1113H Midterm #1

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Phsopholipids

"head" - glycerol and phosphate and polar or charged molecule "tail" - two hydrocarbon chains amphipathic (both polar and nonpolar)

(1) Enzymes speed reaction rates by _______ and lowering activation energy. (2) Enzyme specificity is a function of the active site's shape and the chemical properties of the _______ within the active site. (3) In enzymes, as in many molecules, function follows from _______.

(1) binding substrates, (2) R-groups, (3) structure

Provide two examples of catalytic activities that would have been necessary for ribozymes to replicate in an RNA world.

(1) the production of nucleotides (2) polymerization of RNA It is thought that nucleotides were scarce during chemical evolution, so their catalyzed synthesis by a ribozyme would have been advantageous. Catalysis by an RNA replicase would have dramatically increased the reproductive rate of RNA molecules.

carbohydrates

(C - H2O)n ; n is typically 3-7

gated channels

(Regulated channels) facilitated diffusion (passive) -type of channel that controls membrane permeability -A protein channel in a cell membrane that opens or closes in response to a particular stimulus -binding of a particular substance or voltage ex. K+ channel

Transformation of bacterial cells (horizontal gene transfer)

(delivery of a plasmid) 1. Original bacteria doesn't have resistance to an antibiotic and so should not survive on a selective medium 2. Resistance is bestowed onto said bacteria by plasmids 3. Bacteria that has acquired plasmid should survive in the presence of antibiotic

enzyme regulation by ligands

(non-covalent interactions) and reversible 1. Competititve inhibiiton - regulatory molecules binds to the enzymes active site preventing the substrate from binding - tennis ball in your apples 2. Allosteric inhibition (noncompetitive inhibition) - the active site becomes unavailable (changes shape) when a regulatory molecule binds to a different site on the enzyme 3. Allosteric activation - the active site becomes available (changes shape) when a regulatory molecule binds to a different site on the enzyme

RNA primary structure

- same as DNA, except uracil (U) instead of thymine (T) - base pairs: G-C, A-U -single strands

Organism

-a living thing -have 5 fundamental characteristics -made of cells, can reproduce, process info (genetics/env stimuli), use and need energy, can evolve

ionized form of amino acid

-in water (pH 7) the amino and carboxyl groups ionize to NH3+ and COO- -the amino group acts as a base and attracts a proton -the carboxyl group acts as an acid and donates a proton -the resulting charges help amino acids stay in solution and make the amino acids more reactive

Calculate the pH of a 0.5-M solution of HCl. If you wanted to determine the number of protons in the solution, what additional information would you need?

-log(0.5) = .3 to determine the number of protons in the solution you would need to now the volume

Propose the next step to take if data supports the hypothesis you are testing?

-relate your findings to existing theories and the current scientific literature -communicate your findings with others (peer reviews)

ribose vs deoxyribose

-ribose: has an -OH group at C-2 -deoxyribose: has an -H group at C-2

What evidence supports that all organisms come from a common ancestor?

-similar DNA (4 bases) -DNA encoding scheme -proteins

Describe how biologists go about testing their ideas

-they design and carry out a study (experimental or observational) -they state their ideas as a hypothesis and null hypothesis and make predictions -they analyze and interpret the data they have gathered, and determine whether the data supports their ideas -if not they they resist their ideas and come up with an alternative hypothesis and design another study

If a certain reaction is exergonic and results in a decrease in entropy, is it endothermic or exothermic?

-ΔG = -ΔH + tΔS; exothermic

What are the primary functions of carbohydrates in cells? cell identity, energy storage, raw material source for synthesis, and structure catalysis, energy storage, metabolism, and structure catalysis, digestion, energy storage, and information storage energy storage, information storage, polymerization, and raw material source for synthesis

What type of bond is formed between two sugars in a disaccharide? glycosidic linkage phosphodiester bond peptide bond hydrogen bond

how is the anomeric carbon different from all other carbons in glucose? provides the carbonyl oxygen for cyclization is the most reduced carbon is the most oxidized carbon

Mass of protons and neutrons (in daltons)

1 Da each

How are electron shells numbered?

1,2,3 etc smaller numbers are closer to the nucleus

Identify the electron donors and electron acceptors in the two reactions 1. AH2 + FAD -> A + FADH2 2. BH2 + NAD+ -> B + NADH + H+

1. AH2 is the donor (oxidized) and FAD is the acceptor (reduced) 2. BH2 is the donor (oxidized) and NAD+ is the acceptor (reduced)

A mensicus forms in a glass tube as a result of...

1. Adhesion - at the perimeter of the surface, partial positive charges on water molecules adhere to the negative charges on glass, resulting in an upward pull 2. Cohesion - along the surface, water molecules hydrogen-bond to those next to them and below the, resulting in a lateral and downward pull that resists the upward pull of adhesion creates u shape

Whats the relationship between the 3 uniyfing theories of biology and the five characteristics of life?

1. Cell Theory - all living things are made of cells (cells) and all cells come from other cells (replication), they also require nutrients to survive and thrive (energy) 2. The Chromosome Theory of Inheritance - state that genes are located on chromosomes that carry hereditary/genetic info (information); also the patterns of inheritance are determined by the behavior of chromosomes during meiosis (replication) 3. The Theory of Evolution - organisms evolve over time (evolution)

Why do we need ATP? Why don't sugars directly fuel all the reactions?

1. Energy is released from ATP in a single step, while releasing energy from glucose requires numerous step 2. The amount of energy released by ATP hydrolysis matches a need for most chemical reactions (jujst enough) using glucose would be like using a car battery to power your flashlight. A normal battery is just a better fir for most things.

Protein functions include

1. Enzyme catalysis - speed up chemical reactions 2. Defense - antibodies attack pathogens 3. Movement - move cells or molecules b/w cells 4. Signaling - convey signals to other cells 5. Structure - shape cells and comprise body structures 6. Transport - allow molecules to enter/exit cells or carry them throughout the body

Evaluate the following statements related to the synthesis of nucleic acids. Select True or False for each statement. T/F Ribonucleotides are added to the 3′ end of a DNA strand. T/F Polymerization of nucleic acids occurs by the formation of phosphodiester bonds. T/F Complementary pairing between sugars is required for copying nucleic acids. T/F Strands in a double helix are synthesized in an antiparallel orientation.

1. F 2. T 3. F 4. T

What two factors determine if a reaction will proceed spontaneously?

1. If the products have lower potential energy than the reactants (drop in PE)--that is, when the shared electrons in the reaction are held more tightly than those in the reactants 2. The product molecules are less ordered than the reactant molecules (ex. when glucose is burned it turns into gaseous CO2 and water vapor which are less ordered than glucose molecules)

Important characteristics of a good experimental design

1. Include a control to check for other factors that might influence the experiments outcome; identical conditions except that one that is being tested 2. Randomization and blind experiments; to reduce bias (not always possible) 3. Having a repeatable experiment; need to be carefully controlled and recorded to allow for reproducibility 4. Larger sample size to reduce the amount of distortion in data caused by unusual individuals/circumstances

Describe the PE and KE of a water droplet falling down a waterfall

1. Potential energy: A water drop sitting at the top of a waterfall has a defined amount of potential energy, Ep (top) 2. Kinetic energy: As the drop of water falls, some of the potential energy is converted to kinetic energy, Ek 3. Other forms of kinetic energy: when the water drop strikes the rocks below, its potential energy is now much lower; the change in potential energy has been transformed into an equal amount of Kinetic energy (mechanical energy, heat, sound) Ep(top) =Ep(bottom)+Ek(total) energy is neither created or destroyed; it simply changes form

Peptide bond characteristics

1. Side chain orientation - R-groups extend outward, involved in interactions 2. Directionality - N terminus (synthesized first) to C-terminus 3. Order and flexibility - Peptide bond is planar and therefor rigid - Bonds on either side of peptide bond can rotate

lipid bilayer selective permeability (order)

1. Small nonpolar molecules (O2, CO2, N2) 2. small uncharged polar molecules (H2O, glycerol) 3. large uncharged polar molecules (glucose, sucrose0 4. small ions (Cl-, K+, Na+) -> highly polar

Which of the following correctly describe an active site? Select True or False for each statement. T/F It is the location in an enzyme where substrates bind. T/F It is the place where a molecule or ion binds to an inactive enzyme to induce a shape change to make it active. T/F It is the portion of an enzyme where chaperones bind to help enzymes fold. T/F It is the site on an enzyme where catalysis occurs.

1. T 2. F 3. F 4. T

Which of the following correctly describe an exergonic reaction? Select True or False for each statement. T/F The products have lower Gibbs free energy than the reactants. T/F Activation energy is required for the reaction to proceed. T/F The products always have lower entropy than the reactants. T/F The reaction always occurs quickly

1. T 2. T 3. F; exergonic reactions can occur if the products have lower entropy so long as there is a large drop in enthalpy 4. F; the reaction rate is based on the activation energy, which may be high and result in an exergonic reaction occurring slowly

1. T 2. T 3. F 4. F 3. is false because exergonic reactions can occur if the product have lower entropy so long as there is a large drop in enthalpy 4. reaction rate is based on activation rate

(1) Compare and contrast CO2 and H2O in terms of electronegativity, types of covalent bonds, and overall geometry; and (2) explain why electrical attractions between water molecules would be much weaker if their structure resembled CO2.

1. They both have similar differences between the electronegativity of their atoms. They also both have polar covalent bonds. However, water has unpaired electrons which forces the molecule into a bent shape. Carbon dioxide does not so it remains straight, meaning its two dipoles cancel out making it a non-polar molecule. 2.The electrical attractions would be much weaker if water was a straight molecule since the partial negative charge of oxygen would no longer be as exposed thus decreasing its chances of hydrogen bonding.

In what two ways does energetic coupling happen?

1. Transfer of electrons (redox reactions) 2. The transfer of a phosphate group (ATP donates its phosphate group to another molecule via phosphorylation)

How do we determine protein structures?

1. X-ray crystallography - crystalize proteins - bombard with x -rays - build structure based on electron densities 2. nuclear magnetic resonance (NMR) spectroscopy - incorporate isotopes into protein (C-13, N-15) - Perform experiments in giant magnet (MRI) - Build structure based on protons 3. Cry electron microscopy - analyze flash frozen proteins by electron microscopy - averages over millions of protein particle sin different projections - reconstruct the structure in high resolution

imagine a graph with depicting the rate of product formation vs substrate concentration there are five lines labeled competitive inhibitor, enzyme catalyzed, allosteric activation, uncatalysed and allosteric inhibitor describes would each line would look like

1. at the top would be allosteric activation (it plateaus but pretty much reaches max speed) 2. Underneath it would be an enzyme catalyzed reaction 3. Then competitive inhibitor which is noticeably lower than the other two, it has a more gradual increase but it will eventually reach max speed 4. Under that is allosteric inhibitor that plateaus less than half way (does not reach max speed) 5. at the bottom is uncatalyzed which is a straight line with a very not steep slope

What two environments are believed to have possibly contained the simple molecules of earth that played a role in chemical evolution?

1. atmosphere - probaly full of gas ejected from volcanoes (water vapor, CO2, N, H, CO) 2. Deep-sea hydrothermal vents - CO2, H2, minerals containing reactive metals (Ni and Fe)

chargaff base content rules

1. base composition of DNA varies form one species to another 2. DNA specimens from different tissues of one species have the same base composition 3. Base composition of DNA in a given species does not change with age, nutritional state or env 4. In all cellular DNA, the percent composition %A = %T and %G = %C

What did watson and crick know prior to their discovery?

1. chemical composition of DNA 2. chargaff rules 3. maurice wilkins and rosalind franklin x-ray data suggesting helical nature of DNA

bond strength order

1. covalent 2. ionic interaction 3. hydrogen bond van der waals forces (IMFs) 4. dipole dipole 6. interactions 5. london dispersion (temporary dipole movements)

fats and oils have the same chemical nature except...

1. fats contain mostly saturated fatty acids (no double bonds) - solid 2. Oils contain more unsaturated fatty acids (1 or more double bonds) - liquid

compare and contrast how energy is transferred via redox reactions and ATP hydrolysis.

1. in a redox reaction energy is transferred between molecules are atoms via electrons. When oxidized molecules are reduced, their potential energy increase 2. ATP hydrolysis is often coupled with the phosphorylation of another molecule. The phosphorylation increases the potential energy of the target molecule.

How would each of the following affect membrane permeability? 1. increasing the amount of double bonds 2. increasing the length of hydrocarbons 3. increasing the temperature

1. increase 2. decrease 3. increase

Natural selection occurs when...

1. individuals within a population vary in characteristics that are heritable (traits that can be passed on to offspring) 2. These traits help individuals survive better and reproduce more than others in a particular env if certain heritable traits lead to increased success in making babies, those traits will become more common in the population over time

RNA function

1. info storage and process - messenger RA - transfer RNA - ribosomal RNA 2. Info storage - in RNA viruses 3. Catalyzing chemical reactions - ribozymes (RNA enzymes) - 3D shape is important to function - contains an active site - because DNA is less chemically reactive, it is not a good catalyst

What are three ways monosaccharides differ from one another?

