Biology Chapter 3 Review

The Chemical Building Blocks of Life

Four major classes of biomolecules (macromolecules)

• Carboydrates

• Proteins

• Nuleic Acids

• Lipids

Organic molecules

Carbon-based compounds that usually contain carbon-hydrogen bonds and form the structural and functional foundation of all living organisms

• Can also have nitrogen or oxygen

What are macromolecules made of?

Macromolecules are made of polymers

Macromolecules

A large, organic, carbon-based molecule built from smaller repeating subunits called monomers

• Four primary classes of biological macromolecules are carbohydrates, lipids, proteins, and nucleic acids

Polymers

A large macromolecule formed by linking many smaller, repeating single subunits called monomers together via strong covalent bonds

• Monomers can be the same or different

• Linear polymers

• Branched polymers

How are polymers formed?

Monomers are linked together by covalent bonds to form polymers

Dehydration synthesis: two monomers are linked to form a dimer

A water molecule is formed as the two monomers are linked by a covalent bond

Dehydration synthesis

A chemical reaction that joins smaller sub-units called monomers together to build larger polymers by removing a molecule of water

• Ex; two molecules of glucose are linked to form the disaccharide maltose and a water molecule is released in the process

Hydrolysis

A chemical reaction that uses water to break the covalent bonds holding polymers together, splitting them into smaller monomers

• Breaking polymers into monomers

• Water is needed; one monomer recieves an H and the other recieves OH

• Reverse of dehydration synthesis

Dimer

A macromolecule formed when two identical or similar subunits (monomers) bind together through chemical bonds.

Enzymes

Protein molecules that catalyze or “speed up” chemical reactions in living cells by lowering the required activation energy

• Speed up hydrolysis and dehydration reactions

• Dehydration reactions form new bonds/require energy

• Hydrolysis reactions break bonds/release energy

Macromolecule enzymes

Specific enzymes exist for each type of macromolecule

• Carbohydrates: broken down by amylase, sucrase, lactase, maltase

• Lipids: lipases

• Proteins: pepsin and peptidase

Carbohydrates

Organic macromolecules made of carbon, hydrogen, and oxygen that function in short-term energy storage, cellular fuel, and structural support

• Macromolecule (biomolecule) found in grains, fruits, and vegetables

• Provide quick energy

• Have the general formula (CH2O)n

• Ratio of Carbon: Hydrogen: Oxygen is 1:2:1

Types of carbohydrates

1. Monosaccharides

2. Disaccharides

3. Polysaccharides

Monosaccharides

The simplest, single-unit carbohydrate monomers that act as the building blocks for larger, more complex sugars

• Have 3-7 carbons

• End with -ose (indicates sugar)

• Contain a carbonyl group (C=O)

• Ex; glucose, galactose, fructose

Aldoses

A type of monosaccharide (simple sugar) that contains a carbonyl group (C=O) located at the end of its carbon chain

• Glucose: an aldose

Ketoses

A monosaccharide (simple sugar) that contains exactly one carbonyl group (C=O) located in the middle of the carbon chain

• Its carbonyl group (C=O) is located on an internal carbon atom, typically the second carbon in the chain

• Fructose: a ketose

Types of monosaccharides

Monosaccharides are simple sugars classified by their number of carbon atoms and their functional group (type of carbonyl group- aldose or ketose?)

• Trioses: three carbons

• Pentoses: five carbons

• Hexoses: six carbons

Monosaccharide isomers

formula (C6 H12 O6)

1. Glucose - important source of energy

2. Galactose - part of lactose/milk sugar

3. Fructose - part of sucrose/fruit

• Molecules that share the exact same molecular formula but have different structural arrangements of atoms

Monosaccharides can be linear or ring-shaped molecules

Monosaccharides exist in equilibrium between linear and ring forms

• In ring form OH can be in α or β position

• In aqueous solutions mostly in ring form

• Fructose and ribose also form rings

Disaccharide formation

Form when two monosaccharides are linked in a dehydration reaction

• Ex; Glucose + Fructose = Sucrose (disaccharide)

