Unit 1: Chemistry of Life (copy)

Topic 1.1 - Structure of Water and Hydrogen Bonds

The subcomponents of biological molecules and their sequence determine the properties of their molecules.

How does the structure and the elements water is made of influence its properties?

• Water is made out of 1 oxygen atom and 2 hydrogen atom
• Covalent bonds connect all 3, which results in electrons being shared. However, these bonds are polar as sharing occurs unequally, with oxygen getting more electrons. It results in oxygen being partially negative and hydrogen being partially positive
• This polarity results in ==hydrogen bonds== - weak bonds that occur between a positive and negative regions of two separate molecules.

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Describe hydrogen bonds influence water’s properties. Then describe why these properties are important for living systems.

• Cohesion
• Adhesion
• Surface Tension
• Capillary Action
• Density of Water
• High Specific Heat
• High Heat of Vaporization

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@@Interlude - Recalling Chemistry@@

Subatomic Particles

• Particles that make up an atom
  • Proton - positively charged +
  • Neutrons - no charge, neutral
  • Electrons - negatively charged -
• Protons and neutrons make up the nucleus of an atom.
• Electrons orbit the nucleus in the shells. Valence electrons are electrons found in the outer shell, they determine an elements chemical properties.

==Atom== - building blocks of life, they make up elements

==Elements== - a chemical substance that cannot be broken down to other substances

==Compounds== - chemical bonds between 2 or more elements

• These chemical bonds can include covalent bonds, ionic bonds, or hydrogen bonds
  • ==covalent bonds== - formed when electrons are shared
  • ==polar== - not equal sharing
  • ==nonpolar== - equal sharing

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Topic 1.2 - Elements of Life

Atoms and molecules from the environment are necessary to build new molecules. What elements are important to life, and why?

• Carbon (H), Hydrogen (H), Oxygen (O), Nitrogen (N), and Phosphorous (P). These elements help make up ==macromolecules== - large molecules that are important in biological processes
  • C, H, O make up carbohydrates, lipids, proteins, and nucleic acids
  • Nitrogen makes up nucleic acids and proteins. Phosphorous is also makes up nucleic acids.

Why Carbon is Important?

• Versatile bonding behavior - these atoms can be assembled and remodeled into different compounds, structures, etc.
• It can form up to 4 covalent bonds with other atoms

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Topic 1.3 - Introduction to Biological Molecules

Living systems are organized in a hierarchy of structural levels that interact. Its important to know what macromolecules are composed of, their monomers, and how they are composed. Moreover, its important to know why they are important. Before that, its important to know about processes that help with the creation of such macromolecules (and help break them down)

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==Monomer== - Molecules used as repeatable subunits to build larger molecules

==Polymer== - Larger molecules that are built from chains of monomers

==Dehydration Synthesis== - used to create biological molecules (water is an additional product)

==Hydrolysis== - used to break down biological molecules

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Topic 1.4 & 1.5 - Properties, Structure, and Function of Biological Molecules

The properties and functions biological molecules exhibit occur due to the way their structure or monomers, are assembled.

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Carbohydrates

^^Structure:^^

• Sugar molecules linked together
• Made up of CHO (1:2:1)

Monomer - ==Monosaccharides== (simple sugars)

• Ex. glucose, fructose, galactose
• 1 sugar molecule often glucose
• Used as an energy source

Bonds that Connect Monomer - glycosidic

==Disaccharides== - made up of two monosaccharides joined together (short polymers)

==Polysaccharides== - AKA complex carbs. Polymers of monosaccharides

• ==Starch== - a complex polysaccharide that helps plant store energy and provide sugar to animals
• ==Cellulose== - a polysaccharide that helps make up cell walls
• ==Glycogen== - through hydrolysis, this polysaccharide forms glucose

^^Purpose/Function?^^ Usually used for short-term energy

^^Ecological Origin and Role in Nature?^^ Formed by green plants during the process of photosynthesis. They serve as energy sources and as structural components in organisms (cellulose). Note, ribose is sugar and helps form nucleic acids

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Lipids

Made up of CHO

Monomer - ==Fatty acids & glycerol==

Bonds that Connect Monomer - ==Ester==

Major Classes of Lipids

• ^^Triglycerides^^
  • Made of glycerol and fatty acid chains
  • stores energy for the body
  • Helps store energy for the body
• ^^Phospholipids^^
  • Found in cell membranes
  • Protect cells against harmful substances
  • Consists of a glycerol molecule, two fatty acids, and a phosphate group
• ^^Sterols^^
  • Steroid hormones help with physiological functions such as growth, development, metabolism, homeostasis, and reproduction
  • Found in the blood

^^Purpose/Function?^^

• Long-term energy storage
• Water repellant in aquatic birds and mammals
• Structural component of cell membrane
• Precursors to hormones
• Insulation

^^Ecological Origin and Role in Nature? ^^Essential structural components of membranes, signaling molecules, long-term energy storage, and as chemical identifiers. They originate from biochemical subunits: ketoacyl and isoprene groups.

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Proteins

Made up of CHON

Monomer - ==Amino Acids==

Polymer - ==Polypeptides==, a linear chain of amino acids

Bonds that Connect Monomer - ==Peptide==

Amino Acid Structure

• An amine group (left)
• Carboxyl group (right)
• R group

^^Protein Structures^^

• Primary
  • The sequence of amino acids linked together to form a polypeptide chain
• Secondary
  • Hydrogen bonds between the amino and carboxyl groups of the amino acids
• Tertiary
  • Results in complex globular shape due to interactions between R groups
• Quaternary
  • Association of 2 or more proteins into one large protein

^^Purpose/Function?^^ Helps in all cellular processes. This can include:

• Structure
• Nutrition
• Enzymes
• Transport
• Communication
• Cellular Defense

==Activation Energy== - The minimum energy required for a reaction to occur

==Denature== - Protein changes shape and no longer functions properly

• Heat/Temperature, pH level changes, and chemicals can alter proteins

==Functional Groups== - A group of atoms responsible for the characteristic reactions of a particular compound

==Structural Proteins== - A protein that possesses a characteristic amino acid sequence or motif that repeats and forms a skeleton or contributes to properties of an organism, cell, or material

• help maintain shell shape
• shape skeletons
• mediate processes that are important for biological cells

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Nucleic Acid

Made up of CHONP

Monomer - ==Nucleotide==

Bonds that Connect Monomer - ==Phosphodiester==

^^Structure of a Nucleotide^^

• A phosphate group
• 5-carbon deoxyribose sugar
• A nitrogen base
  • Adenine
  • Thymine
  • Cytosine
  • Guanine

==DNA== - Deoxyribonucleic Acid

• A polymer made of repeating units of nucleotides

==RNA== - Ribonucleic Acid

• Codes for amino acid sequence which in turn codes for proteins

^^Chargeoff’s Rule^^ - The rule that in DNA there is always equality in quantity between A&T and C&G

^^Protein Synthesis^^ - Protein synthesis is the process in which cells make proteins. It occurs in two stages: transcription and translation. Transcription is the transfer of genetic instructions in DNA to mRNA in the nucleus

^^Purpose/Function?^^ DNA carries genetic information required to make proteins, reproduction, etc.

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