Bio 130 Unit One

Organism

A living entity made up of one or more CELLS - five fundamental characteristics

Five fundamental characteristics of organisms

1. Cells - membrane-bound units

2. Replication - an organism’s main goal is to replicate itself

3. Information - process genetic information encoded in genes and also respond and adjust to environmental information to stay alive and reproduce

4. Energy - have to acquire and use energy to stay alive and reproduce

5. Evolution - are products of evolution and continue to evolve today

Theory

An explanation for a very broad class of observed phenomena that is supported by a wide body of evidence - ex. atomic theory, cell theory, theory of gravity, theory of evolution, etc.

Hypotheses

What explains the pattens? What ideas do we have?

• Current observations are the facts

• If (current condition) → and (predicted cause) → then (data/outcome prediction)

To test a hypothesis, it needs to be falsifiable

Eliminating Hypotheses Using Experiments

To test a hypothesis, it needs to be falsifiable - use simple tests first to eliminate variables - you never fully “prove” a hypothesis, you just support it with evidence (never 100%) - fail to reject a hypothesis if observations don’t falsify them - eventually becomes a theory after enough testing - still, corroborating evidence could come in and change the way you think about things

Most Important to Least Important for Science Discoveries

Theory → Hypothesis → Fact

Theories help unify the facts to explain them

Cell Theory

1858 by Rudolph Virchow - All organisms are made of cells and all cells come from preexisting cells - can’t fully be proved but is accepted because there’s no contrary evidence - not a hypothesis anymore becuase of the overwhelming evidence

Theory of Evolution

1858 Charles Darwin - all species descended from a common ancestor - it’s been observed so it’s a fact - also a theory bc it’s still rigorously tested - caused by natural selection

Central Dogma of Biology

The genetic information for life is stored in DNA

1. Replication to form new DNA

2. Transcription to produce RNA

3. Translation of the RNA to produce proteins

Supports identity by descent because of inheritance and nucleotide information

Evaluating Data key points

Know your parameters (i.e. height or lifespan) and then your metric/measurements (i.e. inches or years)

Null Hypothesis

Experiment has no effect, caused by random chance - contrasts hypothesis that states there is an effect - test the null hypothesis vs. the alternative hypothesis for evidence - H_o vs H_a where H_a is “whether” and H_o is “or not” - leads to p-value (type one error) and type two error

Type One Error

AKA p-value - probability of wrongly rejecting the null hypothesis (accepting the alternative hypothesis) - when p is < 0.05, there is >95% probability of correctly rejecting the null (random chance) hypothesis - this means the results are statistically significant

Type Two Error

Falsely accepting the null hypothesis (wrongly rejecting the alternative hypothesis)

Dependent Variable

What you’re measuring (typically y-axis)

Independent Variable

What you’re manipulating (how does it affect the dependent variable) - typically the x-axis

Standard Deviation

A measure of the amount of variation of the values of a variable about its arithmetic average - two samples can have the same. range but completely different standard deviations (amount of variance)

Standard Error

Represents the gap between measured values and the “true measurement” - bigger sample size leads to a smaller standard error

± 2 standard error approximates a 95% confidence interval - non-overlapping error bars indicate a statistically significant difference!

Energy

Energy is stored in chemical bonds - building bonds takes energy and breaking bonds releases it - chemical reactions like hydrolysis occur when there’s enough energy to combine or change bonding - kinetic energy is associated with motion and potential energy is stored in the location of matter, including energy stored in chemical bonds

Electron Positioning

The position of electrons relates to how much energy they contain (further energy shells have more energy) - valence electrons determine chemical behavior of an atom

6 Elements for Most Living Things

Living things are mostly composed of 6 elements:

1. Carbon

2. Hydrogen

3. Nitrogen

4. Oxygen

5. Phosphorus

6. Sulfur

CHO are the main ones for humans and CHON make up 96% of living organisms

Electronegativity

A higher electronegativity means the element is more likely to hog electrons - increases when you move up and right on the periodic table

Hydrogen Bonds

Chemical bond in which a hydrogen is shared between two electronegative elements (usually O or N) - can change shapes of proteins