• Two monomers are joined by glycosidic bond

• Water is released

• Glycosidic linkage is formed between carbon 1 in glucose and carbon 2 in fructose

• Results in 1,2 glycosidic linkage

Glycosidic bond/linkage

A covalent chemical bond that joins a carbohydrate (sugar) molecule to another group or sugar molecule, formed by a dehydration reaction

Other common disaccharides

• Maltose (grain sugar)

• Lactose (milk sugar)

• Sucrose (table sugar)

• All created by covalent glycosidic linkages

Polysaccharides

Long chain of monosaccharides joined together by covalent glycosidic linkages via dehydration synthesis

• Can be branched or unbranched

• May consist of single or multiple types of monosaccharides

• Very large molecule: molecular weight > 10,000 daltons

Plant monomers/polymers

• Monomers: glucose

• Polymers: starch, cellulose

Animal monomers/polymers

• Monomer: glucose

• Polymer: glycogen

Starch

A complex carbohydrate (polysaccharide) made of alpha (α) glucose monomers linked by covalent glycosidic bonds, which serves as the primary energy storage molecule in plants

• Is composed of amylose and amylopectin

• The monomers are joined in two linkage types
  1. α 1-4 glycosidic bonds
  2. α 1-6 glycosidic bonds

Cellulose

A structural polysaccharide (a complex carbohydrate) that makes up the tough cell walls of plants, providing structural support and rigidity

• Glucose monomer in unbranched chains by β 1-4 glycosidic linkages

• Every glucose monomer is flipped relative to the next one resulting in a linear, fibrous structure

Chitin

A structural polysaccharide made up of modified glucose monomers containing nitrogen

• It serves as a durable, rigid macromolecule used by specific organisms for protection and support

Lipids

A diverse group of organic macromolecules composed primarily of carbon, hydrogen, and oxygen that are grouped together because they are nonpolar and hydrophobic ("water-fearing")

• Non-polar hydrocarbons are hydrophobic

Function of lipids

• Long term energy stores

• Provide insulation for plants and animals

• Building blocks for some hormones

• Component of cellular membranes

Types of lipids

• Fats

• Oils

• Waxes

• Phospholipids

• Steroids

Triglyceride

A fat molecule (or triglyceride) is a type of lipid molecule made of one glycerol molecule joined to three fatty acid tails

Fats - contain two main components

1. Glycerol

2. Fatty acids

• Triacylglycerol – formed by joining three fatty acids to a
  glycerol backbone

• The glycerol molecules are attached to the fatty acids

Saturated fatty acids

Long hydrocarbon chains with no carbon-carbon double bonds, meaning every carbon atom is fully "saturated" with hydrogen atoms

• Solids at room temperature (butter, meat fat)

• Packed tightly

• Linked to cardiovascular disease

• High melting point

Unsaturated fatty acids

Have at least one carbon-carbon double bond

• Monounsaturated fat = one double bond

• Polyunsaturated fat = more than one double bond

• Liquid lipids at room temperature are classified as oils

• Not as packed: liquid

• Low melting point

Unsaturated fatty acid configurations

Each double bond of an unsaturated fat may be in one of two positions

• Cis configuration: H on same side

• Trans configuration: H on opposite side

Cis fatty acids

An unsaturated fatty acid where the adjacent hydrogen atoms are on the same side of the carbon-carbon double bond

• They cannot be packed tightly

• Liquid at room temp

• Are bent

Trans fatty acids

Unsaturated fats that contain a carbon-carbon double bond with hydrogen atoms on opposite sides of the chain

• Artificially made; pack tight

• Foods with trans fat increase LDL cholesterol in humans (bad for heart)

• Not bent

Essential fatty acids

Essential fatty acids – required but not synthesized by our body
– must be part of diet

• There fats are heart healthy

• Omega-3 fatty acid (found in salmon, trout, tuna)

Waxes

Long fatty acid chains into long chain alcohols

• a type of lipid made of long-chain fatty acids linked to long-chain alcohols by an ester bond

