chp 2 micro chemical principles (copy)

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78 Terms

1

matter

anything that takes up space ( made of atoms)

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atoms

the smallest chemical units of matter

  • has No net charge

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electrons

negatively charged subatomic particles circling a nucleus

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nucleus

structure containing neutrons and protons

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neutrons

uncharged particles (neutral)

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protons

positively charged particles

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atoms

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element

composed of a single type of atom

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atomic number

equal to the number of protons in the nucleus (determines the identity of an atom)

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atomic mass (atomic weight)

sum of masses of protons, neutrons, and electrons

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electron configurations

  • Only the electrons of atoms interact, so they determine atom’s chemical behavior

  • Electrons occupy electron shells

  • Valence electrons – electrons in outermost shell that interact with other atoms

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atoms

first shell- can hold two electrons

second shell can hold up to 8 electrons

<p>first shell- can hold two electrons</p><p>second shell can hold up to 8 electrons</p>
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valence

combining capacity of an atom (number of extra or missing electrons in outermost shell)

• Atoms are stable when outer electron shells contain eight electrons

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chemical bonds

attachment of atoms combined by sharing or transferring valence electrons

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molecule

two or more atoms held together by chemical bonds

ex: O2 oxygen gas, N2,

<p>two or more atoms held together by chemical bonds</p><p>ex: O2 oxygen gas, N2,</p>
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compound

-molecule made up of two or more different types of atoms. Ex: h2o, NaCl,

CO2 (molecule/compound),

<p>-<span style="font-family: Google Sans, Roboto, Arial, sans-serif">molecule made up of two or more <strong>different</strong> types of atoms. Ex: h2o, NaCl,</span></p><p><span style="font-family: Google Sans, Roboto, Arial, sans-serif"> CO2 (molecule/compound),</span></p><p></p>
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covalent bond

sharing of a pair of electrons by two atoms

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electronegativity

attraction of atom for electrons; the more electronegativity an atom, the greater the pull its nucleus exerts on electrons

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<p>nonpolar covalents bonds</p>

nonpolar covalents bonds

– Shared electrons spend equal amounts of time around each nucleus

– Atoms with similar electronegativities

– No poles exist

– Carbon atoms critical to life; form four nonpolar covalent bonds with other atoms

• Organic compounds contain carbon and hydrogen atoms

<p>– Shared electrons spend equal amounts of time around each nucleus</p><p>– Atoms with similar electronegativities</p><p>– No poles exist</p><p>– Carbon atoms critical to life; form four nonpolar covalent bonds with other atoms</p><p>• Organic compounds contain <strong>carbon and hydrogen atoms</strong></p>
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non polar covalents bonds

  • Strongest covalent bonds in solution

• The most common bonds in living cells

• Form between C, H, O, N, P, S

<ul><li><p><strong>Strongest covalent bonds in solution</strong></p></li></ul><p>• The most common bonds in living cells</p><p>• Form between<strong><u> C, H, O, N, P, S</u></strong></p>
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<p>polar covalent bonds</p>

polar covalent bonds

  • unequal sharing of electrons due to high significantly different electronegativities

  • Most important polar covalent bonds involve hydrogen

    - Allows for hydrogen bonding

<ul><li><p>unequal sharing of electrons due to high significantly different electronegativities</p></li><li><p>Most important<strong> polar covalent bonds involve hydrogen</strong></p><p>- Allows for hydrogen bonding</p></li></ul><p></p>
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hydrogen bonds

– Not a true bond! Actually an Intermolecular force

– Weak forces that combine with polar covalent bonds

– Electrical attraction between partially charged H+ and full or partial negative charge on different region of same molecule or another molecule

Weaker than covalent bonds but essential for life

• Many help to stabilize 3-D shapes of large molecules

**anytime you see H+ bind to N, O, F, they can potentially create a hydrogen bond

VERY WEAK!!!