Hydrophilic

Water-loving - typically polar molecules because they become separated and surrounded by water - ex. NaCl (but not all ionic bonds can dissolve in water i.e. carbonates)

Hydrophobic

Water-hating (don’t separate in water) - typically non-polar compounds that contain many C-C and C-H bonds - ex. oil

Properties of Water

• High specific heat

• High heat of vaporization

• Cohesion (surface tension)

• Expands when becoming a solid

Water Freezing and Energy

When water freezes, the H₂O molecules release energy and actually get a little bit warmer

Why is life carbon-based

Carbon is super abundant and likes to react because it has 4 valence electrons

Macromolecules

Polymers made by the covalent bonding or monomers

• Proteins (>50%)

• Nucleic Acids

• Carbohydrates

• Lipids

Carbohydrates

Sugars - source of stored energy - initially monosaccharides (single sugars that are hexagons of carbon molecules) - these can form a chain to make polysaccharides (starches) - used for fast-acting energy - 3 major roles (structure, identity, energy storage)

Lipids

Fats - store energy in C-C and C-H bonds - play a structural role in cell membranes - fat in animals serves as thermal insulation - saturated fats and unsaturated fats - used for more long-term purposes (padding, insulation, hormones, cell membranes)

Saturated vs. Unsaturated Fats

Saturated fats:

• Straight

• Typically animal-based

• Solid at room temp

• ex. butter

Unsaturated fats:

• Double bonds between carbons leading to kinks in the chain

• Typically plant-based

• Liquid at room temp

• Healthier because they don’t clog blood vessels

• ex. oil

Proteins

Chains of Amino Acids (monomers) - polypeptides are polymers of AAs and proteins are 1+ polypeptides - condensation reaction bonds the amino acids into polypeptides - every protein has an amino group, a carboxyl group, and a different R group that gives proteins their uniqueness - so, each protein has a unique shape for a specific function - used for function throughout the body and makes up over 50% of the body’s macromolecules

Nucleic Acids

Polymers specialized for storage, transmission, and use of genetic information - DNA and RNA are polymers - nucleotides are monomers (phosphate group + 5-carbon sugar + nitrogenous base)

Chemical Bonds

Forces that hold atoms together in a molecule - covalent bonds, ionic bonds, hydrogen bonds, etc.

Covalent Bonds

Chemical bond in which electrons are shared - ex. H₂O, CH₄

Ionic Bond

Chemical bond between ions once one or more electrons ahve been transferred - ex. NaCl is from the attraction between Na⁺ and Cl^-

Solute

A molecule dissolved in a liquid - ex. NaCl is the solute in salt water

Solvent

The liquid in which the molecule is dissolve - ex. H₂O in salt water

Polarity

Carrying a partial positive charge on one side of the molecule and a partial negative on the other - polar molecules are hydrophilic (because water is also polar)

Amphipathic

Containing hydrophobic and hydrophilic elements - ex. tween because it has one polar end and one nonpolar end

Phylogenetics

The scientific study of the evolutionary development and diversification of a species or group of organisms (often called a phylogenetic tree or "family tree" of life) using DNA, genetic data, and physical traits

Positive Control

A test sample or experimental group designed to produce a known, expected positive result

Specific Heat

The amount of energy required to raise the temperature of one gram of a substance by one degree celsius - measures the capacity of a substance to absorb energy - water has an incredibly high SH

Dehydration Reaction

AKA condensation reaction - a chemical reaction where two molecules are joined covalently with the removal of an -OH from one and an -H from the other to form water - mostly involves the joining of monomers into polymers

Hydrolysis Reaction

A chemical reaction where a molecule is split into smaller molecules by reacting with water - mostly involves splitting polymers into monomers

Amino Acid

Building blocks of protein - these are small organic molecules with a central carbon atom bonded to an amino group (-NH3), a carboxyl group (-COOH), a hydrogen atom, and a side chain - when they’re linked together to form protein, they’re known as residues

Enantiomer

A pair of molecules that are non-superimposable mirror images of each other

1st Law of Thermodynamics

Energy is conserved in any process - energy can be transferred and converted into different forms but it cannot be created or destroyed - free energy is the energy that’s useable to do work because not all energy can be used (like how not all the energy from food is used)

2nd Law of Thermodynamics

The entropy of the universe or any closed system always increases

Exergonic Reaction

A chemical reaction that has a change in Gibbs free energy (∆G) less than zero - basically, it releases energy (free energy) into its surroundings - the amount of energy decreases in the thing - ex. fire burning, breaking chemical bonds, etc.

