OAT Boot Day 1

Definitions of Matter, Element, and Atom

• Matter: Anything that takes up space and has mass

• Element: A pure substance that has specific chemical and physical properties and can’t be broken down into a simpler substance

• Atom: Smallest unit of matter that still retains the chemical properties of the element

Definitions of Molecules, Intramolecular Forces, Intermolecular Forces

• Molecule: Two or more atoms joined together

• Intramolecular forces: Attractive forces that act on atoms within a molecule

• Intermolecular forces: Attractive forces that exist between molecules

  • Affect physical properties of the resulting substance

Definitions of Molecules, Intramolecular Forces, Intermolecular Forces

• Monomers: Single molecules with the capability of polymerizing

• Polymers: Substances made of many monomers linked together

• Polymerization: The continuous bonding of one monomer to another, forming a polymer

Dehydration Reaction

A.K.A a condensation reaction:

Polymerization reaction that results in the release of water

Hydrolysis:

Depolymerization reaction which utilizes water to break bonds

Carbs:

• What are they made of

• What are they used for functionally

● Carbohydrates: Molecules used for both fuel and structural support

● Contain: Carbon, hydrogen, and oxygen

● Types: Monosaccharides, disaccharides, polysaccharides

Monosacharides

• Example

• What are they

Monosaccharides: Carbohydrate monomers

● Common examples:

● Ribose: Five carbon monosaccharide

● Fructose: Six carbon monosaccharide

● Glucose: Six carbon monosaccharide

Disaccharides

• Example molecule

• What are they

• What kind of bond do they have

• Disaccharides: Composed of two monosaccharides joined together by a glycosidic bond

• Formation requires a dehydration (condensation) reaction

• Sucrose: Common disaccharide example made of glucose and fructose

Polysaccharides

• What are they

• Examples for plants and animals

● Polysaccharides: Contain multiple monosaccharides held together in a long polymer by glycosidic bonds

• Starch

• Glycogen:

• Celulose

Starch

• Energy storage polysaccharide of glucose monomers held together and used by animals

• Can be hydrolyzed, releasing free glucose monomers which can be utilized for energy

Glycogen

• Energy storage polysaccharide of glucose monomers held together and used by animals

• Can be hydrolyzed, releasing free glucose monomers which can be utilized for energy

Cellulose

• Cellulose: Structural support polysaccharides made of many glucose monomers

• Important component of plant cell walls

What are proteins made of?

• How much is there?

• What does the structure look like.

Amino Acids

There are 20 AA

• They consist of an R group, nitrogen, hydrogen, and oxygen, and carbon.

Polypeptides:

• What are they

• What do they do

• What kind of bonds do they have

• How are these bonds created?

• Polypeptides (proteins): Strands of many amino acids held together by peptide bonds

• Diverse array of structures and functions

• Peptide bonds: Between the carboxyl group of one amino acid and the amino group of another

• created by dehydration (condensation) reactions; broken by hydrolysis reactions

Primary Protein Structure

Primary structure: The simple amino acid sequence resulting from mRNA translation

Secondary Protein Structure

• Structures that show up

• What bonds are present

• Folding patterns of the primary amino acid sequence, including α-helices and β-pleated sheets

• Determined by intermolecular forces between polypeptide backbones excluding R group

• SPECIFICALLY, the C=O in the backbone causes these structural changes.

Tertiary Protein Structure

• Bonds present

• What interactions

• Tertiary structure : Three-dimensional structure resulting from interactions between R groups

• Hydrophobic interactions: Congregation or interaction of nonpolar molecules. Can occur between nonpolar R groups.

• Disulfide bonds: Covalent bonding between two sulfur atoms

• Additional tertiary interactions: Hydrogen bonding and ionic bonding between R groups are also possible

Quatenary Protein Structure

Multiple polypeptide chains come together to form one protein

• Quaternary = tertiary + tertiary +....

Conjugated Proteins Def

• Examples

Composed of amino acids and non-proteins components

EX

• Metalloproteins

• Glycoproteins

Metalloprotein

• Def + Example

Metalloproteins: Proteins which contain a metal ion cofactor

• Ex. hemoglobin contains an iron ion cofactor (Fe2+)

Glycoprotein

• Def + Example

Glycoproteins: Proteins that contain a carbohydrate group

• Ex. mucins can contain various carbohydrates

Protein Denaturation

• Def + what causes it

The loss of protein function and higher order structures

• Primary structures are unaffected by denaturation

Factors that can cause denaturation:

• Extreme temperatures

• pH changes

• Salt concentrations

Protein Functions

• Storage

  • Reservoir of Amino Acids

• Hormones

  • Signaling Molecules that regulate physiological processes (they can be, not all hormones are these). EX: Insulin

• Receptors

  • Some may be able to effect change in the intracellular enviroment

• Structure: Provide strength and support to tissues

• Immunity: Antibodies that protect against foreign substances

• Enzymes: Regulate the rate of chemical reactions

What is a Catalyst

• What does it do?