EX: PROTEINS, DNA

<p>– Not a true bond! Actually an<span style="color: red"><strong> Intermolecular force</strong></span></p><p>– Weak forces that combine with polar covalent bonds</p><p>– Electrical attraction between partially charged H+ and full or partial negative charge on different region of same molecule or another molecule</p><p>–<span style="color: red"> <strong>Weaker</strong></span> than covalent bonds but essential for life</p><p>• Many help to stabilize 3-D shapes of large molecules</p><p><strong>**anytime you see H+ bind to N, O, F, they can potentially create a hydrogen bond</strong></p><p><span style="color: red"><strong>VERY WEAK!!!</strong></span></p><p><span style="color: red"><strong>EX: PROTEINS, DNA</strong></span></p>
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hydrogen bonds

-Weak bond between a H covalently bonded to one molecule and an O or N atom on the same or different molecule + H

- Important in many biological molecules

  • when H+ binds w/ N,O, F you have the capacity to regenerate a super polar covalent bond. And that H+ has the capacity for a special intermolecular force (hydrogen bond)

<p><strong>-</strong>Weak bond between a H covalently bonded to one molecule and an O or N atom on the same or different molecule + H</p><p>- Important in many biological molecules</p><ul><li><p><strong><mark data-color="yellow" style="background-color: yellow; color: inherit">when H+ binds w/ N,O, F you have the capacity to regenerate a super polar covalent bond. And that H+ has the capacity for a special intermolecular force (hydrogen bond)</mark></strong></p></li></ul><p></p>
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<p>ionic bonds </p>

ionic bonds

– Occur when two atoms with vastly different electronegativities come together

– Atoms have either positive (cation) or negative (anion) charges

– Cations and anions attract each other and form ionic bonds (no electrons shared)

– Typically form crystalline ionic compounds known as salts (NaCl)

<p>– Occur when two atoms with vastly different electronegativities come together</p><p>– Atoms have either positive (cation) or negative (anion) charges</p><p>– Cations and anions attract each other and form ionic bonds (no electrons shared)</p><p>– Typically form crystalline ionic compounds known as salts <strong>(NaCl)</strong></p>
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ionic bonds

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hydrophilic

“water-loving” molecules attract water to their surface (polar)

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hydrophobic

“water-hating” molecules repel water (nonpolar)

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amphipathic

“feeling both” molecules have both hydrophilic and hydrophobic properties (polar and nonpolar parts)

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Common Elements in Living Organisms

CHONPS

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pH scale

• Measures the acid concentrations of solutions

• Ranges from 0 (most acidic) to 14 (most basic); 7 is neutral

• pH = -log[H+]

H+ is made of single proton/electron

H+ is a proton

PH high=basic (lots of protons)

PH low= acidic (very low protons)

<p>• Measures the acid concentrations of solutions</p><p>• Ranges from 0 (most acidic) to 14 (most basic); 7 is neutral</p><p>• pH = -log[H+]</p><p>H+ is made of single proton/electron</p><p>H+ is a proton</p><p>PH high=basic (lots of protons)</p><p>PH low= acidic (very low protons)</p>
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Functional Groups of Organic Molecules

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-OH

Hydroxyl

-class of compounds: alcohol, monossacharide, aa

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<p></p>

Ether

-class of compounds: Disaccharide ,polysaccharide

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<p></p>

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chemical reactions

• The making or breaking of chemical bonds

• Involve reactants and products

• Biochemistry involves chemical reactions of living things

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Many biological molecules are composed of

Monomer Units

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Monomer units are joined by

Dehydration synthesis reactions (also called condensation reactions)

<p><strong>Dehydration synthesis</strong> reactions (also called condensation reactions)</p>
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Polymers are broken down by

Hydrolysis reactions

<p>Hydrolysis reactions</p>
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organic molecules