Endergonic Reaction

A chemical reaction that has a change in Gibbs free energy (∆G) greater than zero and is nonspontaneous - basically, it takes energy (free energy) for the reaction to happen - ex. making chemical bonds, or adding phosphate to ADP to make ATP

Equilibrium

When forward reactions and reverse reactions are occurring at the same rate, so the concentration of reactants and products remains the same

Catalysis

The acceleration of the rate of a chemical reaction due to a decrease in the required free energy for the transition state (activation energy) - most catalysts are proteins (enzymes) or a few are RNA - enzymes bring substrates together in precise orientation so the electrons can interact, lowering the energy of activation (E_a)

Enzymes

A protein catalyst used by living organisms to increase the rate of biological reactions - reactants bond to specific active sights on enzymes - each enzyme is highly specific

Two functions:

1. Bring substrates together in precise orientation so the electrons can interact

2. Decrease the amount of kinetic energy (energy of activation) needed

Activation Energy

The amount of kinetic energy required to initiate a chemical reaction - specifically, the energy required to reach the transition state

Theory of Chemical Evolution

Simple chemical compounds in the early atmosphere and ocean combined through chemical reactions to form larger, more complex substances - this eventually led to the origin of life and the start of biological evolution

Nucleotide

A molecule consisting of a five-carbon sugar (ribose or deoxyribose), one or more phosphate groups, and one of several nitrogen-containing bases - Makes up a DNA or RNA nucleic acid - cytosine, uracil, thymine, guanine, and adenine - Cytosine bonds with Guanine - for DNA, Thymine bonds with Adenine, and for RNA, Uracil bonds with Adenine

Activated Nucleotide

Supplies the chemical energy needed to build nucleic acids and drive cellular metabolism - includes ATP, GTP, etc.

Gel Electrophoresis

Used to separate mixtures of DNA, RNA, or proteins according to their molecular size and electrical charge

DNA

Deoxyribonucleic Acid - carries the genetic information - typically a double helix with two intertwined strands held together by noncovalent bonds

RNA

Ribonucleic Acid - usually single-stranded nucleic acid - includes catalytic components of ribosomes (rRNA), transporters of amino acids (tRNA), and messages of the DNA code needed for protein synthesis (mRNA)

5’ end and 3’ end

5’ end is the beginning of the strand where a free phosphate group attaches to the 5’ carbon of the first sugar - 3’ end is the end/tail where an exposed hydroxyl (-OH) group sits on the 3’ carbon of the final sugar

Metabolism

Requires coupling of anabolic and catabolic reactions - anabolic reactions build complex molecules (require energy) - catabolic reactions break down complex molecules (release energy) - not a super efficient system, as anabolic energy required to do a smaller reaction takes the catabolic energy from a bigger reaction - life is generally a constant battle against entropy

Four Main Polymers and Their Monomers

1. Carbs - formed by linking simple sugar monomers (monosaccharides) to form polysaccharides

2. Lipids - Noncovalent forces maintain the interactions between the lipid molecules

3. Nucleic Acids - formed from 4 different kinds of nucleotide monomers

4. Proteins - formed from different combinations of 20 amino acids

Three Major Roles of Carbohydrates

1. Transport stored energy within complex organisms

2. Structural molecules that give many organisms their shpaes

3. Recognition or signaling molecules that can trigger specific biological responses

   1. ex. glycoproteins that are sugar molecules attached to proteins to trigger responses

AKA

1. Cell structure

2. Cell Identity

3. Energy Storage

Monosaccharides

Sugars that can’y be hydrolized to form simpler sugars - shape matters and affects function! (ex. ribose and ddeoxyribose both have 5 carbons, aldose and ketose have same formula but different order, glucose and galactose same thing) - covalently bonded by condensation reactions that form glycosidic linkages - sugars can just get larger and larger and more complex - polysaccharides are super important for structure and energy storage