1. location of carbonyl group 2. number of carbon atoms they contain 3. orientation of their hydroxyl group

Carbohydrate Classification

1. location of the carbonyl group - aldose - carbonyl group at the end of the carbon chain - ketose - carbonyl group in the middle of the carbon chain 2. number of carbon atoms present - triose = three - pentose = five - hexose = six 3. spatial arrangement of their atoms (isomers) - L - isomers have the hydroxyl pointing left - D - isomers have the hydroxyl point right - have to look at the asymmetric center furthest from the carbonyl group 4. Linear and ring forms - sugar typically form ring structures in aqueous solutions - contain an anomeric carbon - alpha isomer - OH at anomeric carbon points up - beta isomer - OH at anomeric carbon points down - can have 6 or 6 atoms -furanose : 5 -pyranose: 6

Mechanisms of catalysis by enzymes

1. orientation/proximity: enzymes bring substrates together in a precise orientation 2. transition state facilitation: enzymes lower Ea by stabilizing the transition state (bonding -> stability) 3. Termination: products have a low affinity for the active site and are released (products shouldn't bind to tightly)

Why is DNA a good molecule for storing information?

1. stable, unreactive structure 2. Its double strand nature serves as a template for its own synthesis

2 step process of hypothesis testing

1. state the hypothesis as precisely as possible and list the predictions it makes 2. design an observational or experimental study that is capable of testing those predictions

DNA sturcture (3)

1. strands held together by hydrogen bonds between one purine and one pyrimidine 2. strands are antiparallel 3. Strands form a double helix - sugar-phosphate backbone faces exterior - nitrogenous bases face interior

Why does ATP have high potential energy?

1. the three clustered phosphates carry four negative charges on their oxygens therefore, if there are four negative charges in close proximity to one another, they will naturally repel each other this makes ATP a relatively unstable molecule because it will want to give away its phosphate groups the (more unstable the more PE) 2. Resonance stabilization of ADP and of Pi is greater than that of ATP The oxygen molecules of the ADP are sharing electrons Those electrons are constantly being passed back and forth between the oxygens, creating an effect called resonance (you can rewrite the structure of ADP in a bunch of ways since the oxygens can bond with any of phosphorous's electrons) This stables the ADP Resonance does not occur in ATP; therefore, it is a more unstable molecule 3. There is a greater degree of solvation of Pi and ADP, relative to ATP This means that it is easier for ATP to lose one of its phosphate groups But, it takes a large amount of water to force ADP to lose one of its phosphates.

In redox reaction, electrons may be gained or lost in 2 different ways

1. transferred electrons may result in a change in the number of electrons in the valance shell of an atom (ex. Fe3+ to Fe2+) 2. or electrons are transferred as new covalent bonds that are formed with other atoms

the number of collisions occurring between the substances in a mixture depends on ...

1. when the concentration of reactants is high, more collision will occur and reactions should proceed more quickly 2. when their temp is high, reactants will move faster and should collide more frequently

How many residues in the backbone connected by a hydrogen bond in alpha helix

Robert Hooke

1665 first crude microscope (30x) examined cork; saw compartment like structures that he coined as "Cells"

Anton van Leeuwenhoek

1700s second microscope (x300) examined pond water saw single cells organisms he called "animalcules"

Carolus Linnaeus

1735 established a system for naming species each organism has a two part name 1. Genus: ex. Homo 2. Species name: ex. Sapiens "scientific name" (descriptive) always italicized genus is capitalized

Gregor Mendel

1850s-1860s discovered the fundamental laws of inheritance deduced that genes come in pairs and are inherited as distinct units; one from each parent peas

Louis Pasteur

1862 wanted to test the spontaneous generation/all-cells-from-cells hypothesis Developed an experiment Wanted to determine whether organisms would spontaneously arise in a nutrient broth or if they would only appear when the broth is exposed to prexisting cells 2 identical treatment groups: expect one was exposed to preexisting cells First round was a fail becasue he used stright neck flasks Even after sterilization, bacteria and fungi latched onto dust particles were able to enter the flask and contaminate the broth He repeated it with swan neck flasks This way water would condence in the crook of the neck trapping any foreign particles No cells grew in the unexposed flask These results were inconsistent with the spontaneous generation hypothesis

Rudolph Virchow

1885 proposed that all cells arise from cells aready in existance

The chromosome theory of inheritance

1902 walter sutton and theodor boveri sea urchin experiments states that genes are found in chromosomes patterns of inheritance (how genes are trasmitted) are determined by the behavior of chromosomes during meiosis suggests that the qualities and properties of the organism are inherited

Erwin Chargaff

1950 Discovered that DNA composition varies, but the amount of adenine is always the same as thymine and the amount of cytosine is always the same as guanine.

When/who discovered the structure of DNA?

1952 James Watson and Francis Crick proposed that DNA is a double stranded helix each strand is made up of varying sequences of 4 types of bases (Adenine, thymine, cytosine, guanine) the two strands are joined by interactions between the base pairs this model came from the structural analyses performed by rosalind franklin

Galapagos island studies

1970s all finches decsended from a common finch beak size varied based on the type of food that had access to

In what century was there enough data for a german biologist to claim that all organisms consist of cells?

19th

Identify two aspects of the structures of cellulose, chitin, and peptidoglycan that correlate with their function as structural molecules.

1: The β-1,4-glycosidic linkages in these molecules result in insoluble fibers that most organisms cannot break down with enzymes 2: When individual molecules of these carbohydrates align, bonds form between them and produce fibers or sheets that resist pulling and pushing forces.

If a solution surrounding a cell is hypertonic relative to the inside of the cell, how will water move? It will move into the cell via osmosis. It will move out of the cell via osmosis. It will not move, because equilibrium exists. It will evaporate from the cell surface more rapidly.

Suppose a cell is placed in a solution with a high concentration of potassium and no sodium. How would the cellular sodium-potassium pump function in this environment? 1. It would stop moving ions across the membrane. 2. It would continue using ATP to pump sodium out of the cell and potassium into the cell. 3. It would move sodium and potassium ions across the membrane, but no ATP would be used. 4. It would reverse the direction of sodium and potassium ions to move them against their gradients.

What type of bond is directly involved in the formation of an α-helix? 1. peptide bonds between amino acid residues 2. hydrogen bonds between amino acid residues 3. van der Waals interactions between nonpolar residues 4. disulfide bonds between cysteine residues

how many bonds to pyrimidines form

You have discovered an enzyme that appears to function only when a particular sugar accumulates. Which of the following scenarios would you predict to be responsible for activating this enzyme? 1. The sugar cleaves the enzyme to form the active conformation. 2. The sugar is an allosteric regulatory molecule for the enzyme. 3. The sugar is a competitive inhibitor for the enzyme. 4. The sugar phosphorylates the enzyme to form the active conformation

If nucleotides from the DNA of a human were quantified and 30 percent of them contained the base adenine, what percentage of them would contain the base guanine? 20 percent 30 percent 40 percent 70 percent

if guanine content is 28%, what is the adenine content

22%

How many molecules of ATP can one glucose molecule make?

29-32

What determines the primary structure of a DNA molecule? 1. stem-and-loop configuration 2. complementary base pairing 3. deoxyribonucleotide sequence 4. hydrophobic interactions and hydrogen bonding

What is a transition state? 1. the shape adopted by an enzyme that has an inhibitory molecule bound at its active site 2. the amount of kinetic energy required for a reaction to proceed 3. the intermediate complex formed as covalent bonds in the reactants are being broken and re-formed during a reaction 4. the enzyme shape after binding an allosteric regulatory molecule

What two functional groups are bound to the central carbon of every free amino acid monomer? 1. an R-group and a hydroxyl group 2. an amino group and a hydroxyl group 3. an amino group and a carboxyl group 4. an N—HN—H group and a (C═O)(C═O) group

Why are proteins not considered to be a good candidate for the first living molecule? 1. Their catalytic capability is not sufficient for most biological reactions. 2. Their amino acid monomers were not likely present in the prebiotic soup. 3. They cannot serve as a template for replication. 4. They could not have polymerized from amino acid monomers under early Earth conditions.

how many bonds to purines form

How many residues per turn in an alpha helix?

3.6 residues per turn

How does pH affect enzyme-catalyzed reactions? 1. Protons serve as substrates for most reactions. 2. Energy stored in protons is used to drive endergonic reactions. 3. Proton concentration increases the kinetic energy of the reactants, enabling them to reach their transition state. 4. The concentration of protons affects an enzyme's folded structure and reactivity

Integral membrane proteins are anchored in lipid bilayers. Which of the following groups of amino acid residues would likely be found in the portion that crosses the lipid bilayer? 1. acidic 2. basic 3. polar uncharged 4. nonpolar

oligopeptide

4-10 amino acids joined together

1 calorie = ____ J

4.184

Single strands of nucleic acids are directional, meaning that there are two different ends. What functional groups define the two different ends of a strand?

5' free phosphate group 3' free hydroxyl group

in what direction are DNA and RNA synthesized?

5' to 3'

What percent of cells are water?

75%

whats a full valence shell?

8 electrons

denature

A change in the shape of a protein that can be caused by changes in temperature or pH also chaotropic agents (urea) disorganize protein structure

prediction

A logical statement about what will happen if the hypothesis is correct. must be correct if a hypothesis is valid

prion

A misfolded, infectious protein

ligand

A molecule that binds specifically to another molecule, usually a larger one.

Zwitterion

A molecule that contains charges, but is neutral overall. Most often used to describe amino acids

Three components of a nucleotide

A phosphate group bonded to 5' carbon of sugar 5' carbon sugar nitrogenous base bonded to the 1' carbon or sugar

peptidoglycan

A protein-carbohydrate compound that makes the cell walls of bacteria rigid linear polysaccharide strands (amino acid chains) are covalently strengthened by peptide links

explain (1) why the same reaction can be nonspontaneous at low temperature but spontaneous at high temperature, and (2) why some exothermic reactions are nonspontaneous.

A reaction is non-spontaneous when ΔG>0 -ΔG = +ΔH - T(+ΔS) only if the temperature is high ΔG = +ΔH - T(+ΔS) Only if the temperature is low The increased temperature represents added thermal energy that may be used to drive an endothermic reaction to completion Some exothermic reactions are non spontaneous when ΔG = -ΔH - T(-ΔS) The temperature is really high Occurs if the result in a large decrease in entropy--meaning the products are more order than the reactants (-ΔS)

Functional groups

A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and involved in chemical reactions exhibit particular chemical properties that it imparts to the organic molecule its attached to

starch

A storage polysaccharide in plants consisting entirely of glucose not as branched as glycogen form helixes has both a 1,4 and a 1, 6 linkages amylose and amylopectin

chitin

A structural polysaccharide found in many fungal cell walls and in the exoskeletons of all arthropods beta 1, 4 linkages forms hydrogen bonds between parallel strands on the Ch2 has N-acetylglucosamine

solute

A substance that is dissolved in a solution.

fiber

A tough complex carbohydrate that the body cannot digest cleans the intesine

Hydrogen bond

A weak electrical interaction between a hydrogen atom with a partial positive charge and another atom (usually O or N) with a partial negative charge

What would be the sequence of the strand of DNA that is made from the following template: 5′-GATATCGAT-3′? (Your answer must be written 5'→3'.) How would the sequence be different if RNA were made from this DNA template?

ATCGATATC AUCGAUAUG

energy within the bonds of glucose is used to make

ATP

How does energy coupling relate to ATP

ATP is a universal high energy molecule hydrolysis of the terminal phosphate groups releases large amounts of energy this is a highly exergonic reaction and can be coupled to drive numerous endergonic reactions

covalent modification of enzymes (reversable)

Addition of phosphate groups enzyme changes shape, which changes its function phosphorylation is produced by enzymes called kinases dephosphorylation is produced by phosphatases unphosphorylated - off phosphorylated - on

Alanine (Ala) Methyl group No charged or electronegative atoms to form hydrogen bonds found in the protein interior important for folding nonpolar

Based on the relative electronegativities of the atoms involved, predict whether each functional group is polar or nonpolar.

All the functional groups except for the sulfhydryl group (-SH), are considered polar. The sulfhydryl group is very slightly polar since sulfur's electronegativity is only slightly higher than that of hydrogen When present on the amino acid cysteine, the sulfhydryl group is classified as nonpolar.

