Biochemistry 1 Exam 1

Superscript 0 delta G aka?

standard state

No superscript above delta G aka?

non-standard state

Biochemistry

describes the structures, mechanisms, and chemical processes shared by all organisms

Which equation would you use to determine "k" or equilibrium?

Standard State Gibbs Free energy

Which equation would be used to determine spontaneity given the molarity of the reactants and products?

Non Standard Gibbs free energy

n in the Biological standard state equation indicates...?

number of Hydrogen/ (products-reactants)

What are the four classes of macromolecules?

carbohydrates, lipids, proteins, nucleic acids

Negative Delta G is spontaneous or non-spontaneous?

spontaneous

Negative voltage is spontaneous or non spontaneous?

non-spotaneous

Rank the molecules from smallest to largest in composition:

Hemoglobin

Ribosomes

Red Blood Cell

Bacterium

Glucose

C-C Bond

Resolution limit of light microscope

C-C

Intramolecular Forces

forces within molecules

Intermolecular forces

forces between molecules

Covalent Bond

sharing of electron pair

Ionic Bond

transfer of electrons to form a bond

Non-polar covalent

equal sharing of electrons

Polar covalent

unequal sharing of electrons

Hydrogen Bonding

the intermolecular forces which bind Hydrogen to F,O,N

coordinated covalent bond

a covalent bond in which one atom contributes both bonding electrons

Intermolecular forces are responsible for what characteristics?

Melting point and Boiling Point

Dipole-Dipole

What has London Dispersion Forces?

everything

The longer the chain, what effect does it have on the LDF?

the stronger the L.D.F

Electrostatic Interaction

an attraction or repulsion that occurs between charged particles

Hydrophobic Interactions

molecules tend to cluster together which results in entropic loss, an exothermic process, making it more favorable.

Positive Delta G is spontaneous or non-spontaneous?

non spontaneous

If you have a high -(Delta G Biological Standard state) what does that mean?

you have a high equilibrium constant (keq) which means you have a lot of products formed

If you have a metabolic step that is Noon Spontaneous as written, you add ATP why?

to make the overall process spontaneous

PkA is what?

how well the species of interest gives away its proton

Low pKA

strong Acid

High PkA

weak acid

when pH>pKA

- lots of OH

-Basic Environment

-Remove all Dissociable Protons

when pH

-Acidic Environment

-lots of H3O

-Attach all Dissociable Protons

Naturally occuring amino acids are

L

Naturally occurring sugars (carbohydrates) are

D

What is the size of an Animal cell?

2-50 micrometers

What is the size of a bacterial cell?

1 micrometer

Cytosol contains what?

enzymes, RNA, amino acids, nucleotides, metabolites, coenzymes, and inorganic ions

How big in diameter are plant and animal cells?

5-100 mircometer

Obligate Anaerobes

die with O2

Facultative Anaerobes

can live with or without O2

How large is one Angstram?

10^-10m

Mitochondria

site of most of the energy extracting reactions of the cell

ER and Golgi

synthesize and process lipids and membrane proteins

Peroxisomes

site of oxidation of fatty acids and detoxification of reactive oxygen species

Lysosomes

filled with digestive enzymes

What organelle is not membrane bound?

ribosome

Endomembrane System

segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reactions occur

What are supramolecular structures?

molecules held together by non-covalent interactions

Non Covalent Interactions include:

hydrogen bonding, ionic interactions, Van der Waals, and the hydrophobic effect

In vitro

in glass

In vivo

in the living

What differentiates us from plants?

Chloroplast and Cell walls

Vacuoles

Stores food, water, wastes, and other materials

Chloroplast

where sunlight drives the synthesis of ATP

Subcellular Fractionation, heavier thinks will be where?

at the bottom

Steps of Subcellular Fractionation

1. lyse cells membrane

2.centrifuge

Cytoskeleton does what?

transfer nutrients, signals

Three types of cytoskeleton

microtubules, intermediate filaments, actin filaments

Carbon atoms have what arrangement

tetrahedral arrangement

Central metabolites

-common amino acids

-nucleotides

-sugars and their phosphorylated derivatives

-mono-, di-, and tricarboxylic acids

metabolome

collection of small molecules in a given cell under a specific set of conditions ( are the end product of metabolic processes like protein synthesis, gene transcription, and mRNA translation)

metabolomics

study of metabolomes

Macromolecules

polymers with molecular weights above 5,000

Oligomers

shorty polymers

Proteome

an organism's complete set of proteins

Polysaccharides

polymers of simple sugars

Glycome

entire complement of carbohydrate-containing molecules

Stereoisomers

molecules with the same chemical bonds and same chemical formula

Enantiomers

mirror images of each other

Diastereomers

not mirror images of each other

What has identical chemical reactivity but different optical activity?

Enantiomers

conformation

spatial arrangement of substituent groups that are free to assume different positions in space

Types of systems

isolated, closed, open

Isolated System

exchange neither matter nor energy with its surroundings

Closed System

exchanges energy but not matter with its surrundings

Open system

exchanges both energy and matter with its surroundings

First law of thermodynamics

the total amount of energy in the universe remains constant, although the form of the energy may change

Translation

decoding of a mRNA message into a polypeptide chain

Transcription

synthesis of an RNA molecule from a DNA template

Exergonic

release of energy

Endergonic

requires energy

Delta G>0 is ender or exergonic?

endergonic

Endergonic reactions are spontaneous or non spontaneous?

non spontaneous

Delta G<0 is ender or exergonic?

Exergonic

Exergonic reactions are spontaneous or non spontaneous?

spontaneous

What angle is Sp3 Hybridized?

109.5

How do you assign priority with E and Z Geometric Isomerization?

atomic number

in newman projections, what arrangement provided the highest potential energy?

Fully eclipsed

in newman projections, what arrangement provided the least potential energy?

anti/ staggered

Mass Action ratio Q

ratio of product concentrations to reactants at a given time. Can be used to calculate how far the reaction is from equilibrium

What function do enzymes actually perform in biochemical reactions?

They increase the rate of the reactions, but not the equilibrium

Pathways

sequence of consecutive reactions in which the product of one reaction becomes the reactant in the next

Catabolism

breaking things down

Anabolism

Metabolic pathways that construct molecules, requiring energy. Synthesize

how to find n in the biological standard state equation?

H30+/H+ of the (products-reactants)

Constitutional isomers

same chemical formula but different branching

Assigning priority for Absolute Configuration

electronegativity

Assigning priority for Relative Configuration

Electronegativity

dextrorotatory +

rotates plane-polarized light clockwise

dextrorotatory -

rotates plane-polarized light counterclockwise