Chapter 5: The Structure and Function of Large Biological Molecules

About how much cellulose does a plant produce per year?

10^4 kg (100 billion tons)

Acidic Amino Acids Names

Aspartic acid (Asp, D) and Glutamic acid (Glu, E).

Acidic Side Chains are…

have negative charge due to presence of carboxyl group, which is usually dissociated (ionized) at cellular pH

Alpha carbon

Asymmetric carbon at the center of an amino acid

Alpha helix

Coil held together by hydrogen bonding between every 4th amino acid, each transthyretin polypeptide as only one helix region

Amino Acid

Monomer subunit of proteins.

Amino acid core structure

Central asymmetric carbon bonded to amino group, carboxyl group, hydrogen, and R group.

Amylopectin

A branched polysaccharide of glucose with 1-6 linkages at branch points, more complex form of starch

Amylose

The simplest form of starch, unbranched polymer of glucose.

Basic Amino Acids Names

Lysine, Arginine, Histidine

Basic Side Chains are…

Positively charged due to the presence of an amino group in the side chain.

Behavior of hydrophobic amino acids in tertiary structure

Cluster at the protein core away from water, held by van der Waals forces.

Beta pleated sheet

Two or more segments of the polypeptide chain lying side by side (beta strands) are connected by hydrogen bonds, make up the core of many globular proteins

Bilayer

Double layer of phospholipids, forming cell membranes.

Bioinformatics

Use of computer software and other computational tools that can handle and analyze these large data sets of genomes

Carbohydrate

Sugars or polymers of sugars, serving as fuel and building material, Most names for sugars end in -ose

Catalyst

Chemical agent that speeds up reactions without being consumed

Cellulose

Structural polysaccharide in plant cell walls; unbranched polymer of glucose with beta linkages.

Chitin

Structural polysaccharide found in arthropod exoskeletons and fungal cell walls, Carbohydrate with nitrogen attachments used in arthropod exoskeletons and fungal walls.

Cholesterol

Common steroid in animal cell membranes; precursor to other steroids and steroid hormone synthesis

Composition of arthropod exoskeletons

chitin embedded in a layer of proteins

Condensation Reaction

Connects monomers or polymers, covalently bonding two molecules with loss of a small molecule.

Dehydration Reaction

A condensation reaction where a water molecule is lost during synthesis.

Denaturation

pH, salt concentration, temperature, or other aspects of its environment are altered, weak interactions may be destroyed, Especially after transfer from aqueous environment to nonpolar solvent

Deoxyribose

The sugar found in DNA

Dietary benefit of indigestible cellulose

Aids digestion by stimulating mucus secretion and promoting passage through the digestive tract.

Disaccharide

Double sugar, consisting of two monosaccharides joined by glycosidic linkages, Must be broken down into monosaccharides to be used for energy

Disulfide bridge

Covalent bond between two cysteine monomers

DNA

Deoxyribonucleic acid; stores genetic information.

DNA Sequencing

Determining the sequence of nucleotides along a DNA strand

Does cellulose have alpha or beta linkages?

All beta linkages but each monomer is alternatively upside down

Does starch have alpha or beta linkages?

Starch has alpha linkages.

Double Helix

Structure of DNA, two polynucleotide strands wound around each other.

Enzyme

Specialized macromolecule that speeds up chemical reactions, Regulate metabolism by acting like catalysts Can perform its function over and over again, facilitate breakdown of polymers

Ester Linkage

Bond formed between glycerol and fatty acids in fats via dehydration, A hydroxyl group (–OH) from a carboxylic acid joins with a hydrogen (–H) from an alcohol

Examples of proteins with quaternary structure

Hemoglobin and collagen are examples of proteins with quaternary structure.

Fat

Energy storage, a gram of this stores more energy than gram of polysaccharide, Consists of a glycerol molecule connected to three fatty acids

Fatty Acid

Long carbon skeleton with a carboxyl group; building block of fats, made of a long hydrocarbon skeleton with a carboxyl group at one end.

Fructose

Isomer of glucose, a ketose sugar, monosaccharide.

Functions of a Protein

Catalysis, defense, storage, transport, cellular communication, movement, and structure.

Galactose

A six-carbon monosaccharide, an isomer of glucose as differs in placement of parts around asymmetric carbon, found in lactose.

Gene

A segment of DNA that codes for a functional product, usually a protein, consist of DNA and programs sequence of amino acids

Genome

The entire sequence of the full complement of DNA

Genomics

Look at problems by analyzing large sets of genes or even comparing whole genomes of different species

Glucose

A six-carbon monosaccharide; the primary energy source for cells, Has carbonyl group, and multiple hydroxyl groups, aldose sugar

Glucose Formula

The molecular formula for glucose is C6H12O6.

Glycerol

An alcohol with three carbons to which fatty acids are covalently bonded to make fats and oils, each with a hydroxyl group; part of fats and phospholipids.

Glycogen

Polymer of glucose, extensively branched, stored in animal liver and muscle cells.

Glycosidic Linkage

Covalent bond formed between two monosaccharides by a dehydration reaction.

Hexoses

Sugars with six carbons in their carbon skeleton, like glucose and fructose.

How arthropod exoskeletons harden

Chitin is embedded in a layer of proteins; then, proteins link or calcium carbonate encrusts it.

How do vertebrates use glycogen?

