons have the most potential energy?

• in the outermost electron shells

Explain how energy moves through biological systems in a molecular form.

cycle

high energy molecule → catabolism, broken down molecules (-deltaG), ATP can be made → low chemical energy molecule with more disorder/entropy → anabolism, energy/ATP is used to build molecules (+deltaG) → high energy molecule

What is the reaction rate of an enzyme reaction?

Reaction rate = (the amount of product formed (or substrate used))(divided by)/time

What is a basic enzymatic reaction equation?

S + E = ES = E + P

s- substrate

E- enzyme

p- Product

ES is a transition state

How does concentration affect reaction rates?

• To proceed

  • One or more chemical bonds have to break

  • Others have to form

• Substances must collide in a specific orientation that brings the electrons involved near each other

• When the concentration of reactants is high

  • more collisions should occur

  • reactions should proceed more quickly

What is v max?

-Enzyme is processing substrate to product as fast as it can (when substrate amount is not limiting)

What happens to reaction rate or velocity as substrate concentration increases?

It will increase and plateau at Vmax

What is Km?

• The substrate concentration needed to get ½ the amount of Vmax

• The affinity of an enzyme for its substrate

• More efficient enzymes have a lower Km

What does having a low Km mean?

• The enzyme binds to the substrate tightly and is very efficient at converting it to product

• has high affinity

What does having a high Km mean?

• The enzyme binds to the substrate loosely and is less efficient at converting it to product

• Has lower affinity

How does enzyme concentration affect Vmax?

• Less enzyme results in a reduced V Max (fewer products in a given time)

• The Km is unchanged

How can we increase v max?

• Increase enzyme concentration

• Vmax is proportional to enzyme concentration

How does increasing enzyme concentration affect Km?

• It doesn’t!

How can enzyme activity be regulated in cells?

• Environmental factors such as temperature, pH etc.

• competitive inhibitors

• noncompetitive inhibitors and activators

How do competitive inhibitors affect an enzyme’s reaction or function?

• They compete with substrate for the active site of enzyme

• they often resemble substrate and can fit into the enzyme

• at high S, substrates out-compete the inhibitor and effective ness decreases

  • Km is always changed

What is a real life example of an enzyme competitive inhibitor?

• HIV protease - an enzyme that cleaves viral polypeptide into functional proteins (Phe & Pro)

  • Competitive inhibitor medications can inhibit HIV proteas

How do non-competitive inhibitors affect an enzyme’s reaction or function?

• Can be both positive and negative

• Also called allosteric regulation which occurs when a regulatory molecule binds away from the active site

  • This can activate or inactivate the enzyme by changing its confirmation

  • It cannot be overcome by excess substrate since the regulator binds away from the active site

  • Allosteric effectors bind at sites other than the active site, or regulatory site

  • It alters properties of enzyme function and certain non-competitive inhibitors can affect Km, but most do not

  • It will always affect Vmax

How can temperature affect the rate of enzyme reaction?

• High temperatures cause proteins to unfold

• low temperature = low kinetic energy

What does pH affect in the rate of enzyme reaction?

• Could affect folding of enzyme

• The substrate’s ability to bind to the active site of the enzyme

What factors affect the rate of an enzymatic reaction?

• substrate concentration

• enzyme concentration

• temperature

• pH (and concentration of other ions)

Cell

lowest level in hierarchy of biological organization
stores & transmits information

What is specific heat capacity, and what biological molecule has a high SHC?

• the energy needed to change the temperature of a substance

• water has a very high SHC and needs 1 calorie/gram

What are the aspects of water that facilitate life chemically?

• cohesion (H-bonds)

• moderation of temperature (high SHC)

• insulation by floating ice (reduced density in solid)

• solvent for polar compounds

How is does pH affect protons?

• acid increases protons

• base reduces protons

• buffer minimizes changes in protons and hydroxide

Theory of Evolution

All species are related by decent from a common ancestor

Natural Selection

Individuals with heritable traits must survive and reproduce better than individuals with other traits

Tree of Life

A diagram depicting the genealogical relationships of all living organisms on Earth, with a single ancestral species at the base.

Archea

Domain of prokaryotic organisms that are biochemically and genetically distinct from bacteria.

Eukaryotes

• membrane-bound nucleus and organelles

• unicellular OR multicellular

• large

Prokaryotes

• Cells that do not contain nuclei, no membrane-bound nucleus/organelles, and are UNICELLULAR

• consists of bacteria and archaea

• smaller

Are organisms multicellular or unicellular?

Both! Ex. bacteria=unicellular, flowering plant= multicellular

Cell Theory

1) Cells are structural units of life
2) Cells are the functional unit of life
3) All cells are fundamentally similar (ie. structure, metabolic strategies, hereditary info). Specific cell functions vary
4) All cells come from pre-existing cells (via cell growth and division)

Define the attributes of a cell.

• enclosed by a plasma membrane that regulates passage of materials in and out of cell

• all use DNA for genetic information

What is 1st and most basic level of protein structure?

primary structure

• linear sequence of amino acids

• held together by covalent bonds (peptide bonds) between the amino acids

What is an atom composed of, and where are these particles?

• protons +

• neutrons

• electrons -

  protons and neutrons are in the nucleus, while electrons are found in orbitals surrounding the nucleus

Protons

Have a positive charge
Atomic number
Found in nucleus
Contributes to atomic mass

Neutrons

Has a neutral charge
Found in nucleus
Contributes to atomic mass

Electron

Negative charge
Found in clouds/orbitals

Mass number

the sum of the number of neutrons and protons in an atomic nucleus

Valence

The electrons in the outermost shell (main energy level) of an atom; these are the electrons involved in forming bonds.

Covalent bond

A chemical bond that involves sharing a pair of electrons between atoms to form an orbital

What are the two types of covalent bonds and how do they differ?

nonpolar

• electrons are shared equally

polar

• electrons are not shared equally, so partial charges exist

What biological molecule is the most electronegative?

oxygen > N > S > C & H

Nonpolar covalent bond

A type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity.

What type of molecules do not easily dissolve in water?

nonpolar covalent molecules

Polar covalent bond

A covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive.

Hydrogen Bond

A type of weak chemical bond formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule.

Ionic Bond

A chemical bond resulting from the attraction between oppositely charged ions.

Cation

Positive Ion

Anion

Negative Ion

Van der Waals

A slight attraction that develops between the oppositely charged regions of nearby molecules.

Cohesion

Attraction between molecules of the same substance

• hydrogen molecules at the surface will hydrogen-bond with the water molecules below; this pulls them downwards

Adhesion

An attraction between molecules of different substances

• water molecules at surface adhere to the glass; therefore can resist downward pull of cohesion