Unit 1 and 2 (Chemistry of Life & Cell Structure and Function)

anion

negative ion

ionic bond

A chemical bond resulting from the attraction between oppositely charged ions

ionic compounds

compounds composed of cations and anions

Hydrogen bond

Weak attraction between a slightly positive hydrogen atom and a slightly negative atom

van der waals interactions

individually weak and occur only when atoms and molecules are very close together.

surface tension

a measure of how difficult it is to stretch or break the surface of a liquid

kinetic energy

the energy an object has due to its motion

thermal energy

the total energy of all the particles of an object

specfici heat

the amount of energy required to raise the temperature of 1 gram of a substance by 1 degree celsius

Heat of vaporization

the quantity of heat a liquid must absorb for 1g of it to be converted from the liquid to the gaseous state

Evaporate cooling

the process in which the surface of an object becomes cooler during evaporation, a result of the molecules with the greatest kinetic energy changing from the liquid to the gaseous state

solution

a liquid mixture of solute and solvent

solute

the substance that is dissolved

a liquid substance capable of dissolving other substances

ocean acidification

decreasing pH of ocean waters due to absorption of excess atmospheric CO2 form the burning of fossil fuels

organic compound

compounds that contain carbon

isomers

compounds with same formula but different structures

structural isomers

have covalent arrangements of their atoms

cis-trans isomers

have the same covalent bonds but differ in spatial arrangements

enantiomers

isomers that are mirror images of each other

enzymes

proteins that speed up chemical reactions

carbohydrates (CHO)

the starches and sugars present in foods

glycosidic linkage

a covalent bond formed between 2 monosaccharides by a dehydration reaction

cellulose

a substance (made of sugars) that is common in the cell walls of many organisms

Fatty acids (CHO)

Does not have monomers

Saturated fatty acid

A long-chain hydrocarbon with single covalent bonds in the carbon chain (lack double bonds) and from animal sources. They are liquid at room temperature.

Unsaturated fatty acids

Contains one or more double bonds (cis) between carbons in the hydrocarbon tail (meaning at the end of the structure). These bonds reduces the number of hydrogen atoms attached to the carbon skeleton. It is solid in room temperature.

Phospholipids

A lipid containing a phosphate group. It has a hhydrophilic head and a hydrophobic tail.

Steroids

Lipids characterized by a carbon skeleton consisting of four fused rings. Examples: sex hormones, cholesterol, and some drugs.

Cholesterol

A lipid that forms an essential component of animal cell membranes and acts as a building block for synthesizing other various important steroids. Their structural role providing stability, and fluidity, cholesterol also plays a crucial role in regulating cell function.

Catalysts

Substances that speed up chemical reactions

Amino acid (CHONS)

A compound with an amino group on one end and a carboxyl group on the other end

Peptide bond

Covalent bond formed between amino acids

Nucleic acid (CHONP)

The monomers are nucleotides which has three components: pentose sugar, phosphate group, and a nitrogenous base. The bonds are phosphodiester bonds and hydrogen bonds.

Phosphodiester bond

A bond between two sugar groups and a phosphate group. Basically, it holds the sugar backbone of DNA.

Type of pentose sugar in DNA and RNA

DNA: deoxyribonucleic acid (lacks oxygen - have one absence of hydroxyl group)

RNA: ribonucleic acid (has oxygen - all hydroxyl groups are present)

Pyrmidine

\`A nitrogenous base that has a single-ring structure: thymin, cytosine, and uracil.

Purine

A nitrogenous base that has a double-ring structure: Adenine and guanine.

Carbonyl group

Polar: C=O

Carboxyl group

COOH (charged)

Amino group

NH2 (charged)

Sulfhydryl group

\-SH (polar)

Phosphate group

PO4 (charged)

Methyl group

A chemical group consisting of a carbon atom bonded to three hydrogen atoms (non-polar): CH3

Valence shells of atoms

Hydrogen: 1

Oxygen: 2

Nitrogen: 3

Carbon: 4

Function of carbohydrates

Provide energy source

Function of lipids

Long-term energy storage

Function of proteins

Essential for the growth. development, and repair of all body tissues

Fucntion of nucleic acids

Store and transmit genetic information

Catabolic reaction

Chemical reaction that breaks down complex molecules into simpler molecules and it releases energy (exergonic)

Anabolic reaction

Chemical reaction that combines simple molecules to build more complex molecules and it requires energy (endergonic).

Exergonic and endergonic

Exergonic: releases energy

Endergonic absorbs energy

Hydrophobic R groups

Long hydrocarbon chains and fold away from water

Hydrophilic R groups

Oxygen or nitrogen, no charges, and folds toward the water

Primary structure of proteins

The amino acid sequence of the polypeptide chain

Secondary structure of proteins

Alpha helices and beta pleated sheets held together by hydrogen bonds.

Tertiary structure of proteins

A folding of the polypeptide structure into a unique three-dimensional conformation: disulfide bonds, ionic bonds, hydrophobic bonds, and Van der Waals interactions.

Quaternary protein structure

Joining of 2 or more tertiary subunits (proteins are made up of multiple polypeptide chains - subunits). Has the same types of bonds that contribute to tertiary structure; for example, hydrogen bonds and London dispersion forces.