• Hydrophobic and prevent water from sticking to surface

• Ex; found on the feathers of some birds and on the surface of leaves from some plants

Phospholipids

An amphipathic lipid molecule made of a glycerol backbone, a polar phosphate head group, and two nonpolar fatty acid tails

Phospholipids are major parts of the cell membrane

• The hydrophillic head face the aqueous solution

• The hydrophobic tails are in the middle of the bilayer

• Phospholipids contribute to dynamic nature of plasma membrane

Steroids

Have a closed ring structure

• Four linked carbon rings

• Many have a short tail

• Structure is different from that of other lipids

Steroid key details

1. They are hydrophobic

2. They are insoluble in water

• Cholesterol is the most common steroid

• Synthesized in liver

• Precursor to other hormones such as testosterone and estradiol

• Precursor to vitamin D

Proteins

Peptide bonds link amino acids together to form chains called peptides, polypeptides, and proteins

Most abundant organic molecules

Very diverse range of functions

• Regulatory functions

• Structural functions

• Protective functions

• Transport

• Enzymes

• Toxins

Enzymes

Biological catalysts, typically proteins, that speed up chemical reactions in living cells by lowering the activation energy required for the reaction to proceed

• Specific enzyme for specific substrate

Catabolic enzyme

A biological catalyst that speeds up the breakdown of large, complex molecules into smaller, simpler ones while releasing energy

• Breakdown substrates

• Exergonic reaction

Anabolic enzyme

A biological catalyst that speeds up reactions which build larger, complex molecules from smaller building blocks

• Build more complex molecules

• Endergonic: require an input of energy

Catalytic enzyme

Affect the rate of reaction

• a biological molecule—usually a protein—that speeds up chemical reactions in living things without being used up or changed

Digestive enzymes

Help in digestion of food by catabolizing nutrients into monomeric units

• Ex; amylase, lipase, pepsin, trypsin

Transport proteins

Carry substances in the blood or lymph throughout the body

• Ex: hemoglobin, albumin

Structural proteins

Construct different structures, like the cytoskeleton

• Ex: Actin, tubulin, keratin

Hormones

Coordinate the activity of different body systems

• Ex: Insulin, thyroxine

Defense proteins

Protect the body from foreign pathogens

• Ex: Immunoglobulins

Contractile proteins

Effect muscle contraction

• Ex: actin, myosin

Storage proteins

Provide nourishment in early development of the embryo and the seedling

• Ex: Egg white (albumin)

Amino acids

The monomers that make up proteins

Structure

• Central carbon atom (α-carbon)

• Amino group (-NH2)

• Carboxyl group (-COOH)

• Hydrogen

• Side chain (R-group)

Amino acids have diverse chemical properties

20 common amino acids found in proteins

Each amino acid has a different R group-

R-groups determine the chemical nature of each amino
acid

• Nonpolar aliphatic-

• Polar

• Positively charged

• Negatively charged

• Nonpolar aromatic

More on amino acids

Amino acids are represented by a single upper-case letter or three letters

• Valine = V or Val

• Aspartic Acid = D or Asp

Essential amino acids

Must be supplied in diet for humans

• Isoleucine

• leucine

• cysteine

Peptide bond formation

Amino acid monomers are linked by peptide bonds (formed through dehydration reaction)

• The carboxyl group (–COOH) of one amino acid reacts with the amino group (–NH₂) of another amino acid

• A water molecule is released

Peptide bond

A covalent chemical bond that links two amino acids together to form the primary backbone of a protein

• Formed through dehydration synthesis

Polypeptide

A linear polymer chain of amino acids linked together by covalent peptide bonds

• a linear polymer chain of amino acids linked together by covalent peptide bonds. It serves as the primary structural building block that folds into a functional protein

Protein

Large, complex biological macromolecules made of one or more linear chains of amino acids called polypeptides that fold into specific three-dimensional shapes

• Has a unique structure and function

Protein shape is crucial to its function

The sequence and number of amino acids determine protein shape, size and function

