Notes for Biochemistry - PBworkstfssbio.pbworks.com/w/file/fetch/41658770/Biochemistry...

Notes for Biochemistry

A. De Jong/TFSS 2011 1 of 13

The information in this document is meant to cover IB topic 3.1-‐3.3 and 7.5. Functional Groups A functional group is a group of atoms that confers highly specific properties to an organic molecule. The functional groups most common to biological molecules are:

Acetyl group

Phosphate group -‐S-‐S-‐ Disulfide group (bridge)

Review of Bondage, I mean Bonding! Matter is anything that has volume and mass. Energy is the ability to do work. All atoms have electrons arranged in shells or energy levels around a nucleus made of 1 or more protons & 0 or more neutrons. All electrons have the same mass and charge – they differ in the amounts of potential energy they possess. Electrons have more potential energy the further they are from the nucleus (i.e. the higher the energy level). The valence electrons occupy the outermost energy level of an atom. The maximum number of valence electrons any atom may have is 8. These are the electrons involved in chemical bonding. Ionic bonds are formed when valence electrons move from one atom to another. Anions (e.g. Cl-‐ and OH-‐) are attracted to cations (e.g. Na+ and NH4

+). Covalent bonds are formed when atoms share valence electrons.

• Non-‐polar covalent bonds are formed when electrons are shared equally between atoms. They may be single (e.g. CH4), double (e.g. O2) or triple (e.g. N2).

• Polar covalent bonds are formed when electrons are shared unequally between atoms. The molecule will have a positive end (where the electrons spend less time) and a negative end (where the electrons spend more time). The more electronegative an atom is, the greater the chance that electrons will be closer to it than a less electronegative atom. Water is a polar covalent molecule.



Hydrogen bonds are formed when a hydrogen atom that is covalently bonded to an electronegative atom is attracted to another electronegative atom on another molecule. Hydrogen bonds typically form between hydrogen and oxygen or hydrogen and nitrogen. Although only about 5% as strong as a covalent bond, hydrogen bonds are usually present in high enough numbers that stability is achieved. (For example, the two strands of the DNA double helix are held together by hydrogen bonds between A=T & C≡G pairs). Van der Waals interactions are non-‐polar bonds caused by accumulations of positive or negative charges at the ends of molecules. They are transient forces & change rapidly.

Image from http://www.columbia.edu/cu/biology/courses/c2005/images/vdw.gif

Hydrophobic interactions occur when hydrophobic substances such as oil droplets are mixed in water. Oil is non-‐polar, so has no real attraction to other oil molecules, but the high attraction between water molecules tends to squeeze oil droplets together, forming larger drops.

Image from http://staff.jccc.net/pdecell/chemistry/hydrophobic.gif



Chemical Elements & Water The most frequently occurring elements in organisms are: carbon C - forms long chains with other carbons

- forms 4 covalent bonds with other atoms oxygen O - forms 2 covalent bonds with other atoms hydrogen H - forms 1 covalent bond with other atoms nitrogen N - found in all proteins and nucleic acids Other elements required by organisms include: sulphur S - found in all proteins phosphorus P - found in nucleic acids & ATP iron Fe - found in the oxygen-‐carrying proteins in RBC’s (hemoglobin) sodium Na - required for nerve impulse transmission potassium K - required for nerve impulse transmission calcium Ca - required for muscle contraction and synaptic transmission Water (H2O) is made from a flammable gas (H) and one that supports combustion (O). Together, they form a liquid that puts out a fire. What makes water special?? Water is a polar molecule.

- water molecules attract each other - hydrogen bonds (+/-‐ attractions) keep water molecules together - melting & boiling points are relatively high for the molecule’s size

hydrogen bond

slight positive charge

slight negative charge



Why is water important to life? - Its transparency allows plants to live in aquatic environments. - Its cohesive properties, a result of hydrogen bonding, allow water to travel up a plant’s

stem. - It is a solvent for ions and polar molecules, particularly those with hydrogen bonded to

oxygen or nitrogen, because hydrogen bonds can form between water and the solute. - Ice floats, leaving a liquid environment beneath for aquatic organisms to inhabit during

the winter. - Its high heat of evaporation (540 cal/g) allows it to act as a coolant (sweating, panting). - Its high heat capacity (1.0 cal/g°C) means that it can absorb a lot of heat without

undergoing a large change in temperature. This helps stabilize body temperature and protects our cells against the ill effects of a large external temperature change.

