Bio1200- Chapter 3

Based off of the slides she provided in class

Organic Compounds

• contain Carbon and Hydrogen

• usually connected by covalent bonds

• living organisms

• May also contain O, N, P, and S

• Some are small, but many are large and complex

ex. lipids, fats, proteins, carbs, nucleic acids

Inorganic Compounds

• contain different elements

• ionic bonds

• found in environment

ex. salt and minerals

Microelements

Needed in much smaller amounts, usually used as cofactors for proper enzyme function

Mg, K, Ca, Fe, Cu

Macroelements

Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur (CHONPS)

Main components of macromolecules

Covalent Bonds

electrons are shared between atoms (strongest bond)

Disulfide bonds

A covalent bond between 2 S atoms

Ionic bond

bond between a neg charged ion and a positive charged ion

Hydrogen bond

bond between an H and an electroneg atom (O or N)

Nonpolar covalent bonds

equally sharing electrons (H2)

Polar covalent bonds

unequally sharing electrons (H20)

Electronegativity

atoms tendency to attract electrons

Functional Groups:

(names, and polar/non, charged or not)

Hydroxyl: R-OH (POLAR)

Carbonyl: R-C=O (POLAR)

Carboxyl: R-COOH (POLAR, charged)

Amino: R-NH2 (POLAR, charged)

Sulfhydryl: R-SH (POLAR)

Phosphate: R-PO4 (POLAR, charged)

Sulfate: R-SO4 (POLAR, charged)

Methyl: R-CH3 (nonpolar)

Review Functional Groups on doc camera

Carboxyl: R-COOH = R-COO-

Amino: R-NH2 = R-NH3

Uncharged and Charged Forms of Amino and Carboxyl in Phenylalanine

See image

Dehydration Synthesis Reaction

to CONNECT subunits together to make a longer polymer (remove H20)

• You have two small molecules (like building blocks).

• They want to join together to make something bigger.

• But to connect, they have to remove a water molecule (H₂O).

  • One gives up an H (hydrogen).

  • The other gives up an OH (hydroxyl).

• Those two pieces (H + OH) combine to form water.

• Now that water is gone, the two molecules are stuck together.

• Imagine trying to snap two Lego bricks together, but there’s a tiny piece of gum between them. You have to pull that gum off (that’s the water), and then the bricks can click together.

Hydrolysis Reaction

to BREAK a large polymer into its subunits (add H20)

• You have a big molecule (like two building blocks stuck together).

• You add a water molecule (H₂O).

• The water breaks the bond:

  • One piece takes the H (hydrogen).

  • The other takes the OH (hydroxyl).

• Now you have two separate smaller molecules again.

• Imagine you want to pull two Lego bricks apart, but they’re stuck super tight. You pour a little water on them, and suddenly they come apart. That water helped break the connection.

The 4 Macromolecules

Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfate

Carbohydrates: CH2O (Sugars, starch)

Lipids: CHO (Fats, oils)

Proteins: CHONS (Enzymes)

Nucleic Acids: CHONP (DNA, RNA)

Carbohydrates

gen formula: CH20

monosaccharides: simple sugars

disaccharides: 2 sugars connected by a covalent bond

Carbohydrate Dehydration Synthesis Model

• 2 simple sugars are combined to form a disaccharide (connected by covalent bond)

• A molecule of water is removed during the reaction

• Sugars are connected by a covalent bond called a glycosidic bond

What shape does the molecule sugar take

Linear and ring form

Sugar diagrams- Every angle represents blank

A Carbon atom

Carbohydrate Polysaccharides

• long polymer made of sugar subunits

• chain of sugars can be straight (unbranched) or branched

Carbohydrate Storage Polysaccharides

• Stored form of energy in the cell

• They are connected by alpha glycosidic bonds

• Most organisms can break alpha glycosidic bonds, so these compounds are easily broken down when the cell needs sugar

  ex. starch, glycogen

Storage Carboohydrates

Plants:

Starch

• Glucose Polymer unbranched or less branched

• alpha glycosidic bonds

Animals:

Glycogen

• glucose polymer

• branched chain

• alpha glycosidic bonds

Structural Polysaccharide

• structural component of the cell

• sugars are connected by beta glycosidic bonds

• most organisms can’t break beta glycosidic bonds, which makes them very stable

  ex. cellulose chitin

Cellulose

(structural polysaccharide)

• glucose polymer

• straight chain

• beta glycosidic bonds

Glycoproteins

Proteins with sugars covalently attached to them

Functions of carbohydrates

• food/energy- mono/disaccharides- used to make short term chemical energy used in enzyme reactions

• storage- storage polysaccharides- stored form of chemical energy, to be used later as food (starch, glycogen)