1. Carbohydrates

2. Proteins

3. Nucleic Acids

4. Lipids

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Carbohydrates

– Organic molecules composed of carbon, hydrogen, and oxygen (CH2O)n

– Functions

• Medium or Long-term storage of chemical energy

• Ready energy source

• Part of backbones of nucleic acids

• Converted to amino acids

• Form cell wall

• Involved in intracellular interactions between animal cells

– Types

• Monosaccharides: single Ex: fructose

• Disaccharides: double. Ex: sucrose

• Polysaccharides. Ex: starch, cellulose

<p>– Organic molecules composed of <strong>carbon,</strong> <strong>hydrogen, and oxygen<u> (CH2O)n</u></strong></p><p>– Functions</p><p>• Medium or Long-term storage of chemical energy</p><p>• Ready energy source</p><p><span style="color: red"><strong>• Part of backbones of nucleic acids</strong></span></p><p>• Converted to amino acids</p><p><span style="color: red"><strong>• Form cell wall</strong></span></p><p>• Involved in intracellular interactions between animal cells</p><p>– Types</p><p>• Monosaccharides: single Ex: <strong>fructose</strong></p><p>• Disaccharides: double. Ex<strong>: sucrose</strong></p><p>• Polysaccharides. Ex: <strong>starch</strong>, <strong>cellulose</strong></p><p></p>
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Carbohydrate synthesis/Hydrolysis

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proteins

– Mostly composed of carbon, hydrogen, oxygen, nitrogen, and sulfur

– Functions

• Structure of cells

• Enzymatic catalysis- speeds up chemical reactions but not consumed in the process

• Regulation

• Transportation

• Defense and offense (immune protein-antibody)

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catalyst

speeds up chemical reaction but is not consumed in the process (meaning not a reactant or product)

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enzyme

is a protein catalysts

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Amino Acids

– The monomers that make up proteins

– Most organisms use only 21 amino acids in the synthesis of proteins

– Side groups affect how amino acids interact with one another and how a protein interacts with other molecules

– A covalent bond ( is formed between amino acids by dehydration synthesis reaction

***** (OH) hydroxyl can run dehydration synthesis******

<p>– The monomers that make up proteins</p><p>– Most organisms use only 21 amino acids in the synthesis of proteins</p><p>– Side groups affect how amino acids interact with one another and how a protein interacts with other molecules</p><p>– A covalent bond (<span style="color: red"> </span>is formed between amino acids by dehydration synthesis reaction</p><p><span style="color: blue"><strong><u>***** (OH) hydroxyl can run dehydration synthesis******</u></strong></span></p>
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amino acids

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Isomers

• Stereoisomers

– are mirror images of one another

– D-isomers bend light to the the right (clockwise)

– L-isomers bend light to the left (counterclockwise)

<p>• Stereoisomers</p><p>      – are mirror images of one another</p><p>       – D-isomers bend light to the the right (clockwise)</p><p>        – L-isomers bend light to the left (counterclockwise)</p>
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Amino Acid Dehydration Rxn.

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Protein structure

KNOW WHERE TO FIND A PEPTIDE BOND!

<p>KNOW WHERE TO FIND A PEPTIDE BOND!</p>
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Primary structure

is the order of amino acids

<p>is the order of amino acids</p>
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secondary structure

is localized modular structure

-determined by the primary structure is a localized 3 dimensional structure that is determined by hydrogen bonding along the peptide backbone

ex: alpha helix, beta sheet

<p>is localized modular structure</p><p>-<span style="color: red"><strong>determined by the primary structure is a localized 3 dimensional structure that is determined by hydrogen bonding along the peptide backbone</strong></span></p><p><span style="color: red"><strong>ex: alpha helix, beta sheet</strong></span></p>
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Tertiary Structure

is the global three-dimensional shape of the polypeptide (chain of AA)

