unit 1 chemistry of life

Polarity

A lack of symmetry; structural differences in opposite ends of an organism or structure, such as the root end & shoot end of a plant.

Hydrogen bonding in water

A type of weak chemical bond that is formed when the slightly positive hydrogen atom of a polar covalent bond in one water molecule is attracted to the slightly negative oxygen atom in another water molecule or in another region of the same molecule

Cohesion

The linking together like molecules, often by hydrogen bonds

Adhesion

The clinging of one substance to another, such as water to plant cell walls in this case by hydrogen bonds

Surface tension

A measure of now difficult it is to stretch or break the surface of a liquid . Water NASA nigh surface tension because of the hydrogen bonding of surface molecules

Macromolecules

A giant molecule formed by the joining of smaller molecules. Polysaccharides,proteins & nuclei acids are macromolecules

Atoms

The smallest unit of matter that retains the properties of an element

Molecules

Two or more atoms held together by covalent bones

Carbon

The foundational chemical element of life. Because it has 4 valence electrons this allows it to form up to 4 strong, stable covalent bonds with other atoms acting as the structural backbone for an biologica, molecules.

Nitrogen

An essential chemical element that makes up 70% of earth's atmosphere.it is a critical component for building life's macromoleculesspecifically proteins & nuclei acids (dna/rna)

Carbohydrates

A sugar (mono - saccharide ) or one of its diners (disaccharides) or polymers ( polysaccharides)

Proteins

A biologically functional molecule consisting of one or-more polypeptides coiled & folded into a specific three dimensional structure

Lipids

Any of a group of large biological molecules including fats, phospholipids& steroids, that mix poorly, it at all, with water.

Nuclei acids

A for proteins polymer ( polynucleotides) consisting of many nucleotide monomers; serves as a blueprint for proteins and, through the actions of proteins for an cellular activities the two types are DNA & RNA

Phosphorous

An essential mineral & chemical element vital for building major macromolecules & storing chemical energy. Most commonly foundin phosphate ion & is akey component of DNA-RNA, ATP& phospholipids

Monomers

The subunit that serves as the building block of a polymer

Hydrolysis

A chemical reaction that breaks bonus between two molecules by the addition of water; functions in disassembly of polymers to monomers

Dehydration synthesis/ dehydration reaction

A chemical reaction in which two molecules become covalently bonded to each other with the removal ofa water molecule

Polypeptide

A polymer of many amino acids linked together by peptide bonds

Primary structure

The level of protein structure ( #1) referring to the specific linear sequence of amino acids

Directionality

The end to end chemical orientation of a biological polymer, the two ends are structurally & chemically distinct

Amino terminus (n-terminus)

The start of the polypeptide chain referring to the free & unbound amine group located at one end of a protein, considered the beginning of the polypeptide in terms of directionality

Carbox yl terminus ( c-terminus )

The end of the polypeptide chain referring to the free unbound carboxyl group located at the terminal end of a protein, the final part of a polypeptide sequencing chain and the carboxyl terminus or the end of the polypeptide chain is where ribosomes create peptide bonds by attaching the amino acid group of an incoming amino acid to the carboxyl terminus to continue to grow the chain

R group

Also known as the side chain is the variable chemical group attached to the central carbon atom of an amino acid. It determines the unique chemical property and identity of each of the 20 amino acids used to build proteins. Since the amino acids share a common backbone made of an amino group a carboxyl group a hydrogen atom and a central carbon atom the R group is the only part that differs between amino acids. This R group determines whether an amino acid is hydrophobic and non polar, hydrophilic and polar, acidic and negatively charged, or basic and positively charged. R group interactions drive tertiary structure and the determination of the final 3d shape of a protein

Ionic

A property that refers to any physical or chemical characteristic of a substance that results from the presence of ionic bonds or charged ions and these ionic compounds dissolve easily in water because the polar molecules attract surround and separate the individual ions and lastly having the ionic property gives the molecules a distinct positive or negative charge which allows them to either stick or repel from other molecules based on their charge like positive sticks to negative and repels from positive and vice versa with the negative charge

Secondary structure

(#2) regions of repetitive coining & folding of the polypeptide backbone of a protein due to hydrogen bonding between constituents of the backbone ( not the side chains )

Tertiary structure

( #3 ) the overall shape of a protein molecule due to interactions of amino acid side chains, including hydrophobic interactions, ionic bonds, hydrogen bonds& disulfide bridges

Quaternary structure

( #4) the particular sharpe of a complex, aggregate protein, defined by the characteristic

