Topic 2: Chemical Principles

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96 Terms

1

What is an atom?

smallest chem. unit of matter which can partake in a chemical reaction

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2

What is an element? State some examples.

matter composed of one type of atom

ex: carbon (C), nitrogen (N), oxygen (O), sodium (Na)

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What is a molecule?

two or more atoms combined

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4

What are the diff. types of molecules?

  • either same type of atom N2

  • or different CO2

    • called a compound

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5
<p>Describe what a nucleus is made up of</p>

Describe what a nucleus is made up of

  • every atom has a central located (atomic) nucleus

    • nucleus is made up of

      • protons (+)

      • neutrons (neutral charge)

        • results in nucleus having a net positive charge

        • stable + does NOT participate in chemical reactions

<ul><li><p>every atom has a central located (atomic) nucleus</p><ul><li><p>nucleus is made up of</p><ul><li><p><strong>protons (+)</strong></p></li><li><p><strong>neutrons (neutral charge)</strong></p><ul><li><p>results in nucleus having a net positive charge</p></li><li><p>stable + does NOT participate in chemical reactions</p></li></ul></li></ul></li></ul></li></ul>
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What are electrons?

exist outside of the nucleus in specialized regions of space called orbitals & are (-) charged

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7

What happens when an atom loses an electron?

It will have a net positive charge

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What happens when an atom gains an electron?

It will have a negative charge

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9

What is the electron ratio to protons?

equal # of electrons & protons ⇒ a net charge equal to neutral

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10

What are electron shells? What do they correspond to?

  • densely packed in nucleus (compared to protons & neutrons), lighter electrons orbit nucleus in “shells”

  • (e-) shells correspond to different energy levels

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11

How do chemical bonds form?

Chemical bonds form between atoms through interactions of (e-) in outer shells with one another

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12

What is the goal of every atom?

goal of every atom is to become chemically stable and do so by filling their outermost shell with electrons

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13

How do atoms achieve their goal of filling their outermost shells?

  • achieved by filling its outermost shell with electrons

    • 1st = 2e-

    • 2nd = 8e-

    • 3rd = 8e-

      • atoms achieve a full complement of electrons by combining together to form molecules

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14

What is an ion?

When an atom has an overall positive or an overall negative charge it is no longer neutral and is referred to as an ion

<p>When an atom has an overall positive or an overall negative charge it is no longer neutral and is referred to as an ion</p>
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What is a cation?

atoms loses an electron, overall (+) charge

ex: NA+

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What is an anion?

atom gains an electron, overall (-) charge

ex: Cl-

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What are chemical bonds?

Chemical bonds form in between atoms when electrons in their outer shells interact with one another

  • Every atom wants to achieve chemical stability and they do this by filling their outermost shell with electrons

  • Atoms achieve a full complement of electrons (8) by combining to form molecules

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18

What are 3 kinds of chemical bonds?

ionic, covalent, hydrogen bonds

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19

What is an ionic bond?

results from attraction between ions of opposite charges

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20

What holds ionic bonds?

anions & cations(attractive force) form ionic bonds → neutralize their charges

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21

What forms from an ionic bond?

  • attraction holds the ions together to form a compound

    • ex: NaCl

      • Na requires the loss of an electron to achieve stability and Cl requires the gain of an electron to achieve stability

      • Cl receives the electron from Na rather than sharing it : Cl becomes Cl- and Na becomes Na

<ul><li><p>attraction holds the ions together to form a <strong>compound</strong></p><ul><li><p><strong>ex: NaCl</strong></p><ul><li><p>Na requires the loss of an electron to achieve stability and Cl requires the gain of an electron to achieve stability</p></li><li><p>Cl receives the electron from Na rather than sharing it : Cl becomes Cl- and Na becomes Na</p></li></ul></li></ul></li></ul>
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22

What are covalent bonds?

Formed when two atoms come together and share electrons within their outer shell

→ strongest bond

Ex: Water is formed as a result of covalent bonds in between Hydrogen & Oxygen

<p>Formed when two atoms come together and share electrons within their outer shell</p><p>→ strongest bond</p><p>Ex: Water is formed as a result of covalent bonds in between Hydrogen &amp; Oxygen</p>
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23

Where are covalent bonds found?

