BIOL 2440 unit 1: chapter 1, 2, & 3

Cell Bio Exam #1

what are the factors of cell diversity?

1. size

2. shape

3. chemical requirements

4. specialization

what are the factors of cell unity?

1. composed of the same molecules

2. same type of chemical reactions

3. same genetic components

4. same basic biochemical machinery

What is created by the central dogma?

DNA—-> RNA—-> protein

what process is used to create RNA from DNA?

transcription

what process is used to create Proteins from RNA?

translation

what are proteins made of?

amino acids

what are DNA and RNA made of?

nucleotides

how do we study cells?

1. cell fractionation, cell homogenate, pellet, supernatant

2. microscopy (17th century)

what is the cell theory that is universally accepted by all biologists ?

1. everything Is made up of cells

2. all cells come from other pre-existing cells

what are the two types of basic cells?

1. prokaryotes

2. eukaryotes

what is a way to distinguish between the prokaryotes and eukaryotes?

eukaryotes have a nucleus, prokaryotes do not

what process does prokaryotic cells go through for cell division?

binary fission

what process does eukaryotic cells go through for cell division?

mitosis

what two processes keep the endomembrane system in equilibrium?

1. endocytosis

2. exocytosis

what is endocytosis?

cells membranes import material through a cavity into the cell

what is exocytosis?

waste is secreted out of the cell through the plasma membrane

why are model organisms used?

to gain knowledge from studying the model

what is the chemistry of life?

1. based on carbon compounds (study of carbon compounds: organic chemistry)

2. chemical reactions take place in a aqueous environment

3. the most complicated chemistry known to man

4. huge polymers

5. highly regulated

what are the three types of chemical bonds?

1. covalent: polar & non polar, e- shared, not transferred

2. ionic: cation (+) and anion (-), electrons. are gained or lost

3. hydrogen: weak interactions

what are the three types of interactions?

1. hydrophilic: water loving

2. hydrophobic: water hating/ fearing

3. Van der Waals: attractive force due to fluctuating electoral charges

what are the characteristics of a acid?

releases H+, has a pH between 0-6, moles/liter: 1 — 10^-6

what are the characteristics of a bases?

accepts H+, removes H+ from solution, has a pH between 8 - 14, moles/liter: 10^{-8 __} 10^-14

what are buffers?

weak acids and bases that readily take up or release protons to keep the environment of the cell relatively constant

what forms macromolecules?

subunits —-—→ macromolecules—-—→ macromolecular assembly

-covalent bonds used to turn subunits to macromolecules

-non-covalent bonds used to macromolecules to macromolecules assemble

(subunits: amino acids, nucleotides)(macromolecules: RNA molecule, protein) (macromolecular assembly: ribosome)

what is needed, not needed, and what kind of reaction is HYDROLYSIS?

water is needed, energy is not needed, energetically favorable reaction, monomer —→polymer

what is needed, not needed, and what kind of reaction is CONDENSATION?

energy is needed, energetically unfavorable, polymer —→ monomer

what is the reaction “equation” for condensation?

A-H +HO-B———condensation——→ A - B ———hydrolysis——> A-H + HO-B

• condensation: releases water, energetically unfavorable

• hydrolysis: takes in water, energetically favorable

what is the general formula for monosaccharides?

(CH₂O)_n ; n=3, 4, 5, 6

what are monosaccharides made?

two or more hydroxyl groups

how are monosaccharides created?

aldehydes and ketones react with the hydroxyl group closing the ring and creating a cyclic structure in aqueous solution.

what are isomers?

same formula, different atom arrangement

(arrangement matters to the cells)

what creates a disaccharide?

it is created when the carbon that carries the aldehyde or the ketone can react with any hydroxyl group on a second sugar

what are characteristics of oligosaccharides?

linear and branched molecules made from simple repeating sugar units, short chains less than 10 units (<10)

what are the characteristics of polysaccharides?

linear and branched molecules made from simple repeating sugar units, long chains greater or equal to 10 units (≥10)

what are fatty acids made of?

1. carboxyl group at one end and long hydrocarbon on other

2. if there is a double bond in hydrocarbon tail, it is unsaturated

3. no double bonds are saturated

what are triacylglycerols?

stored fatty acids, energy reserve, Esther linkage forms to glycerol

what are peptide bonds?

1. bonds that link amino acids together through amide linkage

2. proteins are longer polymers, peptides are shorter polymers

what are nucleotides?

1. subunits of nucleic acids

2. consists of :

   nitrogen containing base, 5-carbon sugar, phosphate group

what are the nomenclatures for Adenine, Guanine, Cytosine, Uracil, Thymine?

Base Nucleoside Abbrv

1. Adenine Adenosine A

2. Guanine Guanosine G

3. Cytosine Cytidine C

4. Uracil Uridine U

5. Thymine Thymidine T

what bonds are nucleic acids joined with?

phosphodiester bonds

what are catabolic reactions?

1. breaking down of LARGE molecules to SMALL to create energy. (polymer —→ monomers)

2. energetically favorable

what are anabolic/ Biosynthetic Reactions?

1. uses energy to build LARGE molecules from SMALL molecules. (monomer —→ polymer)

2. energetically unfavorable

what is metabolism?

the total sum of both the catabolic and anabolic reactions (m=c+a)

what is the 1st law of thermodynamics?

1. energy CANNOT be created or destroyed

2. energy can be converted to another form of energy and transferred to another location

3. heat is a form of energy

4. follows the principle of energy conservation

what is kinetic energy?

the energy of motion

what is potential energy?

energy because of position

what is the energy conversion principle?

potential energy —> kinetic —> heat energy

true or false: universe is a closed energy system-no exchange of energy with surroundings

true

what is the 2nd law of thermodynamics?