Four levels of protein structure

1. Primary structure

2. Secondary structure

3. Tertiary structure

4. Quarternary structure

Primary protein structure

The specific, linear sequence of amino acids in a polypeptide chain held together by covalent peptide bonds

• Protein function can be affected if the order of amino acids changes

• The amino acid sequence is completely specific to a given protein and defines its unique identity

Primary structure

• Amino acid sequence is encoded by genes

• A change in the nucleotide seuqence of DNA could lead to a change in amino acid

• This could lead to a change in protein structure and function

• Ex; a single amino acid change causes sickle cell disease

Secondary protein structure

The local folding of a polypeptide backbone into repeating 3D shapes, stabilized by hydrogen bonds between the backbone atoms

1. α-helix: formed by hydrogen bond between oxygen in
   carbonyl group and an amino acid 4 positions down the chain

2. β-pleated sheet: hydrogen bonding between atoms on the backbone of the polypeptide chain: a type of protein secondary structure where parts of a polypeptide chain lie side by side and connect through hydrogen bonds, creating a folded, sheet-like shape

Graphic representation of secondary protein structure

α-helix and β-pleated sheet are secondary structures of proteins

form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone

• Certain amino acids tend to form an α-helix

• Others amino acid favor formation of β-pleated sheet

What determines the tertiary structure of a protein?

The overall three-dimensional shape of a single polypeptide chain, created when secondary structures fold further due to interactions between amino acid R-groups (side chains)

Tertiary structure of proteins is determined by a variety of
chemical interactions

• hydrophobic interactions

• ionic bonding

• hydrogen bonding

• disulfide linkages

Tertiary protein structure

The overall three-dimensional shape of a single polypeptide chain, created when secondary structures fold further due to interactions between amino acid R-groups (side chains)

• R-groups with like charges are repelled from one another

• R-groups that are hydrophobic will cluster in interior of protein

• Cysteine side chains form disulfide bridges: a strong covalent bond that forms between the sulfur atoms of two cysteine amino acid side chains

What is the tertiary structure?

The overall three-dimensional shape of a single polypeptide chain, created when secondary structures fold further due to interactions between amino acid R-groups (side chains)

• The unique three-dimensional structure of a protein

• Due to chemical interactions between R-groups on amino acids

Quarternary protein structure

The final, highest level of protein organization formed when two or more separate folded polypeptide chains (called subunits) join together to create a single, fully functional protein complex

Interactions between several polypeptides that make up a protein

• Weak interactions between subunits help stabilize the structure

• The assembly of multiple polypeptide chains (subunits) into a single functional complex

Denaturation

When a protein loses its normal three-dimensional shape because changes in temperature, pH, or chemicals break the weak bonds holding it together

• Changes in protein structure that leads to changes in function

Denaturation / protein folding

Protein structure and shape can be changed if chemical interactions are broken

Protein structure/shape can change with altering primary structure due to:

• Changes in pH

• Changes in temperature

• Ex; Heating an egg to extreme temperatures can lead to irreversible denaturation of egg protein (albumin in egg goes from liquid to solid)

Nucleic acids

A biological macromolecule made of repeating monomer units called nucleotides that stores, transmits, and expresses genetic information in living systems

Two types

• Deoxyribonucleic acid (DNA)

• Ribonucleic acid (RNA)

Where are nucleic acids located?

• Nucleus of eukaryotic cells

• Mitochondria

• Chloroplasts

• Prokaryotic cells (bacteria)

Roles of DNA in the cell

• DNA codes for the entire genetic content (genome)

• Chromatin

• Chromosomes

DNA codes for thousands of genes

• Genes contain instructions for producing proteins or
  various forms of RNA

• DNA controls all cellular activities by turning genes on or
  off

Chromatin

A complex mass of DNA and histone proteins located in the nucleus of a eukaryotic cell that packs genetic material into a compact, organized form

Chromosomes

A thread-like structure made of a single long DNA molecule tightly coiled around proteins called histones, which carries genetic information (genes)

Roles of RNA in the cell

RNA is primarily involved in protein synthesis

Nucleotides

Are the monomers of DNA and RNA

Consist of three parts

1. Nitrogenous base

2. Pentose sugar

3. Phosphate groups

DNA exhibits a double helix structure

• The sugar and phosphate lie on outside of helix

• Nitrogenous bases are stacked in the interior

• The strands of the helix run in opposite directions (anti-paralel orientation)

• Each base from one strand interacts by hydrogen bonding with a base from the opposing strand

Base-pairing in DNA

DNA - the two strands run antiparallel to one another

• Adenine forms hydrogen bonds with thymine: A-T

• guanine base pairs with cytosine: G-C

Are all polymers made of the same monomer?

