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Website for the lecture notes. teaching/chem361/chem361-lec01/. Introduction. What is biochemistry (BC)? Reasons why BC is exciting Simple compounds that make macromols Molecular models 3 important non-covalent bonds Properties of water.

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Website for the lecture notes


  • teaching/chem361/chem361-lec01/


  • What is biochemistry (BC)?

  • Reasons why BC is exciting

  • Simple compounds that make macromols

  • Molecular models

  • 3 important non-covalent bonds

  • Properties of water

Biochemistry: An evolving science

  • What is biochemistry (BC)?

  • Reasons why BC is exciting

  • Simple compounds that make macromols

  • Molecular models

  • 3 important non-covalent bonds

  • Properties of water

Definitions of BC

  • Bios(life) + Chem

  • BC seeks to explain life on a molecular level

  • BC is the chemistry of life

  • What makes BC

    • Exciting

    • Unique

    • So important

What makes BC exciting?

  • 1. The chemical mechanisms of many central processes of life are now understood.

  • 2. Common molecular motifs underlie the diverse expressions of life.

  • 3. Biochemistry is profoundly affecting medicine.

  • 4. The rapid progress in biochemistry allows investigators to work on the most challenging topics.

    • How is growth of cells controlled?

    • What are the reasons for cancer?

    • What is the molecular mechanism of memory?

Prelude ends

  • All forms of life arose from a common ancestor. All are subject to the same laws of physics and chemistry. Biochemistry is an intellectually coherent and beautiful discipline because of the underlying unity of life.

Biochemical unity underlies biological diversity

  • The distinct morphologies of the three organisms shown-a plant, and two animals (sea urchins and a common house cat)-might suggest that they have little in common.

  • Yet, biochemically, they have lots in common!

Biochemical unity underlies biological diversity

  • The organisms are remarkably uniform at the molecular level!

  • This means that all organisms on earth have arisen from a common ancestor!

  • Diverse organisms can be divided into 3 domains:

    • Bacteria

    • Eukarya

    • Archaea

How do biochemical reactions differ from ordinary chemical reactions?

  • 1. Chemical reactions can occur in a non-aqueous environment but biochemical reactions always occur in an aqueous environment .

  • 2. Biochemical reactions are faster.

  • 3. Biochemical reactions require the energy source ATP.

  • 4. Biochemical reactions are localized in the cell.

  • 5. Biochemical reactions occur as part of multi-step pathways, biochemical pathways.

  • 6. Biochemical reactions are regulated.

All macromolecules are formed from simple compounds

  • C, H, N, O, P, and S.

  • Organic compounds: amino acids, nucleotides, and mono saccharides (serve as monomeric subunits of proteins, nucleic acids and polysaccharides).

  • Metal ions: K, Na, Mg, Ca, Zn, Fe, Se, etc.

  • E. Coli has 6000 different kinds of organic compounds and 3000 different proteins.

  • Humans may have tens of thousands of different proteins and organic compounds.

Can you guess who is the famous person on this picture?

DNA illustrates the relation between form and function

  • DNA is constructed from four building blocks.

  • Two single strands of DNA combine to form a double helix.

  • RNA is an intermediate in the flow of genetic information.

  • Proteins, encoded by nucleic acids, perform most cell funtions.

Genomic revolution is transforming biochemistry and medicine

In the past decade:

Complete genome sequences of many organisms and human beings (human genome has 3 billion base pairs!)

If we were to include the complete sequence of our genome, the chapter would be 500,000 pages!

This is truly a landmark in human history.

Comparisons are made and mechanisms of genetic disorders are discovered!

Molecular models

1. Space-filling

Most realistic

2. Ball-and-stick

Bonding arrangement is easier to see

3. Skeletal

Very simple model

H------> white, C-------> black, N------> blue, O------> red, P----------> yellow, S------> yellow

Skeletal model good for large molecules

A.skeletalB.ball-and-stick models of ATP

Space filling models of carbon, nitrogen oxygen, phosphorus and sulphur atoms.

Space filling models of water, acetate, formamide, glucose and cysteine

Chemical bonds in biochemistry

A) Covalent Bonds

B) Noncovalent Bonds

  • Electrostatic Interactions

    • E=kq1q2/Dr C, H, N, O, P,and S.

  • Van der Waals Interactions

  • Hydrogen bonds: H is shared by two other atoms.

    H bonds play an important role in biochemistry.

Chemical bonds in chemistry

  • Resonance structures

    • Benzene can be written in two equivalent ways called “resonance structures”.

    • A molecule such as benzene has greater stability than does a molecule without multiple resonance structures.

  • Arrow pushing

    • The flow of electrons in the course of a reaction can be shown by curved arrows.

  • Hydrogen bonds

    • Can be formed between uncharged and charged molecules. H is shared by 2 other atoms.

    • H donor and H acceptor.

    • Donor is usually O or N.

    • Acceptor is usually O or N also!

    • H bonds are stronger than van der Waals bonds but much weaker than covalent bonds.

    Water is a skewed tetrahedral molecule

    Irregular tetrahydron

    The 2 bonds with hydrogen are directed toward 2 corners of the tetrahedron

    the unshared electrons of the 2sp3-hybridized orbitals occupy the 2 remaining corners.

    The angle is 105 which is less than the tetrahedral angle (109.5) means “skewed”

    Because of this, electrical charge IS NOT UNIFORMLY distributed on water molecule!

    The hydrophobic effect: lipid dispersion in water

    What did we learn from Ch.1?

    • The most important achievements of biochemistry in the molecular basis of life and in the advancement of modern biology

    • Molecular models

    • Non-covalent bonds

    • Properties of water

      Next: pH, buffers, and Handerson-Hasselbalch Equation

    Which of the following is considered as a noncovalent bond?

    • electrostatic interactions

    • hydrogen bonds

    • van der Waals interactions

    •  All of the above

    • None of the above






    What pairs of atoms in bases are involved in hydrogen bonds?

    • N—H and O—H

    • N—H and S—H

    • O—H and P—O

    • All of the above

    • None of the above






    What two properties of water are important for biological interactions?

    • the polarity of water

    • the density of water

    • the cohesive properties of water

    • a and c

    • b and c






    List atoms commonly found in biological molecules that are often hydrogen-bond acceptors.

    • carbon

    • oxygen

    • nitrogen

    • b and c

    • All of the above






    What happens to nonpolar molecules in water?

    • They dissolve independently

    • They aggregate together

    • They precipitate

    • All of the above

    • None of the above






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