Bio Chapters 5-7

Polymer

Polymer

a long molecule consisting of many similar or identical building blocks linked by covalent bonds, much as a train consists of a chain of cars

Monomer

repeating units that serve as the building blocks of a polymer are smaller molecules

• Around 40-50 common monomers

Enzyme

a macromolecule serving as a catalyst, a chemical agent that increases the rate of a reaction without being consumed by the reaction

• Most enzymes are proteins

Dehydration synthesis

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

• One monomer provides a hydroxyl group (OH-) while the other provides a hydrogen (H+)

  • This reaction is repeated as monomers are added to the chain one by one, making a polymer (also called polymerization)

Hydrolysis

a chemical reaction that breaks bonds between two molecules by the addition of water

• Functions in disassembly of polymers to monomers

• Hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other

  • Ex: Digestion

Carbohydrate

A sugar (monosaccharide) or one of its dimers (disaccharide) or polymers (polysaccharide)

Monosaccharide

The simplest carbohydrate, active alone or serving as a monomer for disaccharides and polysaccharides

• Also called simple sugars

  • Have molecular formulas that are generally some multiple of CH2O

    • Most common monosaccharide is glucose (C6H12O6)

Depending on the location of the carbonyl group, a sugar is either an

aldose (aldehyde sugar) or a ketose (ketone sugar)

• Ketone - carbonyl group is bonded between two carbon atoms

Aldehyde - carbonyl group is on the end

Another criterion for classifying sugars is the

size of the carbon skeleton, which ranges from three to seven carbons long

• Triose - 3-Carbon sugar

• Pentose - 5-Carbon sugar

• Hexose - 6-Carbon sugar

In aqueous solutions, glucose molecules, as well as most other five- and six-carbon sugars, form rings, because

they are the most stable form of these sugars under physiological conditions

Disaccharide

a double sugar, consisting of two monosaccharides joined by a glycosidic linkage formed by a dehydration reaction

Glycosidic linkage

a covalent bond formed between two monosaccharides by a dehydration reaction

• Ex: maltose, sucrose, lactose

Polysaccharide

a polymer of many monosaccharides, formed by dehydration reactions

• Some polysaccharides serve as storage material, hydrolyzed as needed to provide sugar for cells

• Other polysaccharides serve as building material for structures that protect the cell or the whole organism

Starch

a storage polysaccharide in plants, consisting entirely of glucose monomers joined by glycosidic linkages

• Most of the glucose monomers in starch are joined by 1–4 linkages (number 1 carbon to number 4 carbon)

Glycogen

an extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch

• Glycogen being extensively branched allows more glucose to be released simultaneously

Cellulose

a structural polysaccharide of plant cell walls consisting of glucose monomers joined by b glycosidic linkages

• Cellulose is straight while starch is helical

Chitin

a structural polysaccharide consisting of amino sugar monomers, found in many fungal cell walls and in the exoskeletons of all arthropods

Lipids

any group of large biological molecules including waxes, fats, phospholipids, and steroids, that mix poorly, if at all, with water

• Hydrophobic, made mostly of carbon

  • Wax: protection, waterproofs

  • Fat: energy storage

  • Phospholipids: in cell membrane that acts as a barrier between inside and outside the cell

  • Steroid: hormones that regulate activities in the body

Fat

a lipid consisting of three fatty acids linked to one glycerol molecule

• Triglyceride or triacylglycerol

  • In making a fat, three fatty acid molecules are each joined to glycerol by an ester linkage, a bond formed by a dehydration reaction between a hydroxyl group and a carboxyl group

    • Fat can be storage or cushioning for organs

Fatty acid

a carboxylic acid with a long carbon chain (usually 16-18 carbon in length)

• Fatty acids vary in length and in the number and location of double bonds

Saturated fatty acid

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

• Most animal fats are saturated

Unsaturated fatty acid

a fatty acid that has one or more double bonds between carbons in the hydrocarbon tail, reducing the number of hydrogen atoms attached to the carbon skeleton

• Plant and fish fats are generally unsaturated

Hydrogenated fat

unsaturated fats have been synthetically converted to saturated fats by adding hydrogen, allowing them to solidify

Trans fat

an unsaturated fat, formed artificially during hydrogenation of oils, containing one or more trans double bonds

Phospholipid

a lipid made up of glycerol joined to two fatty acids and a phosphate group

• The hydrocarbon chains of the fatty acid tails act as nonpolar, hydrophobic tails, while the rest of the molecule acts as a polar, hydrophilic head

