microbio chapter 2

proteins

make up more than half of the dry weight of cells some of their most important roles are: catalyzing reactions, transporting molecules, motility, cell framework, sensing and responding to conditions outside the cell, regulating gene expression characteristics of a protein depend on is shape and the sequence of amino acids is one or more long polypeptides folded to create a functional molecule very greatly in size, but an average size polypeptide consists of about 200 amino acids

triglyceride

most common of fats in nature has three fatty acid bound to glycreol

3 different parts of the nucleotides of DNA

nucleobase, deoxyribose, and a phosphate group

sugars

occur in two interchangeable forms: linear and ring both occur naturally in the cell but most are in ring form can exhibit two different forms alpha and beta based on the relative position of the hydroxyl group joined to the number 1 carbon atom

quaternary structure

only proteins that consist of more than one polypeptide have this gives the protein a specific shape resulting from more than one polypeptide held together by many weak bonds

tertiary structure of protein

the entire protein fold into its distinctive 3D shape is is determined by the sequence of amino acids, and whether or not they interact with water. Amino acids that have polar side chains are hydrophilic and are typically located on the outside of the protein molecule, where they can interact with charged polar water molecules non polar amino acids are hydrophobic and their side chains tend to cluster inside the protein molecule

polypeptide

the joining of amino acid subunits by peptide bond

molarity (M)

the number of moles of a compound dissolved in 1 liter of solution.

what makes up the heavier part of the atom

the protons and the neutrons-the nucleus

dipole

the slight separation of charge in polar covalent bonds oxygen is more electronegative than hydrogen, therefore it has a slight negative charge leaving the hydrogen with slight positive charge

Nucleotide

the subunit of nucleic acids

mass number of atom

the sum of the number of protons and neutrons superscript to the left

peptide bonds

this type of covalent bond forms when the carboxyl group of one amino acid react with the amino group of another, releasing water the joining of amino acid subunits by peptide bonds creates a polypeptide

transporting molecules

transport proteins move molecules either into or out of cells

molecule

two or more atoms held together by chemical bonds

hydrophobic

water fearing do not dissolve in water because they cannot form H bonds

hydrophilic

water loving salts and polar molecules

hydrogen bonds

weak bonds formed when a H atom in a polar molecule is attracted to an electronegative atom in the same or another polar molecule usually lasts seconds enzymes are not needed to form or break them H bonds between water molecules are constantly being formed and broken at room temp

hydrogen bond

the attraction between a hydrogen atom in a polar molecule and an electronegative atom in the same or another polar molecule

atom

the basic unit of matter

roles of carbohydrates

- energy source: organisms degrade carbohydrates to harvest the energy they contain -energy storage: organisms can store excess energy and nutrients for later use by producing certain carbohydrates that function as reserve material -source of carbon for biosynthetic products: many microbes can make all of their cell components from a singe carbohydrate- glucose -component of DNA and RNA: the subunits of DNA and RNA contain sugars -structural components of cells: some types of cell wall are composed of sugar containing material

charged amino acids

carry a positive or negative charge because their side chains contain functional groups that can ionize; they include carboxyl groups (acidic) and amino groups (basic)

non polar amino acids

characterized by side chains that lack polar bonds example: methyl grou of alanine

glycerol

3 carbon molecule iwth a hydroxyl group attached to each carbon

one mole

6.022 x 10 23 particles one mole of one molecule has the same number of molecules as a mole of any other

complementary nucleobases

A-T C-G

high -energy phosphate bonds

ATP they release a high amount of energy when the bonds are hydrolyzed indicated by the symbol ~

dehydration synthesis

chemical reaction that removes water requires specific enzymes

what is an atom distinguished by?

By its atomic number- the number of its protons subscript to the left

general chemical formula of carbohydrates

CH2O

element

consists of only one kind of atom and cannot be separated into simpler parts by chemical methods

Shell capactity of an atom

First shell-2 Second shell-8

phospholipids

contain a phosphate group linked to one of a variety of other polar molecules this phosphate containing portion is the polar head and is soluble in water are an essential component of cytoplasmic membranes, the structure that separates the internal contents of a cell from the outside environment phospholipid molecules orient themselves in the membrane as opposing layers, forming a bilayer

compound lipids

contain fatty acids and glycerol as well as elements other than carbon, hydrogen, and oxygen biologically some of the most important of these are phospholipids

simple lipids

contain only one carbon, hydrogen and oxygen most common simple lipids are fats-fatty acids linked to glycerol

What usually breaks ionic bonds?

