Exam 1 Flashcards - BIOC 384

Define biochemistry.

hands-on experimental science that relies heavily on quantitative analysis of data

interested in understanding the structure & function of biological molecules

M1T1

Describe the contribution of Eduard Buchner to the birth of modern biochemistry.

demonstrated that carbon dioxide & ethanol could be produced from sugar using brewer’s yeast extracts in an in vitro reaction

*it showed that fermentation results from chemistry rather than a vital life force

M1T1

What are the five principles of modern biochemistry?

1. hierarchical organization of life

2. DNA is the chemical basis for heredity

3. bimolecular structure determines function (fine tuned by evolution via DNA mutations & natural selection)

4. biochemistry obeys thermodynamic laws

5. life on Earth depends on water

M1T1

Describe the hierarchical structure of nature.

living systems are organized around biomolecules that participate in interconnected metabolic pathways, signal transduction, and ecological networks

M1T2

What is a covalent bond?

chemical link when two atoms share one or more pairs of electrons

bond energies increase in going from single bonds to double bonds to triple bonds

M1T2

Draw the following functional groups: amino, hydroxyl, sulfhydryl, phosphoryl, carboxyl, and methyl,

M1T2

Name the four major classes of biomolecules and the primary functions of each.

1. amino acids: protein function, neurotransmission, nitrogen metabolism, energy conversion

2. nucleotides: nucleic acid function, energy conversion, cell signaling, enzyme catalysis

3. simple sugars: cell wall structure, energy conversion, cell recognition, nucleotide structure

4. fatty acids: cell membranes, energy conversion, cell signaling, energy storage

M1T2

Describe the functions of amino acids relating to proteins.

amino acids are the building blocks for proteins & differ in the side chains attached to the alpha carbon

glutamate & tyrosine derivates are important signaling molecules in neurotransmission

M1T2

Describe the structure of nucleotides and nucleic acids.

nucleotides form nucleic acids

nucleotides are made up of: a nitrogenous base, 5-membered sugar, and phosphoryl groups

nucleotide bases in DNA AND RNA: adenine, guanine, cytosine

nucleotide base in DNA: thymine

nucleotide base in RNA: uracil

M1T2

Describe the functions of sugars and carbohydrates.

monosaccharides & polysaccharides are carbs used as energy sources & structural components of cells

simple sugars form carbohydrates

M1T2

Describe the functions of fatty acids and lipids.

fatty acids contain a carboxyl group (polar) attached to a hydrocarbon chain (nonpolar)

primary components of lipids in the plasma membrane

used as a storage form of energy in the form of triacylglycerols

M1T2

What are the six essential elements in living organisms?

H, O, C, N, P, S

M1T2

What are the building blocks of nucleic acids?

nucleotides

nucleotides consist of: a nitrogenous base (A, G, C, T, or U); 5-carbon sugar (ribose or deoxyribose); 1+ phosphoryl groups

M1T3

Why does base pairing involve hydrogen bonds?

hydrogen bonds form between nucleotide bases provide specificity in DNA replication and RNA transcription

base stacking provides helix stability

G-C pairs contain 3 hydrogen bonds

A-T pairs contain 2 hydrogen bonds (DNA)

A-U pairs contain 2 hydrogen bonds (DNA-RNA or RNA-RNA)

M1T3

How does base stacking stabilize the DNA helix?

deoxynucleotides are linked through a phosphodiester bond that connects the 5’-carbon to the 3’-carbon of the next nucleotide

2 DNA strands in the double helix are antiparallel to each other and run in the 5’ to 3’ direction

M1T3

Describe the central dogma of molecular biology.

genetic info flows from DNA to RNA to protein

DNA replication: copies the genome

Transcription: produces RNA from DNA

• occurs in nucleus & generates mRNA

Translation: uses mRNA to synthesize proteins

• requires protein-synthesizing complex

• charged tRNAs form base pairs with mRNA through codon-anticodon hydrogen bonds

M1T3

What is the main difference between prokaryotic and eukaryotic gene expression?

prokaryotic: gene expression consists of coupled transcription & translation

eukaryotic: gene transcription is separate from translation

M1T3

Is the coding strand of DNA identical or different to mRNA?

coding strand is identical to the mRNA sequence expect that uracil replaces thymine in RNA

M1T3

Based on the protein examples, match the analogy with the protein pair.