Electron shells

An energy level representing the distance of an electron from the nucleus of an atom each contains a specific number of orbitals

glycogen

An extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch. energy storage from alpha 1,6 links for the branches

Which of the following amino acid mutations/substitutions is most likely to be silent 1. Asp to Lys 2. Gly to Phe 3. Arg to Lys

Arg to Lys; they're both charged/basic amino acids and are similar lengths

Arginine (Arg) electrically charged, can thus form ionic and hydrogen bonds define protein charge involved in catalysis typically on the surface Basic

Asparagine (Asn) Partial charges can form hydrogen bonds hydrogen bonds with water within proteins involved in catalysis on the surface polar

Aspartate (Asp) electrically charged, can thus form ionic and hydrogen bonds define protein charge involved in catalysis typically on the surface Acidic

Products of a nonspontaneous reactions have a higher potential energy than the reactants. Which of the following statements are true? Select all that apply. a. ATP hydrolysis is an endergonic reaction that provides energy to drive exergonic reactions b. Energy for nonspontaneous reactions comes from energetic coupling between exergonic and endergonic reactions aka redox reactions. c. Oxidation reactions are the only source of energy for nonspontaneous reactions. d. ATP hydrolysis is an exergonic reaction that provides energy to drive endergonic reactions.

B and D

Explain why reduced molecules with many C—H bonds store more potential energy than oxidized molecules with many C—O bonds.

Because Oxygen has a high electronegativity it would make the C-O shorter. C-H bonds on the other hand are longer and thus has a higher potential energy.

Why can polypeptides flex?

Because groups on either side of each peptide bond can rotate about their single bonds only exception is that 2 atoms cant occupy the same space

Explain what changes when the radioactive isotope tritium (3H) decays and one of its neutrons becomes a proton

Because it gained a proton it has changed from being a hydrogen isotope to being a helium isotope

Why are peptide bonds planar?

Because of the partial double bond character CO-NH are on the same plane

why do ionic bonds form ions

Because the participating atoms either have the lose or gain electrons they no longer have the same amount of protons than electrons ex. Na and Cl -> Na^+ and Cl^- bc Na loses an electron and Cl gains an electron

Why does water have a high specific heat?

Because when a source of energy hits it, hydrogen bonds must be broken before heat can be transferred and the water molecules can begin moving faster as molecules increase in overall polarity and thus in their ability to form hydrogen bonds, it takes more energy to change their temperature

Compare and contrast competitive inhibition and allosteric regulation.

Both are mechanisms that regulate the interaction between enzymes and their substrates. In competitive inhibition, the regulatory molecule binds directly to the active site and interferes with substrate binding. In allosteric regulation, the regulatory molecule binds to a different region and causes the enzyme to change conformation and either open or close the active site.

How are metabolic pathways regulated

By controlling when and where enzymes are active Regulating enzyme activity with allosteric regulation or feedback inhibition the product of metabolic pathways inhibits an enzyme earlier in the pathway product production continues until its concretion is high enough for allosteric binding to result in feedback inhibit once the product concentration goes back down the enzyme will start working again

what bonds in carbohydrates store high potential energy

C-C and C-H (non polar)

Draw a chemical equation to represent the redox reaction that occurs when methane (CH4) burns in the presence of oxygen (O2). Identify the reactant that is reduced and the reactant that is oxidized. Of the four molecules that should be in your equation, point out the one that has bonds with the highest potential energy.

CH4 + O2 -> CO2 + H2O O2 is reduced and CH4 is oxidized. The one with the highest potential bonds is CH4.

Polysaccharides

Carbohydrates that are made up of more than two monosaccharides

Predict what would happen to the concentration of bicarbonate ions if a strong base like sodium hydroxide (NaOH) were added to a solution of carbonic acid.

Carbonic acid would dissociate to release protons and bicarbonate ions The H+ protons released from carbonic acid would react with the OH- ions dissociated from NaOH to form H20, leaving fewer protons free to react with bicarbonate to produce carbonic acid

Who proposed the 3 domain system?

Carl Woese (1990)

negative control

Control group where conditions produce a negative outcome. Negative control groups help identify outside influences which may be present that were not accounted for when the procedure was created.

Cysteine (Cys) stabilization of protein structure due to disulfide bonds forming between them involved in catalysis No charged or electronegative atoms to form hydrogen bonds found in the protein interior important for folding nonpolar

nucleic acid polymer

DNA and RNA

What is responsible for the increased stability of DNA compared to RNA?

DNA lack an OH- groups on its 2' C, so its more resistant to cleavage

DNA is copied by ________ to pass _________ from cell to cell or from one organism to its offspring

DNA polymerase; genetic info

Differentiate between primary, secondary, and tertiary levels of DNA structure.

DNA primary structure is based on covalent bonds and has greater variability compared to the secondary and tertiary levels Secondary structure is based on complementary base pairing and involves two strands of DNA The tertiary structure of DNA often includes proteins

osmosis

Diffusion of water through a selectively permeable membrane (solutes cant diffuse) neutralizes the gradient until equilibrium is reached low to high

who created the period table?

Dmitri Mendeleev

Porin

Doughnut-shaped forms a pore

How do van derr waals interactions play a role in hydrophobic interactions?

Due to the clumping of nonpolar molecules seen in hydrophobic interactions the molecules are all close to one another The constant motion of their electrons then creates a tiny asymmetry in charge thus when nonpolar molecules get extremely close to another, the small partial charge on one molecule induces an opposite partial charge in the other leading to an attraction this can significantly increase the stability of clustered hydrophobic molecules

From what you learned about water, why do coast regions tend to have milder climates with cooler summers and warmer winters than do inland areas as the same latitude?

Due to the hydrogen bonds between water molecules, oceans have high specific heat. Meaning that they are able to absorb large amounts before changing temperature. This means during the summer and a large amount of heat energy is absorbed by the ocean. And during the winter all that heat is released.

Explain how the primary and tertiary levels of protein structure relate to enzyme-substrate specificity.

Enzymes bind to specific substrates based on the structure of their active site An active site is formed when the polypeptide of an enzyme is fully folded into its tertiary structure The information required for directing the polypeptide into this folded state is in its primary structure The primary structure is also responsible for the specific amino acid residues located in the active site that interact with the substrate

Explain how enzymes lower the activation energy of a chemical reaction

Enzymes lower activation energy by destabilizing bonds in the substrates and promoting the formation of the transition state.

What makes up the backbone of amino acids?

Everything except the side chain

T or F: the 4 major classes of biological macromolecules are all polymers

F; lipids aren't polymers proteins nucleic acids carbohydrates are

T/F Proteins have many functions like enzyme catalysis, motion, support, regulation, encoding information and transport

F; they dont encode info

hydroxyl group (formula, family of molecules, properties)

Family of molecules: alcohols Properties: highly polar, so makes compounds more soluble through hydrogen bonding with water; may also act as a week acid and drop a proton

carbonyl group (formula, family of molecules, properties)

Family of molecules: aldehydes (extra h) and ketones Properties: aldehydes, especially, react with certain compounds to produce large molecules; polar

amino group (formula, family of molecules, properties)

Family of molecules: amines Properties: base - tend to attract a proton (forms nitrogen with + charge bonded to 3 hydrogens); polar

carboxyl group (formula, family of molecules, properties)

Family of molecules: carboxylic acids properties: acid - tend to lose a proton in solution (forms C bonded to 2 oxygens, one with negative charge); polar

collagen

Fibrous protein that provides structural support

RNA tertiary structure

Forms when secondary structures fold into more complex shapes RNA is much more diverse in size, shape and reactivity than DNA

Central Dogma

Francis Crick describes the flow of info within cells "dogma" referes to framework for understanding DNA codes for RNA which codes for proteins differences in proteins encoded by different DNA sequences may lead to different physical traits 1. replication: by DNA polymerase - required for cell division 2. transcription: by RNA polymerase - transfer of info from genes to proteins via RNA 3. translation: by ribosomes - protein synthesis

Determine if free fatty acids and fats are amphipathic, and explain why or why not.

Free fatty acids are amphipathic because their hydrocarbon tails are hydrophobic but their carboxyl functional groups are hydrophilic In fats, the charged carboxyl groups of fatty acids are converted to ester linkages. This change reduces the difference in polarity across the molecule, making it more uniformly nonpolar. As a result, fats are not considered amphipathic.

whihc molecule is easier to retrieve form storage depots: fatty acid or glucose

Glucose, because fatty acids are not soluble in water and thus its harder to access its energy; glucose can readily dissolve in water (polar ends)

Glutamate (Glu) electrically charged, can thus form ionic and hydrogen bonds define protein charge involved in catalysis typically on the surface Acidic

Glutamine (Gln) Partial charges can form hydrogen bonds hydrogen bonds with water within proteins involved in catalysis on the surface polar

Glycine (Gly) doesn't have a stereoisomer/chirality center known to break alpha helixes since it's so small and flexible which interfere with relatively constrained α-helical structure. No charged or electronegative atoms to form hydrogen bonds found in the protein interior important for folding nonpolar

positive control

Group expected to have a positive result, allowing the researcher to show that the experimental set up was capable of producing results.

What does water dissociate into

H+ and OH- rearranges s into Hydroxonium (H3O+) ions and hydroxide (OH-) ions since H+ cant exist alone its a proton

Histidine (His) electrically charged, can thus form ionic and hydrogen bonds define protein charge involved in catalysis typically on the surface Basic

How are beta sheets formed?

Hydrogen bonding between the side chains of the Amino acids with each other through turns can be parallel or antiparallel

Explain how regulating the activity of a single enzyme can affect an entire metabolic pathway.

If the regulated enzyme is at the start of a metabolic pathway, then when it is turned off, there will be no product to serve as a substrate for the following reaction. As a result, none of the subsequent reactions would occur, including the formation of the final product.

Explain how the saturation status of hydrocarbon chains affects the physical characteristics of lipids.

In general, unsaturated lipids are more fluid than saturated lipids at a given temperature.

Why is liquid water more dense than ice?

In ice, each water molecules participates in 4 hydrogen bonds creating a regular and repeating lattice structure this structure is fairly open meaning theres relatively large space between molecules when ice is heated, it causes the hydrogen bonds to break, collapsing the crystal structure in liquid water, hydrogen bonds are constantly being formed and broken so the extent of hydrogen bonding in liquid water is much less than in ice thus in liquid water, the molecules are packed closer to together making it more dense also allows ice to float

evaluate the possibility of hydrogen bonding between the nucleotides G-T and A-C. Explain why these pairs of bases are not complementary.

In the G-T pair, only one hydrogen bond could form—between the bottom N-H in guanine and one of the carbonyl groups (C O) of thymine The other two potential H-bonding sites in guanine would repel the similar partial charges in the aligned groups extending from the thymine base No hydrogen bonding would be possible in an A-C pair.

Isoleucine (Ile) No charged or electronegative atoms to form hydrogen bonds found in the protein interior important for folding nonpolar

Whats the geometry of H2O?

It is planar but bent the electrons in the four orbitals of oxygens valence shell repulse each other two of the orbitals in the central oxygen atom are filled with unshared electron pairs, which push the O-H bonds closer together 104.5* apart

what does tRNA do?

It transfers amino acids for translation single-stranded and folds into unique conformations amino acids are added to the 3' end via ester bonds to the carboxyl group the amino group is available for the peptide bond formation

Consider the reaction between CO2 and H20 to form carbonic acid CO2(g) + H2O (l) <=> CH2O3(aq) In the ocean, carbonic acid immediately dissociates to form a proton and bicarbonate ion, as follows: CH2O3(aq) <=> H+(aq) + CHO3- If an underwater volcano bubbled additional CO2 into the ocean, would the reaction shift left or right? How would it affect the pH of the ocean?

It would shift right and produce more carbonic acid, thus increasing the acidity of the ocean (more H+ released)

All amino acids in proteins are __ stereoisomers

Leucine (Leu) No charged or electronegative atoms to form hydrogen bonds found in the protein interior important for folding nonpolar

Lysine (Lys) electrically charged, can thus form ionic and hydrogen bonds define protein charge involved in catalysis typically on the surface Basic

steroids

Made of four rings of carbon cholesterol (cell membranes) hormones (testosterone, estrogen) - long distance signaling derivatives

Methionine (Met) No charged or electronegative atoms to form hydrogen bonds found in the protein interior important for folding nonpolar

lock and key

Model of enzyme activity that explains how a particular enzyme will only fit with one particular type of substrate

Diffusion

Movement of molecules from an area of higher concentration to an area of lower concentration.

What elements can form hydrogen bonds?

N, O, F

Can enzymes increases product concentration?

Do lipids form polymers?

NO, lipids form big molecules made of smaller subunits, but not in a continuing chain

Why doesn't hydrogen have a neutron?

Neutrons usually act as buffers in nuclei Protons are positive and repel positive things that are near them Neutrons, with no charge, thus act as buffers, lessening the amount of repulsive force thus there is no real need for them in Hydrogen since it only has one proton

do thermodynamic state functions (G, H, S) provide information on the rate of reactions?

No they can only tell you how likely or possible it is

Are viruses organism? Are they alive?

No and no; theyre not made of cells and depend on a host for replication, survival and information processing

Predict whether the bonds that chlorine forms with sodium (to form NaCl) and with carbon (to form CCl4) would be the same in both compounds.