• How does it affect Equilibrium Point, Spontaneity, Activation energy, or the Transition State.

Increases reaction rates by decreasing activation energy

• Reduces the activation energy required to reach the transition state

• Do not shift a chemical reaction’s equilibrium point or alter spontaneity

Transition State

Transition state: Unstable intermediate between reactants and products

Enzymes: Def, also what makes up the majority of enzymes

Biological catalysts, most are proteins

Active Sites:

Receptor regions on an enzyme that are specific for a substrate

Specificity constant:

Specificity constant: Measures enzyme binding efficiency for a specific substrate

Kcat/ KM (for past reference)

Explain the Induced Fit theory and the Lock and Key model

• What do enzymes need to work?

• Induced fit theory: Active sites mold to some degree to fit the substrate upon binding

• “Lock and key” model: Outdated theory suggesting active sites are rigid and substrates are shaped perfectly to fit within them

• Protein enzymes can be denatured and require optimal temperature and pH

Examples of Non-protein enzymes

• Ribozymes

• Cofactor

• Coenzyme:

• Holoenzyme

• Apoenzyme

• Prosthetic Groups

Ribozymes

• RNA molecules that are capable of acting as enzymes

Cofactor

Non-protein molecule that helps enzymes function

● Coenzyme: Organic cofactor such as vitamins

● Inorganic cofactors include metal ions

Holoenzyme

Complex formed when an enzyme binds its cofactor.

Prosthetic groups:

Prosthetic groups: Cofactors that are tightly or covalently bound to their enzyme

Apoenzyme:

Enzyme without a bound cofactor

Mechanisms of Enzyme Catalysis

• What do enzymes do to catalyze reactions?

• What kind of interactions do they have with substrates?

• Common ways in which enzymes can catalyze reactions:

• Conformational changes to bring substrates closer together with correct orientation

• Stabilization of the transition state

• Having basic groups that can accept protons from a substrate

• Having acidic groups that can donate protons to a substrate

• Electrostatic interactions between the enzyme and the substrate

Draw out what the mechanism of enzyme catalysis looks like IG.

Phosphatase

They help with the Cleavage of a phosphate group off of substrate molecule

This is also knows as Dephosphorylation

Phosphorylase

• Directly adds a phosphate group to a substrate molecule

• Breaks substrate bonds in order to add the new phosphate group

Undergoes phosphorylation

Kinase

• Indirectly adds a phosphate group to a substrate molecule

• Transfers a phosphate group from an ATP molecule

• No bonds are broken in order to add the new phosphate group

They are more like mediators, since they do not actually hold the enzymes themselves.

What factors influence Enzyme Activity?

• Enzyme reaction rates can be affected if a molecule other than the desired, original substrate for a reaction binds either to the enzyme’s active or allosteric site

What is an active site, what is an allosteric site?

• Active site: Receptor region that is specific for the desired reaction substrate

• Allosteric site: Substrate binding location that is separate from the active site

Competitive Inhibitors

• What do they do on the enzyme

Directly competes with reaction substrates for an enzyme’ active site

Competitive Inhibition

• Effects

Competition between inhibitor and enzyme may cause reaction rate to decrease as inhibitor occupies the active site

Can be overcome by increasing substrate concentration

Enzyme Kinetics

• What does the X axis mean

• What does the Y axis mean

• Enzyme kinetic plots can be used to visual the effects inhibitors have on enzymes

• X-axis: Represents the concentration of substrate available

• Y-axis: Represents the resulting reaction rate or velocity

What is the Vmax and saturation mean on an Enzyme Kinetics Graph?

• V max

  • Represents the maximum reaction velocity

• Saturation: When all enzyme active site are occupied

• Velocity will no longer increase and the graph will plateau

What is a Michaelis Constant?

AKA the KM

• This is inversley related to enzyme substrate binding strenght.

HIGH KM means that more substrate is required to reach ½ Vmax

LOW KM means less substrate is required to reach ½ Vmax

What occurs to the KM and Vmax when there is competitive inhibition.