Unsaturated fatty acid

A fatty acid hat has one or more double bonds between carbons in the hydrocarbon tail. Such bonding reduces the number of hydrogen atoms attached to the carbon skeleton (bends)

Saturated fatty acid

A fatty acid in which all carbons in the hydrocarbon til are connected by single bonds, thus maximizing the number of hydrogen atoms attached to the carbon skeleton

Phospholipids

A lipid made up of glycerol joined to two fatty acids & a phosphate group. The hydrocarbon chains of the fatty acids act as nonpoler hydrophobic tailswhile the rest of the molecule acts as a polar, hydrophilic head. Phospholipids form belayers that function as biological membranes

Polar region

Refers to a part of a molecule where the overall electrical charge is unevenly distributed and these ionic compounds polar regions are driven by electronegativity differences and a highly electronegative atom pulls shared electrons closer to the nucleus and as a result this unequal electron sharing results in partial positive and partial negative charges one charge on one side and the other charge on the other like in a water molecule where the oxygen atoms create a local negative polar region and the hydrogen atoms form a local positive region

Non polar region

Refers to a part of a molecule where elections are shared equally between atoms, resulting in an even distribution of electrical charges & no distinct positive or negative poles & because these regions lack distinct charge oreven charge atall they don't form hydrogen bonds & are therefore hydrophobic or water fearing, these regions are typically built

Polymers

A long m olecule consisting of many similar or identical monomers linked together by covalent bonds.

Nonpolar

The description of a molecule or a covalent bond in which electrons are shared equally between atoms resulting in an even distribution of electrical charge so noatom has a distinct positive or negative charge this results in the compound being nompolar & therefore hydrophobic since the substance lacks the difference incharges to hydrogen bond

Hydrophobic

Having no affinity for water I tending to coalesce & form droplets in water

Hydrophilic

Having an affinity for water

Nuclei's acids

A polymer)poly -nucleotide) consisting of many nucleotide monomers I serves as a blueprint for proteins, and through the actions of proteinsfor all cellular activities the two types are DNA & RNA.

Five carbon sugar / Penrose sugar

A monosaccharide or a simple sugar that contains a skeleton of exactly five carbon atoms & these pentose sugars are critical components of nucleotides,

Deoxyribose

the sugar component of DNA nucleaticles, having one fewer hydroxyl group than ribuse, the sugar component of RNA nucleotides

Ribose

the sugar component of RNA nucleotides

Phosphate

An inorganic chemical compound or a functional group made of one phosphorous atom covalently bonded to four carbon atoms ( important for energy transfer)

Nitrogen base

An organic molecule containing nitrogen that has the chemical properties of a base & forms a keycomponent of a nucleotidethese are the structural molecules responsible for encoding genetic information in DNA and RNA- either pyridine or purine.

Pyrimidine

A single-six membered ringconsists of three nitrogenous bases of cytosine, thymine.& uracil. All of which are found in DNA except for uracil which is found in RNA in place of thymine.

Purine

A double ring which means its six membered ring fused toa five membered ring. The two bases that fall under the purine category are adenine & guanine which both are found in DNA & RNA,

DNA / deoxyribonucleic acid

A nuclei's acid molecule usually a double stranded helix, in which each polynucleotide strand consists of nucleotide monomers with a deoxyribose sugar & thenitrogenous bases: adenine, thymine, cytosine, & guanine; capable of being replicated & determining the inherited structure of cells proteins

RNA / ribonucleic acid

A type of nucreic acid acid consisting of a polynucleotide made up of nucleotide monomers witha ribose sugar & the nitrogenous bases: adenine, uracil, cytosine, & guanine I usually single stranded; functions in protein synthesisingene regulation, &astregenome of some viruses

3’ hydroxyl end (-oh)

Refers to the specific termination point ofa nucleicacid strand of either DNA or RNA where a free unbound hydroxyl group attaches to the third carbon of the five carbon sugar ring, this is the end of the nuclei acid strand I it terminates the hydroxyl group

5’ phosphate end

Refers to the specific termination point of a nuclei's acid strand of either DNA OR RNA where a free, unbound phosphate group attaches to the fifth Carbon of the five carbon sugar ring, considered the structural beginning of the nucleicacia strand, acts as the anchor for the phosphate group that forms the alternating sugar-phosphate backbone,

Antiparallel

Referring to the arrangement of the sugar-phosphate backbones in DNA double helixes since they run in opposite 5’→3 ‘ directions,

Double helix

The form of native DNA, this refers to its adjacent antiparallel polynucleotide strands wound around an imaginary axis into its known spiral shape