No in NaCl it would form an ionic bond while in CCl4 it would form a covalent bond

Are exothermic reactions always spontaneous?

No, If the enthalpy change (ΔH) and the entropy change (ΔS) are both positive or both negative, the spontaneity of the reaction depends on the temperature ex. if they're both negative then: (__)ΔG = -ΔH - T(-ΔS) if the temperature is really high then ΔG would be positive and thus the reaction is not spontaneous but if the temperature is really low then ΔG would be negative and thus the reaction is spontaneous

Does a decrease in disorder always mean a reaction is not spontaneous

Are endothermic reactions always spontaneous?

No, If the enthalpy change (ΔH) and the entropy change (ΔS) are both positive or both negative, the spontaneity of the reaction depends on the temperature ex. if they're both positive then: (__)ΔG = +ΔH - T(ΔS) if the temperature is really high then ΔG would be negative and thus the reaction is spontaneous but if the temperature is really low then ΔG would be positive and thus the reaction is not spontaneous

Does an increase in disorder always mean a reaction is spontaneous

Cooking oil lipids consist of long, unsaturated hydrocarbon chains. Would you expect these molecules to form membranes spontaneously? Why or why not? Describe, on a molecular level, how you would expect these lipids to behave in water.

No, because they have no polar ends to interact with water. Instead these lipids would float on the surface of the water, or collect in droplets suspended in water, reducing their interaction with water to a mininum

Are lipids linked covalenlty?

No, they are brought together due to the hydrophobic effect

Predict where amino acid residues with nonpolar R-groups would be found within the overall structure of a folded globular protein such as chymotrypsin

Nonpolar amino acid residues would be found in the interior of a globular protein like trypsin, grouped with other nonpolar residues due to hydrophobic interactions.

Can a catalyst alone make a nonspontaneous reaction occur spontaneously? Explain why or why not.

No—a catalyst affects only the activation energy, not the overall change in Gibbs free energy (ΔG).

alpha isomers

OH at anomeric carbon points down

beta isomers

OH at anomeric carbons points up

Explain why when an oil is added to water, it forms a separate layer.

Oil is nonpolar, so when it is mixed with water the polar water molecules only interact with each other using hydrogen bonds This oil is thus forced to clump together and separate from the water via hydrophobic interactions.

Discuss this statement: "various species of Galapagos finches are adapted to their particular habitats"

Over time, traits such as a beak shaped to retrieve a certain food type that is especially abundant in a particular habitat will become increasingly frequent in the population

some of the _____ from the oxidation step is used to increase the _____ of a molecule in the reduction step

PE;PE

Phenylalanine (Phe) No charged or electronegative atoms to form hydrogen bonds found in the protein interior important for folding nonpolar

Describe the characteristics of phospholipids that allow them to spontaneously form lipid bilayers in water.

Phospholipids are amphipathic, so their hydrophilic end will interact with water and their hydrophobic end will not Water molecules are more ordered when surrounding the hydrophobic regions When phospholipids are brought together to form a membrane, the hydrophobic regions are tucked away from water and thus the entropy in water increases Events that increase entropy tend to be spontaneous.

Proline (Pro) Only one that forms a covalent bond with the amino group Known to break alpha-helices due to it being so rigid and irregularly shaped (C-NH2 bond cant rotate) No charged or electronegative atoms to form hydrogen bonds found in the protein interior important for folding nonpolar

Explain how secondary, tertiary, and quaternary levels of structure depend on primary structure.

Protein structure is hierarchical: Secondary, tertiary, and quaternary structure all depend on bonds and other interactions between amino acids that are covalently linked in a chain in a specific order (primary structure).

Describe the key attributes of RNA that make it a candidate for the first living molecule.

RNA provides a template that can be copied and can also catalyze the polymerization reaction required for its own replication.

Exceptions of the unidirectional (dna -> rna -> protein) transfer of information

RNA-viruses (contain RNA genome) -> encode unusual enzymes 1. Retrovirus (HIV-1) produces reverse transcriptase (RNA dependent DNA polymerase); converts viral RNA genome into a DNA copy to incorporate into the host genome - reverse transcriptase converts viral genome RNA into DNA, which is then incorporated into he genomic DNA of the host cell 2. Human DNA polymerase η can work as reverse transcriptase (RNA to DNA); it is likely involved in DNA repair (use mRNA to heal double strand DNA breaks) 3. SARS-CoV2 produce RNA-dependent RNA polymerase; converts viral RNA genes into mRNA for virus protein production on ribosomes (doesn't even use DNA)

Explain why the relative activity may appear to drop off in a graph that shows the reaction rates tending to increase at higher temperatures

Reaction rate is based primarily on the activity of the enzyme. Once the temperature reaches a level that causes unfolding and inactivation of the enzyme, the rate decreases to the uncatalyzed rate.

How does water dissolve salt?

Salt is made from positively charged sodium ions and negatively charged chloride ions The partial positive charges on the water's hydrogen atoms attract the Cl ions and the partial negative charges on the water's oxygen atom attract the NA ions which pulls apart the ionic compound into its individual ions

Amyloid fibrils

Self-propagating, stable β-sheet aggregates built from hundreds of identical polypeptide chains that become layered one over the other to create a continuous stack of β sheets The unbranched fibrous structure can contribute to human diseases when not controlled very low potential energy

Serine (Ser) Partial charges can form hydrogen bonds hydrogen bonds with water within proteins involved in catalysis on the surface polar

Peptide

Short chain of amino acids linked by peptide bonds

Monosaccharides

Single sugar molecules glucose, fructose, galactose

atom

Smallest particle of an element and unit of matter

le chatelier's principle

States that if a stress is applied to a system at equilibrium, the system shifts in the direction that relieves the stress shifts counteracts the change

Compare and contrast the structure of a steroid, a fat, and a phospholipid.

Steroids have a distinctive four-ring structure with variable side groups attached fats consist of three fatty acids linked to glycerol many phospholipids also have a glycerol linked to fatty acids, but instead of three fatty acids, they have two plus a hydrophilic, phosphate- containing "head" region.

Why was the formation of earths first ocean important?

Substances are most likely to come into contact with one another and react when they are solutes (dissolved in water) Thus earths first oceans provided a place to allow this process to happen more physical interactions of molecules

How does water dissolve sugar?

Sugar (sucrose) is a polar molecule, due to its O-H bonds and thus has partially positive and negative ends The attraction between the positive and negative ends of water and sugar molecules overcomes the attraction the sugar molecules have for themselves, pulling the individual sugar molecules away from each other the sugar molecules are thus separated from the sugar crystal and surrounded by water

Which of the differences listed here could be found among molecules of the same monosaccharide? Select True or False for each statement. T/F There is a difference in the orientation of a hydroxyl group in the ring form. T/F There is a difference in the number of carbons. T/F There is a difference in the position of the carbonyl group in the linear form. T/F There is a difference in the overall shape of the molecule—one is a ring and the other is linear.

T F F T

Propose a hypothesis to explain why Mg2+ is a common cofactor in enzymes that use ATP to phosphorylate substrates.

The Mg2+ ion carries positive charges that will interact with the negative charges on ATP. This interaction helps the enzyme transfer a phosphate from ATP to its substrate.

Predict the effect on protein function if each polypeptide adopted only a single, inflexible shape based on its primary structure.

The ability to regulate protein activity would be impaired the proteins would be either permanently active or inactive, depending on how they are folded

Explain how the structure of DNA allows it to be copied.

The complementary base pairing in the secondary structure of DNA allows each strand to serve as a template. After separating the strands of a DNA double helix, each template strand can be copied to make two identical double-stranded DNA molecules.

fluid mosaic model

The currently accepted model of cell membrane structure, which envisions the membrane as a mosaic of individually inserted protein molecules drifting laterally in a fluid bilayer of phospholipids

If an base is add to your blood how would it be countered

The decreased proton concentration due to the base, would cause carbonic acid to dissociate into H+ protons and bicarbonate ions

electrochemical gradient

The diffusion gradient of an ion, representing a type of potential energy that accounts for both the concentration difference of the ion across a membrane and its tendency to move relative to the membrane potential (charge gradient and concentration gradient) ions diffuse down their EC gradient unless energy is invested

oxidizing agent

The electron acceptor in a redox reaction.

reducing agent

The electron donor in a redox reaction.

Heat

The energy transferred between objects that are at different temperatures

Describe some ways that the various types of carbohydrates you ate during breakfast today are being used in your body right now.

The energy-storage molecules, like starch, are being hydrolyzed to release glucose Disaccharides like the lactose in milk would be hydrolyzed to release glucose and galactose These sugars may be further broken down to produce ATP and raw materials for building other molecules, such as glycolipids and glycoproteins The insoluble cellulose that makes up dietary fiber does not get broken down, but it will help retain water and support the digestion and passage of fecal material.

Outline the flow of info from the genetic material to the physical appearance of an organism

The flow of info is from DNA to RNA to protein physical traits are a product of proteins produced

quaternary structure

The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits stabilized by bonds and interactions between R groups and between peptide backbones of different polypeptides can be hom- (same protein) or hetero- (different proteins) oligomers

Why is water such a good solvent?

The high electronegativity of water's oxygen creates a polar molecule, thus leading to it having a partially negatively charged oxygen and 2 partially positively charged hydrogens This also leads to its bent shape The partial charges on the water can thus form up to 4 hydrogen bonds (1 on each H and 2 on the O) The positive ends attract the negative ends of water molecules or other polar solutes/ions such as glucose or NaCl Thus why sugar and salt dissolves in water

If an acid is add to your blood how would it be countered

The increased concentration of protons from the acid would react with bicarbonate ions to from carbonic acid

Based on the relative electronegativities of O, N, C, S, and H explain why some R-are nonpolar and some are polar.

The nonpolar R-groups contain mostly C and H, which have roughly equal electronegativities Electrons are evenly shared in C—H bonds and C—S bonds, so the groups are nonpolar The polar R-groups have a highly electronegative oxygen atom with a partial negative charge, making them polar

Explain what happens to the potential energy removed from chemical bonds in reactants after they are converted to products with lower potential energy

The potential energy from the bonds is converted into kinetic energy, which is often in the form of thermal energy The first law of thermodynamics is preserved because the energy is not destroyed, but only transformed.

Predict how energy is transformed in a chemical reaction where the products have much lower enthalpy than the reactants

The potential energy that is lost as the enthalpy is decreased in the products is transformed into kinetic energy, which is most likely in the form of heat or light

predict which structures would be most stable tertiary structure composed mostly of alpha helixes tertiary structure composed mostly of beta pleated sheets tertiary structure rich in disulfide bonds

The tertiary structure that is rich in disulfide bonds would be most stable The covalent bonds formed between cysteines are stronger than noncovalent bonds holding together the structures rich in α-helices and β-pleated sheets.

Explain how the positions of the valence electrons in carbon and hydrogen change as methane (CH4) reacts with oxygen (O2) to produce carbon dioxide and water in the following reaction: CH4 + 2 O2 → CO2 + 2 H2O

The valence electrons are located closer to the nucleus in CO2 due to strong electron affinity of the highly electronegative oxygen

Why do most polar covalent bonds involve nitrogen or oxygen?

They have high electronegativities, so they hold shared electrons tighter than other atoms resulting in polar bonds

Evaluate the claim that polysaccharides are superior to proteins as markers of cellular identity. Cite attributes of carbohydrate structure to support your answer.

This claim is likely correct because carbohydrates have the potential for greater structural variation than proteins Glycosidic linkages between sugar monomers can vary more in location and geometry than can peptide-bond linkages between amino acid residues, which are completely standardized The different monosaccharide monomers vary extensively in their size, the position of the carbonyl group, the orientations of hydroxyl groups, and the presence of modifications in the polymerized forms (e.g., modified sugar residues in chitin and peptidoglycan).

Threonine (Thr) Partial charges can form hydrogen bonds hydrogen bonds with water within proteins involved in catalysis on the surface polar

Tryptophan (Trp) most fluorescent No charged or electronegative atoms to form hydrogen bonds found in the protein interior important for folding nonpolar

Tyrosine (Tyr) Partial charges can form hydrogen bonds hydrogen bonds with water within proteins involved in catalysis on the surface polar

Valine (Val) No charged or electronegative atoms to form hydrogen bonds found in the protein interior important for folding nonpolar

Hydrophobic

Water fearing typically nonpolar moleculues

"the universal solvent"

Water- due to its polarity and ability to dissolve many different solutes

Contrast the effect of water on dissolving NaCl versus glucose

When NaCl is dissolved, water disrupts the ionic bond between sodium and chloride and surrounds each of the ions When glucose is dissolved, the covalent bonds are not disrupted, but water surrounds it by hydrogen-bonding with different parts of the molecule

Hydrophobic interactions

When hydrophobic molecules are introduced to water, the surrounding water molecules are forced to create more hydrogen bonds with each other forming a highly organized "cage" around the hydrophobic molecules This level of organization is unfavorable so the hydrophobic molecules cluster together to minimize the energy required for forming multiple cages This thus decreases organization and increases entropy (disorganization)

What makes an atom electrically neutral?