KM is increased but V max does not change

• Normal V max can still be reached with an increased substrate concentration

Noncompetitive inhibition changes to KM and VMAX

VMAX is decreased but KM does not change

• Reduction in active enzymes available

• Normal V max cannot be reached with increased substrate

Product Feedback Regulation (enzymes)

Describe how the product of a reaction affects the rate of the reaction itself

Negative Feedback Regulation (enzymes)

Reaction products will slow or inhibit the original reaction

Positive Feedback Regulation (enzymes)

Reaction products will activate or increase the original reaction

Lipids:

• What are they made of?

Carbon, Hydrogen, Oxygen

What are fatty acid Tails

Long hydrocarbon tails with hydrophobic properties

Hydrophobic, Hydrophilic, Lipophillic, Amphipathic

Hydrophobic: Repels Water

Hydrophilic: Attracts Water

Lipophillic: Attracts Lipids

Amphipathic: Molecule with hydrophobic and hydrophilic parts

• Another way to say this would be they have a hydrophilic and a lipophilic portion (ig)

Fatty Acids

• Differences between Saturated and Unsaturated.

• What are they?

• What do they do to fluidity?

• Saturated: Hydrocarbon chain without any double bonds

  • Single bonded chains packed tightly together

• Unsaturated: Hydrocarbon chain with double bonds

  • Double bonding may produce a kink in the hydrocarbon chain

  • Unsaturated fatty acids pack less tightly together

  • Increase membrane fluidity

Triglycerides

Triglyceride (triacylglycerol):

• Lipid type containing a glycerol backbone and three fatty acids

  • Most triglycerides are completely nonpolar and hydrophobic

What is a glycerol backbone?

Three carbons that serve as anchors for the fatty acid chains

Phospholipids

• Composed of a glycerol backbone, one phosphate group, and two fatty acid tails

  • Amphipathic: Phosphate “head group” is polar and hydrophilic while the fatty acids are nonpolar and hydrophobic

  • Spontaneously form bilayers in aqueous solutions

Factors that Affect Membrane Fluidity

• Temperature

• Cholesterol

• Degrees of Saturation

How do these factors affect fluidity:

• Temperature

• Cholesterol

• Degrees of Saturation

• Temperature

  • Fluidity Increases with higher temperatures and decreases with lower temperatures

• Cholesterol

  • Holds membranes together at high temperatures and keeps the membrane fluid at low temperatures

• Degrees of Saturation

  • Fluidity increases when many kinked, unsaturated fatty acids are present in the membrane and decreases as saturated fatty acid concentrations rise.

Cholesterol

DEF: Amphipathic lipid component of cell membranes

• Precursor molecule to steroid hormones (4 hydrocarbon rings), vitamin D, and bile acid

• Maintains membrane stability at both high and low temperatures

Lipoproteins

• DEF + What are they used for

• Lipoproteins: Round complex of lipids and proteins that can carry lipophilic (hydrophobic) molecules through the blood

• Outer coat composed of phospholipids, cholesterols, and proteins

• Can carry molecules like cholesterol and proteins

Waxes and Carotenoids defs

• What are they made of, what do they do

• Waxes: Simple lipids with long fatty acid chains connected to alcohols

• Carotenoids: Lipid derivatives containing long carbon chains conjugated double bonds that function mainly as pigments

Sphingolipids

• Sphingolipids: Lipids with a backbone containing aliphatic (non-aromatic) amino alcohols

• Important functions in structural support, signal transduction, and cell recognitions

Glycolipids

Lipids found in plasma membranes with carbohydrate groups bound rather than a phosphate group

• Amphipathic with a polar head and nonpolar tail

What are nucleic acids?

Nucleic acids: Diverse molecule class composed of sugar monomers

• Functions including genetic information storage, transfer of other molecules, gene silencing, etc.

• DNA and RNA are the two main types of nucleic acids

Nucleoside vs Nucleotide

Nucleoside: Made of 1 ribose or deoxyribose sugar and 1 nitrogenous base

Nucleotide: Made of 1 ribose or deoxyribose sugar, 1 nitrogenous base, and

phosphate(s)

• Name depends on the amount of phosphate groups

• Ex. Nucleotide containing 3 phosphates is a nucleoside triphosphate

• Mnemonic: Nucleosides are sugars with bases; nucleotides have phosphates

RNA

• RNA (ribonucleic acid): Molecule containing ribose sugar nucleotides that is typically single stranded

• Ribose sugar with hydroxyl groups (-OH) on both the 2’ and 3’ carbons
  

DNA

DNA (deoxyribonucleic acid): Antiparallel double helix molecule containing deoxyribose sugars

Deoxyribose sugars with a hydroxyl group on only the 3’ carbon, not the 2’