• structure- polysaccharides- structural component of cells, like cell wall, shell/ exoskeleton of insects, extracellular matrix of animals (cartilage)- cellulose

Proteins

• made up of amino acids

• amino group: NH2 or NH3+ (pH7)

  carboxyl group: COOH or COO-

Types of Amino Acids

NOT SOLUABLE

• Non polar or totally uncharged Amino acids that are hydrophobic

• Polar (partially charged) (uncharged)

• Polar (charged)

Non polar Amino Acids

Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan, Cysteine, Methionine

Polar Uncharged Amino Acids

Serine, Threonine, Asparagine, Glutamine, Tyrosine

Polar, Charged Amino Acids

Aspartic Acid, Glutamic Acid, Histidine, Lysine, Arginine

Peptide Bonds

SUB GROUP OF COVALENT BONDS

• connect amino acids

• OH of amino acids combines with an H from AA to form H20

• The C if the carboxyl of Amino Acid1 is connected to the N of the amino group 2

Formation of Peptide Bond

• 2 amino acids are connected together

• a molecule of H2O is produced

• Reaction: Dehydration Synthesis

Polypeptide

chain of amino acids

• front group- amino group, Nitrogen terminus

• rear end- carboxyl group and is called Carbon terminus

Protein structure

• primary structure- sequence of amino acids connected by peptide bonds

• secondary structure- localized folding of polypeptide chain (interaction between nearby amino acids), held together by H bonds

• tertiary structure- final 3D structure of a polypeptide chain, interactions between distant amino acids

• quaternary structure- different protein subunits interact to form the whole protein (only proteins that have more than one subunit have this structure)

Protein Denaturation

• unfolding of proteins so that they no longer function properly

• cause: bonds involved in 3D structure are broken

H bonds, Ionic, Disulfide, Hydrophobic Interactions

Protein Functions

• enzymes- perform chemical reactions

• structural proteins- can build things out of proteins

• receptor proteins- communications

• transport proteins- in and out of the cell

• hormones- long distant signal molecules

Nucleic Acids

• made out of nucleotides

• 5 carbon sugar, phosphate, nitrogen base

Nucleotide Structure

• RNA- sugar ribose in ribonucleotides (NTPs)- breaks easily

• DNA- contains sugar deoxyribose in deoxyribonucleotides (dNTPs)

Nucleic Acid Nitrogenous Bases

Purines: bases with 2 rings

ex. Adenine, Guanine

Pyrimidines: bases with only 1 ring

ex. Cytosine, Thymine, Uracil

Nitrogenous bases in RNA

AGCU

Nitrogenous bases in DNA

AGCT

Phosphodiester Bonds

connect nucleotides on the same strand

• covalent bonds

DNA structure

• Double stranded

• antiparallel

• connected by phosphodiester bonds to make sugar-phosphate backbone

• bases in opposite strands are connected by H bonds so that they can make base pairs

pairs by complement bases

A-T

G-C

Complementary Bonds

held together by H bonds

Functions of DNA

• genetic blueprint

• contains genes

• genes are code for proteins

What is RNA

made of ribonucleotides= NTPs

• sugar=ribose

• bases are GACU

• single-stranded

Functions of RNA (the different types)

• mRNA- codes for proteins

• tRNA- brings AA to ribosomes during protein synthesis

• rRNA- structural part of the ribosome

• snRNA- RNA splicing

Lipids

• gen formula- CHO

• chem properties- lg and hydrophobic (only group not soluble in water)

ex. fats, oils, steroids, fatty acids, triglycerides, phospholipdis

Liquid types

• triglycerides- used for stored foods

• phospholipids- struct part of membrane

• steroids

Lipids as Amphipathic

• amphipathic molecules have both a polar and non polar end

ex. fatty acids, phospholipids

Triglycerides/ structure

LIPIDS

function is to store energy

Glycerol, 3 fatty acids, triglyceride

LIPIDS

g- 3C alc

3FA- carboxyl group+ long hydrocarbon chain

T- glycerol + 3 fatty acid molecules

Saturated vs Unsaturated fats

LIPIDS

sat- solid at room temp, single bonds in fatty acids- all three fatty acids are sat

unsat- liquid at room temp and there will be at least one double or triple bond (tendency to kink)- bond has at least one unsat FA, kink

Phospholipids

component of membrane (phospholipid bilayer)

Structure-

• glycerol

• 2 fatty acids

• phosphate group

• polar headgroup

Phospholipids assemble

• into bilayer

• hydrophobic tails face one another

• polar headgroups- exposed to water

Steriods (structure and function)

LIPID

• most are hydrophobic

Structure: 4 characteristic rings, and side chain

Function: component of membranes, hormones