1.1 structure of water and hydrogen bonding

• High electronnegtive= attracts more electrons

• Low electronegativity= Less ability to attract electrons

• Nonpolar bond

  • Atoms share electrons equally

  • Nonpolar molecules are hydrophobic

• Polar bond

  • Atoms with different electronegativity do not share electrons equally: one atom has a more negative charge, and the other is more positive

  • Polar molecules are hydrophilic

Water:

• Unique properties of liquid water raided because of the water molecules’ polarity

• Universal Solvent

• The oxygen atom has a slightly negative electronegativity

• Hydrogen atoms are slightly positive

• Cohesion and adhesion

  • Cohesions: Water moles tick on one another

  • Adhesion: When water molecules cling to the other surface

• High surface tension

• High heat capacity

• Changes in density based on temperature

Hydrogen bond:

• Weak attraction between a highly electronegative atom and a hydrogen atom

• Hydrogen atoms take part in a separate polar covalent bond

• Do not form molecules and are not chemical bonds

• Stabilize the strictures of large biological molecules

Acids

• Donate hydrogen ions in a water solution

• pH below 7

Bases

• Accept hydrogen ions in a water solution

• pH above 7

Buffer

• Srt of chemicals (weak acids or base and its salt) that can keep the pH of a solution stable

1.2 Elements of Life

Carbon

• 4 electrons in its outer energy level

• Can bond up to four other atoms to complete its outer shell

• Can bond two, three, or four atoms

• Form polar or nonpolar

• can form chains or ring

• Be assembled and remolded many organic compounds

• Work as a framework of many sugars, starches, and fats

Organic

• Molecules are complex molecules of life built on a framework of carbon atoms

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Monomers

• Molecules are used as subunits to build larger molecules

Polymers

• Larger molecules that are chains of monomers

Dehydration synthesis (condensation reaction)

• Joins monomers into polymers

• water is realize

• Covalent bonding of two molecules to form a larger molecule

• Water forms as a product

Hydrolysis

• Breaks polymers into monomers

• Water is added to break polymers into monomers

• Reverse of condensation

• Cleavage creation splits larger molecules into smaller ones

• Water is split

Function groups:

Hydroxyl

• Strong polar

• Alcohols is an example of a hydroxyl

• Interaction that links subunits together to form larger molecules

Amino groups

• Nitrogen-containing amino groups tend to make a molecule basic

• Takes up hydrogen ions

• Enter into reactions with other groups to form covalent linkages

• Amino groups can react with a carboxyl group of another amino acid to form a peptide bond

Carboxyl group

• Give up hydrogen ions easily

• Organic acids like amino or fatty acids are characterized by the presence of it

• Carboxyl group can enter to combine subunits

Phosphate group

• Related hydrogen ions

• Form chemical bridges that link subunits together to form larger molecules

• Storage of chemical energy within the cell involves the phosphate-containing nucleotide (ATP

Sulfhydryl group

• Highly reactive

• Two different molecules can form disulfide linkages

• Stabilize many biological molecules

  

Aldehyde group

• Serve as a potential linkage site in biosynthetic reaction

• React to form acids or alcohols

• Important in the synthesis and breakdown of fats and carbohydrates

1.3

Carbohydrates

• ose means sugar

• 1:2:1 ratio (Carbon, Hydrogen, and Oxygen)

• CH2O)n is the formula and n is the number of carbon in the molecule

• MOnosaccharides

  • Simpliest carbohydrates

  • Used as an energy source

  • Backbones of 5 oe 6 carbons

  • Very Soluble in water

  • Ex, Glucose

• Oligosaccharides

  • Short chains of monosaccharides

    

• Poly saccharide

  • Straight or branched chains if many sugar monomers

  • The most common are cellulose, starch, and glycogen

  • Consists of glucose monomers

  • Different patterns of covalent bonding and different chemical properties

  • Cellulose

    • Major structure in plants

    • Long, straight chains of glucose monomers

    • Do not dissolve in water

    • In our vegetables

  

Starch

• Energy reservoir in plants

• Covalent bonding pattern between monomers make a chain that coils up into a spiral

• Does not dissolve easily in water but is less stable then cellulose

• Imporant in human food

Glycogen

• Polysaccharides

• Covalent bonding pattern forms highly branched chains of glucose monomers

• Energy rsevior in animals cells stores in muscle and liver cells

  

Chitin

• Nitrogen containing polysaccharide

• Strengthen the hard parts of animals like crabs a

• Also the strong cells walls of fungi

Lipids

• Fat, oils, or waxy organic compounds that are insoluble in water

• Function as the body's major energy reservoir

• Structural foundation of cell membrane

• Sime organic compound with carboxyl group joined to a backbone of 4-36 carbon atoms

Saturated fatty acids (Animal fats)