  • When phospholipids are added to water, they self-assemble into a double-layered sheet called a “bilayer” that shields their hydrophobic fatty acid tails from water

  • Phospholipids form bilayers that function as biological membranes

    • The hydrophilic heads of the molecules are on the outside of the bilayer, in contact with the aqueous solutions inside and outside of the cell

    • The hydrophobic tails point toward the interior of the bilayer, away from the water

Steroid

a type of lipid characterized by a carbon skeleton consisting of four fused rings with various chemical groups attached

Cholesterol

a steroid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids, such as many hormones

• (High density lipoprotein) HDL: good cholesterol; high protein to lipid ratio

  • Regulates LDL storage and promotes excretion

• (Low density lipoprotein) LDL; bad cholesterol; low protein to lipid ratio

  • Stores cholesterol in the bloodstream

• Cholesterol is nonpolar and does not dissolve in blood

Adipose tissue

tissue that cushions vital organs and insulates the body

Protein roles

some proteins speed up chemical reactions, while others play a role in defense, storage, transport, cellular communication, movement, or structural support

Catalyst

a chemical agent that selectively increases the rate of a reaction without being consumed by the reaction

Proteins are all constructed from the same set of

20 amino acids

Polypeptide

a polymer of many amino acids linked together by peptide bonds

• Polypeptides range in length from a few amino acids to 1,000 or more

  • One end of the polypeptide chain has a free amino group (the N-terminus of the polypeptide), while the opposite end has a free carboxyl group (the C-terminus)

Protein

a biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific three-dimensional structure

Amino acid

an organic molecule with both an amino group and a carboxyl group

• Serve as the monomers of polypeptides

Peptide bond

the covalent bond between the carboxyl group on one amino acid and the amino group on another, formed by a dehydration reaction

Protein structure

4 types of structure in final protein shape

• Primary structure

  • Order of letters in a long word

• Secondary structure

  • The result of H-bonds between the repeating constituents of the polypeptide backbone

    • Alpha helix or beta pleated sheets

• Tertiary structure

  • The overall shape of a polypeptide results from interactions between R groups, rather than interactions between backbone constituents

• Quaternary structure (only some proteins have this)

  • Two or more polypeptide chains forming subunits

Types of proteins:

Enzymatic proteins: selective acceleration of chemical reactions

Structural proteins: support

Storage proteins: storage of amino acids

Transport proteins: transport of other substances

Hormonal proteins: coordination of an organism’s activities

Receptor proteins: response of cell to chemical stimuli

Contractile and motor proteins: movement

Defensive proteins: protections against diseases

Sickle-cell-disease

a recessively inherited human blood disorder in which a single nucleotide change in the a-globin gene causes hemoglobin to aggregate, changing red blood cell shape and causing multiple symptoms in afflicted individuals

Denaturation

in proteins, a process in which a protein loses its native shape due to the disruption of weak chemical bonds and interactions, thereby becoming biologically inactive

• In DNA, the separation of the two strands of the double helix

• Denaturation occurs under extreme (noncellular) conditions of pH, salt concentration, or temperature

X-ray crystallography

a technique used to study the three-dimensional structure of molecules

• Depends on the diffraction of an X-ray beam by the individual atoms of the crystallized molecule

Gene

a discrete unit of hereditary information consisting of specific nucleotide sequence in DNA (or RNA, in some viruses)

Nucleic acid

a polymer (polynucleotide) consisting of many nucleotide monomers

• Serves as a blueprint for proteins and, through actions of proteins, for all cellular activities

Deoxyribonucleic acid (DNA)

a nucleic acid molecule, usually a double-stranded helix, in which each polynucleotide stand consists of nucleotide monomers with a deoxyribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and thymine (T)

• Capable of being replicated and determining the inherited structure of a cell’s proteins

Ribonucleic acid (RNA)

a type of nucleic acid consisting of a polynucleotide made up of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U)

• Usually single-stranded

• Functions in protein synthesis, gene regulation, and as the genome of some viruses

Gene expression

the process by which information encoded in DNA directs the synthesis of proteins or, in some cases, RNAs that are not translated into proteins and instead function as RNAs

Polynucleotide

a polymer consisting of many nucleotide monomers in a chain

• Can be nucleotides of RNA or DNA

Nucleotide

the building block of a nucleic acid, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and one to three phosphate groups

Pyrimidine

one of two types of nitrogenous bases found in nucleotides, characterized by a six-membered ring