-what determines tertiary structure?: interaction of the R groups

<p>is the <span style="color: red"><strong>global</strong></span> three-dimensional shape of the polypeptide (chain of AA)</p><p><span style="color: red"><strong>-what determines tertiary structure?: <u>interaction of the R groups</u></strong></span></p><p></p>
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quaternary structure

is the association of more than one polypeptide chains coming together to make a protein

  • Ex of quaternary structure- hemoglobin

<p>is the association of more than one polypeptide chains coming together to make a protein</p><ul><li><p><span><strong>Ex of quaternary structure- hemoglobin</strong></span></p></li></ul><p></p>
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Protein Denaturation

– causes loss of 3D structure

– protein unravels and looses function

– can be caused by

• heat

• acids

• bases

• harsh chemicals

•mechanical action

<p>– causes loss of 3D structure</p><p>– protein unravels and looses function</p><p>– can be caused by</p><p>           • heat</p><p>           • acids</p><p>           • bases </p><p>           • harsh chemicals</p><p>           •mechanical action</p><p></p>
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enzymes

• Nearly always proteins

• Biological catalysts critical for life

• Active site

• Substrate(s) – acted on by enzymes to make products

• Cofactors – often required (ATP, NADH, etc)

<p>• Nearly always proteins</p><p> • Biological catalysts critical for life </p><p>• Active site</p><p>• Substrate(s) – acted on by enzymes to make products </p><p>• Cofactors – often required (ATP, NADH, etc)</p>
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DNA

• DNA is genetic material of all organisms and of many viruses

• Carries instructions for synthesis of RNA and proteins; controls synthesis of all molecules in an organism

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RNA

• functions in protein synthesis (mRNA, tRNA, rRNA)

• is the genetic material of some viruses

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Nucleotides

• Monomers that make up nucleic acids

• Composed of three parts

– Phosphate

– Pentose sugar: deoxyribose or ribose

– One of five cyclic nitrogenous base

<p>• Monomers that make up nucleic acids</p><p>• Composed of three parts</p><p>– Phosphate</p><p>– Pentose sugar: deoxyribose or ribose</p><p>– One of five cyclic nitrogenous base</p>
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Nucleic acid structure

• H bonds form between C and G and between T and A in DNA

– Two H bonds form between U and A in RNA

• DNA is double stranded in most cells and viruses

– Two strands are complementary

– Two strands are antiparallel

<p>• H bonds form between C and G and between T and A in DNA</p><p>          – Two H bonds form between U and A in RNA</p><p> • DNA is double stranded in most cells and viruses</p><p>             – Two strands are complementary</p><p>             – Two strands are antiparallel</p>
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lipids

– Not composed of regular subunits, but are all hydrophobic

– Four groups

• Fats

• Phospholipids

• Waxes

• Steroids

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sterols

• Multi-ring structure

• Used in membranes cholesterol

• Bile acids (help digest food)

• Hormones ( chemical signal released by the cell)

<p>• Multi-ring structure</p><p>• Used in membranes cholesterol</p><p>• Bile acids (help digest food)</p><p>• Hormones ( chemical signal released by the cell)</p>
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<p>macromolecules</p>

macromolecules

plasma membrane composed of phospholipids

cell wall made out of carbohydrates

flagella made out of protein

<p>plasma membrane composed of phospholipids</p><p>cell wall made out of carbohydrates</p><p>flagella made out of protein</p>
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cells

• The fundamental unit of life is the cell

• All cells:

– Have a cytoplasmic membrane

– Have chromosomes made of DNA

– Have ribosomes for protein synthesis

– Reproduce to form progeny cells

– Obtain energy from their environment

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eukaryotic cells

– Animals, plants, fungi, and protists

– Have a nucleus and cellular organelles

– Tend to be large

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Prokaryotic cells

– Bacteria and Archaea

– No nucleus or other membrane-bound organelles

– Tend to be smaller

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DNA monomer unit us

nucleotides

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amino acids monomer unit is

polypeptide or protein

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cofactors

something an enzyme needs in order to do it’s job

Example:(ATP, NADH)

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