No, not all polymers are made of the same monomer

What do dehydration reactions need/release?

Dehydration reactions need:

1. -H molecule

2. -OH molecule

Dehydration reactions release: a water molecule (H2O)

What are three characteristics of monosaccharides?

• Have 3-7 carbons

• End with -ose

• Contain a carbonyl group (C=O)

What are disaccharides joined by?

All disaccharides are joined by covalent glycosidic bonds

What are the monomers of carbohydrates?

Monosaccharides

• Ex: glucose, fructose, galactose

What is the link between two sugar (monosaccharide) molecules called?

A glycosidic bond

• Covalent bond that joins a carbohydrate (sugar) molecule to another group or molecule, such as another monosaccharide

• Formed through dehydration synthesis

Common disaccharides

• Sucrose

• Lactose

• Maltose

Starch

A storage polysaccharide made of glucose monomers linked by α-1,4 and α-1,6 glycosidic bonds, serving as the primary energy storage molecule in plants

• Ex: potatoes, wheat, rice

Cellulose

A structural polysaccharide that makes up the tough cell walls surrounding plant cells, providing them with shape and rigidity

• Most abundant carbohydrate; insoluble

• Cows & sheep can digest it: cellulose- digesting bacteria

• beta monomers

Glycogen

A highly branched polysaccharide polymer made of glucose monomers that animals use to store extra energy

• energy source in animal tissue

• Stored in liver & muscle cells

Two components of fat and which one is hydrophobic:

A fat (triglyceride) molecule is made of glycerol and fatty acids, and the fatty acid tails are the hydrophobic components

• An isolated glycerol molecule is hydrophilic (water-loving), but when it is bound inside a fat molecule like a triglyceride, it behaves as part of a hydrophobic structure

What is the difference between saturated and unsaturated fatty acids?

Saturated fatty acids have only single carbon-carbon bonds and are full of hydrogen atoms, while unsaturated fatty acids have at least one double carbon-carbon bond which creates a bend

What are steroids and their function?

A type of lipid molecule characterized by a core chemical structure of four fused carbon rings

• Membrane Fluidity (Cholesterol): Cholesterol embeds itself in animal cell plasma membranes. It acts as a fluidity buffer

• Cholesterol serves as the vital starting material or precursor used to synthesize important steroid hormones, including testosterone, estrogen, progesterone, and cortisol

• Cell Signaling and Gene Expression

The three main functional groups of amino acids:

• Amino group (-NH2)

• Carboxyl group (-COOH)

• R-group (Side chain): a unique chemical group that gives each specific amino acid its distinct size, charge, and function

R-group

The variable chemical group attached to the central carbon of an amino acid that determines its unique identity, chemical properties, and behavior

R-groups can be:
• Nonpolar (hydrophobic)
• Polar
• Positive charged
• Negative charged
• Nonpolar aromatic (rings)

Differences between DNA and RNA: (bases, sugars, number of strands)

Sugars:

• DNA uses deoxyribose, which lacks one oxygen atom on the second carbon (2'-H)

• RNA uses ribose, which has a full hydroxyl group (-OH) on the second carbon

Nitrogenous Bases:

• DNA contains Adenine (A), Cytosine (C), Guanine (G), and Thymine (T)

• RNA contains uracil (U) instead of thymine

Number of Strands:

• DNA is typically double-stranded, forming an antiparallel double helix that protects genetic information

• RNA is typically single-stranded, allowing it to fold into various shapes for protein synthesis (such as mRNA, tRNA, and rRNA)