BiochemistrySixth Edition

Chapter 1:Biochemistry: An Evolving Science

Berg • Tymoczko • Stryer

Tips on note taking...• Remember copies of my lectures are

available on my webpage– If you forget to print them out before class, or if

you don’t want to print them out due to the new copying policy, I suggest the following…

I am more interested in your listening and involvement in our discussion….take notes on that

• try this format:• slide 1: ………notes…….

– Later, compare notes for slide 1 with slide 1

Perspective of this Course

• This course is taught as pure science• emphasis on evolution

– from molecular evolution to organismal evolution

• This is a purely-scientific explanation of the development of life on earth and our understanding of the biochemical principles that sustain it.

Outline

• DNA illustrates the Relation between Form and Function

• Biochemical Unity Underlies Biological Diversity

• Chemical Bonds in Biochemistry• Biochemistry and Human Biology

On Life and Chemistry...

1. Living things are composed of lifeless molecules

2. Chemistry is the logic basis of biological phenomena

Hierarchy in Biology

• The top of the list depends on lower levels!• Order: Ecosystems, communities, populations,

organisms, organs systems, organs, tissues, CELLS, (these are the living components)

• organelles, MOLECULES, atoms, subatomic particles. (these are nonliving components)

Properties of Life

Who’s this guy?

Form Follows Function…

Molecules act Like Organisms

• Subjected to Evolutionary pressures• A molecule’s Form determines its

functions

DNA is a good example…

• James Watson and Francis Crick…• 1953…hypothesized about the structure (the

form) of DNA.• With the molecule’s form established…its

function could be supported.

I wonder How this works?~1953 ~2003

DNA is a 2-stranded Molecule

The building blocks of DNA

• The nucleotides • These are the nitrogen bases

Nucleotides are joined togetherto form one strand…

(a nucleic acid)DNA is made from a “polyester linkage” between nucleotides

NOT THAT KIND OFPOLYESTER…

Rather, its called a Phosphodiester linkage…These bonds hold all Nucleic acids together.!

Can you draw an ester?Can you draw a diester?Can you draw a phosphodiester?

A phosphate containing polyesterAKA the sugar phosphate backbone.

One nucleotide is chemically bonded to the next.

The two strands are held together to form the DNA double helix!

• Again…form eludes to function…• The nitrogen bases’ shape suggested how they

might work to hold the double helix together.

DNA can replicate because of its form…

Because of its shape…DNA is the long term storage molecule for

Genetic Information• Another nucleic acid helps the process

though…• RNA• RNA is chemically different from DNA

– Different sugar used…a ribose sugar– Different base is used…uracil

RNA has a Different shape than DNA

• RNA is a SINGLE STRANDED molecule…not a double helix.

• It can twist into many different shapes..• With many different possible shapes…• You have many different….?

RNA functions

• Genetic info access (transcription)• Ancient genetic info storage ?• Catalytic functions

– Ribozymes• New functions…

– Aptamers.

The type of molecule with the greatest repertoire of Functions…

(that we’re currently aware of)• The proteins• A linear arrangement of their building

blocks – Amino acids

• The arrangement of amino acids in the proteins determines the shape of the protein (a process called protein folding)

• And also its function.

Protein folding

Dysfunctional proteins..

• Come from anything that changes the shape of the protein

• Genetic mutations• Environmental factors.

– If you restore the shape, you restore the function.

1.2 Biochemical Unity underliesBiological Diversity

• Many different types of Life on earth• All with different morphologies….

Though Biologically Diverse…All life has Biochemical Unity

• All life is made out of the same stuff– Atoms and molecules

• All life uses DNA as a genetic storage molecule

• All life uses similar metabolic pathways to power living processes.– Glycolysis

• A common ancestor for all life?

Phylogenetic Tree of life(using molecular evolution data)

Chemical Bonds in Biochemistry

• The important “molecules of life” are organic compounds

• They can be composed of many thousands of atoms chemically joined together.

• Even though they are huge…the atoms that comprise them follow the same chemistry as their smaller molecular relatives

Biomolecules: The Molecules of Life

H, O, C and N make up 99+% of atoms in the human body

ELEMENT PERCENTAGEOxygen 63Hydrogen 25.2Carbon 9.5Nitrogen 1.4

Biomolecules: The Molecules of Life

• What property unites H, O, C and N and renders these atoms so appropriate to the chemistry of life?

• Answer: Their ability to form covalent bonds by electron-pair sharing.