• Cytosine, thymine, uracil

Purines

one of two types of nitrogenous bases found in nucleotides, characterized by a six-membered ring fused to a five-membered ring

• Adenine and guanine

Deoxyribose

the sugar component of DNA nucleotides, having one fewer hydroxyl group than ribose

Ribose

the sugar component of RNA nucleotides

Double helix

the form of native DNA, referring to its two adjacent antiparallel polynucleotide strands wound around an imaginary axis into a spiral shape

Antiparallel

referring to the arrangement of the sugar-phosphate backbones in a DNA double helix

Scanning electron microscope

a microscope that uses an electron beam to scan the surface of a sample, coated with metal atoms, to study details of its topography

• 3D image

Transmission electron microscope

a microscope that passes an electron beam through very thin sections stained with metal atoms and is primarily used to study the internal structure of cells

• 2D image

Centrifuge

a device that uses centrifugal force to subject a specimen to a specified constant force

All cells are bounded by a selective barrier, called the

plasma membrane (also referred to as the cell membrane)

Cytosol

the semifluid portion of the cytoplasm

Chromosomes

carry genes in the form of DNA

Ribosome

tiny complexes that make proteins according to instructions from the genes

Eukaryotic cell

a type of cell with a membrane-enclosed nucleus and membrane-enclosed organelles

• Ex: protists, plants, fungi, and animals (called eukaryotes)

Prokaryotic cell

a type of cell lacking a membrane-enclosed nucleus and membrane-enclosed organelles

• Ex: bacteria and archaea (called prokaryotes)

  • Some prokaryotes contain regions surrounded by proteins (not membranes), within which specific reactions take place

Nucleoid

a non-membrane enclosed region in a prokaryotic cell where its chromosome is located

Fimbriae

attachment structures on the surface of some prokaryotes

Glycocalyx

outer coating of many prokaryotes consisting of a capsule or slime layer

Cytoplasm

the contents of the cell bounded by the plasma membrane

• In eukaryotic cells, the portion exclusive of the nucleus

Eukaryotic cells are generally much larger than prokaryotic cells

• The smallest cells known are bacteria called mycoplasmas, which have diameters between 0.1 and 1.0 µm

  • Typical bacteria are 1–5 µm in diameter, about ten times the size of mycoplasmas

  • Eukaryotic cells are typically 10–100 µm in diameter

Plasma membrane

the membrane at the boundary of every cell that acts as a selective barrier, regulating the cell’s chemical composition

The need for a surface area large enough to accommodate the volume helps explain the microscopic size of most cells and the narrow, elongated shapes of others, such as nerve cells

Microvilli

tiny finger-like projections found on the surface of certain cells to increase the surface area of a cell

Plasmodesmata

tunnel like structure between two plant cells

• Transports stuff between cells

Nucleus

the organelle of a eukaryotic cell that contains the genetic material in the form of chromosomes, made up of chromatin

Nuclear envelope

the double membrane that surrounds the nucleus, perforated with pores that regulate traffic with the cytoplasm

• The outer membrane is continuous with the endoplasmic reticulum

  • The nuclear membrane is a double membrane

Nuclear lamina

a netlike array of protein filaments that lines the inner surface of the nuclear envelope and helps maintain the shape of the nucleus

Chromosomes

a cellular structure consisting of one DNA molecule and associated protein molecules

• A eukaryotic cell typically has multiple, linear chromosomes, which are located in the nucleus

• A prokaryotic cell often has a single, circular chromosome, which is found in the nucleoid, a region that is not enclosed by a membrane

Chromatin

the complex of DNA and proteins that makes up eukaryotic chromosomes

• When the cell is not dividing, chromatin exists in its dispersed form, as a mass of very long, thin fibers that are not visible with a light microscope

  • Typical human cell has 46 chromosomes; exceptions are the sex dells with 23

Nucleolus

a specialized structure in the nucleus, consisting of chromosomal regions containing ribosomal RNA genes along with ribosomal proteins imported from the cytoplasm

• Site of rRNA synthesis and ribosomal subunit activity

Ribosome

a complex of rRNA and protein molecules that functions as a site of protein synthesis in the cytoplasm

• Consists of a large and a small subunit

  • In eukaryotic cells, each subunit is assembled in the nucleolus

• Free ribosomes are suspended in the cytosol, bound ribosomes are attached to the outside of the endoplasmic reticulum or nuclear envelope