Vertebrates store glycogen mainly in liver and muscle cells for energy, breakdown of glycogen in these cells releases glucose when the demand for energy increases

How does the α helix compare in globular and fibrous proteins?

In globular proteins, α helices are short, while in fibrous proteins, they are long, Other globular proteins have multiple stretches of this separated by nonhelical regions Some fibrous proteins, have this formation over most of their length

Hydrocarbon Chains of Saturated Fatty Acids

Lack double bonds, allowing tight packing and solid state at room temperature, their flexibility allows the fat molecules to pack together tightly

Hydrolysis

Bond between monomers is broken by the addition of a water molecule, hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other

Hydrophilic

Tending to attract water; characteristic of polar molecules.

Hydrophobic

Tending to repel water; characteristic of lipids.

Hydroxyl group position on glucose C1 ring

Alpha glucose has hydroxyl on C1 below the ring plane; Beta glucose has it above, above or below the plane of the ring.

Interactions stabilizing tertiary structure

Hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges, Hydrogen bonds between polar side chains and ionic bonds between charged side chains.

Key characteristic of all lipids

They are hydrophobic, consisting mostly of nonpolar C-H hydrocarbon regions.

Lactose

A disaccharide composed of glucose and galactose; broken down by lactase.

Lactose Intolerant

Humans lack lactase, enzyme to break lactose Sugar instead broken down by intestinal bacteria, causing gas and cramping Avoided by taking the enzyme lactase

Lipid

Diverse group of hydrophobic molecules, mostly nonpolar.

Macromolecule

Large, complex molecule made of polymers; e.g., carbohydrates, proteins, nucleic acids.

Maltose

A disaccharide formed by linking two glucose molecules via a glycosidic linkage.

Microfibril

Bundles of cellulose molecules held together by hydrogen bonds, forming structural units in plant cell walls.

Monomer

Bundles of cellulose molecules held together by hydrogen bonds, forming structural units in plant cell walls.

Monosaccharide

Simplest carbohydrate or sugar; a monomer from which more complex carbohydrates are built.

Monosaccharide Formula

CnH2nOn, where n is a multiple of 3 to 7.

mRNA

Carries genetic information from DNA to ribosomes for protein synthesis, Information given by DNA can direct protein synthesis Prokaryotic cells lack nuclei but still use mRNA to convey a message from the DNA to ribosomes

Nitrogenous Base

Each nitrogenous base has one or two rings Called bases because nitrogen atoms tend to take up H+ from solution

Nonpolar Amino Acids Names

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline.

Nonpolar Side Chains are…

Hydrophobic; these amino acids tend to cluster in the protein's core.

Nucleic Acid

Store, transmit, and help express hereditary information, Polymers made of nucleotide monomers Types: DNA and RNA

Nucleoside

A nucleotide without any phosphate groups

Nucleotide

Monomer subunit of nucleic acids, consisting of a sugar, phosphate, and nitrogenous base.

Nucleotide Parts

A sugar (pentose), one to three phosphate groups, and nitrogenous base.

Pentoses

Sugars with five carbons, forming part of nucleic acids.

Peptide Bond

Amino group of one amino acid to carboxyl of other can become connected through dehydration reaction

Phosphodiester linkage

Covalent bond joining adjacent nucleotides in a polynucleotide

Phospholipid

Molecule with two fatty acids and a phosphate group attached to glycerol; forms cell membranes.

Phospholipid structure

Two fatty acids and a phosphate group attached to glycerol; has hydrophilic head and hydrophobic tails.

Polar Amino Acids Names

Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Tyrosine (Tyr, Y), Asparagine (Asn, N), Glutamine (Gln, Q).

Polar Side Chains are

Hydrophilic amino acid side chains that have a partial positive or negative charge.

Polymer

Long molecule consisting of many similar/identical building blocks linked by covalent bonds.

Polynucleotide

Polymer of nucleotides that makes up nucleic acids, Linkage requires condensation reaction Adjacent nucleotides are joined by a phosphodiester linkage

Polynucleotides Beginning Monomer

A nucleotide with three phosphate groups, losing two during polymerization.

Polynucleotides Ends

One end has a phosphate on the 5' carbon, the other has a hydroxyl on the 3' carbon, we refer to these as the 5' end and the 3' end

Polypeptide

Polymer of amino acids linked by peptide bonds.

Polysaccharide

Carbohydrate macromolecule composed of many monosaccharides joined by glycosidic linkages, Function is determined by its monosaccharides and by the positions of its glycosidic linkages

Primary structure

The specific sequence of amino acids in a polypeptide, Determined by inherited genetic information Dictates secondary structure due to chemical nature of backbone and interactions of the side chains

Protein

Include a diversity of structures, resulting in a range of functions.

Protein definition

Biologically functional molecule made of one or more polypeptides, folded into a specific 3D structure, constructed from 20 amino acids

Proteomics

Study of the full set of proteins and their properties.

Purine

Nitrogenous base with a 6-membered ring fused to a 5-membered ring (Adenine, Guanine)

Pyrimidine

Nitrogenous base with one 6-membered ring of carbon/nitrogen atoms (Cytosine, Thymine, Uracil)

Quaternary structure

Functional macromolecule composed of two or more polypeptide chains

R group

The side chain of an amino acid that determines its properties

Ribose

The sugar found in RNA

RNA

Ribonucleic acid; involved in protein synthesis and gene regulation.