Topic 3: Macromolecules

organic molecules

complex molecules based on carbon

inorganic molecules

all other substances (including a few small carbon-containing molecules that occur in the environment, CO₂)

what is the simplest hyrdrocarbon?

methane, CH₄

what are more complex hydrocarbons composed of?

2 or more carbon atoms arranged in a linear unbranched chain, linear branched, or a structure with 1 or more rings

functional groups

small, reactive groups of atoms which give

ex of functional groups

hydroxyl, carboxyl, carbonyl, amino, phosphate, and sulfhydryl

How are functional groups linked?

linked to C atoms through covalent bonds

are carbon atoms linked to 4 different atoms or functional groups symmetrical or asymmetrical?

asymmetrical

isomers

two forms of C molecules with the same chemical formula, but different molecular structures

what is an example of an isomer?

glyceraldehyde. —H and —OH groups take 2 positions (L/R) on the C chain

stereoisomers

isomers that are mirror images of each other (glyceraldehyde); typically, only 1 of the 2 forms (L-form/D-form) can enter into a reaction

structural isomers

2 molecules with the same chemical formula, but atoms are arranged in different ways

ex of structural isomers

glucose (an aldehyde) and fructose (a ketone)

dehydration synthesis reaction/condensation reaction

when water components (—H and —OH) are removed in reactions involving functional groups; joins separated units

hydrolysis

water components are added in a reaction involving functional groups; separates joined unites

polymers

assembled from subunit molecules (monomers) into a chain by covalent bonds

polymerization

polymers are assembled from monomers by dehydration synthesis reactions

macromolecule

a single polymer molecule with a mass of 1,000 Da (Dalton) or more (carbohydrate, proteins, and nucleic acids

What vital functions do proteins perform?

• structural support

• enzymes

• movement

• transport

• recognition and receptor molecules

• regulation of proteins and DNA

• horomones

• antibodies

• toxin and venom

monomer of a protein

amino acid

components of an amino acid

• C atom

• carboxyl group (COOH) — c terminal

• amino group (H₂N) — n terminal

• R group (brings identity to the amino acid)

How do amino acids act as acids or bases?

• the amino group can accept H⁺ (base)

• the carboxyl group can give up H⁺ (acid)

What are reactive side groups?

—NH₂, —OH, —COOH, —SH

What bonds do sulfhydryl groups (in cysteines) produce?

disulfide bonds (—S—S—) that help hold proteins in their 3D shape

peptide bonds

link amino acids into polypeptide chains (subunits of proteins); form a dehydration synthesis reaction between —NH₂ and —COOH groups

primary structure

unique sequence of amino acids that creates a polypeptide chain

secondary structure

produced by twists and turns of the amino acid chain; formed by hydrogen bonds

tertiary structure

folding of the amino acid chain to form the overall 3D shape; formed by bonds between R groups

quaternary structure

formed from more than 1 polypeptide chain

How can you alter any level of protein?

by changing 1 amino acid

What is the secondary structure made of

alpha helix and beta sheets

alpha helix

twists into a regular right-handed spiral

beta sheet

zigzags in a flat plane that form a sheet

What do random coils in the secondary structure allow?

they allow for flexible sites that let a-helical and b-strand segments to bend or fold back on themselves; act as hinges

conformation

3D shape of a protein given by tertiary structure; disulfide bonds, hydrogen bonds, and the 2nd structure plays a major role, as well as attractions between positively and negatively charged side groups

chaperone proteins/chaperonins

bind temporarily with newly synthesized proteins, directing their conformation into the correct tertiary structure and inhibiting incorrect arrangements

What does the tertiary structure determine and how?

solubility of a protein; depends on the arrangement or polar (hydrophobic) and nonpolar (hydrophobic) segments, which are determined by R-groups

Why are conformational changes important?

important to enzymes, proteins involved in cellular movements or transport through the cell membrane

proteins + lipids =

lipoproteins (make up parts of cell membrances

proteins + carbohydrates =

glycoproteins (enzymes, antibodies, recognition and receptor molecules. and parts of extracellular support)

proteins + nucleic acids =

nucleoproteins (form structures like chromosomes)

monomers of nucleic acids

nucleotides

DNA (deoxyribonucleic acid)

stores hereditary info responsible for inherited traits in all eukaryotes, prokaryotes and a large group of viruses

RNA (ribonucleic acid)

hereditary molecule of another larger group of viruses — 3 major types involved in protein synthesis

three parts of a nucleotide?

1) nitrogenous base - formed from rings of carbon and nitrogen

2) 5-carbon, ring-shaped sugar

• ribose (OH) in RNA

• deoxyribose (H) in DNA

3) 1 to 3 phosphate groups

what are the pyrimidine nitrogenous bases?

uracil (only RNA)

thymine (only DNA)

cytosine

What are the purine nitrogenous bases?

adenine

guanine

What type of bonds link nitrogenous bases and 5-carbon sugar?

covalent bonds

a necleotide is a…

nucleoside phosphate

examples of nucleoside phosphates

• adenosine monophosphate (AMP)

• adenosine diphosphate (ADP)

• adenosine triphosphate (ATP)

nucleoside

a structure containing only a nitrogenous base and a 5-caborn sugar

phosphodiester bond

one nucleotide linked to another creating a polynucleotide chain

How is one nucleotide linked to the next?

bridging the phosphate group between 5’ C of one sugar and the 3’C of the next

What forms the backbone of the nucleic acid chain?

the alternating sugar and phosphate groups

What do RNA strands form when folded back on themselves?

double-helical regions

Why do “hybrid” double helices (DNA chain paired with RNA) temporarily form?

so RNA can copy DNA

domains

large subdivisions caused by the folding of the amino acid chain/chains, in proteins with multiple functions, individual functions are often located in different domains

What must you give hemoglobin to make it give up O₂?

• give it something else to bind with (CO₂)

  • changes the optimal active site (molecular geometry) which then changes the binding affinity

How does H⁺ denature hemoglobin?

• makes it more acidic

• temporarily changes its conformational shape

What are the downsides of chaperonins?

• gene mutations can lead to incorrect folding with are “highly contagious” or self-replicating when consumed

• ex: mad-cow disease

polymerase

an enzyme that makes RNA and DNA

biomineralization helps to create…

lipoproteins, glycoproteins, and nucleoproteins

What are the functions of carbohydrates?

• storing energy (starch for plants; glycogen for animals)

• providing structure (cellulose in the cell wall of plants)

What elements do carbohydrates have and what is the ratio?

1C:2H:1O or CH_²O

monosaccharides

monomers that contain 3-7 C atoms

disaccharides

2 monosaccharides polymerized together

polysaccharides

carbohydrate polymers with more than 10 linked monosaccharides monomers; only occur as monosaccharides or as polymers of monosaccharide units

examples of monosaccharides

glucose, fructose, galactose

examples of disaccharides

lactose (glucose + fructose)

sucrose (glucose + glucose)

maltose (a-glucose + a-glucose)

monosaccharides with 5 or more C (like glucose) …

can fold back on themselves through a reaction between 2 functional groups to assume a ring form

what are the two enantiomers in which glucose exists?

a-glucose and B-glucose

a-glucose

has an —OH group pointing below the plane of the ring

B-glucose

has an —OH pointing above the plane of the ring

how is chitin assembled?

from glucose units modified by the addition of N-containing groups

How can polysaccharides be structured?

• may be linear, unbranched molecules

• may contain one or more branches in which side chains or sugar units are attached to a main chain