Free ribosome

• Suspended in the cytosol

• Most proteins created by free ribosomes function within the cytosol

Bound ribosome

• Bound/attached to the ER or nuclear envelope

• Generally make proteins destined for

  • insertion into membranes

  • packaging within certain organelles such as lysosomes

  • export from the cell (secretion)

Endomembrane system

the collection of membranes inside and surrounding a eukaryotic cell, related either through direct physical contact or by the transfer of membranous vesicles

• Includes the plasma membrane, nuclear envelope, smooth and rough endoplasmic reticulum, the golgi apparatus, lysosomes, vesicles, and vacuoles

  • This system carries out a variety of tasks in the cell, including synthesis of proteins, transport of proteins into membranes and organelles or out of the cell, metabolism and movement of lipids, and detoxification of poisons

Vesicles

a membranous sac in the cytoplasm of a eukaryotic cell

Endoplasmic reticulum (ER)

an extensive membranous network in eukaryotic cells, continuous with the outer nuclear membrane and composed of ribosome-studded (rough) and ribosome-free (smooth) regions

The ER membrane separates the internal compartment of the ER, called the ER lumen (cavity) or cisternal space, from the cytosol

Cisternae

a network of membranous tubules and sacs called that make up the ER

Smooth ER

the portion of the endoplasmic reticulum that is free of ribosomes

• Synthesis of lipids (oils, steroids[sex hormones], and new membrane phospholipids), metabolism of carbohydrates, detoxification of drugs and poisons, and storage of calcium ions( for muscle contraction)

Rough ER

the portion of the endoplasmic reticulum with ribosomes attached

• Has bound ribosomes, which secrete glycoproteins (proteins covalently bonded to carbohydrates)

• Distributes transport vesicles, secretory proteins surrounded by membranes

• Is a membrane factory for the cell

Glycoproteins

a protein with one or more covalently attached carbohydrates found in the plasma membrane

Transport vesicles

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

Golgi apparatus

an organelle in eukaryotic cells consisting of stacks of flat membranous sacs (cisternae) that modify, store, and route products of the endoplasmic reticulum and synthesize some products, notably non cellulose carbohydrates

• Warehouse for receiving, sorting, shipping, and even some manufacturing of macromolecules

  • Here, products of the ER, such as proteins, are modified and stored and then sent to other destinations

Products modified during their transit from the cis region to the trans region of the Golgi apparatus

Lysosome

a membrane-enclosed sac of hydrolytic enzymes found in the cytoplasm of animal cells and some protists

• Work best in acidic environments

  • If a lysosome breaks open or leaks its contents, the released enzymes are not very active because the cytosol has a near-neutral pH

  • Lysosomes also use their hydrolytic enzymes to recycle the cell’s own organic material, a process called autophagy

Phagocytosis

a type of endocytosis in which large particulate substances or small organisms are taken up by a cell

• Carried out by some protists and by certain immune cells of animals (in mammals, mainly macrophages, neutrophils, and dendritic cells

Autophagy

lysosomes use their hydrolytic enzymes to recycle the cell’s own organic material

Vacuoles

a membrane-bound vesicle whose specialized function varies in different kinds of cells

Food vacuole

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

Contractile vacuoles

a membranous sac that helps move excess water out of certain freshwater protists

Central vacuole

in a mature plant cell, a large membranous sac with diverse roles in growth, storage, and sequestration of toxic substances

Mitochondria

an organelle in eukaryotic cells that serves as the site of cellular respiration

• Uses oxygen to break down organic molecules and synthesizes ATP

  • Mitochondria are generally in the range of 1–10 µm long

Chloroplast

an organelle found in plants and photosynthetic protists that absorbs sunlight and uses it to drive the synthesis of organic compounds from carbon dioxide and water

• 3-6 µm in length

Endosymbiont theory

he theory that mitochondria and plastids, including chloroplasts, originated as prokaryotic cells engulfed by a host cell

• The engulfed cell and its host cell then evolved into a single organism

Organelles of the endomembrane system, mitochondria and typical chloroplasts have two membranes surrounding them as well as circular DNA & ribosomes

Crista

an infolding of the inner membrane of a mitochondrion

• The inner membrane houses electron transport chains and molecules of the enzyme catalyzing the synthesis of ATP

Mitochondrial matrix

the compartment of the mitochondrion enclosed by the inner membrane and containing enzymes and substrates for the citric acid cycle, as well as ribosomes and DNA

Thylakoids

a flattened, membranous sac inside a chloroplast

• Often exist in stacks called grana that are interconnected

  • Membranes contain molecular “machinery” used to convert light energy to chemical energy