Diffusion

Movement of molecules from an area of higher concentration to an area of lower concentration

Osmosis

Diffusion of water through a selectively permeable membrane

Hydrogenation

The process of converting unsaturated fats to saturated fats by adding hydrogen

Alpha helix and beta pleated sheet

Alpha helix: a spiral shape made through hydrogen bonds

Beta pleated sheet: The polypeptide chain folds back and forth and is also held together by hydrogen bonds.

Disulfide bridge

The covalent bond between two sulfur atoms (-S-S) linking two molecules or remote parts of the same molecule

Amphipathic/amphiphilic

Having both a hydrophilic region and a hydrophobic region

Difference between prokaryotes and eukaryotes

Mitochondria is absent in prokaryotes.

Eukaryotes have a nucleus

Prokaryotes doesn’t have organelles enclosed in plasma membranes.

Cytosol and cytoplasm

Cytosol is the fluid contained in the cell cytoplasm while cytoplasm is the entire content within the cell membrane.

Nucleoid

A non-membrane-bounded region in a prokaryotic cell where the DNA is concentrated

Glycocalyx (prokaryote)

layer of sticky carbohydrates covering plasma membrane, provides strength, attachment and cell-cell recognition, anchored to the plasma membrane by carbohydrates bonded to proteins and lipids in the membrane.

Flagella (prokaryote and eukaryote)

A long, whip=like filament that helps in cell moving.

Microvilli (eukaryote)

Projections that increase the cell’s surface area

Microfilaments (eukaryote)

Threadlike proteins found in the cell’s cytoskeleton

Chromatin

Material consisting of DNA and proteins; visible in a dividing cell as individual condensed chromosomes. It consists of DNA tightly coiled around histones.

Plasmodesmata

Cytoplasmic channels through plant cell walls that connect the cytoplasms of adjacent cells

Free ribosomes and bound ribosomes

Free ribosomes: ribosomes suspended in the cytosol

Bound ribosomes: Attached to the outside of the ER or nuclear envelope

Vesicles

Small membrane sacs that specialize in moving products into, out of, and within a cell.

Smooth Endoplasmic Reticulum (SER)

It synthesizes lipids, phospholipids (as in plasma membrane), and steroids. It is associated with carbohydrate metabolism, calcium concentration, drug detoxification, and attachment of receptors on cell membrane proteins.

Rough Endoplasmic Reticulum (RER)

Contains small ribosomes for protein synthesis for the rest of the cell to function.

Glycoproteins

Proteins with carbohydrates covalently bonded to them

transport vesicles

A small membranous sac in eukaryotic cell’s cytoplasm carrying molecules produced by the cell

Golgi apparatus

Stack of membranes in the cell that modifies, sorts, and m\[packages proteins from the endoplasmic reticulum

Cisternae

Membrane-bound compartments that make up the golgi apparatus

Cis face to Trans face of golgi apparatus

Receiving side to shipping side of the golgi apparatus

Lysosome

A membrane-enclosed sac of hydrolytic enzymes that many eukaryotic cells use to digest (hydrolysis) macromolecules

Phagocytosis

A type of endocytosis in which a cell engulfs large particles of whole cells

Auotphagy

A process in which lysosomes digest damaged organelles to reuse their organic monomers

Food vacuoles

A membranous sac formed by phagocytosis of microorganisms or particles to be used as food by the cell

Contractile vacuoles

A membrane-bound organelle (eukaryotes) which controls the intracellular water balance by accumulating gathering) and expelling (force out) excess water out of the cell.

Central Vacuole

In plant cells which storages, breakdown of waste products, and hydrolysis of macromolecules. Enlargement of the vacuole is a major mechanism of plant growth.

Mitochondria (eularyote)

Processes cellular respiration and energy production for cell’s biochemical reaction

Endosymbiosis theory

Eukaryotic cells engulfed a mitochondria (nonphotosynthetic prokaryotes) and chloroplasts (photosynthetic prokaryotes).

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Endosymbiont: a cell that lives within another cell

Cristae

Infoldings of the inner membrane of a mitochondrion that houses the electon transport chain and the enzyme catalyzing the synthesis of ATP.

Chloroplast

organelle in plant cells and some other organisms that captures the energy from sunlight and converts it into chemical energy

Chlorophyll

Green pigment in plants that absorbs light energy used to carry out photosynthesis

Thylakoids and granum

A flattened membrane sac inside the chloroplast, used to convert light energy to chemical energy.

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Granum: stack of thylakoids

Peroxisomes (animal cells)

An organelle that contains enzymes involved in a variety of metabolic reactions.

Cytoskeleton

A network of fibers extending throughout the cytoplasm that holds the cell together, helts the cell to keep its shape, and aids in movement

Motor proteins

An ATP powered protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell.

Microtubules

Hollow tubes in the cytoskeleton that maintain cell shape, cell movement (outside the cell), chromosome movement in cell division.

Intermediate filaments

fibrous proteins coiled into cables in the cytoskeleton that marination cell shape, anchorage of nucleus and other organelle and the formation of nuclear lamina

Centrosomes and centrioles (animal cells)

Centrosome: a region where microtubules are initiated

Centriole: structure in an animal cell that helps to organize cell division in anaphase (located in the centrosomes)