Exam 1 part 1 (lectures 1-3)

biochemistry

application of chemistry to understand biological processes of cells and living organisms at the molecular level

core concepts of biochemistry

1. energy + metabolism

2. structure + function

3. information storage + transfer

4. Homeostasis

5. Evolution

Organic molecules that biochemistry focuses on

1. carbohydrates

2. lipids

3. proteins

4. nucleic acids

5. high-energy compounds (ATP)

(T/F) ALL of the organic molecules listed before are polymers

FALSE - lipids are NOT polymers

Why care about biochemistry?

provides underlying principles that govern life in all its diverse forms, helps understand mechanisms of disease, drug + vaccine development

Definition of life

1. ability to acquire, store and transport energy

2. organization in membrane-bound compartments (cells)

3. self-contained genetic information (nucleic acids)

4. ability to replice

   1. evolves/changes over time - growth and response to stimuli

3 domains of life

bacteria, eukaryotes, archaea

LUCA

last universal common ancestor - most recent form from which all surviving life on Earth is descended

(T/F) LUCA is the first life on Earth

FALSE

which rRNA genes are most used for making phylogenetic trees?

16S or 18S

Why is 16S or 18S rRNA genes most used for making phylogenetic genes?

because they are the most conserved between species

Prokaryotes are unicellular

Eukaryotes can be unicellular OR multicellular

prokaryotic cell vs eukaryotic cell

prokaryotic

1. nucleoid

2. no membrane-bound organelles

eukaryotic

1. nucleus

2. membrane-bound organelles

what determines a cellular size LOWER limit?

size of genetic information, cell structure, biomolecules

what determines a cell UPPER limit?

efficiency of nutrient uptake, transport, and metabolism

source of chemical elements of life

big bang → star formation → star lifecycles

What are the most common elements making up life?

CHNOPS (over 97% of the mass of cells)

Why is carbon so well suited for life?

1. widespread abundance

2. ability to form stable bonds with numerous elements

3. ability to form polymers at common Earth temperatures

methyl

RCH3

phenyl

aromatic carbon group

carbonyl (aldehyde)

RHC=O

carbonyl (ketone)

RRC=O

carboxyl

ROC=O

hydroxyl

ROH

amino

CNH3

amide

O=CNH2

sulfhydryl

RSH

disulfide

RSSR

thioester

RC=OSR

purposes of functional groups

1. structure + stability

2. molecular interactions with water or other biomolecules

3. activity (enzymes)

   1. energy storage/transfer

different ways to visualize biomolecules

fischer projection, Lewis strucures, bond-line formation, ball-and-stick, wireframe, backbone

stereoisomers (spatial isomers)

same molecular formula, unique 3D orientations of atoms in space

structural/constitutional isomers

same molecular formula, differ in the way that the atoms are connnected

enantiomers

mirror images, identical physical configuration (type of stereoisomer)

diastereomers

non-mirror images, can have unique chemical properties (type of stereoisomer)

most biomolecules are ___ and __

chiral, have a few chiral centers, and are a single type enantiomer

Cells primarily synthesize _ amino acids and _ sugars

L-amino acids, D-sugars

(T/F) biomolecules are static

FALSE - undergo conformational changes where stereochemistry is importanta

thermodynamics

energetics of chemical reactions and molecular interactions in cells

first law of thermodynamics

cells absorb/release energy and convert it into different forms

second law of thermodynamics

overall randomness (entropy) in the universive tends to increase over time

* cells release energy as heat which increases S(surr)

Gibbs free energy equation

delta G = delta H - T(delta S)

delta G in the Gibbs equation

Gibbs free energy, change in energy available for work (units: kJ/mol)

delta H in Gibbs equation

enthalpy, change in heat content (units: kJ/mol)

delta S in the Gibbs equation

entropy, change in degree of disorder (units: kJ/Kelvin\*mol)