When the number of protons and the number of electrons in an atom are the same

Is this reaction spontaneous C₆H₁₂O₆ + 6O₂ -> 6CO₂ + 6H₂0

Yes, the potential energy decreased from the reactants to the products. There was also a phase change from solid and gas to gas and liquid, which shows an increase in entropy. So ΔH<0 and ΔS>0

Phylogentic tree

a branching diagram that depicts the evolutionary relationships among species or other taxa the main node is the common ancestor of all living organisms constructed by analyzing DNA sequences of genomes and looking for similarities similar sequence = similar genes = closely related "last universal common ancestor" - LUCA

amino acid structure

a carboxyl group, amine group, and R group not possible in solution, cause one end should be protonated

endothermic

a chemical reaction that absorbs heat absorbed by the system delta H > 0; enthalpy of the products is higher than the enthalpy of the reactants of the system

exergonic

a chemical reaction that has a ΔG less than 0 spontaneous and release energy

acid-base reaction

a chemical reaction that involves a transfer of protons

exothermic

a chemical reaction that releases heat to the environment increases disorder of the surroundings at the same time that order is increased in the system water vapor -> liquid water delta H < 0; enthalpy of the products is lower than the enthalpy of the reactants of the system

dimer

a compound whose molecules are composed of two identical monomers (dipeptide)

What two conditions must be present for osmosis to occur?

a concentration gradient and a membrane that allows water to pass, but not the solute, must be present

System

a defined set of interacting chemical components under observation the substances you want to focus attention on

Population

a group of individuals of the same species living in the same geographic area at the same time

Organic compounds

a group of molecules that include at least one carbon atom; most have C-H bonds and C-C bonds

control

a group of organisms or samples that do not receive the experimental treatment but are otherwise identical to the group that does

A predication specifies what should be observed if...

a hypothesis is correct

null hypothesis

a hypothesis that specifies what the results of an experiment will be if the main hypothesis being tested is wrong often states that there will be no difference between the experimental groups

polymer

a large number of monomer bonded together proteins, nucleic acids and polysaccharides

Temperature

a measure of how much thermal energy (KE) its molecules posses hot -> fast & cold -> slow

electronegativity

a measure of how strongly an atom pulls shared electrons toward itself in a bond can lead to polar covalent bonds depends on the number of protons in the nucleus and the distance between the nucleus and the valence shell becomes stronger as you move to the upper right hand corner of the periodic table

a measure of the concentration of protons in a solution and thus how acidic or basis the solution defined as the negative of the base 10 logarithm of the proton concentration pH = - log [H+] [H+] = antilog(-pH) = 10^-pH acids < 7 bases > 7

Tree of life

a phylogenetic tree that includes all organisms distinguishes 3 major groups (domains of life) -bacteria -archaea -eukarya

metabolic pathways

a series of enzymatic reactions that converts one biological material to another.

Pathogenic mutations in primary protein structure (hemoglobin example)

a single amino acid change can radically alter the function ex. in normal hemoglobin tetramers are not connected to each other in a regular way. single amino acid mutation makes them sticky - they form fibers that deform and break down the RBC membrane switches from an electrically charged amino acid to a nonpolar one, which affects protein folding

monomer

a small molecule that can covalently bind to other similar molecules to form a larger macromolecule

Chemical equilibrium

a state of balance in which the rate of a forward reaction equals the rate of the reverse reaction and the concentrations of products and reactants remain unchanged no work can be done

Hypothesis

a testable statement that explains a phenomenon or a set of observations explanation for more tightly focused questions

dalton (Da)

a unit of mass approximately equal to the mass of one proton or one neutron

radioactive isotopes

a version of an element that has an unstable nucleus which will release radiation energy as it decays to a more stable form decay often results in the radioisotope losing protons and becoming a different element timing of decay is specific to each radioactive isotope (can be used in estimating the dates of events)

Van Der Waals interactions

a weak electrical attraction between two nonpolar molecules or parts of molecule that have been brought together, often by hydrophobic interactions attractions occurs due to the constant motion of electrons giving the molecules a tiny asymmetry in charge this this induces an opposite partial charge in nearby molecules when two get close very weak relative to covalent and hydrogen bonds

Important properties of water

able to absorb large amounts of energy high specfic heat (amount of energy required to raise the temp of 1 gram by 1*C) high heat of evaporation (amount of energy required to change 1 gram from liquid to gas)

Spontaneous chemical reaction

able to proceed on its own, without any continuous external influence such as added energy negative delta G exergonic (occur without the addition of energy) If the products have lower potential energy than the reactants

hydroxyl groups

act as weak acids and may drop a proton alcohols many times, the protons involved in acid-base reactions that occur in cells come from these groups on organic compounds are highly polar, so it makes compounds more soluble through hydrogen bonds oxygen and hydrogen

enzymes lower ___

activation energy

Substrates bind to and react in an ___

active site

kinases

add a phosphate group (phosphorylation)

Cell Theory

all organism are made of cells all cells come from preexisting cells

What are the two implications of speciation?

all species come from preexisting species all species, past and present, trace their ancestry back to a single common ancestor

Although cellulose and starch are identical in terms of stored chemical energy, our ability to harvest the energy from these two polysaccharides differs considerably. What is responsible for this difference?

alpha 1, 4 glycosidic linkages in starch form helical structures that can be easily hydrolyzed by enzymes found in most humans beta 1, 4 glycosidic linkages result in large fibers and sheets that exclude water, so they resist hydrolysis

pH and pOH of pure water

also pH + pOH = 14 at 25*C

active sites normally have one or more _______ essential for catalysis

amino acid residues

The most important types of amino and carboxyl-containing molecules are...

amino acids can be linked together by covalent bonds that form between amino and carboxyl groups

1 calorie

amount of energy required to raise the heat of water by 1*C at 1 atm pressure

High specific heat (how does it relate to water)

amount of energy required to raise the temperature of 1 gram by 1*C Water can absorb lots of heat before changing temperature

Specific heat

amount of energy required to raise the temperature of 1 gram of a substance by 1* C

High heat of evaporation (how does it relate to water)

amount of heat required to change 1 gram from liquid to gas Hydrogen Bonds have to be broken before evaporation can occur, and thus it takes a large input of heat

If you hold a salty cracker in your mouth long enough, it will begin to taste sweet. What is responsible for this change in taste?

amylase breaks done the starch in the cracker into glucose monomers that are sweet

ion

an atom or molecule that carries a charge unequal proton/electron ratio

anion

an atom that gains an electron and becomes - charged

cation

an atom that loses an electron and becomes + charged

Species

an evolutionary independent popultion or group of populations generally distinct from other species in appearance, behavior, habitat etc can only produce fertile offspring among organisms from their same species

Fitness

an individuals ability to produce viable offspring relative to other individuals abilities high fitness -> produce many surviving offspring

Carl Woese

analyzed the molecular components of organisms as a way to understand their evolutionary relationships wanted to understand which organisms are closer versus distantly related looked at a specific RNA molecules (codes for an essential part of the machinery that all cells use to grow/reproduce) examined the sequence of its building blocks

Fungi is more related to ____ than _____

animals; plants

base

any compound that accepts protons or gives up electrons accepts hydrogen ions when dissolved in water lower hydronium ion/hydrogen concentration of water

acid

any compound that gives up protons or accepts electrons releases hydrogen ions when dissolved in water increases hydronium ion/hydrogen concentration in water

Adaption

any heritable trait that increases the fitness of an individual with that trait in a particular env ex. finches on the Galapagos islands

macromolecules

any large organic molecule made up of smaller molecules (monomers) joined together into a polymer proteins, nucleic acids and polysaccharides

taxon (taxa)

any named group of organisms at any level of a classification system

isotopes

any several forms of an element that differs in the number of neutrons contained in their nuclei isotopes of the same elements have different masses

Compounds

any substance that consists of more that one different type of element chemically bonded together

All of the chemical reactions in the body take place in an _____ env

aqueous

Concentration of H+ of pure water

at 25*C its 1.0x10^-7 M

Adhesion

attraction between water and other molecules typically between a liquid and a solid surface defines capillary effect (allows trees to bring water high to leaves and branches) water adheres to surfaces that have any polar or charged components

Cohesion

attraction between water molecules leads to high surface tension (walking on water) caused by hydrogen bonds

When H2 and CO2 react, acetic acid can be formed spontaneously while the production of formaldehyde requires an input of energy. Which of the following conclusions may be drawn from this observation? a. More heat is released when formaldehyde is produced compared to the production of acetic acid. b. Compared to the reactants from which it is formed, formaldehyde has more potential energy than does acetic acid. c. Entropy decreases when acetic acid is produced and increases when formaldehyde is produced. d. The mineral catalyst involved in acetic production provides energy to make the reaction spontaneous.

Which of the following occurs when a covalent bond forms? a. electrons in valance shell are transferred from one atom to another b. electrons in valence shells are shared between atoms c. partial charges on polar molecules interact d. nonpolar molecule are pushed together by surrounding water molecules

Smallest organisms known today

bacteria

3 fundamental groups of organisms

bacteria (mostly one celled/no nucleus) archaea (mostly one celled/no nucleus) eukaryotes (have nucleus)

why is RNA 100 fold more prone to hydrolysis

because of the 2' - OH (less stable/more reactive)

taxonomy

branch of biology concerned with describing, naming and classifying groups of organisms

reducing agents (proteins)

break disulfide bonds (cysteine) diothiotreitol (DTT) and Beta-mercaproethanol

catabolic pathways

breakdown macromolecules typically release energy production of ATP

glycogen phsophorylase

breaks down glycogen

How do peptide bonds form?

by a dehydration reaction between the carboxyl group of one amino acid and the amino group of another electron sharing between the Nitrogen and Oxygen gives it the characteristics of a partial double bond forms water

How are phylogenetic trees constructed?

by analyzing DNA sequences of genomes and looking for similarities

What holds cellulose molecules together in bundles large enough to form fibers? the cell wall peptide bonds hydrogen bonds hydrophobic interactions

Which of these molecules would you predict to have the largest number of polar covalent bonds based on their molecular formulas? a. C2H6O (ethanol) b. C2H6 (ethane) c. C2H4O2 (acetic acid) d. C3H8O (propanol)

c (theres more oxygens)

Which of these functional groups is known to be used for storing large amounts of chemical energy? a. amino b. carbonyl c. phosphate d. sulfhydryl

c (think ATP)

Open system

can exchange energy with environment can exchange matter with environment ex. humans

active transport

can transport against gradient (creates gradient) primary - requires energy (ATP or other exergonic reaction) ex. sodium-potassium pump 3 NA- out and 2 K+ in secondary - cotransport; uses gradient provided by a primary transporter to power the movement of a different molecule against its gradient ex. Na Glucose cotransporter - electrochemical gradient established by Na-/K+ - Na- diffuses into cell, bringing glucose with it

Why can't humans digest cellulose?

can't break beta 1, 4 linkage; don't have cellulase strong linear fibers enforced by numerous H-bonds exclude water from accessing the linkages

Isolated system

cannot exchange energy with environment cannot exchange matter with environment ex. universe

whats our blood's buffer

carbonic acid

what functional groups does carbohydrates contain

carbonyl (C=O) many hydroxyls (O-H) many C-H bonds

aldose

carbonyl group at end of carbon chain

ketose

carbonyl group in middle of carbon chain

phosphate groups

carry negative charges on two of their oxygen atoms when transferred from one organic compound to another, the change in charge often dramatically affects the structure of the recipient molecule when bonded together they store large amounts of chemical energy that can be used in chemical reactions polar

Using what you have learned about changes in Gibbs free energy, would you predict the ∆G value of catabolic reactions to be positive or negative? What about anabolic reactions? Justify your answers using the terms "enthalpy" and "entropy."

catabolic reactions often have -delta Gs based on a decrease in enthalpy and increase in entropy anabolic reactions are the opposite (increase one enthalpy and decrease in entropy)

diffusion of ions and other solutes may be facilitated by

channels (or pores)

What protein can assist with folding

chaperones black inappropriate interactions provide space for folding

What are the two fundamental nutritional needs of Organisms?

chemical energy in the form of ATP molecules that can be used as building blocks for the synthesis of DNA, RNA, proteins, the cell membrane and other large complex compounds required by the cells the ways organisms obtain these materials widely varies

hydrolysis

chemical reaction in which a molecule is split into smaller molecules by reacting with water splitting polymers into monomers

endergonic

chemical reaction that has a Δ G greater than 0 nonspontaneous and require an input of energy to proceed

How does cholesterol affect membrane permeability

cholesterol molecules interact with the hydrocarbon tails making them more tightly packed thus decreasing permeability

covalent modification of enzymes (irreversable)

cleavage of peptide bonds can convert inactive proenzyme into its functional form ex. activation of pancreatic proteases in the intestine