Blood is 50% water. Cells are about 70% water. The human body is about 60% water by weight. Carbohydrates Carbohydrates are a loosely defined group of molecules containing carbon, hydrogen & oxygen:

• energy is stored in the many C-‐H bonds • simplest are monosaccharides (single sugars), with an empirical formula of (CH2O)n

o glucose, galactose and fructose are monosaccharides • disaccharides are linked monosaccharides (complex sugars)

o maltose, lactose and sucrose are disaccharides - maltose is a disaccharide of α-‐glucose - lactose is a disaccharide of α-‐glucose and galactose - sucrose is a disaccharide of α-‐glucose and fructose

• polysaccharides are polymers of monosaccharides, normally glucose o starch, glycogen and cellulose are polysaccharides

- starch is a linear polymer of α-‐glucose - glycogen is a branched polymer of α-‐glucose - cellulose is a linear polymer of β-‐glucose

• branched polysaccharides are more water-‐soluble than straight polysaccharides Functions of Carbohydrates

• α-‐glucose is the main source of energy for cells o β-‐glucose is not used by most cells, because they cannot break down cellulose

• lactose is the sugar found in milk & dairy products • glycogen is an energy storage molecule for animals • fructose (fruit sugar) is produced by cellular respiration, and is used to make sucrose • sucrose is produced by photosynthesis in leaves and transported in the phloem to other

parts of a plant to be used as food energy • cellulose is the primary structural component of the cell walls of plants • starch is an energy storage molecule for plants • ribose and deoxyribose are structural components of nucleic acids



Structure of Monosaccharides

Di-‐ and polysaccharides are produced by dehydration synthesis (condensation) reactions. Synthesis of Maltose



Synthesis of Cellulose

Lipids Lipids are a loosely defined group of hydrophobic molecules containing carbon, hydrogen & oxygen:

• energy is stored in the many C-‐H bonds • fats and oils (triglycerides) are composite molecules built from two different sub-‐units:

o glycerol, the “backbone” to which fatty acids are attached (IUPAC name is propane-‐1,2,3-‐triol)

o fatty acids, which may be saturated (all single -‐C-‐C-‐ bonds) or unsaturated (having one or more double -‐C=C-‐ bonds)

• fats and oils are also called neutral fats because they are not electrically charged o fats are solid at room temperature; oils are liquid at room temperature

• waxes are also lipids – composite molecules built from fatty acids and a “backbone” other than glycerol

o waxes form protective coatings on feathers, leaves, etc. • phospholipids are composite molecules built from glycerol, fatty acids, and a negatively-‐

charged phosphate group o phospholipids form the bulk of the cell membrane

• steroids are hydrophobic molecules composed of four fused carbon rings



Phospholipid

Steroid (cholesterol)

**Both of these molecules are components of biological membranes. Building Blocks of Triglycerides Glycerol

Fatty Acids

Functions of Lipids

• energy storage (triglycerides) • thermal insulation (adipose tissue, primarily triglycerides) • structural component of cell membranes (phospholipids & cholesterol) • steroid synthesis (cholesterol is turned into vitamin D & steroid hormones) • chemical messengers (testosterone, estrogen, progesterone) • protection (waxes prevent dehydration)



Synthesis of Triglycerides

Proteins Proteins are un-‐branched polymers of amino acids joined by peptide bonds. For this reason, they are often called polypeptides. Amino acids are small molecules with the same general structure (at right). The “R” group can be as simple as a single hydrogen atom, as with glycine, or as complex as a benzene ring, as in phenylalanine.



Synthesis of Dipeptides Amino acids are connected together by peptide bonds. A dipeptide consists of two amino acids connected by one peptide bond.

Synthesis of Tripeptides A tripeptide consists of three amino acids connected in a chain by two peptide bonds.



Levels of Protein Structure 1. Primary structure is the order of amino acids in the polypeptide, as determined by DNA:

met-‐ala-‐gly-‐phe-‐cys-‐ etc. 2. Secondary structure is the folding (β-‐pleated sheet) or coiling (α-‐helix) of the chain,

caused by interactions between side chains (R-‐groups):

Image from http://kvhs.nbed.nb.ca/gallant/biology/secondary_structure.jpg

3. Tertiary structure is the overall three-‐dimensional shape

of the polypeptide. - Globular proteins have a spherical structure.

Enzymes (e.g. catalase) and some hormones (e.g. insulin) are globular proteins.

