What are the type of covalent bonds for: 1. Proteins? 2. Carbohydrates 3. Lipids 4. Nucleic acids

1. Peptide 2. Glycosidic 3. Ester 4. Phosphodiester

Exam 1 Lectures 1-3 Flashcards by Z Chin

Properties of a covalent bond include:

Atoms are close together ie strong, short bonds because sharing electrons

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properties of a non-covalent bond

Attractive forces ie do not not need to be close to one another. Weak and long bods. Includes ions

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Covalent bonds make molecules: T/F?

True

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What are the type of covalent bonds for:

Proteins?
Carbohydrates
Lipids
Nucleic acids

Peptide
Glycosidic
Ester
Phosphodiester

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How is the strength of a covalent bond measured?

Measured by how much energy is needed to break apart. High energy needed bc of closeness

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How is the strength of a non-covalent bond measured?

Measured by how much less energy is needed to break bond. Bc of how far apart they are, requires less energy.

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What are the types of non-covalent interactions:

Charge-charge
Dipole
Hydrogen Bond

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What are 2 examples of charge-charge bonds?

Ionic bonds and salt bridges

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If F>0 what does that tell us about charge?

Positive number bc 2 pos charges = a pos number which means they are like charges and REPEL

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What does F<0 tell us:

Negative number bc one is bigger than the other and 2 opposite charges ie ATTRACTIVE

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In a vacuum we use __ law but in a biological environment, we use __?

Coulomb’s law and Relative permittivity (D)

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What is D?

Dielectric constant accounts for “stuff” that prevents electrons from interacting with one another

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What is the energy of interaction

Energy required to separate 2 ions

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E<0 means:

Considering the attraction

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What is a dipole interaction?

Deals with partial charges; similar to charge-charge interactions

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Dipole interactions are highly dependent on what?

Distance

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T/F: dipoles can be permanent (polar) or induced (polarizable)?

True

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What exactly is a H bond?

Sharing of a H+

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What is an example of H bond?

Nucleotide base pairing

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Wha is the nature of interaction for Van der Waals?

Charge attraction

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H20 is what type of interaction?

Non-covalent

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What are characteristics of H20 as a solid?

Has optimal H bonds and bonds are long

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What are characteristics of H20 in a liquid state

Suboptimal H bonds, back and forth motion of bonds (far and close)

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What are the characteristics of H20 as a gas

No H bonds

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Is ice less/more dense than liquid H20?

Less

What is specific heat capacity?

Amount of heat needed to change the temp of 1g of a given substance by +/- 1 degree Celsius

What is heat of vaporization defined as:

Amount of energy needed to change 1g of a given substance from liquid to gas

H bonds __ energy to break and ___ energy when they form

Use and release

What is cohesion?

Attraction to self

What is adhesion?

Attraction to other

What creates surface tension

Cohesion

What creates capillary action

Cohesion and adhesion working together

Charged/polar molecules are in H20 solvent?

Hydrophilic and dissolve

Nonpolar molecules are what in H20 solvent?

Hydrophobic and separate

Covalent bonds ___ energy when broken

Release

Covalent bonds __ energy to form

Use

Noncovalent interactions __ energy to break

Use

Noncovalent interactions __ energy when formed

Release

T/F: everything is reversible

True

HA <=> A- + H+ What is the donor? What is the acceptor?

HA is the weak acid donor | A- is the conjugate base acceptor

A weak acid’s Ka is smaller/larger and why?

Smaller bc not likely to fall apart

A strong acid Ka is smaller/larger and why?

Larger bc falls apart completely (large numbers of conj base and H+)

Energy of interaction is smaller larger in a weak acid? Why?

Larger because 2 ions are more attractive to one another

Weak acid has smaller/larger pka?

Larger

Strong acid has smaller/larger pka? Why?

Smaller bc how attractive conj base is to H+

Energy of interaction in strong acid is smaller/larger

Smaller

B + H20 <=> BH+ + OH- What is the acceptor? What is the donor?

B is the weak base acceptor | BH+ is the conjugate acid donor

Strong base has smaller/larger Kb?

Larger

Strong base has smaller/larger pKb?

