Chapter 2: Biological Chemistry Flashcards by Phuoc Tran

Atom is

The basic unit of matter

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Proton

Positive charge (+), having mass

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Neutron

Neutral (no charge), having mass

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Electron

Negative charge (-), essentially no mass

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Element

The substance that cannot be chemically broken down into any other substance
1) Ex: hydrogen (H), oxygen (O)
2) Life requires ~ 25 elements
3) Your body is almost entirely composed of 10 elements (Nitrogen-fixing bacteria)
4) 15 are trace elements, those found in very small concentration

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Electron Shells (Level max)

1) Max 2 electrons on the inner shell
2) Max 8 electrons in the outermost shell

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Octet rule

Atoms will gain or shed electrons to attain a full outermost shell

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Atoms that lose or gain electrons become

Ions (charged atoms)

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Molecules

Two or more atoms held together

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Compound

A molecule containing two or more elements

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Covalent bonds

Sharing of electrons

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Ionic bonds

Attraction of charges

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Hydrogen bonds

1) Weak bonds that form between Hydrogen and other polar molecules
2) Weaker than ionic or covalent bonds
3) Hydrogen bonds cause many unusual properties and characteristics

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Water is

an excellent solvent because it is polar

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Hydrophilic molecules (water-loving) are

Polar & form hydrogen bonds; they are water-soluble

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Hydrophobic molecules (water-hating) are

Non-polar & do not bond with water, and they are not water soluble

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Solutions are formed when

Solutes are dissolved in solvents

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If the solute increases H+ (hydrogen ion) it is an

Acids

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If the solute reduces H+ it is a

Base

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Rigid, crystalline structure as

Solid

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As a liquid, H-bonds constantly break & form, pulling molecules in

More closely

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Liquid water is

More dense than solid water

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Ice floats, preventing what?

Bodies of water from freezing solid

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The high specific heat energy is required to

Change temperature

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Oceans store solar heat without

Large temperature changes

Oceans without temperature changes include:

1) Mild coastal climates 2) Life exists within a small temperature window

Also allows evaporative cooling

Aka sweating

Cohesion

1) "Gripping" of other water molecules via H-bonds 2) Makes it difficult to separate

Adhesion

1) "Gripping" of substances 2) Allows water transport against gravity

Surface tension

1) Difficulting of breaking the surface 2) Animal can walks in water

Macromolecules (Polymer)

Large molecules

Macromolecules (Monomers)

Composed of chains of monomers

Major macromolecule groups:

1) Carbohydrates 2) Proteins 3) Nucleic acids

Lipids aren't macromolecules or polymers, but are necessary for, what?

For life

Lipids aren't macromolecules or polymers, but are necessary for, what?

For life

Carbohydrates - Typically consist of C, H, and O

C-H bonds are easily broken to release energy

Carbohydrates function

1) Fuel (energy source) for cellular functions 2) Flexible uses: immediate use, storage 3) Support cell structures (building materials)

Simple (monosaccharides ) or, what else?

Complex (polysaccharides)

Non-food structure roles

1) Chitin (the reason bugs and other invertebrates are crunchy) 2) Cellulose (plant cell walls) aka "fiber"

Indigestible by most animals

Require microbes to chemically break down

Lipids

Not formed from polymers 1) Unlike carbs, no distinct monomers 2) Categorized by behavior: Always hydrophobic (oily or greasy)

Lipids including:

1) Fats 2) Sterols 3) Phospholipids

Structure of Fat

All fats have a head + 2 or 3 tails

Fat head =

glycerol

Fat tails =

fatty acids

2 tails =

diglyceride

3 tails =

Triglyceride

Uses of Fats Energy storage:

A molecule of fat has more than twice the energy of a molecule of carb or protein

Uses of Fats Examples:

1) Blubber 2) Adipose tissue

Uses of Fats because of the energy

Humans crave fats (milk)

Types of Fats

Two different types: 1) Saturated fat 2) Unsaturated fat

Saturated fat

Fatty acids filled with H

Unsaturated fat

Have one or more double bonds that cause kinks

Anything that is partly hydrogenated has

Unsaturated fat with H added to it to improve the texture

AKA trans fat

Increase bad cholesterol production; decrease good cholesterol

Sterols

1) Crucial to growth & development 2) Modification of a basic 4-carbon ring structure 3) Cholesterol at high blood concentrations can attach to vessel walls, thickening or blocking 4) Necessary to form sex hormones

Phospholipids

1) Necessary to form cell membranes 2) Similar in structure to fats, but have an extra phosphorus group on the glycerol head & 2 tails

Proteins

1) 50% of cellular dry weight 2) Uses: 1. Structural support 2. Storage 3. Transport 4. Signaling (hormones) 5. Movement 6. Defense against the foreign substance 7. Enzymes

Protein structure

Made of amino acids (AAs) 1) Organic molecules with a carboxyl and amino group + varying functional group 2) 20 AAs make up all proteins connected by covalent peptide bonds

The Importance of Shape

For proteins to work, need the correct shape

Denaturation

A protein loses its 3D structure

Primary structure

AA sequence (order)

Secondary structure

H-bond patterns

Tertiary structure

Bending/folding

Quaternary structure

Subunits

Proteins structure is determined by

Genes, which are nucleic acids

Store information

Blueprint

Nucleic acids are composed of

Monomers known as nucleotides

Nucleic Acids (two types):

1) Deoxyribonucleic acids (DNA) 2) Ribonucleic acids (RNA)

Nucleic Acid Structure

Composed of sugar-phosphate backbone plus nitrogen-containing bases

Nucleic Acid Structure information is stored by

1) Varying the sequence of bases 2) Bases in DNA: 1. Adenine (A) 2. Thymine (T) 3. Guanine (G) 4. Cytosine (C)

DNA

1) Has a double helix structure (2 strands twisted together) 2) Held together by base-pair bonds (A-T and C-G)

Strands are complementary:

The sequence is predictable between one strand and the other

RNA

Differences between DNA/RNA

1) RNA is a single strand 2) Extra oxygen on backbone 3) Exchanges T with U (Uracil)

Lots of monosaccharides

++ Orange/red

Some of the monosaccharides

+ Yellow/green

No monosaccharides

- Blue

Positive starch

+ Blue/black

Negative starch

- Yellowish

Positive protein (peptide bonds)

+ Violet

Negative protein (peptide bonds)

- Blue

Positive fat

+ Bright/orange

Negative fat

- Dull red