Biology 1110 Exam 1

What does it mean to say something is alive?

• There is no single, well accepted definition of life

• life is recognized by what living things do

What is life?

We define “life” interns of a set of shared characteristics

• all living things are compose of one or more cells

• living organisms use energy and are made of matter

• living organisms interact with their environment

• living organisms maintain homeostasis

• genetic material provides a blueprint that allows organisms to grow, develop, and reproduce

• populations of organisms evolve from one generation to the next

The nature of science

science is a way of thinking

• someone wonders about why something is the way it is and then decides to try and find the answer

• the scientific method, or the process of science, are the practices that produce scientific knowledge

Science cannot:

• tell us morally right or wrong

• explain subjective experiences like feelings

• address the existence of god or other supernatural beings

The scientific method

1. make observations

2. formulate a hypothesis

3. devise a testable prediction

4. conduct a critical experiment

5. draw conclusions and make revisions

Step one: Make observations

• on observation is a description, measurement, or record of any object or phenomenon

• what we see, hear, smell, read, experience, etc.

Step 2: Formulate a hypothesis

a scientific hypothesis is:

• an informed, logical, and plausible explanation for observations of the natural world

• a statement, not a question

Step 3: Devise a testable prediction

hypothesis must be

• testable

• helps us to make predictions expressed as “if…. then” statement

under certain conditions, we will make certain observations

Step 4: Conduct a critical experiment

• an experiment is designed to text a hypothesis

• it is a repeatable manipulation of one or more aspects of the natural world

• experiment makes it possible to decisively determine whether a particular hypothesis is correct

Elements of a well designed experiment (variables)

• Variables are characteristics of an object or an individual organisms that can change

• in an experiment, the researcher will manipulate or change the independent variable from one group to another

• the dependent variable responds, or could potentially respond, to changes in the independent variable

elements of a well designed experiment (experiments)

Experiments are divided into two groups

1. Control Group:

• is maintained under a standard set of conditions

• no change in the independent variable

2. Treatment group:

• is the experimental group

• is maintained under the same standard set of conditions as the control group

• the independent variable, is however, manipulated

elements of a well designed experiment (strategies)

Blind/double-blind strategies

• the experimental subjects do not know which treatment (if any) they are receiving

Randomized

• the subjects are randomly assigned into experimental and control groups

Step 5: Draw Conclusions, make revisions

• what conclusions can you draw from the experiment?

• were the predictions and hypothesis supported?

(Step 6): publish

• Peer-reviewed publications are found in scientific journals that publish research after it has passed the scrutiny of experts who have no direct involvement in the research under review

scientific literacy

• more claims that we are exposed to each day are NOT TRUE

• Scientific literacy is an understanding of the basics of science and the scientific process

• enables us to evaluate the evidence behind scientific claims and uses critical thinking to make informed decisions

correlation doesn’t equal

causation

Why chemistry in important in Bio?

• we are all just a bunch of chemicals

• in order for our bodies to move, to think, to grow, to do anything, chemical reactions have to occur

4 main chemical elements essential for life in most organisms

• Oxygen: 65% human body mass and 25.5% all atoms in human body

• Carbon: 18% human body mass and 9.5% all atoms in human body

• Hydrogen: 9% human body mass and 63.0% all atoms in human body

• Nitrogen: 3% human body mass and 1.4% all atoms in human body

Atoms

• atom is the smallest piece of an element that retains the characteristics of the element

• atoms can be broken down further into subatomic particles:

protons and neutrons are located in the nucleus; electrons move rapidly around the nucleus forming a “electron cloud”

chemical bonding

• a chemical bond is an attraction force that holds atoms together and link them into a molecule

• atoms combine with other atoms in ways that complete their outermost valence shell

• they can either share, donate or steal valence electrons

covalent bond

is the sharing of a pair of valence electrons by two atoms

electronegativity

• electronegativity is the strength with which atoms pull electrons toward themselves

• the more electronegative an atom, the more strongly it pulls shared electrons toward itself

Non polar and Polar Covalent bonds

1. Non polar covalent bonds: electrons are halfway between the two atoms, shared equally

2. Polar Covalent: electrons are not shared equally, so partial charges exist on the O and H atoms

Ionic Bonds

• some atoms have such different electronegativity that one atom completely pulls an electron away from the other