A. apple tree and pear tree

B. lemon and tennis ball

C. boat and submarine

Ribonucleotide reductase (bacteria) and ribonucleotide reductase (mouse) → apple tree and pear tree

• same enzyme in two relared species mean same structure and function

Porin channel protein and green fluorescent protein → lemon and tennis ball

• porin and GFP share a beta-barrel shape but do unrelated jobs

GR transcription factor and GCN$ transcription factor → boat and submarine

• GR and GCN4 are both DNA-binding transcription factors that act through different structures

CS-01

Put the following hierarchical levels in the correct order representing the structured organization of life on Earth. 1 is the lowest hierarchical level (base) and 7 is the highest hierarchical level (top).

glucose, glycolysis, hydroxyl group, liver cell, Great Barrier Reef, manta ray, glycogen

1. hydroxyl group

2. glucose

3. glycogen

4. glycolysis

5. liver cell

6. manta ray

7. Great Barrier Reef

functional group → molecule → macromolecule → metabolic pathway → cell → organism → ecosystem

CS-01

Describe the First Law of Thermodynamics and provide examples.

energy cannot be created or destroyed, it can only be transformed or transferred from one form to another

ex 1: amount of energy available from the oxidation of 1 gram of glucose is exactly the same regardless of the physical or biological process required for oxidation to occur

ex 2: thermogenesis in a hibernating bear results from oxidizing fat stores that are required to keep the bear alive during winter

CS-01

Describe the Second Law of Thermodynamics and provide examples.

total entropy always increases over time during any spontaneous process

ex 1: unplugging an ice maker results in a puddle of water on the floor because the energy required to form ice crystals is not available

ex 2: staying as far away from the equilibrium with the environment as possible is the only way to stay alive, this requires a constant input of energy

CS-01

Describe Gibbs Free Energy.

the difference between the enthalpy (bond energy) and entropy (energy dispersion) of a reactant and product at a given reaction temp

positive value indicates that the reaction as written is spontaneous in the reverse direction

CS-01

Describe the equilibrium constant.

ratio of the concentration of products divided by the concentration of reactants when the rate of product formation is equal tot he rate of reactant formation

value greater than 1 indicates that the reaction as written is spontaneous in the forward direction

CS-01

A mutation changes the active site of an enzyme critical for metabolism. Which outcome is most likely?

the protein function changes due to altered molecular structure

• structure determines function so changing the active site’s structure changes the enzyme’s function

CS-01

Why is the equilibrium with the environment equivalent to death in living organisms?

living organisms maintain order by resisting entropy through energy source

• life maintains order by continuously spending energy to resist entropy

• at equilibrium no free energy is available to do biological work, which is death

*life requires homeostasis not equilibrium

CS-01

Define divergent evolution.

two species with a common ancestor evolve specific traits to optimize life in their own unique environment which are very different

ex. the whale in the ocean & hippopotamus on land

M1T4

Define convergent evolution.

two species that are unrelated or very distantly related evolve similar traits because they live in the same environment and natural selection drives adaptation

ex. wings on bats & birds

M1T4

Duplication of an ancestral gene leads to three distinct outcomes. What are they?

1. the 2nd gene provides an evolutionary advantage

2. 2nd gene diverges and acquires a new beneficial function

3. 2nd gene diverges and acquires deleterious mutation

M1T4

What are the differences between paralogous and orthologous genes?

• paralogous: genes that share similar sequences within a species are paralogous (within species)

  • ex. alpha-globin and beta-globin

• orthologous: genes conserved across species (between speces)

  • ex. human & mouse alpha-globin and beta-globin

M1T4

What determines protein function and what are the different protein-structure function relationships?