Found in many compounds ⇒ especially those containing carbon

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24

What is formed with covalent bonds?

almost all organic matter formed with carbon

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25

Are covalent bonds strong or weak?

very strong bonds

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26

How many covalent bonds can carbon atoms form?

4 covalent bonds

  • ex: methane CH4

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27

What is the difference between ionic & covalent bonds?

depends on conditions (pH, temp.) / covalent bonds are typically stronger ⇒ require more energy to be broken

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28

How do hydrogen bonds occur? State an example

  • occur when hydrogen is covalently bound to oxygen or another electron loving molecule such as nitrogen

    • since the atom bound to hydrogen is ‘electron loving; it holds the shared electrons closer to its nucleus than hydrogen

      • ex: when two hydrogens are bonded to oxygen, the larger oxygen atom tends to pull the electrons closer to itself

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29

Compare the electronegativity of H & C to H & O

  • H : C

    • Carbon is not more electron loving than Hydrogen, thus the electrons are equally shared in between the two atoms

  • (partial positive)H : O(partial negative)

    • Oxygen is more electron loving than Hydrogen, thus the electrons are not equally shared in between the two atoms and are held more closely to the oxygen nucleus

<ul><li><p>H : C</p><ul><li><p>Carbon is not more electron loving than Hydrogen, thus the electrons are equally shared in between the two atoms</p></li></ul></li><li><p>(partial positive)H : O(partial negative)</p><ul><li><p>Oxygen is more electron loving than Hydrogen, thus the electrons are not equally shared in between the two atoms and are held more closely to the oxygen nucleus</p></li></ul></li></ul>
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30

What do hydrogen bonds result in?

Because the electrons are not equally shared in between the two atoms there is a resulting partial positive charge on the hydrogen atom (d+ )and a partial negative charge (d- )on the electron loving atom (oxygen in this case)

  • Unequal sharing leads to:

    • creates a region w/ partial negative charge (O)

    • and partial positive charge (H)

      • ex: H2O

  • on the electron loving atom (oxygen in this case)

  • regions can now participate in hydrogen bonding

    →displays polarity

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What are polar molecules?

Molecules that contain unequal sharing of electrons

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32

Which elements have the most electronegativity?

Oxygen & Nitrogen

→Electron greedy

Highly electronegative!

C & H are non polar covalent bonds

  • (lipid) non soluble because of its equal charge and not partial charge

O & H

  • polar(unequal charge)

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33

What type of attraction is between oppositely charged regions of different molecules (hydrogen bonds)?

  • loose attraction between oppositely charged regions of different molecules

    • partial positive charge on hydrogen atom is attracted to partial negative charge on atoms within other molecules

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Are hydrogen bonds stronger than ionic & covalent bonds?

  • weaker than ionic & covalent bonds

Covalent bonds → ionic bonds → hydrogen bonds

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35

How do hydrogen bonds form?

These bonds form when Hydrogen is covalently bound to oxygen or another
electron loving molecule such as nitrogen

1 water molecule will be attracted through covalent bonds

4 charges (2 partial negative & 2 partial positive)

<p>These bonds form when Hydrogen is covalently bound to oxygen or another<br>electron loving molecule such as nitrogen</p><p>1 water molecule will be attracted through covalent bonds</p><p>4 charges (2 partial negative &amp; 2 partial positive)</p>
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36

What do hydrogen bonds do?

  • serves to bridge separate molecules together

    • ex: in H2O the H’s of one molecules are attracted to the O’s of the other molecule

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37

What do hydrogen bonds result in?

Networks of molecules of different molecules

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38

What are organic compounds?

Organic compounds are compounds which contain Carbon

  • Carbonic acid, Carbon dioxide, & Carbon monoxide (inorganic - exception)

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39

What are inorganic compounds?

Inorganic compounds are compounds which do not contain Carbon

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40

What kind of compounds do organisms require?

Organisms require a wide variety of inorganic compounds in order to live & reproduce

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41

What is the most inorganic molecules found in living systems?

  • Water accounts for approximately for 75% of cell weight

  • Since water is used to dissolve materials it is a solvent and because electrons are not shared equally in between the hydrogen and the oxygen atoms, it is a polar solvent

Like dissolves like (polar & polar: yes/polar & non-polar: no)

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42

How is water an excellent solvent?