1. in any isolated system, the degree of disorder can only increase

2. spontaneous change towards arrangements with greatest probability

3. arrangements with greatest probability are more disordered

what is entropy?

1. measure of disorder of a system

2. disorder more likely than order

how are living cells related to the 2nd law of thermodynamics?

1. living cells must take in some types of energy, uses the energy to create order within itself with many chemical reactions specified to create order

2. some energy is converted to heat energy, following the 2nd law of thermodynamics

what is heat energy?

1. disordered form of energy, random movement of molecules.

2. heat is quickly dispersed into the cells surrounding causing more motion and chaos

what is photosynthetic process?

1. the energy of sunlight is absorbed by the plants, algae , and some bacteria

2. the plants, algae, or bacteria takes in H₂O and CO₂ that is expired by living organisms to create sugars, O₂, and other organic molecules

3. O₂ is respirated by most living organisms who expire CO₂

4. respiration is useful energy for cells

5. cycle gets repeated

what is oxidation?

• L: loss of

• E: electrons

• O: oxidations

• O: oxidation

• I: is

• L: loss of electrons

what is reduction?

• G: gain of

• E: electrons

• R: reduction

• R: reduction

• I: is

• G: gaining of electrons

what are energetically favorable reactions?

downhill reactions, release of energy, hydrolysis

what are energetically unfavorable reactions?

uphill reactions, intake of energy, condensation

what is activation energy?

initial input of energy to give a boost over the energy barrier

what are enzymes?

• biological catalyst

• reduces the activation energy needed for reactions

• enzymes are the most effective catalyst

• speeds up reactions 10¹⁴ times faster than without a enzyme

• the activation energy is aided by enzymes

• chemical reactions would not occur without enzymes

• highly selective with an active site

what is the relationship between enzymes and substrates?

• substrate bonds to active site on enzyme

• both must collide with each other for reaction to occur

• 1000 reactions per second

• increased substrate concentration = increased rate of reaction until enzyme is saturated

what is the Michaelis-Menton Model of Kinetics

• V_max= enzyme is saturated

• K_M= Michaelis’ constant, substrate value when enzyme is working at ½ V_max

• If lower K_M- substrate binds tightly to enzyme

• if higher K_M- weak binding

what is the equilibrium constant?

[AB]/ [A][B] = K_on/K_off = K + equilibrium constant

what are inhibitors?

they stop or block substrates from binding with a enzyme

what are competitive inhibitors?

inhibitors that block the active site so a substrate can’t bind (compete with substrate for bonding to the enzyme)

what are noncompetitive inhibitors?

inhibitors do not bind directly to the active site, but instead bind to another area on the enzyme causing the enzyme to change shape and the substrate cannot bind

what are cofactors?

nonprotein partners that are essential for function, bind to enzymes and change shape of active site

what are coenzymes?

they are organic cofactors made from water-soluble vitamins and it transfers electrons between enzymes

what is a allosteric enzyme?

enzymes that change shape with binding of an effector

what is a allosteric site?

the site where the inhibitor or activator binds

what is a allosteric inhibitor?

a substrate that binds to the allosteric site to inhibit enzyme activity

what is a allosteric activator?

a substrate that binds to the allosteric site to activate enzyme activity

what is energy coupling? (hardest part of test apparently)

1. enzymes cannot force unfavorable reactions

2. cells need energetically reactions to occur to grow, divide, and live

3. occurs when the energy produced by one reaction or system is used to drive another reaction or system

what is a exergonic reaction?

has less free energy, favorable, is spontaneous

what is a endergonic reaction?

has more free energy, unfavorable, less spontaneous

what goes first, exergonic or endergonic?

exergonic goes first

what is the equation for free energy?

(ΔG) = (+ΔG) + (-ΔG)

(ΔG)= free energy

what are activated carrier molecules and some examples?

• energy that is stored as a chemical bond energy in a carrier molecule

• molecules readily diffuse through the cell and carry their bond energy with them to release at another faction of the cell

• ex: NADH, NADPH, ATP

what are the characteristics of Adenosine Tri-Phosphate (ATP)?

• technically a nucleotide

• very abundant

• does cellular work

• 10,000,000 ATP molecules are used and generated per sec in each cell

• ATP transfers terminal phosphate to another molecule in phosphorylation reaction

• ATP used to power the pumps in membrane transport

• 30% of ATP is used by the sodium pump

• breaks down food in the body

why is ATP so important?

• ATP takes metabolized food molecules and delivers the energy that is needed to power cell reactions throughout the cell

what is NADH?

• nicotinamide adenine dinucleotide

• catabolic, energy favorable

• intermediate in catabolic system of reactions that generate ATP through oxidation

what is NADPH?

• nicotinamide adenine dinucleotide phosphate

• anabolic/biosynthetic, energy unfavorable

• works with enzymes to catalyze anabolic reactions

what are NADH and NADPH?

cofactors that carry high energy electrons and hydrogen atoms.

exam questions: what is the hypothesis of the article?

UCYN-A is becoming a nitrogen fixing organelle in marine alga

exam questions: what were the findings from the article?

• UCYN-A lost its genome size causing shrinking

• a criteria of organelle is to be in sync with the rest of the cell. UCYN-A has synchronized with its “host” cell, B. bigelowii making it one step closer to being a organelle

• proteins cannot be made in genome

• UCYN-A can be taken encoded by the marine alga

exam questions: what were the weaknesses from the article?

• really strong language for results but not strong enough for the information

• redox reaction has indications but doesn’t know the mechanism. didn’t word it with the “standards”

• a lot of unknown

• title is off

• abstract is off from the actual paper

• vagueness on data but over done conclusion

exam questions: what was the conclusion of the article?

suggests UCYN-A is going through evolution to become a nitrogen fixing organelle, nitroplast