Molecules and Cells: Water, Nucleic Acids, and Protein

3.3, 3.12, 3.13, and 3.15

Four main classes of molecules

carbohydrates, lipids, proteins, and nucleic acids

macromolecules

big molecules. cells make most of their macromolecules by joining smaller molecules into chains called polymers

polymer

long molecules consisting of many identical or similar building blocks strung together

order of building blocks for a macromolecule

monomer, polymer, macromolecule

dehydration reaction

the process of removing a molecule of water as two molecules become bonded together (cells linking monomers together to form a polymer by removing one monomers H and another monomers OH)

hydrolysis

breaking down a large polymer to smaller ones that can enter the cells (adds the H and OH back in)

enzymes

specialized macromolecules that speed up chemical reactions in cells - both dehydration and hydrolysis reactions require enzymes

peptide bond

the bond formed by dehydration reaction between two monomers

what reactions must occur for protein in cheese to be broken down into amino acid monomers and then for the monomers to turn to protein?

proteins are broken down to amino acids by hydrolysis. the new proteins are formed in body cells from those monomers in dehydration reactions

protein

a polymer of small building blocks called amino acids (the most structurally and functionally elaborate and varied life molecule)

List some types of proteins

• enzymes

• transport proteins

• defensive proteins

• signal proteins

• receptor proteins

• contractile proteins

• collagen structural proteins

• storage proteins

transport protein

move sugar molecules and other nutrients into your cells

defensive proteins

antibodies of the immune system

signal proteins

hormones and other chemical messengers that help coordinate your body’s activities

receptor proteins

receive and transmit signals into cells

contractile proteins

muscle cells for muscle contraction

collagen structural proteins

fibers that make up tendons and ligaments - accounts for 40% of the protein in the body

storage proteins

supply amino acids to developing embryos

does the shape of a protein effect function?

YES

globular/fiborous

refers to proteins general shape

denaturation

the unraveling of a protein, losing its specific shape and therefore, loses its function. Without the shape, a protein loses its proper function and diseases occur from the accumulation of misfolded proteins

amino acids

all have an amino group and a carboxyl group

dipeptide

a product made from two amino acids

polypeptide

additional amino acids added to the chain of amino acids

an amino acid has two groups, what are they?

amino group and carboxyl group

When two amino acids join together, a dehydration reaction occurs to the OH of the carboxyl group of one amino acid and the H of the amino group of the other amino acid. This water molecule is removed and a bond is formed between the C and N. What is that bond called and what is the new name for the joined amino acids?

a peptide bond; dipeptide

what makes the unique sequence of amino acids?

the different polypeptides

R-group

influences protein structure

Hydrophobic

amino acids may cluster together in the center of a globular protein

hydrophillic

amino acids face the outside, helping proteins dissolve in aqueous solution of a cell

DNA and RNA are information…

rich polymers of nucleotides

gene

the amino acid sequence of a polypeptide programmed by a discrete unit of inheritance. Consists of DNA

DNA

deoxyribonucleic acid. one of the two types of polymers called nucleic acids

RNA

assembles polypeptides according to DNA instructions

nucleotides

nucleic acid monomers

polynucleotides

nucleic acid polymer built from it monomers through dehydration reactions

a nucleotide has three parts. What are they?

phosphate group, deoxyribose (sugar), and nitrogeneous base

True or False: a polynucleotide is connected nucleotides to form a chain

true

RNA consists of how many strands of a polypeptide?

one (half the double helix)

DNA contains how many strands of a polynucleotide?

two (double helix)

The two polypeptide chains are held together by what kind of bond between the base pairs?

hydrogen bond

A pairs with ___, T pairs with ____, C pairs with_____, G pairs with _____

A-T, T-A, C-G, G-C

chromosomes

long structures that house DNA and carry 100s of genes.

How is DNA duplicated for daughter cells?

the double helix of DNA unzips into the two strands of RNA. New polypeptide chains form and match its complimentary base pairs with the original RNA strand. This cycle creates identical matches of the original DNA pairs.

Gene expression

a gene first directs the synthesis of RNA molecule. RNA then interacts with the cells protein-building machine. There the “nucleic acid language” (ACTG), is translated to protein language.

The flow of genetic information that leans to gene expression can be summarized like what?

DNA→RNA→protein→information

Flow of genetic information in protein building

gene (DNA) →transcription→RNA→translation→protein

what do genes determine in proteins?

genes determine the proteins and the structures and functions of the body

In order, list the largest to smallest parts of a genetic information

genome, chromosome, gene/DNA, polynucleotide, nucleotide

Solvent

substance that can dissolve other molecules and compounds

Solute

molecules and compounds that are dissolved into a solvent

aqueous solution

solutions with water as the solvent

is water polar or nonpolar?

polar

polar molecule

neutral, uncharged, but has an asymmetrical internal distribution of charge, leading to partially positive and negative regions

hydration shell

formation of a 3D sphere of water molecules from many water molecules relative to solute molecules

types of non covalent bonds and their features

ionic: strongest-atoms have full charges

Hydrogen: atoms have partial permanent charges

Van der Waals Interactions: weakest-very temporary bonds between partially charged electrons

Because organisms are primarily made of water…

water plays an important role in how molecules in cells interact

A water molecule has ____ partial negative charges and ____ partial
positive charges (equal numbers)

TWO, TWO

MANY hydrogen bonds =

STRONG interactions between water molecules

Unique properties of water

High boiling: lots of hydrogen bonds between water molecules means it takes a lot of energy to pull them apart

Evaporative cooling: lots of hydrogen bonds between water molecules means it takes a lot of energy to pull them apart

Cohesive: strongly cohesive meaning it sticks to itself really well

Expands when freezes: hydrogen bonds hold water molecules apart in ice

• liquid: more dense and molecules are moving too much to form four hydrogen bonds

• Solid: less dense and hydrogen bonds hold water molecules apart (more space=less dense)

Hydrophilic

molecules interact well with water (have atoms with full and/or partial charges")

hydrophilic molecules are polar molecules

Hydrophobic

molecules do NOT interact well with water (few/no atoms with any kind of charge)

hydrophobic molecules are nonpolar

nonpolar bonds have what kind of charge?

no charge.

What kind of bond, links nonpolar covalent oil molecules together?

van der waals

can molecules have both hydrophobic and hydrophilic parts?

yes

Nucleic Acids main function

instructions required to create and maintain cells

Gene

instructions to make a specific protein or RNA

Nucleotides

• smaller molecules (monomers) used to form nucleic acids, DNA, and RNA

• some also act as energy currency in cells - transfer energy between cellular reactions (ex: ATP)

DNA & RNA are…

chains (polymers) of nucleotides connected by covalent bonds

main function of proteins

speed up chemical reactions in cells that form, break down, and change cellular molecules

Amino acids

building blocks (monomers) of proteins

• set of twenty common to ALL cells

• share common structure

• unique properties determined by R group

polypeptides

chains of amino acids (polymers) connected by covalent bonds

• fold into complex structures that are essential for proper function - held together by noncovalent bonds

• on specific type of covalent bond (disulfide bonds) that are important for 3D structure

• shape determined by composition AND order of amino acids

• a protein can have one or more polypeptide chains