Molecules of life | Quizlet

What is an organic molecule?

carbon-based molecules

there are two types of electrons in atoms name them and tell how are they different

core and valence electrons

valence electrons are found on outer energetic layer=on them do chemichal reactions depend

which particle makes up most of the volume in atom?

electrons(cloud) do = imporntant for molecules formation

what is the electronegativity trend across the periodic table?

more right and more up electronegativity increases

what is an alternative name for energy level?

shell

what is an alternative name for shell in atoms?

energy leve

what are core electrons?

electrons in the inner shell(s)

what are calence electrons?

electrons in the outer shell

by which 3 rules can ground -state electron configuration be built?

1. Aufbau principle: An electron goes into the atomic orbital with the lowest energy.

2. Pauli exclusion principle: No more than two electrons can be in an atomic orbital.

3. Hund's rule: An electron goes into an empty degenerate orbital rather than pairing up

define Aufbau principle

An electron goes into the atomic orbital with the lowest energy.

define Pauli exclusion principle

No more than two electrons can be in an atomic orbital.

define Hund's rule

An electron goes into an empty degenerate orbital rather than pairing up.

what are degenerate orbitals?

Degenerate orbitals are orbitals that have the same energy. They are different (they may display differently in space around the nucleus) but they are associated to the same energy.

define octet rule

atom is most stable(energetically favorable)when outer shell is filled or empty

what dipole moment of the bond tells us about bond polarity?

Greater dipole moment = more polar

how to calculate a formal charge?

formal

charge= # of valence electrons -(# of lone-pair

electrons + # of bonds)

Name steps of drawing molecule in Levis structure

1. Determine the total(if minus or plus is present in molecule it means more or less electrons correspondingly) number of valence electrons

2. Distribute the atoms

3. Form bonds and fill octets with lone pairs

4. Check for formal charges

what is C hybridization when it has 4 bonds?what is its geometry and angle?

sp3,tetrahedral,angle=109.5

what is hybridization of C when it has one double and two single bonds?what is its geometry and angle?

sp2,trigonal planar,angle>120

what is hybridization of C when it has one triple and one single bond?what is its geometry and angle?

sp,linear angle=180

what is hybridization of O when it has two single bonds?what is its geometry and angle?

sp3,bent >109.5

what is hybridization of O when it has one double bond?what is its geometry and angle?

sp2,linear angle=180

what is hybridization of N when it has three single bonds?what is its geometry and angle?

sp3,tetrahedral(with lone pair taking one angle) angle>109.5

what is hybridization of N when it has one double and two single bonds?what is its geometry and angle?

sp2 trigonal planar(?)

what is hybridization of N when it has one triple bond?what is its geometry and angle?

sp just nitrogen

what is the shape of an s orbital?

a sphere

what is the shape of a p orbital?

dumbbells(гантели) in 3 planes(x,y,z)

by which two orbitals is σ (sigma) bond formed?

by two s orbitals

what kind of bond will two s orbitals form?

σ bond

what is VSEPR(Valence-shell electron repulsion model )

Bonding electrons and lone-pair electrons around an

atom are positioned as far apart as possible!

what kind of bond do two p orbitals form?

π (pi) bond

with which orbitals can π bond be formed?

with two p orbitals

how to distinguish cis and trans?

when there is a C=C bond the groups with the highest priority on one side is cis

on the opposite sede is trans

how to distinguish E and Z iizomers?

Z=zamen/samen =highest priority on the one side

E =on diff sides

how to distinguish R and S iizomers on asymm.center?

from highest to lowest priority turning to lower and lower

R rotation clockvise

S=counterclockvise

how to rotate molecule for better R and S configuration?

how to distinguish cis & trans,Z & E isomers?

in cis and Z groups with the highest priority are on one side of the molecule

where can Φ angle be found in a peptide bond?

α-N

(since protein starts from N terminus and goes to C terminus by convention ,then Ф on the left, Ψon the right side of α carbon)

(alpha carbon to N connection)(alpha carbon is the carbon which is attached to amine group and Carboxylic group)

where can Ψ angle be found in a peptide bond?

α-C

(since protein starts from N terminus and goes to C terminus by convention ,then Ф on the left, Ψon the right side of α carbon)

(alpha carbon to Carboxyl group connection)(alpha carbon is the carbon which is attached to amine group and Carboxylic group)

what will happen to the proton if pKa is higher than pH?

H+ remains

what will happen ito the proton if pKa is lower than pH?

H+ will be removed

what will happen if pH is higher than pKa?

H+ will be removed

what will happen if pH is lower than pKa?

proton stays

what is a A nucleophile?

something that has a negative charge(-) or a lone pair.

free e pair,donates e pair

better e- accomodation=weaker nucleophile

what is An electrophile?

something that hasa positive charge(+),

a partial positive charge,

or an incomplete octet.(has a free orbital to accept electons)

how to find a rate determining step for sure?

it has the highest transition state

give an equation of a reaction rate

Rate=k{product}

Rate=k{product1}{product2}

how do curved arrows indicate movement of electrons?

a curved arrow indicates a movement of an electron pair,half arrow indicates movement of a single electron

what are rules concerning use of arrows to show a movement of e-/e- pairs?

e- always moves towards positive charge

Octet rule=if 5th thing attaches to a carbon then one thing has to leave

Arrows go according to the electron flow. So an arrow goes from negatively charged atom and/ot point out to the positively charged one

Arrows show the movement of electrons, not atoms

Arrow heads always point to an atom or a bond. Never to space.

Arrows always start at electron source (bond, electron pair), never at an atom

what are rules for drawing curwed arrows?

