Chapter 5. Macromolecules
Macromolecules Smaller organic molecules join together to form larger molecules macromolecules 4 major classes of macromolecules: carbohydrates lipids proteins nucleic acids
Polymers Long molecules built by linking chain of repeating smaller units polymers monomers = repeated small units covalent bonds
How to build a polymer Condensation reaction dehydration synthesis joins monomers by taking H 2 O out 1 monomer provides OH the other monomer provides H together these form H 2 O requires energy & enzymes
How to break down a polymer Hydrolysis use H 2 O to break apart monomers reverse of condensation reaction H 2 O is split into H and OH H & OH group attach where the covalent bond used to be ex: digestion is hydrolysis
Nucleic Acid Notes AP Biology
NUCLEOTIDES AND NUCLEIC ACIDS INFORMATION FLOW IN CELLS = Central Dogma of Molecular Biology DNA RNA PROTEINS FUNCTION DNA- genetic code contains info that programs cell activities RNA-carries message from DNA to cell; protein synthesis
BASIC STRUCTURE NUCLEOSIDE = nitrogenous base + sugar NUCLEOTIDE = nitrogenous base + sugar + phosphate group PURINES = 2 rings; Adenine (A), Guanine (G) PYRIMIDINES = 1 ring; Cytosine (C), Thymine (T), Uracil (U)
Nitrogen Bases Nitrogen bases A purine always bonds with a pyrimidine.
NUCLEOTIDES Can have one, two, or three phosphate groups (mono, di, triphosphates) O O O - O - P ~ O - P ~ O - P - O - O - O - O - High energy bond between phosphate groups is important energy transport
Nucleotides are. Named for nitrogen base and number of phosphate groups EX: adenosine triphosphate (ATP) cytosine diphosphate (CDP) guanosine monophosphate (GMP)
IMPORTANT NUCLEOTIDES ADENOSINE TRIPHOSPHATE (ATP) = main energy currency in ALL living things (GTP & UTP also used) CYCLIC AMP (camp)- Second messenger Important in cell signaling and response to hormones COENZYMES- Many coenzymes are nucleotides or their derivatives (vitamins) EX: Flavin adenine dinucleotide (FAD) & nicotinamide adenine dinucleotide (NAD) used in cellular respiration nicotinamide adenine dinucleotide phosphate (NADP) used in photosynthesis
NUCLEIC ACIDS (DNA & RNA) DEHYDRATION SYNTHESIS forms polymers of nucleotide building blocks PHOSPHATES and SUGARS form backbone
Bonds in DNA To distinguish sugar and nitrogen base carbon atoms when numbered, sugar atoms have a prime ( ) Phosphate group attached to 5 carbon on one sugar and the 3 carbon of next sugar PHOSPHATE LINKAGE between carbon 3 of one sugar and carbon 5 of the next 3 5
RIBONUCLEIC ACID (RNA) Single stranded Sugar = ribose Nitrogenous bases = A, U, G, C Can fold up in 3D shape
NUCLEOTIDE SUBUNITS: SUGAR = Ribose (RNA) OR Deoxyribose (DNA) NITROGEN BASES: DNA Adenine Guanine Cytosine Thymine RNA Adenine Guanine Cytosine Uracil
DEOXYRIBONUCLEIC ACID (DNA) Double stranded Sugar = deoxyribose Nitrogenous bases = A, T, G, C Strands run in opposite directions (ANTIPARALLEL) Backbone = sugars and phosphates
DNA Structure Rungs of ladder = nitrogenous bases Hydrogen bonds between nitrogenous bases hold sides of ladder together Purine always bonds to a Pyrimidine CHARGAFF S RULE: A = T; G = C
The double strand twists around its axis like a spiral staircase, forming a DOUBLE HELIX
Evolutionary significance DNA and protein sequences can be used as tape measures of evolution linear sequences of nucleotides in DNA molecules are passed from parents to offspring more distantly related species have chains that are less similar
PROTEINS- Cellular toolbox Make up 50% or more of dray mass of most cells Humans have tens of thousands of different proteins Typical protein = 200-300 amino acids; biggest known = 34,000 We know the amino acid sequences of > 875,000 proteins/3d shapes of about 7,000 Scientists use X-ray cystallography to determine protein conformation A protein s function = determined by its conformation