Pyrimidines vs Purines

Pyrimidines (one ring): Cytosine, Uracil, Thymine

Purines (two rings): Adenine, Guanine

ATP

Energy formed from DNA - it’s a nucleotide triphosphate (nucleotide with just three phosphates) - ATP powers cellular work because a phosphorus can detach and attach to an inactive protein, giving it energy (ATP + Inactive Protein → ADP + Active Protein) - can be mechanical, transport, or chemical work

RNA

Single-stranded, very flexible in shape (hairpins, stem loops, etc.) - combines A, C, G, and U - different from DNA because RNA is more exposed and flexible - RNA has an extra hydroxyl group also

DNA

Has complimentary base-pairing (hydrogen bonds form a double-stranded helix) - bonds purines with pyrimidines (C+G or A+T - C+G is stronger because it has 3 hydrogen bonds) - One strand is 5’ to 3’ and the other is 3’ to 5’ - helix shape forms major grooves and minor grooves

Generally-Accepted Characteristics of Life

1. Reproduction

2. Metabolism

Could DNA or RNA possible be the first “life form?”

What makes RNA a good candidate for the first “living” entity?

• Can catalyze its own replication

• Shared in all living organisms

• Stores information (DNA, info for protein formation, ribosome stuff, etc.)

Isomers

All amino acids in living systems are “left-handed” (L form) - AA enantiomers (“right-handed”) are found in meteorites and in space but not on Earth!

Different Types of Protein

• Antibodies (defense)

• Contractile and Motor (movement)

• Enzymes (catalyze chemical reactions)

• Hormones (act as signals)

• Receptors (receive chemical signals)

• Structural (structure)

• Transport (move substances across cell)

Four Levels of Protein Structure

1. Primary

2. Secondary

3. Tertiary

4. Quaternary

Primary Structure of Proteins

Unique sequence of amino acids - determines all three other structures based on the unique R-groups in the sequence - determines folding - amino acid substitution radically canges protein function and cell function (i.e. sickle-cell anemia)

Secondary Structure of Proteins

Formed by hydrogen bonds - either a beta-pleated sheet or an alpha helix

Tertiary Structure of Proteins

Interaction between R-groups that causes the polypeptide chain to be bent and folded - outer surfaces present functional groups that can interact with other molecules - hydrogen bonds, disulfide bonds, ionic bonds, hydrophobic interactions, etc.

Quaternary Structure of Proteins

Interaction between more than one protein - i.e. hemoglobin combines four proteins

Mechanisms of Catalysis

• Inducing strain (bonds are stretched)

• Substrate orientation (substrates brought together so bonds can form)

• Adding chemical groups (R groups may be directly involved) (lowers activation energy)

Reaction can be sped up by adding more enzymes, turning up the temperature, etc.

Competitive Inhibition

Regulatory molecule binds with active sights so the substrates can’t bind - sometimes, the regulatory molecule is the product of the reactants themselves (feedback inhibition)

Allosteric Regulation

Inhibitory molecule binds with one part of the enzyme which changes its shape so substrates don’t fit

Feedback Inhibition and Example

The regulatory molecule is the product of the reactants - Enzyme one makes A which does to enzyme 2 to make B to go to enzyme 3 to make product - the product does allosteric binding with enzyme 1 to regulate how much of it is made - happens because of high accumulation of product!

Cellular Respiration

Exergonic Reaction - synthesizes ADP and P_i into ATP - occurs in the cytoplasm and mitochondria - differs from combustion because the reactions are carefully controlled - about 40% of energy in glucose is transferred to ATP (the rest is lost to heat) - about 30 ATP produced!