  • Can dissolve many ionic compounds such as NaCl

    • Not covalent because its polar (like dissolves like)

  • Ions (Na+, Cl-) remain dissolved in water to form a solution

  • This solution forms because the partial + regions within the water molecules surround the (-) ions Cl- & the partial (-) regions within the water molecules surround the positive ions (Na+) holding them in solution

<ul><li><p>Can dissolve many ionic compounds such as NaCl</p><ul><li><p>Not covalent because its polar (like dissolves like)</p></li></ul></li><li><p>Ions (Na+, Cl-) remain dissolved in water to form a solution</p></li><li><p>This solution forms because the partial + regions within the water molecules surround the (-) ions Cl- &amp; the partial (-) regions within the water molecules surround the positive ions (Na+) holding them in solution</p></li></ul>
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43

Does water have an equal charge distribution, why or why not? In relation to temperature?

  • has an unequal charge distribution

    • each water molecule can form up to four hydrogen bonds with other water molecules → excellent ability to hydrogen bond allows water to form networks of interconnected water molecules which gives water:

      • a high boiling point (100°C)

      • makes water resist rapid changes in temp. (keeps it in liquid state in most of the places found on Earth

        • great temp. buffer because of its strong hydrogen bonds

<ul><li><p>has an unequal charge distribution</p><ul><li><p>each water molecule can form up to four hydrogen bonds with other water molecules → excellent ability to hydrogen bond allows water to form networks of interconnected water molecules which gives water:</p><ul><li><p>a <strong>high boiling point (100°C)</strong></p></li><li><p>makes water resist rapid changes in temp. (keeps it in liquid state in most of the places found on Earth</p><ul><li><p>great temp. buffer because of its strong hydrogen bonds</p></li></ul></li></ul></li></ul></li></ul>
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44

Can water be easily split into its component ions?

Yes it can be easily split into its component ions H+ & OH-

  • This characteristic allows water to play key roles in many chemical reactions

<p>Yes it can be easily split into its component ions H+ &amp; OH-</p><ul><li><p>This characteristic allows water to play key roles in many chemical reactions</p></li></ul>
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45

What kind of solvent is water & why?

water ⇒ universal solvent (reach 4 degrees - highest density of water, closer to each other) (polar solvent)

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46

What does water allow due to its unequal charge of distribution?

unequal charge of distribution allows it to dissolve many ionic compounds

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47

What does the (+) region of water do?

  • (+) region of water molecules surround (-) ions

    • holds ion in solution

      • ex: NaCl easily dissolves into Na+ & Cl- in water

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48

What does water’s polarity facilitate?

  • water’s polarity facilitates the splitting & joining of hydrogen ions H+ & hydroxide ions OH-

    • makes these ions available for chemical reactions

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49

What does the pH scale describe?

  • pH scale describes the concentration of $H^+$ ions in a solution

    • measures of acidity

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50

What does a ph of 7 mean? below 7? above 7?

  • pH 7 = neutral (pure water)

  • pH below 7 = acidic

  • pH above 7 = basic or alkaline

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51

What are organic molecules? Why is it so?

any molecule that contains both carbon & hydrogen

  • reason: each C atom can participate in 4 covalent bonds, carbon can be used to build an enormous variety of compounds

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What are the four major classes of organic molecules?

Carbohydrates, Lipids, Proteins, Nucleic Acids

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53

What is a carbohydrate?

large group of compounds including sugars & starches

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54

What do Carbohydrates contain? State an example of a compound using this ratio

all contain the elements C, H, & O and ratio is C1 H2 O1

  • C6 H12 O6

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Are carbohydrates polar?

generally polar (so they dissolve in water)

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56

What is carbohydrates used for?

  • ready source of energy for cells

  • unsaturated = healthy

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57

What is the organ that is given glucose(prioritized) in a fight or flight response?

The brain

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Can carbohydrates be insoluble?

Yes and it is dependent on size (smaller-soluble; larger: not soluble)

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59

What are the diff. types of carbohydrates?

monosaccharides

disaccharides

polysaccharides

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60

What are monosaccharides? Example?

  • mono = one

    • simple sugars, ex: glucose

    • more stable - least amount of repulsion

<ul><li><p>mono = one</p><ul><li><p><strong>simple sugars, ex: glucose</strong></p></li><li><p><strong>more stable - least amount of repulsion</strong></p></li></ul></li></ul>
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What are disaccharides? Example?