Surface tension

cohesive forced caused by attraction between the molecules at the surface of a liquid thereby resisting deformation of the liquids surface and minimizing surface area why tiny bugs can walk on water

The more recent a ___________, the more related two species are

common ancestor

ionic compound

compound composed of ions held together by ionic bonding is neutral overall, but consists of cations and anions crystalline structure dissolve in water; very polar

A reaction links monomers together to form polymers (condensation or hydrolysis?), resulting in (increase or decrease?) in the entropy of a molecule

condensation; decrease

Provide an example of how an experimental study could span more than one level of biological organization?

consider the experiment on navigation in ants In addition to testing how the ants use info on stride length and number to calculate how far they are from the nest (multicellular organism and population levels), researchers could also test how the "pedometer" works at the level of cells and molecules

sulfydryl group

consist of sulfur atoms bonded to a hydrogen atom thiols can link one another via disulfide (O-H) bonds when present in proteins can form disulfide (S-S) bonds that contribute to proteins structure (tertiary) nonpolar

secondary active transport

cotransport; uses gradient provided by a primary transporter to power the movement of a different molecule against its gradient ex. Na Glucose cotransporter - electrochemical gradient established by Na-/K+ - Na- diffuses into cell, bringing glucose with it can transport against gradient (creates gradient)

If you were to expose glucose to oxygen on your lab bench, why would you not expect to see it burn 1. The reaction is endergonic and requires an input of energy. 2. The reaction is not spontaneous unless an enzyme is added. 3. The sugar must first be phosphorylated to increase its potential energy. 4. Activation energy is required for the sugar and oxygen to reach their transition state.

d. energy, such as the thermal energy in fire, must be provided to overcome the activation energy

How does hydrocarbon tail saturation affect membrane permeability

decreases as saturation increase saturated fatty acids have straight hydrocarbon tails that pack together tightly, leaving few gaps

Condensation reactions

dehydration reactions a chemical reaction in which two molecules are joined covalently with the removal of an -OH from one and an -H from another to form water normally involve joining monomers in polymers newly formed bonds result in the loss of a water molecule requires energy to happen

nucleic acid dimer

dinucleotide

rRNA

direct the catalytic steps of protein synthesis

What happens when mistakes in DNA are made?

dna sequence changes may lead to changes in proteins changes in proteins may change their function dna sequences changes lead to heritable variations that underlie diversity in life

cells in isotonic solution

do not change size -no osmosis

DNA tertiary structure

double helix forms compact structures by twisting into supercoils or wrapping around proteins (+ histones) nucleosomes both provide better compact structures for better storage

Why is carbon so versatile?

due to its four valence electrons its capable of forming 4 covalent bonds

descent with modification

each living species has descended, with changes, from other species over time from generation to generation

How are orbitals filled?

each orbital in a shell is loaded with one electron before any orbital is filled with a second paired electron electrons fill the innermost shell first before filling outer shells

which provides more energy electric gradient or chemical gradient

electric

Polar vs nonpolar covalent bonds

electrons in compounds are not always shared equally determined by an atoms electronegativity (increases left to right) the more electronegative = the more affinity for electrons nonpolar: symmetrical bond

most of an atoms volumes is...

empty space

Energetically unfavorable reactions are called

endergonic they require energy

Cell are maintained by chemical reactions that requires ____

energy

first law of thermodynamics

energy is conserved in any process energy can be transferred and converted into different forms, but it cannot be created or destroyed

Where does ATPs energy come from

energy is released upon cleavage of phosphoanhydride bonds

Kinetic energy

energy of motion the more KE and more heat there is (moves faster)

Carbohydrate function

energy storage cell/cell recognition/cell identification structural support

5 fundamental characteristics of life

energy, cells, information, replication, evolution

if ΔS>0

entropy is high increased disorder spontaneous reaction (not necessarily always) favored

if ΔS<0

entropy is lower more organized non spontaneous (not necessarily always) non favored

amylase

enzyme that breaks down starch

How do enzymes affect the yield of chemical reactions in equilibrium?

enzymes do not affect the equilibrium, therefore the yield of products is not affected they only reduce activation energy

Standard free-energy change

equation used to measure delta G calculates changes in delta H and delta S delta G < 0 when spontaneous delta G > 0 when not spontaneous ΔG = ΔH - TΔS T stand for temperatures measured on the kelvin scale

Biological consequence of water having a high heat of vaporization

evaporation of water from an organism cools the body

Are coupled reactions exergonic or endergonic?

exergonic there needs to be enough or more than enough energy from the exergonic reaction to power the endergonic reaction

Energetically favorable reactions are called

exergonic dont require energy

sugar-phosphate backbone faces the ______

exterior

electrons

extremely small negatively charged particles that orbit the atomic nucleus

channels

facilitated diffusion (passive) are selective (wont accept glucose - too big) residues facing inside pore are hydrophilic allow passage of specific types of molecules or ions ex. aquaporins - allow water

carrier proteins

facilitated diffusion (passive) - cant create a gradient "pickup" a molecule on one side of the membrane, then change the conformation to "drop it off" on the other side ex. glucose

passive transport

facilitates diffusion substances diffuse across membrane down the concentration gradient energy is not required or consumed

phosphate group (formula, family of molecules, properties)

family of molecules: organic phosphates properties: molecules with more than one phosphate linked together store large amounts of chemical energy (ATP); polar

sulfhydryl group (formula, family of molecules, properties)

family of molecules: thiols properties: when present in proteins, can form disulfide (S-S) bonds that contribute to protein structure; non polar

Why do fats contain more energy than carbohydrates?

fats acids are almost all nonpolar -> longer bonds containing more potential energy fats also contain almost no water, so the concentration of energy molecule sin fat (adipose) tissue is much higher than in glycogen

why molecule contains more potential energy: glucose or a fatty acid

fatty acid - is less oxidized and has more non polar bonds -> 2.2 times more energy can be released upon oxidation glucose - partially oxidized at some bonds (c-o) and are polar -> less energy can be released upon oxidation - since polar shorter bonds the longer the bond the more potential energy

Are proteins flexible or rigid?

flexible

diffusion within leaflets enables

fluidity, plasticity and self repair

experimental conformation of the fluid mosaic moedl

freeze fracture preparations allows biologists to view membrane proteins smooth side ad rough side (proteins)

How are polypeptides read

from N-terminus to C-terminus N-terminus is typically the amino group C-terminus is typically the carboxyl group

What kind of charge do ionic bonds form?

full positive and negative charges

Structure affects ____

function

sugars with 5 membered rings

furanose

Chromosome

gene carrying structure that consists of a single long molecule of double stranded DNA and any associated proteins prokaryotic cells normally have a single circular chromosome (plasmid) eukaryotic cells have multiple

Phylogeny

genealogical relationship between organisms

Chymotrypsin

globular binds substances (enzyme)

enzymes hydrolyze polysaccharides to release

glucose alpha glycosidic linkages easy to hydrolyze

Why would glucose bind to an enzyme before ATP?

glucose binds first to make sure ATP isn't hydrolyzed ahead of time

There is only 1 amino acid out of the 20 that does not have a chirality center--who is it?

glycine

What R groups are known for breaking alpha helixes?

glycine - it small and flexible which disrupts the relatively constrained α-helical structure proline - it's so rigid and irregularly shaped (C-NH2 bond cant rotate)

Contrast the structure of glycogen and chitin in terms of their monosaccharides, glycosidic linkages, and interactions between polysaccharide chains.

glycogen consists of glucose residues that are connected by alpha 1, 4 glycosidic linkages with branches arising from alpha 1, 6 glycosidic linkages chitin is made up of modified glucose residues that are connected by beta 1, 4 glycosidic linkages with no branching chitin polymers interact with one another view hydrogen bonds, glycogen molecules do not

sugar (carbohydrate) sugars are link be

glycosidic linkage

RNA secondary structure

hairpins instead of a full double helix because RNA is single stranded they are not stabilized by complementary strands instead interactions within the same strand form hairpins and helixes unpaired regions form hairpin loop

amphipathic

having both a hydrophilic region and a hydrophobic region

What problem would arise if Pasteur had (1) put different types of broth in two treatments, or (2) used a ceramic flask for one treatment and a glass for the other

he would have had more than one variable in the experiment critics could claim he got different results because of those differences instead of exposure to preexisting cells

do unfolded proteins have high or low potential energy

high, very unstable

Longer, weaker bonds with shared electrons have ___ PE and shorter, stronger bonds with unequally shared electrons have ____ PE

high; low CH (nonpolar) is weak OH (polar) is strong

Products of a nonspontaneous reactions have a (higher/lower) potential energy than the reactants

higher

lipids are mostly made of

hydrocarbons (C-H)

why are carbohydrates preferred fuel sources as compared to hydrocarbons polyalcohols

hydrocarbons are not water soluble polyalcohols dont have a carbonyl group

What kind of bonding that water use?

hydrogen bonding a weak attraction between a hydrogen atom with a partial positive charge and another atom with a partial negative charge

what stabilizes nitrogenous bases

hydrogen bonds

how is the protein backbone bonded?

hydrogen bonds between carbonyl and amino groups

How are alpha helices stabilized?

hydrogen bonds between carbonyl i and amino group of residue i + 4 I + 4 donate hydrogen through a hydrogen bond to the carbonyl

Why can alpha helixes be called 3.6₁₃ helixs

hydrogen bonds occur every 3.6 amino acids the last third of i (carbonyl group) bonds with the first third of i + 4 (amino group) there are also 13 atoms between the hydrogen bond include oxygen and nitrogen 3.6 = residues it takes to complete 1 per helical rotation 13 = hydrogen bond enables the formation of 13 atom ring

What are the most abundant elements found in organisms?

hydrogen, carbon, nitrogen, oxygen, phosphorus, sulfur carbons the best for building up things since it has 4 bonding points

What is more energetically favorable hydrolysis or condensation?

hydrolysis it increases entropy

What is the primary driving force in protein folding

hydrophobic effect nonpolar side chains collapse together to minimize low entropy water cages

Spontaneous generation

hypothesis from the mid-1800s organisms can arise spontaneously under certain conditions believed because bacteria and fungi would appear in nutrient-rich media such as milk and wine when they spoiled

Biological consequence of water being denser as a liquid than a solid

ice floats, insulating bodies of water and preventing them from freezing solid

Whats the advantage of using larger experimental populations?

if you used a smaller group, the interpretation of the data would not likely change, but you would have less confidence in the conclusion drawn less affected by outliers

what does the free energy diagram show?

illustrates the relationship between the activation energy, the free energy of the reaction, and the free energy of the system

Second law of thermodynamics

in all spontaneous reactions, entropy always increases when both the system and its envrionment are taken into account entropy of the universe or any closed system always increases

What happens to the concentration of protons in black coffee after you add milk?

in decrease; milk is more basic

If we lower the temperature on an endothermic reaction the equilibrium will shift to the _____?

in endothermic reactions heat is a reactant thus here were are removing a reactant from the system, and therefore, by Le Chatelier's principle, it shifts to the left

If we raise the temperature on an endothermic reaction the equilibrium will shift to the _____?

in endothermic reactions heat is a reactant thus here were essentially adding more reactant to the system, and therefore, by Le Chatelier's principle, it shifts to the right

If we raise the temperature on an exothermic reaction the equilibrium will shift to the _____?

in exothermic reactions heat is a product thus here were are adding product to the system, and therefore, by Le Chatelier's principle, it shifts to the left

If we lower the temperature on an exothermic reaction the equilibrium will shift to the _____?

in exothermic reactions heat is a product thus here were are removing products from the system, and therefore, by Le Chatelier's principle, it shifts to the right

phylum

in linnaeus system, a texonomic category above the class level and below the kingdom level major lineages within each domain

Phosphorolysis

in some cases, degradation of a polymer is accompanied by the addition of a phosphate group, not water ex. phosphorolysis of starch or glycogen produces phosphorylated glucose (glucose - 1P)

double bonds (decrease/increase) melting temperature?

increase (i.e. unsaturated fatty acids)

The outcome of state functions (ex. the ratio between reactants and products at equilibrium) is (dependent/independent) on the conversion pathway

independent it doesn't matter how it got there just where it is

Natural selection acts on ________, while evolutionary change occurs ________

individuals; in populations

Nucleic acid functions

info storage info passage (RNA) catalysis (RNA only) energy storage and conversion ATP Enzyme cofactors in redox reactions, electron transport (NAD+, NADP+, FAD)

what 3 key characteristics of life does rna satisfy

info storage and replication info processing catalysis

nitrogenous bases face the _____

interior

The amount of PE in bonds is (inversely/directly) related to the strength of bonds

inversely longer, weaker bonds have more PE than shorter stronger bonds

polymerization of nucleotides

involves condensation reactions (forms water) phosphodiester linkage forms between the 3 carbon hydroxyl group and phosphate hydroxyl group and the 5 carbon CH2 group and phosphate O

What kinds of interactions occur in the tertiary protein structure?