C₆H₁₂O₆ + 6O₂ → 6CO₂ +6H₂O + ATP

Glucose is oxidized into CO₂ and O₂ is reduced into H₂O

Steps are glycolysis, citric acid cycle (krebs cycle), and oxidative phosphorylation (electron transport chain)

Reduction

Molecules that gain an electron are reduced - they often also gain a proton (H+) - compouns may have many C-H bonds - i.e. 6O₂ → 6H₂O in cellular respiration

Oxidation

Molecules that lose an electron are oxidized - they often also lose a proton (H+) - may have many C-O bonds - i.e. C₆H₁₂O₆ → 6CO₂ in cellular respiration

Glycolysis

In cytoplasm - one glucose (six carbons) broken down into two pyruvate (three carbons each) - this. also generates a small amount of ATP and produces NADH through oxidation of glucose

ATP + Glucose → NADH, ATP, Pyruvate (x2)

Citric Acid Cycle (Krebs Cycle)

After glycolysis, if oxygen is present, pyruvate is transported into the mitochondrial matrix where it’s converted to Acetyl-CoA - the cycle then fully oxidizes the remaining carbons of glucose - produces high-energy electron carriers (NADH and FADH₂) and releases CO₂ as a waste product - runs TWICE for every glucose molecule (two pyruvate from glucose) - goal is to transfer energy onto NAD+ and FADH so they can carry them to the electron transport chain

Pyruvate (oxidized to Acetyl CoA) → NADH, FADH₂, ATP, CO₂

Oxidative Phosphorylation (Electron Transport Chain)

ATP production through electron transport - in the inner membranes of the mitochondria, four protein complexes are arranged in order of electronegativity - NADH and FADH₂ are broken by enzymes (NADH first!!), releasing electrons and H+ that activate the electron transport chain - electrons go into the membrane which powers the four protein complexes - the four protein complexes funnel H+ through them, creating an electrochemical gradient - then, the H+ diffuses back through the membrane through ATP Synthase - the diffusion creates mechanical work (spinning) so the ATP Synthase can catalyze ADP and P_i into ATP (like a hydroelectric dam) - creates 26 ATP!!!

O₂ bonds with leftover electrons and H+ to clear the waste

NADH + FADH₂ + O₂ → ATP + H₂O

Regulation of Cellular Respiration

Regulated through feedback inhibition - Glycolysis is inhibited by high ATP concentrations - Krebs Cycle is inhibited by high ATP and NADH and accelerated by AMP, Acetyl CoA, and NAD+

What happens if you stop the electron transport chain?

For example, cyanide blocks Complex IV in the electron transport chain, causing quick death :(

Photosynthesis

Performed by autotrophs (plants, algae, protists, etc.)

1. Sunlight

2. Light Capturing Reactions

3. Calvin Cycle

6CO₂ + 6H₂O + Energy → Glucose + 6O₂ (respiration backwards!)

Light-Capturing Reactions for Photosynthesis

In the chloroplasts, H₂O is broken into O₂ (waste product), H+, and low-energy electrons - these low-energy electrons are transported to Photosystem II inside the Thylakoids - when Photosystem II is struck by protons (sunlight), electrons are promoted to a high-energy state - pheophytin takes the high-energy electrons and transports them down an electron transport chain, which allows H+ to be pushed into the thylakoid from the stroma - the H+ diffuses back to the stroma through ATP synthase which makes ATP - electrons go through another electron transport chain which allows them to be accepted/carried by NADP+ - ATP and NADPH used in Calvin Cycle

Calvin Cycle

1. Fixation - 3 Rubisco (RuBP) + 3 CO₂ → 6 3PGA

2. Reduction - 6 3PGA + 6 ATP + 6 NADPH → 6 G3P (one G3P per cycle saved to make one half of glucose molecule)

3. Regeneration - 5 G3P + 3 ATP → 3 Rubisco (so you can reuse it)

This allows CO₂ to be reduced and energy from ATP and NADPH to be stored long-term in glucose

Cyclic Phosphorylation

Way for plants to make more ATP without making oxygen or NADPH - electron in Photosystem I excited by sunlight, transferred to Ferredoxin, ATP produced through proton-motive force in the cytochrome complex, them back to Photosystem I

Z-Scheme

Process of Photosynthesis where electron in Photosystem II gets excited by sunlight to the Pheophytin, down ETC to Photosystem I, excited by sunlight to high-energy state, then down another ETC to form NADPH

Smooth Endoplasmic Reticulum

Makes fats/lipids (hormones, bilayer, etc.(

Rough Endoplasmic Reticulum

Sit where proteins are made (ribosomes on the rough ER actually make the proteins)

Ribosomes

Make protein