  • di = two

    • two monosaccharides come together to form a disaccharide

    • ex: glucose + fructose = sucrose (table sugar)

      • covalently bonded together through a dehydration reaction

<ul><li><p>di = two</p><ul><li><p>two monosaccharides come together to form a disaccharide</p></li><li><p>ex: glucose + fructose = <strong>sucrose (table sugar)</strong></p><ul><li><p><strong>covalently bonded together through a dehydration reaction</strong></p></li></ul></li></ul></li></ul>
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62

What are polysaccharides? Solubility? Examples?

  • poly = many

    • hundreds of monosaccharides

    • often not soluble in water (too large)

      • ex: glycogen, starch, cellulose (cannot digest)

<ul><li><p>poly = many</p><ul><li><p>hundreds of monosaccharides</p></li><li><p>often not soluble in water (too large)</p><ul><li><p>ex: <strong>glycogen, starch, cellulose (cannot digest)</strong></p></li></ul></li></ul></li></ul>
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63

What are lipids & their importance?

  • includes fats, complex lipids (ex: phospholipids) & steroids

  • essential to the structure & function of membranes

    • comprises the lipid portion of the phospholipid bilayer

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64

What are lipids used for?

used for energy storage

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65

Are lipids polar or non-polar?

non-polar molecules: hydrophobic ⇒ water hating

  • Non-polar (equal sharing) which means no regions of partial (+) or (-) →not attracted to water molecules (polar-unequal sharing)

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66

What are fats made from?

  • made from a glycerol backbone +1 or more fatty acids(non-polar; hydrophobic)(function: holds heat in body):

    • monoacylglycerides: glycerol + 1 fatty acid

    • diacylglycerides: glycerol + 2 fatty acids

    • triacylglycerides: glycerol + 3 fatty acids

<ul><li><p>made from a glycerol backbone +1 or more fatty acids(non-polar; hydrophobic)(function: holds heat in body):</p><ul><li><p>monoacylglycerides: glycerol + <strong>1 fatty acid</strong></p></li><li><p>diacylglycerides: glycerol + <strong>2 fatty acids</strong></p></li><li><p>triacylglycerides: glycerol + <strong>3 fatty acids</strong></p></li></ul></li></ul>
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What can fatty acids be?

  • fatty acids can be:

    • saturated ⇒ no double bonds, saturated with hydrogen atoms

      • pack closer together - forms more bonds (more solid)

    • or unsaturated ⇒ at least one double bond, fewer hydrogen atoms

      • has “kinks” therefore influences its fluidity

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What makes up a phospholipid?

in complex lipids

contain glycerol, 2 fatty acids, & a phosphate group

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Where are phospholipids found?

In membranes of living cells & they are the primary component of prokaryotic & eukaryotic plasma membranes

<p>In membranes of living cells &amp; they are the primary component of prokaryotic &amp; eukaryotic plasma membranes</p>
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70

What makes up a phospholipid?

Included in complex lipids

  • glycerol & phosphate group

    • hydrophilic - likes water

  • fatty acid tails are non-polar

    • hydrophobic - hates water

    • has two fatty acid tails

      • has permeability to enable certain ions to travel through cell membrane (small non polar material; polar material can’t because of the lack of charges in phospholipid tails(repelled))

<p>Included in complex lipids</p><ul><li><p>glycerol &amp; phosphate group</p><ul><li><p><strong>hydrophilic - likes water</strong></p></li></ul></li><li><p>fatty acid tails are non-polar</p><ul><li><p><strong>hydrophobic - hates water</strong></p></li><li><p>has two fatty acid tails</p><ul><li><p>has permeability to enable certain ions to travel through cell membrane (small non polar material; polar material can’t because of the lack of charges in phospholipid tails(repelled))</p></li></ul></li></ul></li></ul>
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What does the fatty acid tails allow the phospholipids to do?

  • allows phospholipids to form membranes in water

    • saturated fatty acids tend to form membranes that are more solid

    • unsaturated fatty acids - more fluid

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What are biological membranes made from?

are made from a phospholipid bilayer

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What are biological membranes?

are semi-fluid (contain a mix of saturated & unsaturated fatty acids)

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What are biological membranes function?