- Fibrous proteins have a tertiary structure that is a long, coiled chain and have long, narrow shapes. Keratin (hair & nails), collagen (bone & tendon) and myosin (muscle) are fibrous proteins.

4. Quaternary structure occurs in some proteins, and is the

interaction of two or more polypeptide chains (e.g. hemoglobin), or a polypeptide chain and a prosthetic group.

Image from http://www.uccs.edu/~rmelamed/MicroFall2002/ Chapter%202/protein%20types.jpg



Polar & Non-‐Polar Side Chains Of the 20 amino acids, 8 have non-‐polar side chains, and 12 have polar side chains. This helps drive protein structure:

• non-‐polar AAs cause channel proteins to embed in a membrane, while polar AAs at either end allow it to retain position among the hydrophilic heads of phospholipids

• polar AAs line the pore of a channel protein to allow charged particles like ions to pass through a hydrophilic channel and bypass the hydrophobic fatty acid tails

• polar AAs on the surface of a protein (like an enzyme) allow it to dissolve in aqueous solutions such as cytoplasm or plasma.

• polar and non-‐polar AAs contribute to the specificity of enzymes ■ polar AAs on the active site attract polar substrates ■ non-‐polar AAs on the active site attract non-‐polar substrates

Functions of Proteins

• enzymes are biological catalysts • chemical messengers (e.g. the hormone insulin) • antibodies (immune response) • structural proteins (e.g. collagen in tendons & skin) • transport (e.g. hemoglobin transports oxygen in blood)

Can you un-‐fry an egg? The tertiary structure of a protein is the result of different types of bonds between R-‐groups of its amino acids.

• Hydrogen bonds form between H & O or H & N • Van der Waals & hydrophobic interactions • Ionic bonds (salt bridges) • Disulfide bonds form between the R-‐groups of cysteine

Image modified from http://www.westga.edu/~chem/courses/chem1152/lectures/112Fe2599/img023.JPG



When “something” causes these bonds to be broken, the protein is denatured. That “something” could be:

1. Heat – high temperatures break hydrogen bonds. This makes a globular protein more linear, decreasing its solubility in water. Albumin is a protein in egg white, and it is soluble until it is heated – it turns white when you cook an egg.

2. High or Low pH – changes in pH disrupt ionic bonds & Van der Waals forces 3. Reducing Agents – break disulfide bonds (e.g. perming your hair breaks –S-‐S-‐ bonds &

then reforms them in new places) So…the final word is, NO, you can’t un-‐fry an egg. DNA Structure of DNA:

• DNA is a double helix – it looks a bit like a twisted ladder • It is made of two polynucleotide strands wound around each other. • The “backbone” of the molecule consists of alternating deoxyribose (sugar) and

phosphate groups • The “rungs” of the molecule are pairs of nucleotides, attached to the deoxyribose on

each strand. o Each base pair consists of one purine (adenine or guanine) and one pyrimidine

(thymine or cytosine). Adenine forms two hydrogen bonds with thymine Guanine forms three hydrogen bonds with cytosine Within one full turn of the double helix, there are approximately 25

hydrogen bonds, which gives the molecule a great degree of stability. • Adjacent nucleotides in the DNA molecule are connected by phosphodiester linkages

These are the monomers that make up the DNA molecule:



A nucleotide is made up of one sugar, one phosphate, and one purine or pyrimidine.

Image from http://www.msu.edu/course/isb/202/ebertmay/drivers/ nucleotide.jpg

Image from http://www.accessexcellence.org/RC/VL/GG/images/ dna_molecule.gif

Energy Storage in Food Molecules Lipids and carbohydrates, while both composed of carbon, hydrogen and oxygen, are very different with regards to energy storage and availability.

Role Lipids Carbohydrates - energy storage - more energy per gram than from

carbohydrates - carbon in lipids is more reduced than in

carbohydrates - 9 kcal/g

- less energy per gram than from lipids

- 4 kcal/g

- metabolic water source

- much metabolic water is produced on oxidation

- desert animals such as the camel retain most of this water when there is none available for drinking

- less metabolic water is produced on oxidation

- solubility - insoluble in water - does not cause osmotic water uptake

- highly soluble in water - cause osmotic water uptake

- ease of breakdown

- not quickly ‘digested’ - digestion does not begin until the small

intestine

- more easily hydrolyzed - energy transferred quickly - digestion begins in the

mouth

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