Biochem Midterm 1

We not only want to know how nature is but also

 know why nature is such and not otherwise

Chemistry

composition, structure, properties, and

reactions of a substance or matter, especially of atomic

and molecular systems

Biochemistry

science concerned with all aspects of the chemistry of

living organisms.

_ elements are essential for life.

~25

elements that make up 99% of total mass. 

CHON

atomic number =

number of protons and electrons

group number tells you

the number of valence electrons in outermost shell

show where C N O S P H are

Organic chemistry

chemistry of carbon-containing

compounds

organic chemistry is initially from

living organisms

2 reasons Why carbon (>50% of the total mass) 

Ability to form stable covalent bonds

Bonding versatility

bond energy of C-C single bonds

346 kJ/mol

Why must carbon bonds be stable but not too strong?

They need to be strong enough to hold molecules together, but not so strong that they cannot be broken during reactions.

Bonding versatility:

Can form single, double, triple bonds with itself or other atoms, H, O, N, S

Can form molecules of different sizes and shapes creating many combination and complex molecules

 Electron configuration:

1s22s22p2

astrobiology

look for life in the universe.

carbon bonds cannot be too _ or too _ because…

strong, stable, it needs to be broken

sp3 hybridized carbon atoms have 3 characteristic

1) tetrahedral arrangement of their four single bonds

2) free rotation around each single bond

3) limited rotation about the axis of a double bond

Incorrect statement?

1) Life is carbon-based because C forms stable, but not too strong, bonds with itself

3) Life is carbon-based because C forms stable, diverse bonds, including single, double, triple bonds, with itself and with many other atoms

4) Carbon has four valence electrons and forms four single bonds

5) Carbon is the most abundant element in the Earth's crust, which is the primary reason it became the building block of life on this planet. 

5) Carbon is the most abundant element in the Earth's crust, which is the primary reason it became the building block of life on this planet. 

Carbon is the most abundant element in the Earth's crust, which is the primary reason it became the building block of life on this planet.  Why is this incorrect?

Carbon is not the most abundant element in the Earth's crust. Oxygen and silicon are far more abundant.

Chemical “personality” (property) of a compound is determined by

the chemistry of its (2)

 functional groups and their deposition in 3D space

Molecule

aggregate of a few atoms that is the

fundamental building block of matters, held together by

covalent bonds between the atoms.

Mole (mol)

A collection of 6.022E23 molecules

One mole was first defined as the number of 

atoms in 12 grams of Carbon-12

Avogadro’s number was measured as the number of atoms in

one mole.

Molarity (M)

 concentration unit defined to be

the number of moles of solute per liter of solution

The concentration of water in pure water in molarity is

55.5 mol/L or 55.5 M.

Supramolecular Structures are held together by

noncovalent interactions 

4 types of noncovalent bonds

1) London dispersion force

2) ionic bonds

3) hydrogen bonds

4) hydrophobic effect

noncovalent interactions dont actually

share electrons

DNA has what kind of bonds

hydrogen

water has a high boiling point and we are able to cook because of

hydrogen bonds

Hydrogen bonds are based on

electronegativity

Ionic interactions

 electronic attractions between oppositely

charged ions

van der Waals interactions – London dispersion force

Short-range intermolecular forces driven by induced

electrical (dipole-dipole) interactions between two

molecules that are very close to each other

Weakest among the four noncovalent interactions

van der Waals interactions – London dispersion force

how do you know what amino acid has more van der walls?

chose the option with more phenol

van der walls individually the weakest but cumulatively

significant due to their sheer number (protein intereriors)

weakest → strongest noncovalent

van der waals

hydrogen bonds

ionic interactions

hydrophobic force

distance going from weakest → strongest

0.3-0.6

0.3

0.25

varies

how we used to write values

Macromolecules

Major Constituents of Cells

High Mr polymers assembled from

 relatively simple precursors

molecular weight above >5000 is a

macromolecule

proteins

long polymers of amino acids

amino acids

sub units

proteins can function is 4

enzymes, structural elements, signal

receptors, transporters

enzymes

catalyze conversion of molecules into different molecules

a chain on amino acids is a

protein

example of what a signal receptor would do

break glycogen into glucose when needed in exercise

proteome

sum of all the proteins functioning in a cell, body, organism

proteomics

systematic characterization of this protein complement under a specific set of conditions (study of proteome)