*structure determines function

evolution through natural selection influences macromolecular structure & function

DNA mutations in protein coding genes can alter protein structure & function depending on type of mutation

1. same structure & function

2. similar structure & different function

3. similar function & different structure

M1T4

What are some similarities and differences between autotrophs and heterotrophs?

photosynthetic autotrophs use solar energy produced by sun for photosynthesis

both heterotrophs & autotrophs use O2 and glucose (C6H12O6) for aerobic respiration, which is a form of chemical energy conversion

*photosynthesis & aerobic respiration are redox-driven energy conversion processes that are required for life on Earth

M1T5

Define oxidation.

reduction reactions in photosynthetic autotrophs convert solar energy into chemical energy

chemical energy is transformed into osmotic work, chemical work, mechanical work

M1T5

Does life require homeostasis or equilibrium?

life requires homeostasis NOT equilibrium

organisms must maintain a steady state that is far from equilibrium with respect to temp, concentrations of biomolecules, etc.

when an organism cannot maintain a steady state using energy conversion, the concentrations of metabolites & macromolecules equilibrate with the environment & organism dies

*organisms require energy to perform osmotic, chemical, and mechanical work (energy ultimately comes from solar energy)

M1T5

Define redox reactions and identify their importance.

photosynthesis & aerobic respiration convert energy using oxidation & reduction reactions to transfer electrons since they cannot exist freely

reduction: gain of electrons

oxidation: loss of electrons

a compound cannot be reduced without another compound being oxidized

M1T5

What is the first law of thermodynamics?

reaction that gives off heat is exothermic & has negative delta H value

reaction that absorbs heat is endothermic & has positive delta H value

change in Gibbs free energy reveals if reaction is favorable (-deltaG) or unfavorable (+deltaG)

M1T5

What is the second law of thermodynamics?

solids (ex. ice) has lower entropy than liquid because water molecules in the ice have limited motion

gases (ex. steam) has the highest entropy because of increased motion of molecules

M1T5

Why is Gibbs free energy important?

Gibbs free energy changes predict if chemical reactions are thermodynamically favorable under standard (detlaG0’) and actual conditions (deltaG)

the difference between the change in enthalpy (detaH) and change in entropy (deltaS) at know temp in kelvin

deltaG0’ refers to constant pressure (1 atm), temp (298K) and the rxn is at pH 7 with water concentration fo 55.5M

M1T6

What is the equilibrium constant?

Keq is defined by the concentrations of A, B, C, & D when the rxn has reached equilibrium

Keq>1 then rxn favors C and D, proceeds left to right, deltaG0’<0 and is exergonic

Keq<1 then rxn favors A and B, proceeds right to left, deltaG0’>0 and is endergonic

M1T6

What is the mass action ratio?

under conditions where reactants and products are NOT at 1 M initial concentrations

Q is the ratio of initial concentrations of products over reactants

M1T6

Does delta G indicate thermodynamic favorability or rate of reaction?

thermodynamic favorability

M1T6

Calculate the delta G value (actual change in free energy) at 25 degrees C for the aldolase reaction, which converts F-1,6-BP to DHAP and GAP. Given the delta GO’ value of +23.8 kJ/mol and concentrations of these metabolites at a steady state:

F-1,6-BP = 15 mM

DHAP = 4×10^-5 M

GAP = 0.04 mM

-15.8 kJ/mol

MR-01

Write the equation that describes the equilibrium reaction: aA + bB ←→ cC + dD

MR-01

Identify the numbered compound functions as a hydrogen bond donor, acceptor, or neither.

1 is donor

2 is acceptor

3 is neither

4 is acceptor

MR-01

T/F: Heterotrophs depend on autotrophs for conversion of light energy to chemical energy.

True

MR-01

T/F: Heterotrophs are dependent on autotrophs to generate O2 from H2O in order to support aerobic respiration.