Water in an aqueous solution, salts are electrolytes, meaning they conduct electricity electrical charges from the heart are conducted by electrolytes

when are atoms most stable?

With the exception of H, biologically important atoms are most stable when they have 8 valence electrons (octet rule)

ionic bond

a chemical bond resulting from the attraction between positively and negatively charged ions;ions from when electrons leave one atom and become part of the other.

carbohydrate

a compound containing principally carbon, hydrogen and oxygen in a ration of 1:2:1 diverse group of compound that include starches and sugars

organic compound

a compound that has a carbon atom covalently bonded to a hydrogen atom

inorganic compound

a compound that is not organic

protein domains

a distinct protein part associated with a certain function large proteins sometimes contain many domains, whereas a small protein may contain only one. domains usually consist of 40 to 350 amino acids are connected by polypeptides

nucleic acid

a macromolecule consisting of chains of nucleotide subunits to from either DNA or RNA

protein

a macromolecule consisting of one more chains of amino acid

pH

a measure of the hydrogen ion concentration of acidity of a solution on a scale of 0 to 14 lower the number the more acidic

covalent bond

a strong chemical bond formed when two atoms share electrons indicated by a dash or two between two symbols double bonds are stronger than single bonds the stronger the bond the more difficult to break these bonds usually do not break unless exposed to certain chemicals or large amounts of energy (heat) enzymes break covalent bonds at lower temps

amino acid

a subunit of a protein

macromolecule

a very large molecule usually consisting of repeating subunits are usually polymers (joining of subunits together) the joining of subunits involves dehydration synthesis (removal of water)

an especially important small organic molecule is

adenosine triphosphate (ATP)

examples of polysaccharides

agar: gelling agent in bacteriological media,extracted from cell wall of some algae cellulose: main structural polysaccharide in plant cell walls most abundant organic molecule on earth chitin: exoskelton of insects dextran: stroage product in some bacterial cells glycogen: main storage polysaccharide in animal and bacterial cells starch: main storage product in plants

ion

an atom or molecule that has gained or lost one or more electrons

lipid

an organic molecule that is insoluble in water

polysaccharides

are large molecules composed of long chains of monosacchardie subunits or their derivatives often contain only glucose molecules, but are structurally diverse beause some polymers are branched some have linkages between alpha forms and beta forms the position of the carbon atoms involved in the bonding can also differ

steroids

are simple lipids that have a characteristic structure consisting of four connected rings chemical structure is different from fats they are insoluble in water therefore classified as lipids if hydroxyl group is attached to one of the rings: sterol (ex: cholesterol) other steroids include the hormones: cortisone, progesterone, and testosterone

disaccharides

are two monosaccharides joined together by covalent bonds most common examples are sucrose and lactose (sucrose composed of glucose and fructose, lactose is composed of glucose and galactose) to form disaccharides two monosaccharides are joined by the dehydration reaction between a pair of ther hydroxyl groups

hydrolysis

breaking down of subunits by a chemical reaction by adding water requires specific enzymes

What elements are living things usually made of?

carbon, hydrogen, oxygen, and nitrogen phosphorus and sulfur

the side chain

distinguishes different amino acids and gives it its characteristic properties

valence electrons

electrons found in the outer shell

catalyzing reactions

enzymes are proteins that speed up the various chemical reactions in cells

non-polar covalent bonds

form when the electrons are shared equally, such as when identical atoms share electrons, or between different atoms if both have a similar attraction for electrons examples H-H and C-H

isotopes

forms of the same chemical element containing different number of neutrons are useful in research