Smaller

Energy of interaction smaller/larger in strong base?

Larger

Weak base has smaller/larger Kb?

Smaller

Weak base has smaller/larger pKb?

Larger

Weak base has smaller/larger energy of interaction?

Smaller

Low pH means what about the H+

More (most) H+

What is the purpose of a buffer?

Weak acid base that help stabilize pH able to absorb change in H+ concentration

How dos gel electrophoresis work?

Direction of migration based on net charge of molecule

Wha is the isoelectric point (pI)

The pH where ALL molecules of a given species in sol’n have an overall average charge of 0

Ph is less than pI

Molecule has a positive charge

pH>pI

Molecule has negative charge

pH=pI

Molecule has no net charge

What happens if there are 3 pKas and trying to find pI?

All we care about are the 2 pKas that get us to our species isoelectric point (2 pKas for average)

Protein stops moving in isoelectric focusing when...

pH = pI (separating based on pI of protein)

Are proteins soluble when pH=pI

What is the 1st law of thermodynamics

Energy is neither created or destroyed in a CLOSED sys

Can you convert btwn energy (PE & KE) without violating the 1st rule of thermodynamics?

Yes

What is PE?

Position, potential to do work.

What is KE?

Motion, performing work

What is an example of PE?

Chemical energy- PE within chemical bonds. Electrons with an atom (push/pull of e-s and protons)

What is an example of KE?

The atom itself

How does energy function in a closed system?

Energy cannot leave in or out

What is an example of a closed system?

The universe

How does energy function in an open system?

Energy exchanged btwn system and surroundings (can go and come as it pleases to surroundings) can add and subtract

What is an example of an open sys

A cell. The universe is the surroundings

What is the 2nd law of TD?

Disorder is increasing

What is disorder seen as in TD?

Entrophy seen as heat bc we are in pieces/mobile which generates heat

Which is more disordered: anabolic or catabolic?

Anabolic

Define anabolic

Synthesis. Monomers into polymers; assembly of many pieces into 1 piece

Define catabolic

Breaking polymers into monomers

How do we measure energy in TD?

Gibbs free

``` What is: Delta G Delta H T Delta S ```

Delta G = change in energy Delta H = change in total energy = enthalpy in sys T = kelvin (+273) Delta S = entropy change in disorder

What drives the sign of delta G?

TdeltaS

-deltaH and +deltaS =

Spontaneous at all temps

+deltaH and -deltaS =

Non spontaneous at all temps

+deltaH and +deltaS =

Spontaneous only at high temps

-deltaH and -deltaS =

Spontaneous only at low temps

When deltaG is negative:

Free energy released; EXERGONIC favorable rxn (to products)

When deltaG is positive:

Free energy required; ENDERGONIC rxn unfavorable (reverse rxn to reactants)

When do you need high disorder?

To do work; energy is added to the sys thus incr deltaH and incr deltaS

When do you need low disorder?

For disorder to ‘go away’ energy is releases from the open sys

What is important about a state function and examples:

We only care about where we end ie deltaG, deltaH, and deltaS

Most energetic state is _ state and what does this mean?

Transition state and very unstable

What lowers the activation energy and how?

Enzymes by stabilizing the transition state

What are the 4 ways to stabilize the transition state?

1. Substrate orientation 2. Straining substrate bonds 3. Favorable microenvironment 4. Covalent bonding with substrate

Protein folding: spon or non spon?

Spontaneous!

Net effect is equal to:

Sum all sources of energy

T/F: reactions exist in a vacuum?

FALSE. Reactions do no exist in a vacuum thus non-equilibrium concentrations

What is the equilibrium constant?

“Q” = products/reactants

Q less than K

Rxn towards products (forward to the right)

Q>K =

Rxn towards reactants (to the left; reverse)

Movement of e-s and concentration gradients across a barrier account for influences of process happening in a __

Cell

What is biology standard state concentration?

1M except H+ (=10^-7M)

How do we drive and unfavorable reaction?

1. Use up the products! | 2. Couple it to a favorable exergonic rxn ie ATP hydrolysis

T/F: reaction and deltaG values can be summed

True

Exam 1 Lectures 1-3 Flashcards

(103 cards)