ionic hydrogen disulfide (covalent) hydrophobic effect

Why is base pairing important in DNA?

it allows DNA to be copied and faithfully preserves the info encoded within DNA since the strands can be split it allows for replications

is water and acid or a base

it can act as both (extremely weak)

Does the process of water freezing increase entropy or decrease entropy?

it increases it the process of turning from liquid to solid requires a loss of energy (exothermic) and thus entropy increase ik its weird but its right

delta H

its value is primarily based on the differences in PE between products and reactants

Galactosemia is a potentially fatal disease that occurs in humans who lack the enzyme that converts galactose to glucose. If you were a physician treating a person with this disease, which of the following would you have them exclude from their diet? maltose starch mannose lactose

lactose

In ______ molecules, London forces tend to be stronger than dipole-dipole force

large

Cooling the temperature of system drives the equilibrium to the ___

left removing heat from reactants

which way does the hydroxyl point in L - isomers

left (look at the last carbon) before the group at the end)

beta 1,4 linkage

links diagonally; O is oriented upwards

alpha 1-4 linkage

links side to side to create a straight line; O is oriented downwards

what kind of lipids would arctic fish have

lipid bilayers with short and unsaturated tails since they can remain fluid at lower temperatures

How does lipid structure affect membrane permeability?

lipid bilayers with short unsaturated tails have higher permeability and fluidity lipid bilayers with long saturated tails have lower permeability and fluidity

How does hydrocarbon tail length affect membrane permeability

longer hydrocarbon tails have more interactions (membrane is more dense -> decrease in permeability)

do folded proteins have high or low potential energy

low

Physical and chemical changes tend to proceed in the direction that results in...

lower potential energy increased entropy or both

How does decreasing temperature affect membrane permeability

lower temp slows movement of hydrocarbon tails, allowing more interactions (membrane is more dense)

Reactions tend to proceed in the direction of ______ potential energy and ______ entropy

lower; higher

spontaneous chemical reactions run in the direction that (raises/lowers) the free energy of the system

lowers

Proteins

macromolecules consisting of one or more polypeptide chains each polypeptide has a unique sequence of amino acids each protein generally possesses a characteristic 3D shape

ball and stick models

make the bonding arrangment of atoms (colored balls) easier to see because the bonds are represented as sticks provide info on the 3D relationships also relative atom size

lipid functions

membrane structure energy storage signaling

mRNA

messengers of the DNA code required for protein synthesis

cofactors

metal ions that assist enzymes with catalysis bind to the enzyme ex. Zinc, Magnesium , iron

how do lipids self organize in solution?

micelles: fatty acids or other single chain form into a circle; the hydrophilic heads interact with water and the hydrophobic tails interact with one another - the heads are bigger/wider than the tail (triangle shape) phospholipids: two chains; hydrophilic heads interact with water and hydrophobic tails interact with each other - same width head/tail (rectangular shape)

When did the main theorys relating to life emerge?

mid-1800s

Buffers

minimize changes in pH reduce the impact of adding acids or bases to the overall pH weak acids or bases important for homeostasis

Organic molecule

molecule that contains carbon bonded to other elements, linked in a chain or ring

equilibrium (in terms of diffusion)

molecules moving randomly in both directions but there is not more net movement (no concentration change)

Why is waters ability to absorb energy critical to the theory of chemical evolution?

molecules that were formed in the ocean were well protected from excessive heat or sources of energy that could break them apart this allowed them to persist and slowly increase in concentration over time, making them more likely to react and continue the process

double strand DNA is (more/less) thermostable than DNA

Why is ATP the universal energy currency?

most enzymes are optimized to use ATP therefore the cell can focus on producing only ATP in large quantities some enzyme are optimized for UTP, CTP, or GTP these nucleotides can easily be produces from ATP ex. most cars are optimized for regular gas (its just more convenient)

Biological consequence of water being a solvent for charged or polar compounds

most reactions important for life take place in aqueous solutions

delta h of exothermic reactions

negative since it releases heat, the products have less PE than the reactants

If a reaction is exothermic (ΔH is _______) and the Δs is _________ , the ΔG is always ____________ and the reaction is always (spontaneous/non spontaneous)

negative; positive; negative; spontaneous

nucleoside

nitrogenous base + sugar

Can peptide bonds rotate?

can passive transport create a gradient

Does all genetic info descend from ancestor to offspring?

no horizontal gene transfer symbiotic fusions

do catalyzed reactions reach the maximum speed

no but they still approach it (eventually plaqteau)

Is DNA copying perfect

no, but it is overall highly accurate

Can thermodynamics predict how quickly a reaction will occur?

no, only the direction of the reaction (speed would be kinetics)

Do all side chains have functional groups?

no, some only consist of carbon and hydrogen atoms these are nonpolar, involved in folding and interactions with other proteins not as reactive

Did the beak shape of the finches change within their lifetimes?

no, the change occurred in the characteristics of the population over time

Are viruses alive?

no, they are not made of cells and require other organisms to process information and reproduce

neutron

non charged particles in the atomic nucleus every element except hydrogen has one or more neutrons in its nucleus

ΔG > 0

non spontaneous endergonic

Prosthetic groups

non-protein atoms or molecules permanently attached to proteins that assist enzymes with catalysis ex. retinal (vitamin A) and FAD

would a C-H bond be polar or nonpolar

nonpolar because they have approximately equal electronegativities

what do free fatty acids consist of

nonpolar hydrocarbon tail attached to polar carboxyl group

Where do you expect hydrophobic and polar residues to be found in protein

nonpolar inside and polar on the outside (exposed to solvent)

Nucleic acid monomer

nucleotide

monosaachride classification

number of carbon atoms and location of the carbonyl group ex. aldotriose and ketotriose

Atomic number

number of protons in the nucleus of an atom specific to the identity of each element written as a subscript to the left of an elements symbol

translation

occurs in the ribosome, which contains rRNA and many proteins in translation, anti-codon of tRNA that carries a respective amino acid to the ribosome binds to its complement sequence (codon) in the mRNA template amino acid sequence is dictated by the genetic code

How to tell if a molecule is polar

often molecules that contain nitrogen or oxygen atoms are polar since they're very electronegative theyre shape is bent dissolve in water

nucleic acid oligomer

oligonucleotide

glycolipid

oligosaccharides link to lipids

glycoprotein

oligosaccharides link to proteins

Residues

once in a polymer, monomers are referred to as residues amino acid residue nucleotide residue sugar residue

Chemical reaction

one substance is combined with others or broken down into another substance typically chemical bonds are broken and new bonds form

What kind of questions do scientists ask?

ones that can be answered by observing or measuring things--collecting data

What kinds of question cant scientists answer?

ones that don't result in data ex. religious things

sacharrides

other word for carbohydrate

In living organisms, energy for driving unfavorable reactions is generated through

oxidation, carbohydrate, fats and proteins

O2 is a very effective ______ agent

oxidizing

In a neutral solution what is the relationship between pH and pOH

pH=pOH

What kind of charge to polar covalent bonds form?

partial positive and negative charges

Amino acids are linked by

peptide bonds

What bonds are between the phosphate groups in ATP

phosphoanhydride bonds

what are nucleic acids linked by

phosphodiester bonds

what stabilizes sugar phosphate bonds

phosphodiester bonds

What forms the sugar phosphate backbone?

phosphodiester linkages

How are genes transferred by plasmids/other DNA vectors?

plasmids - cyclic DNA elements that can replicate independently of the chromosomes plasmids are very useful for gene manipulations & protein expression very common for bacterial toxins and antibiotic resistance factors shared between different bacteria can be easily lost when the election factor is missing can be obtained from other bacteria when the selection factor is present

Genes can be transferred horizontally by:

plasmids or other DNA vectors (typically by bacteria- conjugation or transformation) viruses/bacteriophages or acquired from genome fragments of deceased organisms (less common)

carbonyl groups

polar includes ketones and aldehydes have sites that link molecules into more complex compounds, especially aldehydes carbon double bonded to an oxygen

Is the amino acid backbone polar or non polar?

polar; bunch of N-H & O-C bonds

cellulose

polysaccharide consisting of glucose monomers that reinforces plant-cell walls linear molecules instead of helical since every glucose molecule is flipped tougher and flat rigid structure hard to hydrolyze requires complex enzymes

Smallest scale of organisms that can experience evolution

population

If a reaction is endothermic (ΔH is ________) and the ΔS is _________, ΔG is always ___________ and the reaction is never (spontaneous/non spontaneous)

positive; negative; positive; spontaneous

protons

positively charged particles in the atomic nucleus

delta h of endothermic reactions

postive since heat is taken up during the reaction (products have higher PE than the reactants)

Which level of protein structure is least affected by disruption of hydrogen bonds?

primary

Polymerization

process of covalently linking monomers together

What are state functions?

properties that are determined by the state of the system, regardless of how that condition was achieved or what path it had to take such as enthalpy, entropy

domain

proposed by Woese a taxonomic category, based on similarities in basic cellular biochemisrty, above the kingdom level bacteria, archaea and eukarya

What determines an enzymes optimal temp and pH

protein folding and denaturing protonation states of active residues

secondary structure of protein

protein structure is formed by folding and twisting of amino acid chain stabilized by hydrogen bonding between groups along the peptide bonded backbone (carbonyl group of one amino group of another) also forms alpha helix and beta-pleated sheets

tertiary structure of protein

protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3D structure stabilized by bonds and other interactions between R groups and peptide bonded backbone (both long and short of any shape and complexity) some proteins stop here

In overall shape, ______ are the most diverse class of molecules known

proteins

What are the 4 major classes of biological macromolecules?

proteins nucleic acids carbohydrates lipids

how do proteins span the mebrane

proteins can be amphipathic polar and charged amino acids (hydrophilic) are on the ends while nonpolar residues (hydrophobic) are in the middle and interact with the nonpolar tails this is how alpha helixes sit in the membrane

Theory of Evolution

publication - 1856 Book "origin of species" - 1858 Charles Darwin and Alfred Russel Wallace Made two claims: 1. all diverse species are related by a common ancestry 2. the characteristics of species can be modified from generation to generation (descent with modification) via natural selection, genetic drift, gene flow and mutation Darwin published "on the origin of species" relates to changes in allele frequencies DNA is copied by DNA polymerase to pass genetic info from cell to cell or from one organism to its offspring copying DNA is highly, but not perfectly, accurate

sugars with 6 membered rings

pyranose

ΔG = 0

reaction is at equilibrium

Explain the lock-and-key model of enzyme activity. What is incorrect about this model?

reactions proceed when the reactant model (key) fits snugly into the active site of an enzyme (the lock) this model assumes that enzymes are rigid, however that are in fact flexible and often change their shape to bind substrates

redox reactions

reduction-oxidation reactions chemical reactions that involve the loss or gain of one or more electrons represent the energetic coupling of two half reactions, one exergonic and one endergonic

The transition from compounds with high enthalpy to compounds with low enthalpy is accompanied by heat (gain/release)

release

phosphatases

remove phosphate groups (dephosphorylation) from proteins

life origin conundrum

replication of genetic material and its transcription is ineffective without catalysis cell catalysts (proteins) are encoded by DNA which evolved first catalysts or genetic material? proteins or DNA?

R group (side chain)

represents part of amino acid core structure that makes each of 20 amino acids unique properties of amino acids vary due to these side chains contain functional groups - can participate in chemical reactions

primary active transport

requires energy (ATP or other exergonic reaction) ex. sodium-potassium pump 3 NA- out and 2 K+ in can transport against gradient (creates gradient)

Any force that depresses a water surface meets with _____

resistance this resistance makes a water surface act like an elastic membrane hydrogen bonds cause it to be stronger than that of other liquids

Ionic bonds

result when electrons are transferred from one atom to another to give both atoms full valence shells the attraction between oppositely charged ions

Raising the temp of the system drives the equilibrium to the ___

right adding heat to reactants

which way does the hydroxyl point in D - isomers

right (look at the last carbon) before the group at the end)

TATA box binding protein

saddle shaped, binds DNA

how does fatty acid saturation affect structure

saturated - single bonds only with max number of hydrogen (straight) unsaturated - one or more double bonds (forms kinks)

order of protein folding

secondary structures (a-helices are faster than B sheets) then they fold in local foci - nuclei of folding then proteins fold in globular, but loose structures - molten globules finally, molten globules optimize the bonds to become mature proteins

Oligomers

short polymer chains that consist of just a few monomers oligopeptides or peptides

structural formulas

show which atoms in a molecule are bonded to each other single, double and tirple bonds are visible indicate geometry in 2D useful for planar molecules like water and carbon dioxide

How are chemical reactions written?

similar to mathematical equations the initial or reactant, molecules are shown on the left and the resulting, or product, molecules are shown on the right arrows in between are like equal signs (means matter has transformed) the number of atoms of each element in the reactant must be equal (balanced with) the atoms of each element in the products

Molecular formulas

simply list the atoms present in a molecules subscripts indicates how many of each atom are present

In which direction will the equilibrium shift if the temperature is raised on the following reaction? N2O4(g)⇌2NO2(g) ΔH=+57.2

since ΔH is positive this is an endothermic reaction and thus we can treat heat as a reactant this means it would shift right, producing more NO2

Types of covalent bonds

single, double, triple, polar and nonpolar

Dipole-dipole forces are stronger than London forces in _____ molecules

small

oliogosaccharides

small polymers of monosaccharides

Orbital

specifc regions in which electrons move around the atomic nuclei each orbital can hold up to 2 electrons grouped in levels called electron shells

catalyst

speeds up a chemical reaction without being used up or changed in the process specific for a particular reaction

Pathogenic mutations in primary protein structure (SARS-COV2 example)

spike protein mediates virus entry The furin cleavage site in the spike protein is mutated to be effectively cleaved by human furin this allows it to infect human cells

CH4 + 2 O2 → CO2 + 2 H2O Determine if the reaction above is spontaneous or not, addressing both potential energy and entropy.

spontaneous The reactants have higher potential energy than the products due to the strong electron affinity seen in the products due to the Oxygens electronegativity (shorter bonds). This is also a combustion reaction meaning heat is released (exothermic) and thus entropy increases.