T in Gibbs equation

temperature (units: Kelvin)

delta G degree in Gibbs equation

standard free-energy change - G at “standard conditions”

reactions where delta G are < 0 are ___

spontaneous

reactions where delta H < 0

reaction releases heat

when delta S < 0

reaction is more ordered

Reactions in cells need to be __ or become coupled with other favorable ones

spontaneous

what signs should delta H and delta S be for a spontaneous reaction

negative delta H and a positive delta S

endergonic reaction

energy is absorbed, delta G > 0, not spontaneouse

exergonic

energy is released, G < 0, spontaneous

kinetics

speed/rate that chemical reactions and molecular interactions occur in cells

equilibilrium

occurs when the rate of product formation is equal to the rate of reactant formation

Q

reaction quotient

Keq - equilibrium constant

relative amounts of products vs reactants at equilibrium

when Keq>1

more products at equilibrium, delta G < 0

when Keq

more reactants at equilibrium, delta G > 0

when Keq = 1

equal amounts of products and reactants at equilibrium, delta G = 0

equation relating delta G to Keq

Le’Chateliers principle

passive process - when equilibrium is disturbed the equilibrium shifts to counteract and reestablish equilibrium

homeostasis

dynamic steady state at cellular level, active process requiring biomolecules

Le-Chatelier vs homeostasis

both resist changes to a system, Le’Chatlier is passive while homeostasis is active

steady state vs equilibrium

equilibrium is a reversible process A→B AND B→A

steady state requires more steps A→B→C

metabolism

set of life-sustaining chemical reactions in a cell

metabolite

an intermediate or end product of metabolism

metabolic pathway

coordinated series of chemical reactions (product of one reaction becomes the substrate for the next reaction)

anabolic

the building up (synthesis) of metabolites and biomolecules

* usually consumes/requires energy

catabolic

breaking down of compounds

* energy is either stored or released as heat

chemical oxidation is to _ as sunlight is to _

cellular respiration, photosynthesis

cellular respiration

glucose is oxidized with oxygen to release ATP (spontaneous)

photosynthesis

light drives synthesis of glucose and oxygen from CO2 and H20

are humans aerobic or anaerobic?

aerobic

ATP

energy currency of the cell, hydrolyzed to release ADP and energy

reaction coupling

pairing a energetically favorable reaction with an energetically unfavorable reaction (add the delta Gs of both reactions)

activation energy (Ea)

minimum energy required to cause a process to occur

what is the source for activation energy needed to push reactions forward

catalysts or heat energy from the surroundings

catalysts

enzyme or RNA that increases the rate of a chemical reaction

G++

activation free energy - catalysts lower this

(T/F) Catalysts alter delta G\*

FALSE - enzymes lower the activation free energy G++

gene

region of DNA that encodes cellular function

genome

entire set of DNA found in a cell

allele

different versions of a gene

central dogma

DNA→RNA→proteins (in reality it goes in many directions)

modern view of central dogma

central dogma + works in the reverse direction/proteins can create more proteins

evolution

change in heritable characteristics of bio populations over successive generations

5 forces of evolution

1. mutation - mistake/change in DNA

2. genetic drift - random small population

3. gene flow - movement of people/migration

4. non-random mating

5. natural selection

homolog

proteins diverged from a common origin

ortholog

genes which evolved from a common ancestral gene by speciation that usually have retained a similar function in different species

paralog

genes related by duplication within the genome and often they acquire a new function

germline mutation

occur in sperm and egg, more important to evolution, can be passed on to offspring

somatic mutations

occur in body cells, NOT passed on to offspring

gene duplications

• source of genetic novelty that can lead to evolutionary innovation w/o deactivating original gene function

• common cause of disease (cancer)

• can occur as the result of an error in recombination or replication

• often immune to selective pressure under which genes normally exist

water is some form (liquid, ice, vapor) is necessary for every llife form, which is why

we are looking for water on other planets

role of water in biochemistry

1. water as a solvent - chemical reactions in a cell or btwn a cell and the environment occurs in aqueous solutions

2. water actively participates in many biochemical reactions (30-50% of known biochem reaction involve water consumption or production)

3. biomolecules assume their shapes and function in response to the properties of water

4. the reactivity of the functional groups in many biomolecules depends on the relative concentration of H+ and OH- in solution

5. properties of water shape homeostasis and the evolution of life

(T/F): Water is just a medium/solvent

FALSE - is also an active chemical participant

water dictates almost all of what process?

cellular metabolism

condensation

dehydration synthesis - molecules combined with the loss of a water