EXAMPLES OF VARIETY OF PROTEINS/FUNCTIONS: Structural: hair, fingernails, bird feathers (keratin); spider silk; cellular cytoskeleton (tubulin & actin); connective tissue (collagen) Storage: egg white (ovalbumin); milk protein (Casein); plant seeds Transport: Transport iron in blood (hemoglobin); Hormonal: Regulate blood sugar (insulin) Membrane proteins (receptors, membrane transport, antigens) Movement: Muscle contraction (actin and myosin); Flagella (tubulin & dynein); Motor proteins move vesicles/chromosomes Defense: Antibodies fight germs Metabolism: Enzymes act as catalysts in chemical reactions Toxins (botulism, diphtheria)
AMINO ACIDS Central (α carbon) with CARBOXYL, AMINO, H, and R groups attached 20 common amino acids used by living things; lys-arg-his-asp-glu-ala-val-leu-ile-pro-phemet-trp-gly-cys-ser-thr-tyr-asn-gln
Essential AA s VEGGIE ALERT! 9 essential amino acids can t be synthesized by humans; must come from diet especially Lysine and tryptophan (in low amounts in most plant proteins) Strict vegetarians need to make sure that their diet contains sufficient amounts of these
In cells, protein structure changes depending on ph
Bonds in Proteins POLYPEPTIDE = polymer of amino acid subunits connected in a specific sequence An enzyme joins the carboxyl of one amino acid and the amino group of another via DEHYDRATION SYNTHESIS condensation reaction to form a PEPTIDE BOND Peptide bonds are rigid, planar structures The -NH bond and the -C=O bond, point away from each other so these groups can hydrogen bond to other parts of chain
LEVELS OF PROTEIN ORGANIZATION/3- STRUCTURE Primary Structure =unique sequence of amino acids; determined by DNA code; unique for each protein Secondary Structure: Determined by amino acid sequence; HYDROGEN BONDS (between the oxygen of C=O and the hydrogen of N-H of peptide bonds) stabilize structure & form pattern
Α HELIX- polypeptide chain winds clockwise like a spiral staircase EX: KERATIN, the main protein component of hair, nails, horns Β PLEATED SHEET- chains joined together like the logs in a raft EX: SILK Tertiary Structure: Hydrogen bonding, ionic interactions, hydrophobic interactions, and disulfide bridges between R groups stabilize 3 D shape
hydrop hyllic Tertiary Structure hydrop hob ic io nic + - S S S disu lfid e hydrog en
Quaternary Structure: protein made up of more than one amino acid chain EX: COLLAGEN 3 polypeptide chains twisted in super coil EX:HEMOGLOBIN 4 polypeptide chains
What Do You Call It? two or more amino acids bonded together = PEPTIDE chain of many amino acids = POLYPEPTIDE complete folded 3D structure = PROTEIN Final overall protein shapes - FIBROUS. - long fiber shape EX: actin or collagen - GLOBULAR - overall spherical structure EX: hemoglobin
MUTATIONS CAN CHANGE PROTEIN SHAPE Since shape is determined by amino acid sequence; changing sequence changes 3D shape EX: Sickle cell anemia mutation changes one amino acid in the sequence (glu ala) Abnormal hemoglobin molecules crystallize; cause blood cells to become sickle shaped
FACTORS AFFECTING CONFORMATION Folding occurs as protein is synthesized, but physical/chemical environment plays a role DENATURATION: = unraveling/ loss of native confirmation makes proteins biologically inactive ~ Reason high fevers can be fatal does NOT break peptide bonds so primary structure remains intact may regain its normal structure if conditions change sometimes = irreversible (ie. cooking an egg)
Denaturing CAUSED BY changes in ph (alters electrostatic interactions between charged amino acids) changes in salt concentration (does the same) changes in temperature (higher temperatures reduce the strength of hydrogen bonds) presence of reducing agents (break S-S bonds between cysteines)
Other Kinds of Proteins- Simple proteins contain only amino acids Conjugated proteins contain other kinds of molecules Ex: glycoproteins contain carbohydrates, nucleoproteins contain nucleic acids, lipoproteins contain lipids