Complementary base pairing in DNA

When base pairing in DNA we always complementary pair with having the strands pair inte opposite direction but even before that it has to be understood that adenine + thymine always complementary pair & so does cytosine + guanine. So when we pair: 5’ ACCGGA 3’ the complementary base pair would be: 3’ TGGCCT 5’ since we pair in the opposite direction

A-T two hydrogen bonds ( also a-u )

The adenine-thymine pair is held together by onlytwo hydrogen bonds & this is the complementary base pairing rule these ensures the double helix DNA due to proper nitrogenous base pairing. Due to the nitrogenous bases of adenine& thymine perfectly aligning it is due to their partial positive & partial negative regions where opposites attract to form exactly two weak hydrogen bonds, these two hydrogen bonds help create one set of rungs for the double helix ladder , less thermal energy is needed to separate these two bonds

C-G three hydrogen bonds

The cytosine-guanine pair is held together by three hydrogen bonds, & this complementary base pairing helps to ensure the correct structure of theDNAs double helix. Thereason for the three hydrogen bonds is because of the molecular structure being able to possess three complementary donor-acceptor sites in order to form three hydrogen bonds from apartial positive hydrogen to attach to an electronegative atom aite donor & these must align perfectly with a sone pair of electrons on anotur electronegative atom acceptor), this pairing has a stronger binding than a-t due to the extra hydrogen bond-higher thermal energy to break apart

Alpha helices

A coiled region constituting one form of the secondary structure of proteins, arising from a specific pattern of hydrogen bonding between atoms of the polypeptide backbone & this doesn't include the side chains.

Beta-sheets / beta pleated sheets

One form of the secondary structure of proteins in which the polypepticle chain folds back & forth instead of coiling. Two regions of the chain lie parallel to each other & are held together by hydrogen bonds between atoms of the polypeptide backbone which again doesn't include the sidechains

Carbohydrate polymers - linear or branched

Carbohydrate polymers or polysaccharides can either be linear or branched e this variation determines their biological function, separating them into either strong e structural molecules or easily accessible storage molecules- the shape of the polymer also depends on which carbon atoms connected by glycosidic linkages during dehydration synthesis, linear or structural polysaccharides are long unbranched chains of glucose monomers e these chains can pack rightly parallel to one another I cellulose & chitin are some examples, cellulose has 1-4 beta glycosidic linkages these polymers create structural mesh that builds plant cell walls & chitin is used to build the hard & crunchy exoskeleton on an insect& the strong fungi cell walls. Branched polysaccharides containa main chain of glucose monomers with side chains splitting Off at various intervals & this exposes more ends on the molecule which allows enzymes to break it down rapidly when the cell needs more energy : starch, glycogen ave examples -plants store energy as starch & amylose linear but amylopectin is branched & has 1-6 glycosidic linkages at branch spots , glycogen is branched & found in animals to help them store energy in liver & muscle tissues,these branched structures help enzymes attack free ends torelease glucose monomers & speed cellular respiration up

Monosaccharides

The simplest carbohydrate monomers, such as glucose and fructose, which serve as fuel and carbon sources to be converted to other molecules or polymers.

Disaccharides

Carbohydrates composed of two monosaccharides, with examples including lactose and sucrose.

Cellulose

A polysaccharide that strengthens plant cell walls.

Starch

A polysaccharide in plants used to store glucose for energy.

Glycogen

A polysaccharide in animals used to store glucose for energy.

Chitin

A polysaccharide that strengthens animal exoskeletons and fungal cell walls.

Triacylglycerols

Fats or oils composed of glycerol and three fatty acids that serve as an important energy source.

Phospholipids

Lipid molecules composed of glycerol, a phosphate group, and two fatty acids; they form the lipid bilayers of membranes.

Steroids

Lipids characterized by a backbone of four fused rings with attached chemical groups; they function as components of cell membranes (cholesterol) and signaling molecules (hormones).

Amino acid

The monomer of a protein, of which there are $20$ types, each containing an $\text{R}$ group.

Enzymes

Specific proteins that catalyze chemical reactions.

Defensive proteins

Proteins that protect against disease.

Transport proteins

Proteins responsible for the transport of substances.

Nucleotide

The monomer of a polynucleotide, consisting of a phosphate group, a sugar, and a nitrogenous base.

DNA (Deoxyribonucleic Acid)

A usually double-stranded nucleic acid containing deoxyribose sugar and nitrogenous bases $C, G, A, T$; it stores hereditary information.

RNA (Ribonucleic Acid)

A usually single-stranded nucleic acid containing ribose sugar and nitrogenous bases $C, G, A, U$; it functions in gene expression and carries instructions from DNA to ribosomes.