• electrons will completely transfer over to highly electronegative atoms

Molecular shape

• actual shape of more complex molecules is rarely planar

• molecular shape is critical! it determines how biological molecules specifically recognize and respond to one another

• geometry of bond angles may also impact overall polarity

opiates, such as morphine, and naturally produced endorphins have similar effects because their shapes are similar and the bind to the same receptors in the brain

Bonding and interactions between molecules

In hydrogen bonds, the hydrogen atom from one polar molecule is attracted to an electronegative atom of another

• represented as dashed or dotted lines

• individually, these are weak bonds that can form and break easily, collectively, many H bonds can be strong overall

Van der Waals dispersion forces are temporary attractive forces due to location of electrons

• electrons in outer shells of atoms may be equally or unequally distributed and fleeting attractions to other molecules may arise

hydrogen bonds between water molecules

water emergent properties

1. Cohesion, adhesion, and surface tension

2. water as an efficient solvent

3. Expansion upon freezing

4. Moderation of temperature

5. Water and Acid-Base reactions

1. Cohesion, adhesion and surface tension

• attraction between water molecules is call Cohesion

• Attraction between water and other polar or charged molecules is called Adhesion

• Surface tension- cohesive force caused by stronger attraction between molecules at surface of liquid

2. Water as an effective solvent

• hydrophilic (“Water-loving”) molecules

ions and polar molecules stay in solution due to their interactions with water’s partial charges

• hydrophobic (“water-fearing”) molecules

Uncharged and non polar compounds do not dissolve in water.

Hydrophobic molecules interact with each other through hydrophobic interactions

3. Expansion upon freezing

• as the water freezes into ice, it forms a relatively open crystal structure

• ice is less dense than liquid water- this is why ice floats

• ice forms an insulating “blanket” on waters surface

Ice: water molecules are less likely to move apart due to decrease heat energy. Hydrogen bonds are more stable, resulting in an orderly array of molecules

Liquid water: water molecules are in rapid motion, and hydrogen bonds continually break and re-form

4. moderation of temperature

• water has a very high specific heat (specific heat- amount of energy needed to raise the temperature of 1 gram of a substance by 1 degree celsius)

• water resists changes its temperature- cools and heats up very slowly

5. Water and Acid-base Reactions

• water molecules dissociate into Hydrogen ion H+ and a Hydroxide ion OH-

H₂O — H⁺ + OH^-

• only one water molecules in every 554 million is dissociated, concentration of each ion in pure water is 10-7 M (0.0000001 M)

10-7 H⁺ and 10-7 OH^-=10-14 ions

• The pH scale expresses proton concentration [H+] in a solution- negative base 10 logarithmic scale

pH= -log[H+]

pH= -log[10-7]=7 for pure water

The pH reveals acidic or basic solutions

• Acids: substances that give up protons during chemical reactions (adding acid to solution increases proton concentration of solution)

• Bases: Substances that acquire protons during chemical reactions

pH scale

• acids have a pH of less than 7

• Bases have a pH of greater than 7

Carbon provides a molecular skeleton

• organic molecules: molecules that contains carbon bonded to other elements, linked in a chain or ring

except for water, almost all molecules found in organisms contain carbon

(Functional groups with biological importance) Amino

-NH₂

• Examples: Amino Acids

• Properties: weakly basic (can accept H+); polar; forms part of peptide bonds

(Functional groups with biological importance) Carbonyl ketone/ aldehyde

-CO

• Examples: Steroids, waxes, proteins

• properties: Polar; highly chemically reactive; forms hydrogen bonds

(Functional groups with biological importance) Carboxyl

-COOH

• Examples: Amino Acids, Fatty Acids

• Properties: Acidic (gives up H+ in water); forms part of peptide bonds

(Functional groups with biological importance) Hydroxyl

-OH

• Examples: steroids, alcohol, carbohydrates, some amino acids

• Properties: polar; forms hydrogen bonds with water

(Functional groups with biological importance) Methyl

-CH₃

• examples: may be attached to DNA, proteins, and carbohydrates

• properties: non polar

(Functional groups with biological importance) Phosphate

-PO₄^2-

• Examples: Nucleic acids, ATP, and phospholipids

• properties: Polar; weakly acidic and thus negatively charged at typical pH of living organisms