Arrows go according to the electron flow. So an arrow goes from negatively charged atom and/ot point out to the positively charged one

Arrows show the movement of electrons, not atoms

Arrow heads always point to an atom or a bond. Never to space.

Arrows always start at electron source (bond, electron pair), never at an atom

what does thermodynamics looks at?what does it tells us?

difference in energy between a reactant and a product

It tells us:

what is more energeticaly stable

how good is the reaction in terms how much of a product is formed

what does kinetics looks at?what does it tells us?

activation energy

how unwillingly something rqcts

how fast the reaction happen

do they and how do rate constant and reaction rate change if concentration of reactants changes?

Rate Constant always stays the same

Reaction rate changes

(if there are two reactants and we decrease concentration of one of them=reaction rate decreases)

what atoms are parts of a planar double bond system?

carbons which are connected to a double bond & atoms connected to them

what is a Reaction coordinate diagram?

energy diagram

describe/define transition state

higher in energy than a reactant and a product

bonds are partially broken and partially formed

state Le Chatelier principle

if an equilibrium is disturbed,the system will adjust to offset the disturbance and maintain the equilibrium.

how can we use Le Chatelier principle to increase the number of reaction products?

Add more of one of the reactants

Remove the product in another reaction (or physical process

A + B to C to D

give an equation for Gibbs free energy and annotate what stands for what

ΔG=ΔH-TΔS

ΔH=change in enthalpe

T=change in temperature

ΔS=entropy

when can ΔS be ignored?

the temperature is low AND

The enthalpic therm is not close to zero AND

We expect the So to be small

This gives a good estimation if Go is favorable, but not of exact value

what value does ΔG has to be for a reaction to occur?

negative

how to find ΔH of the reaction?

Look at the dissociacion enthalpies (DH) of bonds being broken and formed

ΔH(broken during reaction) - ΔH(being formed)

what determines rate of the reaction?

(number of collisions per unit of time)x(fraction of collisions with sufficient energy to break/form bonds)x(fraction with proper geometry=molecules do have to hit each other with a correct sight)

which configuration E or Z is lower in energy?what is the reason behind it?

E

orbitals overlap a bit in cis isomer while they don't in trans

how to arrange carbons around carbons which are connected by double bond so it is more energetically favorable?

attach as many other carbons to carbons connected by a double bond as much as possible

define Thermodynamic stability

indicated by G°. If G° is negative, then the product is

Thermodynamically stable compared with the reactant; if G° is positive, then the product

is thermodynamically unstable compared with the reactant.

definne Kinetic stability

indicated by G‡. If G‡ is large, then the reactant is kinetically stable

because it reacts slowly. If G‡ is small, then the reactant is kinetically unstable—it reacts

rapidly. Similarly, if G‡ for the reverse reaction is large, then the product is kinetically

stable, but if it is small, then the product is kinetically unstable.

how can we improve a reaction rate?

Increasing the concentration increases the rate

Increasing the temperature increases the rate.

Adding a catalyst increases the rate.(lowers activation energy by making an intermediate more stable)

what is Boltzmann distribuion show?

it compares number of particles,ther energy and how much particles have sufficient energy for a succesfull collision for two different temperatures

distinguish between enantiomers,diasteomeres and stereoisomers

what is an angle between atoms jn tetrahedral molecules?

109.5

how is Keuke drawing different from Lewis?and in N with 3 bonds?

Keuke draws with perspective.In N 107.3

what is relation between bond length and its strenth?

shorter the bond=stronger

the stronger s character then ... the bond

shorter and stronger

distinguish localized and delocalized electrons

localized electrons belong to 1 atom or are shared by 2 atoms

delocalized electrons are shared by 3 or more atoms

distinguish resonance contributors and resonance hybrids

resonance contributors are approx. structures with localized e

resonance hybrids are structures with delocalized e- shown.

what is a requirment for delocalization?

p-orbitals must lie in the same plane and overlap for delocalization.

rules for drawing resonance structures and hybrids

1. Only electrons move, atoms never move!

2. Only π-electrons and lone pair electrons move!

3. Move electrons always to an sp2 or sp hybridized atom!

4. The number of electrons in the molecule does not change!

5. Do never break a σ-bond!

lone pair e- can move to an sp2 carbon but not to a sp3 carbon

where can lone pair e- move in resonance structures?

lone pair e- can move to an sp2 carbon but not to a sp3 carbon

which chair configuration is more stable?

distinguish enantiomers, diastereomers, and meso compounds

if a group points towards you how will it point on the chair configuration?

it will point up

what will happen to a geometry of a compound during sn2 substion reaction?

int will invert

define apo enzyme

enzyme without a cofactor

define holo enzyme

apo enzyme with a cofactor

what is active site of an enzyme?

a site to which substrate(s) bind

which bond is longer sp2-sp2 or sp3-sp2

sp3-sp2 since less s character=longer bond

prostetic group

tightly bound to enzyme cofactor

holoenzyme

apo enzyme +cofactor

coenzyme

losely bound cofactor

induced fit model

when substrate binds to an enzyme and enzyme chages its shape to better interract with a substrate

to have a better binding

burst phase(of a reaction)

rapid release of a product in the very beginning of the reaction(initially all of enzymes are occupied

(first phase)

catalytic triad

A catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes.

what does kinase enzyme do?

it phosphorelates specific compounds making them more negatively charges and often reactive

in which direction proteins go?

from N to C

basicity trnd in periodic table

bacisity increases up and right in periodic table

how to determine the strongest base in the molecule

further from electronegative parts=stronger base

meso compounds

same molecules

in terms of bacisity which are good leaving groups?

weak bases

what is a good nucleophile?

negatively charged molecule