“-ome”

complete set of a particular type of

biological entity in an organism

“-omics”

systematic study of that complete set, often using

high-throughput techniques

how many genes, proteins can we study at a time

one

Q) Proteins are classified as macromolecules because they:

A. can associate noncovalently into very large structures.

B. are polymers with molecular weights above ~5,000.

C. can function as enzymes, structural elements, signal

receptors, or transporters.

D. are composed of multiple oligomers.

B. are polymers with molecular weights above ~5,000.

macromolecules are assembled from

relatively simple precursors.

nucleic acids

DNA and RNA

 polymers of nucleotides

nucleic acids

role of nucleic acid

store and transmit genetic information

some RNA molecules have structural and catalytic

roles in

supramolecular complexes

example supramolecular complexes

ribosomes

genes encode a _. It will be _into mRNA. It will be _.

protein. transcriped. Translated

genome

complete set of genetic material in an

organism

genetic material is expressed in different _ under different _.

cells, conditions

does the number of genes we carry stay the same or change our whole life?

stays the same

genomics

characterization of the structure, function,

evolution, and mapping of genomes

transcriptome

complete set of RNA transcripts in a cell, tissue, or organism,

under given conditions.

transcriptomics

study of an organism's complete set of RNA transcripts.

polysaccharides

polymers of simple sugars

polysaccharides are _ fuel stores

energy rich

polysaccharides are used for _ energy source

immediate

polysaccharides have rigid structural components of

cell wall in plants and bacteria

polysaccarides have _ that bind to proteins on other cells.

extracellular recognition elements

if the cell is recognized what will happen

it will not attack

glycome

entire complement of carbohydrate-containing

molecules

lipids

water-insoluble hydrocarbon derivatives

lipids are structural _

components of membranes

lipids are energy _

rich fuel stores

lipids have _

pigments

lipids have intracellular signals meaning

protein will bind to lipid and go to another area

lipidome

the lipid containing molecules in a cell

lipidomics

study of lipids

Metabolites

Cells Contain a Universal Set of Small Molecules

central metabolites: 4

1) amino acids

2) nucleotides

3) sugars and their phosophorylated derivatives

4) mono, di, and tricarboxylic acids

secondary metabolites 

specific to the organism

example of secondary metabolites

skin colour that protects from UV, plants make flower colours that are useful for polination.

metabolome

entire collection of small molecules in a

given cell under a specific set of conditions

metabolomics

the systematic characterization of the

metabolome under very specific conditions

The systematic characterization of the entire collection of

small molecules in a given cell under a specific set of

conditions is called:

A. genomics.

B. proteomics.

C. lipidomics.

D. metabolomics.

D. metabolomics.

Metabolomics is the systematic characterization of the

metabolome under very specific conditions such as

following administration of a drug, or a biological signal such as insulin

Genomics question

What is different in the DNA of cancer cells compared with normal cells?

genomics what was measured.

DNA mutations, copy- number changes, methylation, etc.

genomics key insight

Cancer is not one disease but a collection of molecularly distinct diseases driven by different genomic alterations

Trasciptomics _ → _→ _

Thousands of mRNAs → expression pattern → disease classification

Trasciptomics what was measured

Expression of

thousands of genes

using DNA microarrays

transcriptomics key insight

Gene-expression patterns could distinguish acute myeloid leukemia (AML) from acute lymphoblastic leukemia (ALL) without being told beforehand which genes to look for

Proteomics question

If we know the DNA and the mRNA, do we necessarily know the protein? NO