(Functional groups with biological importance) Sulphate

-SO₄^2-

• examples: may be attached to carbohydrates, proteins, and lipids

• properties: polar; negatively charged at typical pH

(Functional groups with biological importance) Sulfhydryl

-SH

• Examples: proteins, amino acid cysteine

• properties: polar; forms disulfide bridges in many proteins

small organic molecules can assemble int large molecules

• biological macromolecules (except lipid) are also call polymers - large molecules made of smaller subunits

• a monomer is a single structural unit of a polymer

forming macromolecules

• Condensation (dehydration) reactions join monomers into polymers

• result in the loss of water molecules

breaking macromolecules

• hydrolysis is the reverse reaction of dehydration

• breaks polymers apart by adding a water molecule

(4 major organic molecules) carbohydrates

• Structure: the general formula is Cn(H₂O)n, where n is a whole number

• Key Functions: simple carbohydrates are broken down to make ATP, used as a source of energy. Larger carbohydrates store energy or may play a structural role, as in plant cell walls. Some carbohydrates function as molecular tags, allowing recognition of specific cells and molecules

• Examples: simple sugars such as glucose; large polymers such as starch and cellulose

(4 major organic molecules) Lipids

• structure: lipids are non polar molecules primarily composed of carbon and hydrogen, with some oxygen

• Key functions: lipids are key part of cell membranes and function as hormones and in energy storage. In animals, they act as insulators and shock absorbers

• Examples: phospholipids, estrogen, testosterone, triglycerides

(4 major organic molecules) proteins

• structure: a polypeptide is a structural unit composed of a linear sequence of amino acids. A protein is a functional unit composed of one or more polypeptides

• key functions: proteins play a key role in cell structure and preform diverse cellular functions, including gene expression and regulation, movement , defense, signing, metabolism, and transport.

(4 major organic molecules) Nucleic acids

• Structure: linear sequence of nucleotides. DNA is double stranded.

• Key Functions: DNA stores genetic information in genes. RNA is made from DNA and provides access to that information

• examples: DNA and RNA

Carbohydrates

• Composed of Carbon, Hydrogen, and Oxygen atoms

• Cn(H₂O)n

Commonly found as:

• Monosaccharides (One sugar)- simple sugars

• disaccharides (two sugars)

• polysaccharides (many sugars)- polymers

Monosaccharides

• the most common types have five or six carbons

• may exist in a linear structure, but in living cells they usually occur in a ring structure

• Molecules with identical formulas but different structures and called Isomers

Isomers

differing effects of isomers demonstrate that organisms are sensitive to even subtle variations in molecules

• ibuprofen: reduces inflammation and pain

• Albuterol: relaxes bronchial (airway) muscles, improving airflow in asthma patients

Disaccharide

• compose of two monosaccharides

• joined by dehydration reaction- the bond formed is call a glycosidic bond

• Examples: Sucrose, Maltose, Lactose

energy storage polysaccharides

• polymers of glucose

• starch- stored in chloroplasts of plant cells (moderately branched) (a-1,4-glycosidic linkages from linear chains and a-1,6-glycosidic linkages from branches)

• Glycogen- stored in liver and muscle cells (highly branched)(a-1,6-glycosidic linkages create more branches in glycogen)

• the way the glucose molecules are linked allows branching and highly solubility in water

structural polysaccharides

• cellulose: the way the glucose molecules are linked allow straight, rodlike molecules held together by hydrogen bonds (unbranched)( B-1, 4-glycosidic linkages from chains without any branching)

• leads to a rigid structure that is insoluble in water and undigestible by humans

• Peptidoglycan- cell walls of bacteria

• Chitin- cell walls of fungi; exoskeletons of insects, arachnids, crustaceans

proteins involved in gene expression and regulation

• Make mRNA from a DNA template; synthesize polypeptides from mRNA; regulate genes

• Examples: RNA polymerase assists in synthesizing RNA from DNA

Motor proteins

• Initiate movement

• Example: myosin provides the contractile force of muscle

Defense proteins

• protects organisms against disease

• Examples: antibodies help destroy bacteria or viruses

metabolic enzymes (proteins)