Is protein folding spontaneous or nonspontaneousq

spontaneous folded molecules are more energetically stable than unfolded molecule (less potential energy)

ΔG < 0

spontaneous exergonic

Are most common isotopes stable or nonstable?

stable

Thermodynamics operates by _________

state functions

Major types of lipids

steroids fats/oils phospholipids waxes

potential energy (in general/in molecules)

stored energy an object gains or loses its ability to store energy due to its position in molecules PE is related to the position of shared electrons in covalent bonds when the shared electrons are far from the atomic nuclei, the bond is long and weak if the electrons are shifted closer to one or both of the atoms, the bond becomes shorter and stronger

Thermodynamics

studies properties of chemical reactions like whether or not a chemical reaction will occur

elements

substances that consist entirely of a single type of atom each atom of an element has a specific number of protons

Reactants are called

substrates

Common sources of energy

sunlight (plants, algae, some bacteria) organic molecules reduced inorganic molecules

cell in hypotonic solution

swells

Anabolic pathways

synthesize macromolecules typically require energy hydrolysis of ATP

What affects pH

temperature atm pressure breathing rate (blood in people)

Amino and carboxyl functional groups

tend to attract or release a hydrogen ion (proton) when in solution amines and carboxylic acids amino groups function as bases--tend to attract a proton (get an extra H with a positive charge) carboxyl groups act as acids--tend to lose a proton (lose H on hydroxide, O has negative charge) participate in hydrogen bonding

Whats the geometry of CH4?

tetrahedral the repulsive forces between electrons push the four C=H bonds as far apart as they can get each bond is 109.5* from one another

Mole

that amount of a substance that contains 6.022 x 1023 of its elemental entities the mass of one mole of an atom is the same as its atomic weight expressed in grams

Energy

the ability to do work or supply heat

entropy

the amount of disorder of any system, such as a group of molecules increases in the a system when the products of a chemical reaction are less ordered than the reactant molecules s

rate of reaction is defined by...

the amplitude of the activation energy

Chemical bonds

the attractive forces that hold atoms together

atomic weight

the average mass of an element that is based on the relative proportions of all its naturally occurring isotopes

why do alpha helixes form bonds faster than beta sheets?

the bonds are always formed between i and i+4 they are near by residues they are right there they don't need to look for it its always there

Dissociation reaction

the chemical reaction that takes place between water molecules H2O <=> H+ + OH- Produces a hydrogen and hydroxide ion hydrogen is a proton tho and protons cant just exist by themselves so the equation is more accurately written as 2H2O <=> H3O+ + OH- The water molecule on the left gives up a proton and the other water molecule accepted a proton

What caused the Hindenburg to explode? What if He was used instead of H?

the combustion reaction between Hydrogen and Oxygen gas 2H2 + O2 -> 2H2O H2 and O2 have more potential energy than water, thus meaning this was an exothermic reaction That extra energy was released as heat causing the blimp to explode Helium is a noble gas and thus stable and nonreactive If the blimp only used helium the explosion would not have occurred.

What is pH determined by?

the concentration of protons (the more H+ -> more acidic)

What do enzymes not change?

the delta G of the reaction the energies of the reactants or products

What factors contribute to bond strength?

the electronegativity of atoms affect the position of shared electrons Stronger EN leads to shorter stronger bonds increased bond strength also occurs as more electron pairs are shared when double and triple bonds are formed

Gibbs free energy

the energy of a system that can be converted into work amount of this energy that is available can be measured only by how it changes in a reaction (delta G) determines whether a chemical reaction is spontaneous

second law of thermodynamics

the entropy of an isolated system always increases amount of disorder/randomness how much energy is disspersed

Why does the catalyzed reaction rate eventually reach a plateau

the enzymes get busy, theres no where for the extra substrates to attach

RNA world hypothesis

the first life form used RNA ribosomes contain RNA and proteins bacterial ribosomes contain less proteins than eukaryotic ones various forms of RNA are requires to make proteins, so RNA likely exists first RNA satisfies 3 key characteristics of life - info storage and replication - info processing - catalysis

monosacharides polymerize through

the formation of glycosidic linkages between carbon 1 and carbon on the other side condensation reaction forms water

transition state

the intermediate point between breaking old bonds and forming new bonds very unstable = very high energy

Thermal energy

the kinetic energy of molecular motion the total KE of a system that includes the motion of matter and is measured as temperature

Closed system

the mass of reactants is always equal to the mass or products can exchange energy with environment cannot exchange matter with environment ex. thermos

energetic coupling

the mechanism by which energy released from an exergonic reaction is used to make an endergonic reaction spontaneous in cells it either occurs through the transfer of electrons or the transfer of a phosphate group (phosphorylation)

activation energy

the minimum amount of energy required to form the transition state

Space filling models

the most realistic way to represent a chemical structure spheres representing atoms show their true relative sizes depicts spatial relationships

valence

the number of unpaired electrons in the valence shell when an atom is involved in covalent boding, valence often determines how many covalent bonds the atom can form

Molarity

the numbers of moles of a solute present in 1 liter of solution

Which molecule would have the highest potential energy? C₆H₁₂O₆ (glucose) C₃H₇O₆P (Glyceraldehyde 3-phosphate) CH₁₁N₂O₃ (Glutamine)

the one with the most nonpolar bonds (glucose)

What type of information is used to direct different polypeptides to fold into different shapes?

the order and type of amino acids (primary structure)

In cases where more free energy is lost by oxidation than is necessary for reduction...

the overall reaction is exergonic

sandwich model of membrane structure

the plasma membrane consists of an inner layer of phospholipid sandwiched between two outer crusts of protein wrong cause proteins extend out and within the membrane

One of the factors that define potential energy of chemical bonds is...

the position of shared electrons in covalent bonds if shared electrons are far from the atoms nuclei--bonds are long and high in energy if shared electrons are shifted closer to one or both nuclei--bond becomes shorter and contain less potential energy

Chemical energy

the potential energy stored in chemical bonds between atoms atoms bound together with weak bonds have a greater capacity to be broken apart to reform into new, stronger bonds during a reaction than do atoms held together by strong bonds

fats and oils

the primary function is energy storage glycerol + 3 fatty acids (hydrocarbon tail) most nonpolar fats and oils have the same chemical nature except... 1. fats contain mostly saturated fatty acids (no double bonds) 2. Oils contain more unsaturated fatty acids (1 or more double bonds)

How does the PE in most chemical reactions vary between the reactants and products

the products formed often have shorter, stronger covalent bonds than the reactants thus the PE stored within the bonds decreases the differences in PE between the reactants and products is transformed into an equal amount of KE

What determines a proteins fold, properties and functions?

the sequence of R groups

solvent

the substance in which the solute dissolves

Molecular weight

the sum of the atomic weights of all the atoms in a molecule roughly, the total number of protons and neutrons in the molecule

mass number

the sum of the protons and neurons in an atom subscript to the top left of its symbol

Biological consequence of water having a high specific heat

the temperature of aqueous solutions change slowly, oceans moderate coastal climates

enthalpy

the total energy in a molecule (H) chemical potential energy

where do base pairs rotate

the two paired bases rotate at the carbon - nitrogenous base bond (glycosidic)

Chemical Evolution

theory that simple chemical compounds from th early atmosphere and ocean combined through chemical reactions to fom larger, more complex susbatnces, eventually leading to the origin of life and start of biological evolution so life did at one point arise from nonlife

phospholipid mobility within membranes

they are in constant lateral both, but rarely flip to the other side, the other leaflet (hydrophilic head wouldn't want to go through hydrophobic tails) - allows for membrane polarity phospholipids are not covalently attached so the diffuse leaflets in natural membranes typically have a different composition diffusion within leaflets enables fluidity, plasticity and self repair

Whats the geometry of N2 and CO2?

they are linear in N2 there are only 2 atoms so it has to be linear in CO2 the electrons in the two C=O bonds repel one another also making them linear

What factors determine whether a chemical reaction is spontaneous or not?

they can proceed on their own--without any continuous external influence if the PE of the products and less than the reactants it is spontaneous (ΔH<0) If there is an increase of entropy it is spontaneous

secondary structure elements are very common because

they depend on the universal backbone they only weakly depend on side chains (R) yet, side chains may favor one vs another (glycin and proline are known to break alpha helixes)

why cant humans digest lactose?

they dont produce beta - D - galactosidase (lactase)

why are hydrogen bonds important

they keep our DNA together and are behind many of waters properties

Why are isotopes important science tools?

they're heavy and can be used to trace compounds their nuclei have magnetic momentum and can be used to determine the structure by NMR can be used for imaging in medicine (MRI) carbon dating

What DNA strands have the highest melting temperatures

those with purine bonds (G-C)

How do active sites hold substrates in a precise orientation

through hydrogen bonds and other weak interactions

A cell in a hypertonic solution will

to shrink

coenzymes

transiently attached organic molecules (not permanent) that assist enzymes with catalysis more complex than cofactors ex. NAD+, Coenzyme-A

tRNA

transporters of amino acids

chirality or stereoisomerism

two molecules that aren't identical, but relate as mirror images of each other L - D isomers middle carbon is the chiral center

Molecule

two or more atoms held together by covalent bonds

primary structure of protein

unique sequence of amino acids stabilized by peptide bonds disulfide bonds between cysteine groups

The number of __________ determines that number of bonds an atom can make

unpaired electrons

Induced fit

upon binding substrates, enzymes change conformation ex. stretching a bond to make it more likely to break

Covalent bonds

valence electrons are shared by two atoms molecules are held together by covalent bonds

outmost electron shell

valence shell elements want to have a full outermost shell noble gasses have full shells

conformations

variations of the final fold of a protein proteins often adopt different conformations to function

How are genes transferred by viruses?

viruses can get integrated into and released from genomes some information can be transferred ex. bacteriophages into bacteria

What is the most abundant molecule in organisms?

water

Why is sweating an effective way to cool off?

water has to absorb a great deal of energy to evaporate due to its hydrogen bonds thus the water molecules in sweat absorb a lot of energy from your body before they evaporate, so you lose heat

Hydrophilic

water loving typically polar compounds containing partially or fully charged atoms

Explain the importance of eating breakfast in the morning?

we need it to stay alive the molecules we obtain from it can be used as building blocks for DNA, RNA, proteins etc. and for making ATP

Theory

well-tested explanation that unifies a broad range of observations not a guess or speculation framework for hypothesis

reduction

when an atom or molecule gains one or more electrons (hydrogen) nonspontaneous, endergonic half of coupling reaction increases the potential energy of a reactant

oxidation

when an atom or molecule loses one or more electrons (hydrogen) the spontaneous, exergonic half of coupling reactions lowers the potential energy of a reactant

When is an atom most stable?

when its valence shell is filled

Speciation

when natural selection causes populations of one species to diverge and form other new andmore distinct species ex. finches

When did the process of evolution by natural selection take over?

when the original molecule was able to start self multiplying

when is delta s positive

when the products of a chemical reaction become less ordered than the reactant molecules entropy increases and is +

Are all proteins polypeptides?

yes

Is F-H polar

yes

Is N-H polar

yes

Can ionic compounds dissolve in water?

yes dissolve by separating into ions and interacting with the partial charges of water (ex. NaCl) other molecules with many polar groups can also dissolve in water (ex. glucose)

Do proteins fold quickly?

yes microsecond to millisecond time scale

Why is it better to cut the waters surface with your fingertips when you dive into a pool, instead of doing a belly flop

you have to break the surface of the water to enter when you use your fingers it creates an entry point for you body to glide in when you belly flop, you're relying on the flat surface of your whole body to break the water the larger the surface area of something hitting the water, the larger the resistance force of the water pushing back will be

1113H Midterm #1

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