6 carbon sugars

glucose, galactose, fructose, mannose

monoglyceride

has only one fatty acid bound to glycerol

trans fat

have hydrogen atoms on opposite side of the double bond

substituted proteins

have other molecules covalently bonded to the side chains of some of their amino acids many proteins found on the surface of cells are substituted the proteins are named after the molecules covalently joined to the amino acid (sugar molecule- glycoprotein; lipids- lipoprotein)

polar amino acids

have side chains that contain a polar bond example: hydroxyl group of serine

protein denaturation

high temperature, extreme pH and certain solvents can break bonds within a protein causing its shape to change. They protein then no longer function. if the denaturation agent is a chemical the protein may refold if that chemical is removed

amino acids

subunits that make up proteins all amino acids have a carbon atom bonded to a carboxyl group , an amino group and a side chain are subdivided into several different groups based on properties of their side chains are held together in an unbranched chain by peptide bonds

water

hydrogen bonds play a critical role in the properties of water the extent and stability of H boning between water molecules depends on the temp. liquid water is denser than ice the polar nature of water molecules accounts for water's ability to dissolve a large number of compounds to dissolve compounds must be polar or have a positive or negative charge water containing dissolved substances freezes at a lower temp. some microorganisms can multiply below 0 C because some of the water remains liquid

polar covalent bond

if one atom in a covalent bond is significantly more electronegative than the other

organic small molecules (subunits) in cells or macromolecules

include amino acids, nucleotides, and various sugars

about 1% of a bacterial cells dry weight is composed of :

inorganic ions

ATP

is an effective energy carrier because the three negatively charged phosphate groups repel each other , so the bonds joining them are inherently unstable, they are easily broken to release a sufficient amount of energy to drive a cellular process

primary structure of proteins

is determined by the number and sequence of amino acid in the polypeptide (about 250 amino acids) it determines the final shape of the protein and thus is responsible for its properties

adenosine diphosphate (ADP)

is formed along with inorganic phospate when the terminal bond of ATP breaks

secondary structure of proteins

is the 3D shape of localized regions certain amino acid sequences lead to characteristic spirals and folds due to weak forces such as hydrogen bonds. A spiral or helical structure is an alpha helix whereas parallel strands make up a beta pleated sheet

electronegativity

is the ability of an atom to attract electrons to itself in a molecule

DNA

is the master molecule of the cell the information in DNA is translated in RNA which is then translated into making proteins

nucleic acids consists of

linear chains of nucleotide subunits with a covalent bond between the phosphate of one nucleotide and the sugar of the next this results in the sugar phosphate backbone

fatty acids

long chains of C atoms bonded to H atoms, with a carboxyl group on one end the length of the chain varies, depending on the fatty acid, which usually has an even number of carbon atoms. fatty acids can join to glycerol via covalent bonds between a hydroxyl group of glyerol and the carboxyl group of the fatty acid

lipids

play an indispensable role in all cells they are critically important in the structure of membranes, which function as a cell's gatekeepers are a very diverse group of non polar, hydrophobic molecules single common feature is that they are only slightly soluble in water but highly soluble in organic solvents such as ether, benzene, and chloroform thus their defining characteristic is a physical rather than a chemical property lipids are not composed of similar subunits; rather they consist of a wide variety of chemically distinct substances

motility

proteins are essential components of flagella and cilia, structures that move cells

regulating gene expression

proteins bind to DNA and regulate gene expression

cell framework

proteins make up the exoskeleton, the structural framework of many cells

sensing and responding to conditions outside the cell

proteins on the cell surface recognize conditions in the external environment and relay that information to the cellular machinery

four major classes of macromolecules

proteins, carbohydrates, nucleic acids and lipids

5 carbon sugars

ribose (component of RNA ) and deoxyribose (component of DNA)

the result of the ionic bonds is called

salt (common type of salt is sodium chloride Na+Cl-

two goups of fatty acids

saturated: have no double bonds between carbon atoms (they have the maximum number of hydrogen atoms) unsaturated: contain one or more double bond (monounsaturated: that have one double bond, polyunsaturated have multiple double bonds)

oligosaccharides

short chains of polysaccharides

monosaccharides

simple sugars have only a single unit they are classified by the number of carbon atoms most common monosaccharides have 5-6 carbon atoms

protein chaperones

sometimes help the protein fold in the "correct" functional shape

buffers

stabilize the pH of solutions they are frequently added to bacterial growth media to prevent a dramatic rise of fall in pH resulting from metabolic processes this is important because most bacteria are able to live within a narrow range of pH usually close to neutrality

RNA

structure resembles that of DNA but there are several differences nucleotides of RNA contain the pyrimidine uracil in place of thymine and the sugar ribose in place of deoxyribose DNA is long RNA is shorter and exists as a single chain of nucleotides although single stranded it may form short double stranded stretches as a result of H bonding between complementary nucleobases in the singe strand