  • separate the watery inside of the cell from the watery environment

    • one saturated & unsaturated, this is what enables the entrance of certain elements through the cell membrane

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What is the difference between steroids & other lipids?

structurally different from other lipids

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76

What are steroids built on?

built on a hydrophobic 4 ring structure

  • on exam, portrayed as true or false

<p>built on a hydrophobic 4 ring structure</p><ul><li><p><em><span>on exam, portrayed as true or false</span></em></p></li></ul>
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77

Where are steroids found in?

  • generally found in eukaryotes (more complex organism) not in prokaryotes(bacteria)

    • ex: Cholesterol ergosterol(thermostability) & vitamin D

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78

What are proteins made up of?

made up of building blocks: amino acids (individual units)

<p>made up of building blocks:<strong> amino acids (individual units)</strong></p>
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79

What do proteins contain?

all contain: C, H, O, N (& some have S)

  • proteins typically contain: 20 different amino acids

    • have at least one amino -NH2 & one carboxyl (-COOH) group

    • side groups(different on each amino acid) determine properties of amino acid

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80

What are functions of proteins?

  • required in all aspects of cell structure & function

    • some are structural

    • but most act as enzymes - increase the rate at which chemical reactions take place in living organisms

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What bonds turn amino acids to proteins?

amino acids are joined to make proteins by covalent peptide bonds

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82

What is a chain of amino acids?

protein= polypeptide = chain of amino acids

short chain of amino acids are called peptides

<p>protein= <strong>polypeptide</strong> = chain of amino acids</p><p>short chain of amino acids are called <strong>peptides</strong></p>
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What is the shape & function of protein determined by?

shape & functions of the protein is determined by the sequence of amino acids

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84

How is protein required in all aspects of cell structure & function?

  • Structural components of the cell:

    • Membrane channels

  • Enzymes

    • Increase the rate of chemical reactions that occur within the cell

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85

What are the 9 amino acids essential for life?

  • needs to obtain from other sources

    • histidine, isoleucine, leucine, lysine, methionine (AUG is the starting column), phenylalanine, threonine, tryptophan, and valine

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86

What are types of nucleic acids?

  • (double strands)DNA transcribes to RNA then to (single strand) RNA become translated to amino acids (series of amino acids)→ proteins (enzymes or structural)

  • DNA = deoxyribonucleic acid

  • RNA = ribonucleic acid

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87

What are nucleotides made up of? Describe the 3 building blocks.

  • built of building blocks called nucleotides

  • each nucleotide has 3 parts

    1. Nitrogenous Base:

      1. Purine → 2 rings = Guanine (G) & Adenine (A)

      2. Pyrimidine →1 ring = Cytosine (C), Thymine (T) or Uracil (U)

        1. Uracil is the change due to evolutionary change to increase genetic stability

    2. Pentose sugar → 5 carbon sugar

      1. ribose or deoxyribose

        1. deoxyribose - no oxygen therefore “dehydrated”

    3. Phosphate group

      1. A phosphate group is attached to the nucleotide and serves as the site of attachment for the next nucleotide

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What is DNA made up of?

  • nucleotides: A, G, T, & C

  • sugar deoxyribose

  • double stranded with each strand together by hydrogen bonds

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89

What does DNA do?

stores the genetic info of all cellular organisms (what genes are composed of)

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90

What is the direction of DNA?

forms a double helix

  • 5 prime to 3 prime

    • The order of the nucleotide sequence is very specific and forming the genetic instructions for the organism

      • there are viruses that contain DNA

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91

How many base pairs in DNA?

3 billion base pairs in DNA

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92

What is RNA made up of?

  • A, G, U, & C

  • sugar ribose

  • single stranded

    • except in viruses; can be double stranded

<ul><li><p><strong>A, G, U, &amp; C</strong></p></li><li><p>sugar ribose</p></li><li><p>single stranded</p><ul><li><p>except in viruses; can be double stranded</p></li></ul></li></ul>
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What is RNA involved in?

involved in communicating the instructions stored in DNA(transcription)

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What is the direction of RNA?

  • 3 prime to 5 prime

    • SARS covid 2(viruses that contain RNA)

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95

What is the DNA structure composed of?

  • each strand is built from a sugar phosphate backbone

  • 2 strands are held together by hydrogen bonds between nitrogenous bases

  • forms the double helix

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96

What nitrogenous base pairs are paired in DNA?

  • A pairs w/ T

  • G pairs w/ C

    • order of bases is specific & forms the genetic instructions for the organisms

      • ex: genes

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