• Fatty acids with only single covalent bonds

• Molecules are packed tightly; solid at room temperature

Unsaturated fatty acids (Vegetable Oils)

• Fatty acids with one or two more double bonds

• MOlecules are liquid at room temp

Triglycerides

• Natural fats with three fatty acids attached to glycerol

• The most abundant energy source in vertebrates

• Concentrated in adipose for insulation and cushioning

Trans Fats

• Partially hydrogenated vegetables formed by the chemical hydrogenation process

• Double bond straightens the molecule

• Pack tightly; solid at room temp

• Bonds can be either cis or trans, depending on how hydrogen is arranged

Phospholipids

• Molecules with a polar head containing phosphate and two nonpolar fatty acid tails

• Heads are hydrophilic and tails are hydrophobic

• From lipid bilayers with hydrophobic tails sandwiched between hydrophilic heads

Steroids

• Lipids with a rigid backbone of four carbon rings and no fatty acid tails

Protein

• An organic compound composed of one or more chains of amino acids

  • A small organic compound with an amine group (-NH3+) or a carboxyl group (COO) and one or more R group

Polypeptide

• Chain of amino acids bonded together by peptide bonds

• Condensation reaction between the amine group of one amino acid and the carboxyl group of another amino acid

Protein Structure

• Primary Structure

  • Unique amino acid sequence of a protein

• Secondary Structure

  • Polypeptide chain golds and form hydrogen bonds between amino acids

• Tertiary Structure

  • Secondary structure is compacted into structurally stable units called domains

  • Form a function protein

  • QUatemary structure

    • Proteins consist of two or more folded polypeptide chains in close association

    • Ex.Hemoglobin

Proteins must contain their correct three-dimensional shape

Change in protein shape may have drastic consequences or could be denatured

• Head

• Changes in pH

• Salts and detergent can disrupt the structure of it

Prion

• Misfolded proteins cause diseases

• Mad cow disease

• Creutzfeld-Jakob

• Scrapie in sheep

Nucleotides

• Small organic molecule consisting of sugar with a five-carbon ring

• Nitrogen-containing base

• One or more phosphate group

ATP (Adenosine triphosphate)

• A nucleotide with three phosphate groups

• Important in phosphate group energy transfer

Nucleic Acids

• Polymers of nucleotides

• sugar one is attached to a phosphate group of the next

• RNA and DNA are nucleic acids

RNA (ribonucleic acid)

• Contains four kinds of nucleotdies, monomers, including ATP

• Consits of:

  • Ribose

  • Phosphate

  • One of the four nirogenous bases: Adeinine, Uracil, Guanine, or Cytosine

  • Imporant in protein synthesis

  • Messgenger, trasnfer, and ribosomal are three types of RNA

DNA (Deoxyribonucleic acid)

• Nucleotides consists of

  • Sugar

  • Phosphate

  • One of the four nitrogen bases

    • Adenine

    • Thymine

    • Guanine

    • Cytosine

  • Two chains of the nucleotides twist together into a double hlex helped by hydrogen bonds

  • Inherited information necessary to buikld an organism

  • Codee in the order of nucleotide bases

• Pyrimidines

  • In DNA they have cytosine and thymine

  • RNA: Cyotine and uracil

  • One ring structure

• Purines (Larger then pyrimidines

• Two ring structure

1.6 Nucleic Acids

• Nucleotides are the monomers of nucleic acids like DNA and RNA

• Some have a metabolism

Nucleotide

• Small organic molecule consisting of a sugar with a five-carbon ring

• Nitrogen-containing base

• One or more phosphate groups

• Essentials for replication of DNA

• Transcription of RNA in rapidly diving stages

• Either synthesized from small molecules and amino acids or acquired in the diet

• Essential in providing the cellular energy sources (ATP and GTP)

• Involved in numerous other metabolic roles

• Chains of nucleotides is a nucleic acid

• Sugar of one nucleotide is covalently bonded to the phosphate group of the next

• Forming sugar-phosphate backbone

ATP

• Energy carrier in cells

• It consists of 3 phosphate groups (High energy)

  • Adliene

  • Sulfur

• Hydrolysis

  • Removing something

  • Ex. During ATP, the third phosphate gets removed for energy forming Diphosphate

Ribose

• Primes (5’3) refer to the numbering system

• Carbon atoms in the ribose

  

RNA

• the main type of RNA include

  • Messenger

  • Transfer

  • Ribosomal

• RNA contains four kinds of nucleotide monomers

  • Adenine and Guanine (Purines)

  • Cytosine and URacil (Pyrimidine)

• Important in protein synthesis

DNA

• Two chains of nucleotides twist together into a double helix

• Held by hydrogen bonds between base pairs

• Base pairs are easily separated during replication and transcription

• Contains all the information built into an organism

• coded in the order of nucleotide bases

• Covalent bonds (Backbone) of DNA