Two complementary strands wind around each other

Sugar Phosphate Backbone of DNA

• Sugar-phosphate backbone: Structural chain of alternating sugars and phosphates held together by phosphodiester bonds

• Terminal ends will be one 3’ hydroxyl group and one 5’ phosphate group

• Phosphodiester bonds: Condensation reaction used to link nucleotides together

• Bond between the 5’ phosphate group of one nucleotide and the 3’ hydroxyl group of another nucleotide

OK, so here is a much easier explanation. At the ribose 3 prime end, there is a phosphate attatched. That phosphate connects to a 5,4 prime end of ribose (it really is just the 4’ end though). Then at the 1’ end, of the ribose, a nitrogenous base is added (like adenine, guanine, cytosine, etc)

Nucleic Acid polymerization

• Nucleic acid polymerization: Nucleic acids elongate as nucleoside triphosphates (DUMB WAY OF SAYING IT IS A NUCLEOTIDE :p) are continually added to the free 3’ hydroxyl group of the molecule.

ESSENTIALLY, WE ADD STUFF TO THE 3 PRIME HYDROXYL END.

mRNA

Single stranded molecule resulting from DNA transcription

• Contains the information required to create proteins

tRNA

tRNA (transfer RNA): Participates in protein synthesis by carrying amino acids to ribosome enzymes

rRNA

ribosomal RNA: Participates in protein synthesis by complexing with proteins to make the ribosome enzyme that reads mRNA molecules

miRNA

microRNA: Capable of silencing gene expression

• Base pair to mRNA molecules to prevent them from being read by ribosomes

dsRNA

double stranded RNA:

• Genetic information reservoir used by some viruses instead of DNA

• Pro-Tip: dsRNA must have complementary base pairing and therefore will have equal amounts of A/U and G/C

What is a hypothesis and a theory

• Hypothesis: A proposed explanation of a scientific phenomena that is based on prior knowledge but requires further testing and scrutiny

• Theory: Explanation of a scientific phenomena that has been accepted due extensive testing yielding repetitive results

Primordial Earth Theory (11 points)

Biological Hypotheses and Theories | Biology

• Theory explaining how early Earth provided the conditions needed for life

1. The Universe is approximately 13.8 billion years old

2. Primordial atmosphere: Comprised of inorganic compounds creating a reducing environment (low O2 gas)

3. Earth cooled and gases condensed, formed the primordial sea

4. Simple compounds evolved into more complex organic compounds

5. Organic monomers linked into polymers

6. Protobionts: Abiotic, lipid capsules that emerged as a precursor to cells

7. The first cell arrived on Earth 3.5 billion years ago

8. Heterotrophic, obligate anaerobic prokaryotes developed

9. Autotrophic prokaryotes, such as cyanobacteria capable of photosynthesis, formed
   a. Led to oxygen production and accumulation, creating an oxidizing

10. Primitive eukaryotes emerged

• Support for the endosymbiotic theory

11. More complex eukaryotes and multicellular organisms evolved

Modern Cell Theory: 7 points

• Theory describing how cells govern high order iterations of life

1. All lifeforms have one or more cells

2. The cells is the basic structural, functional, and organizational unit of life

3. All cells come from other cells via cell division

4. Genetic information is stored and passed down through DNA

5. An organism’s activity is dependent on the total activity of its independent cells

6. Metabolism and biochemistry (energy flow) occur within cells

7. All cells have the same chemical composition within organisms of similar species

Central Dogma of genetics

• Central dogma of genetics: Information is passed from DNA to RNA to proteins

• Exceptions include reverse transcriptase and prions

PRIONS: Self replicating

REVERSE TRANSCRIPTASE: RNA to DNA

RNA world Hypthesis

1. The first nucleic acids were RNA molecules that formed when nucleotides combined in the primordial soup

2. Early life relied on self-replicating RNA both to store genetic information and to catalyze chemical reactions before the evolution of DNA and proteins

3. RNA is unstable

a. DNA replaced RNA as the prominent genetic storage mechanism

b. Proteins largely replaced RNA as biological catalysts (ribozymes remain)

Endosymbiotic Theory

• Theory describing how eukaryotes came to house membrane-bound organelles

1. Eukaryotes developed when aerobic bacteria were internalized as mitochondria while the photosynthetic bacteria became chloroplasts

2. Evidence for this theory includes the similarities between mitochondria and chloroplasts

a. They are similar in size

b. They possess their own circular DNA

c. They have ribosomes with a large and small subunit

d. They reproduce independently of the host cell

e. They contain a double membrane