True

MR-01

Describe which of the four building block biomolecules this term belongs to:

palmitate

fatty acid

MR-01

Describe which of the four building block biomolecules this term belongs to:

cytidine monophosphate

nucleotide

MR-01

Describe which of the four building block biomolecules this term belongs to:

ribose

simple sugar

MR-01

Describe which of the four building block biomolecules this term belongs to:

aspartate

amino acid

MR-01

The enolase reaction has a positive ΔG°′ yet proceeds forward in the cell; what best explains this?

Cellular concentrations make the mass-action ratio low, giving a negative actual ΔG.

TopHat Sep 1

A reaction has a large negative ΔG; what does this tell you about how fast the reaction will occur?

Nothing, because ΔG indicates favorability but not the reaction rate

TopHat Sep 1

Why is reaching chemical equilibrium with the environment fatal for a living organism?

A living cell must use energy to maintain a steady state far from equilibrium

TopHat Sep 1

Why does oxidizing one gram of glucose release the same energy in a bomb calorimeter and in a living mouse?

The energy released depends only on the reactants and products, not the path

TopHat Sep 1

The porin channel and green fluorescent protein share a β barrel structure; what does this comparison demonstrate?

Similar structures can carry out different functions in different proteins

TopHat Sep 1

What element must a molecule contain to be considered organic? Why is the element critical to formation of organisms?

1 or more carbons

carbons can make up to 4 covalent bonds & provides stable structural backbones for complex organic molecules

Chapter 1

Name 4 important functions of nucleotides

energy conversion, coenzymes, information storage, signaling

Chapter 1

Name 5 types of RNA describe their functions

mRNA - template for protein synthesis

small nuclear RNA - role in RNA processing

micro RNA - regulates translation

rRNA - component of ribosomes

tRNA - provides amino acids to ribosome for translation

Chapter 1

How can DNA mutations have deleterious effects?

mutations in gene can change codons in mRNA transcript

leads to changes in AA and therefore protein

can lead to protein denaturation (unfolding) which could affect function

Chapter 1

What is the process in which ATP is formed by phosphorylation rxn using energy released from redox rnx in photosynthesis?

photophosphorylation

transforms light energy into usable chemical energy

ATP used to convert carbon dioxide into glucose which is consumed by plants or animals that eat plants

Chapter 2

What are amphipathic molecules? Why are they important?

contain hydrophobic & hydrophilic regions

form membranes that are impermeable to polar molecules

maintains separation of inside of cells from environment & allows compartmentalization ithin cells

In a redox reaction, when does a reduced compound become oxidized?

a reduced compound becomes oxidized only when it transfers an electron to an oxidized compound

SW 1

Sort the molecules into their oxidized and reduced forms.

NADP+, NADH, NADH, NAD+, Ubiquinone (Q), Ubiquinol (QH2)

Oxidized: NADP+, NAD+, ubiquinone (Q)

Reduced: NADH, NADPH, NADPH, ubiquinol (QH2)

SW 1

Within this molecule, identify the amount of peptide bonds and amino acids. Which bimolecular class does this structure belong to?

2 peptide bonds & 3 amino acids

protein

SW 1

Rank the list according to the hierarchical levels of organization. The most complex is 1 and least complex is 6.

elements & functional groups

cells

organisms

macromolecules

biomolecules

metabolism

1. organisms

2. cells

3. metabolism

4. macromolecules

5. biomolecules

6. elements & functional groups

SW 1

Sort the following terms into the appropriate hierarchical complexity level.

oxygen

DNA & RNA

proteins

carbon

amino acids

citrate cycle

glucose

glycolysis

nucleotides

Macromolecules: proteins, DNA & RNA

Elements: oxygen & carbon

Metabolism: glycolysis, citrate cycle

Biomolecules: amino acids, nucleotides, glucose

SW 1

Describe the pKa of a weak acid.

pKa is an intrinsic property of a molecule in question & depends on how tightly bound the acidic H+ is

SW 1

Given a solution is made up of equal volumes of 0.05M acetic acid & 0.1 sodium acetate, what statements are true?

doubling conc of acetic acid & sodium acetate will double the pH capacity

adding acetic acid will decrease the pH of a solution

SW 1

Match the letters to regions on the figure.

HA < A-

HA = A-

HA > A-

A. HA = A-

B. HA < A-

C. HA > A-

SW 1

Which statement about phospholipids is false?

A. phospholipids orient in lipid bilayers with the hydrophobic tails pointing inward, interacting with each other

B. polar head group of phospholipids is hydrophilic

C. polar head group of phosphatidylcholine cannot form hydrogen bonds

D. the hydrocarbon tail of phospholipids is hydrophobic

C

phosphatidylcholine is an amphipathic phospholipid

polar heads can form hydrogen bonds with water molecules & polar molecules

SW 1

When is a reaction thermodynamically favorable or unfavorable?

unfavorable: delta G > 0

favorable: delta G < 0

total delta G of couple reactions is additive (share intermediates)

M2T1

Is ATP hydrolysis exergonic or endergonic?

ATP hydrolysis is an exergonic rxn

energy is absorbed to break the phosphate bond = endergonic

the formation of new bonds releases more energy = exergonic

OVERALL exergonic rxn

M2T1

List some examples of ATP hydrolysis being used for protein conformational changes:

• muscle contraction involving conformation changes in myosin protein

• conformational changes in the Na+-K+ ATPase protein that mediate ion transport

M2T1

How does the cell maintain ATP levels? What is energy charge?

maintains ATP levels within a narrow range by interconverting ATP, ADP, and AMP using phosphoryl transfer rxns

use ratio of the concentration of ATP to conc of ADP and AMP to measure energy state of cell called energy charge (EC)

M2T1

How do cells maintain energy charge (EC)?

by regulating metabolic flux through anabolic and catabolic pathways

when EC is near 0.7 = ATP levels are now & ADP levels are near max

when EC is at 0.9 = ATP levels are near max & AMP levels are very low

M2T1

What is the difference between catabolic and anabolic pathways?

catabolic: extracting energy from metabolic fuels which convert fuel into high potential energy compounds ATP and NADH

anabolic: high potential energy compounds used for biosynthesis of biomolecules

under conditions of low nutrients/sunlight = catabolic pathways degrade stored metabolic fuels to generate ATP

when nutrients/sunlight are high = ATP used to replenish supplies of stored metabolic fuel

M2T1

Describe hydrogen bonding between water molecules.

each H2O can donate 2 hydrogens for hydrogen bonds with other molecules

flickering clusters: constant forming & breaking of hydrogen bonds between water molecules

^ short lifetime

proton hopping happens vert fast bc it relies on H bonds forming & breaking not actual movement of ion

M2T2

Describe osmosis.

diffusion of H2O molecules (solvent) across semipermeable membrane from a solution of high H2) conc to low H2O concentration

at equilibrium, conc of H2O on both sides will be equal

hypotonic solution: water molecules move into cell causing it to burst

hypertonic: water molecules rush out causing it to shrink

M2T2

What are the three types of noncovalent interactions.

permit unstable structures to briefly form which allows complexes to dissociate or reform as needed for regulation & catalysis

1. hydrogen bonds

2. ionic interactions

3. van der Waals

M2T2

Describe van der Waals interactions.

motions of electrons in nonpolar molecules that result in temporary dipoles

nearby dipoles that are aligned with opposite charges close together will attract

M2T2

How do hydrophobic effects alter protein structure?

protein folding results from hydrophobic effect

hydrophobic effect = LACK of interaction

hydration layer around polypeptide is minimized by the hydrophobic nonpolar amino acids

hydrophobic molecules disrupt hydrogen bonding in water, lowering entropy so hydrophobic groups aggregate to reduce surface area

ex. leucine & isoleucine are hydrophobic

M2T2

Where are hydrogen bonds and ionic interactions most likely to occur?

H bonds are commonly found within & between proteins

ionic interactions occur near the surface

M2T2

What chemical properties of water make life possible on Earth?

1. solid water is less dense than liquid water

2. water is liquid over a wide range of temps

3. water is an excellent solvent bc of H-bonding abilities

4. high heat capacity water functions as temp buffer

• H bonds account for high viscosity, boiling point, & melting point of water

M2T2

What is the water ionization constant?

Kw

water molecules self ionize in a reversible rxn to form H3O+ and OH-

H+ is never free in an aqueous environment & is always hydrated as H3O+

M2T3

How can we find the pH of a solution?

change in one pH unit is equivalent to a 10-fold change in H+ concentration

M2T3

When is a solution basic or acidic?

acidic: pH less than 6.5 (high H+)

neutral: between 6.5 and 7.5 (H+ = OH-)

basic: pH greater than 7.5 (low H+)

M2T3

Do strong acids have a high or low pKa? What about weak acids?

strong acids have a low pKa

strong acids hold onto hydrogen ion very weakly in presence of OH- and is easily dissociated

• low amounts of OH_ are needed to remove H+ from acid to form H2O

weak acids have high pKa

hold onto H+ strongly

• high amounts of OH- are needed to remove the H+ from acid to form H2O

M2T3

Although Watson and Crick could construct a DNA double helix with A-A and C-C base pairs, there were two reasons why this arrangement was unlikely to be valid. What are the reasons.

1. Erwin Chargaff showed that the abundance of A equaled T and G equaled C nucleotides, so A-A and C-C base pairs is inconsistent with these data

2. Distance between the ribose sugars in A-A and C-C base pairs are significantly different, whereas purine-pyrimidine base pairs are equally spaced

Chargaff’s rules (A=T, G=C) rule out like-with-like pairing

only a purine-pyrimidine pair gives uniform helix width (A-A is too wide, C-C is too narrow)

CS-02

Why was Franklin’s B-form DNA diffraction pattern so decisive in solving the DNA structure?

it revealed helical geometry with uniform spacing

the X-shaped B-form pattern with regular spacing is the signature of a uniform helix, which is what constrained the structure

M2T3

Linus Pauling proposed a triple helix structure for DNA that had the phosphate backbones of the three strands facing inward and the nucleotide bases facing outward. What are two reasons why this structure did not make sense based on the chemical properties of DNA?

1. the ring structures of nucleotide bases have hydrophobic properties and would more likely associate with each other in the interior of the helix

2. the charged polar phosphoryl groups will form hydrogen bonds with water in and be more stable facing outward toward the aqueous environment

The hydrophobic bases are more stable packed inside the helix and the charged, polar phosphates are more stable facing outward where they hydrogen bond with water — the opposite of Pauling's inside-out model

CS-02

Match the letter corresponding to the figure below with the descriptions.

A = hydrogen bond

B = 5’ hydroxyl

C = phosphoryl group

D = ribose sugar

E = minor groove

F = major groove

G = 5’ hydroxyl

H = nucleotide base

CS-02

Why is SSB binding to single-stranded DNA considered sequence-independent?

it interacts primarily with the sugar-phosphate backbone

SSB binds the sugar-phosphate backbone, which is identical in every sequence, so its binding does not depend on base sequence

CS-02

Why is the hydrolysis of ATP an overall exergonic reaction even though breaking its phosphoanhydride bond requires energy?

forming new bonds with an acceptor releases more energy than breaking the phosphoanhydride bond absorbs

TopHat Sep 3

Why do nonpolar amino acids such as leucine and isoleucine cluster in the interior of a folded protein?

clustering minimizes the ordered water hydration layer around the nonpolar groups

TopHat Sep 3

What happens to a red blood cell placed in a hypotonic solution, and why?

it swells and may burst bc water moves into cell by osmosis

TopHat Sep 3

Why does adding a small amount of base to a buffered solution cause only a small change in pH?

conjugate acid donates a proton to the added hydroxide to form water

TopHat Sep 3

According to the Henderson-Hasselbalch relationship, when does the pH of a solution equal the pKa of the acid?

when the concentrations of the conjugate base and acid are equal

TopHat Sep 3