• increase rate of chemical reactions important in energy balance

• example: hexokinase is an enzyme involved in glucose metabolism

cell-signaling proteins

• enable cells to communicate with each other and to sense the environment

• Example: notch proteins coordinate growth of cells in developing animals

structural proteins

• support and strengthen structures

• Examples: actin provides shape to the cytoplasm of plant and animal cells. Collagen gives strength to tendons

transporters (proteins)

• mediate movement of solutes across membranes

• Examples: glucose transporters move glucose from outside cells to inside cells, where it can be used for energy

Nonpolar and polar amino acid drawing

• amino group: positively charged at neutral pH

• Carboxyl group: negatively charged at neutral pH

Amino acids like to form polypeptides

• amino acids are joined together when a bond forms between a carboxyl group of one amino acid and an amino group of another

• the resulting C-N bond is called a peptide bond

a linear chain of amino acids

primary (1^o) structure

• unique sequence of amino acids

• limitless number of possibilities (know proteins from <100 to ~30,000 amino acids)

• Specific order of R-group determines a protein’s fold, properties, and functions

secondary (2^o) structure

• formed by hydrogen bonds between an amino group of one amino acid and a carboxyl group of another

Tertiary (3^o) Structure

Overall distinct shape of polypeptides

Formed by interactions between R-groups

• hydrogen bonds, hydrophobic interactions, van der walls forces, ionic interactions, disulfide (covalent) bonds

Quaternary (4^o) structure

results when two or more separate polypeptide chains interact with each other to form one functional protein

AI can be used to predict the three-dimensional structure of proteins

Demis Hassabis, John Jumper, and colleagues from DeepMind developed AlphaFold, an AI program that can predict the structure of proteins

• in 2022, DeepMind released the 3D structures of more than 200 million proteins predicted by alphafold

• in 2024, they were awarded the Nobel Prize in chemistry for this achievement

• Can be applied in structural biology, drug discovery, protein-protein interactions prediction of protein functions, vaccine design.

Normal folding is crucial to function

• Normal protein folding is crucial and often spontaneous folded molecule is more energetically stable

• a denatured (unfolded) protein is unable to function normally

Nucleic acids

• nucleic acids are macromolecules responsible for the storage, expression, and transmission of genetic information.

two Classes:

• Deoxyribonucleic (DNA) store genetic information encoded in the sequence of nucleotide monomers

• Ribonucleic acid (RNA) decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain, involved in translation

nucleic acids are polymers of…

nucleotides

polymerization of nucleotides

• dehydration reactions link the OH group of the sugar of one nucleotide to a phosphate group of another

Nucleic acids, like proteins, have directionality

• one end has a free 5’ phosphate

• other end has a free 3’ hydroxyl group (OH)

DNA structure

• A DNA molecules consists of two strands of nucleotides coiled around each other to form a double helix

• the two strands run in opposite directions- antiparallel

• the two strands are held together by hydrogen bonds between complementary bases on opposite strands

Adenine (A) pairs with thymine (T) via two hydrogen bonds

Cytosine (C) pairs with guanine (G) via three hydrogen bonds

RNA structure

• RNA usually remains single-stranded

• the sugar is ribose (not deoxyribose)

• RNA has uracil (U) instead of thymine (T)

• Base pairing can occur within a single strand, leading to formation of hairpins

lipids

• lipids are not polymers (no monomers that are linked together by dehydration reactions)

• the unifying feature is they do not dissolve in water (hydrophobic)

• predominantly hydrocarbon (made only of C and H)

three types: fat (triglycerides), phospholipids, steroids

fats provide long term energy storage

Triglycerides - three fatty acids linked to a glycerol

• two groups of fatty acids: carboxyl group, 14-20 carbons

phospholipids are a major component of the…

cell membrane

steroids

• all contain the same four-ring structure

• cholesterol regulates the fluidity of animal cell membranes and its used to synthesize other steroids

all cells share common features

all cells have:

1. proteins: preform most of the cell’s functions

2. nucleic acids: store, transmit, and process information

3. carbohydrates: provide chemical energy, carbon, support, and identity

4. cell (plasma) membrane: serves as a selectively permeable membrane barrier

structure of bacteria cell

Eukaryotic cells

three key differences between eukaryotic and prokaryotic cells:

1. eukaryotic cells are generally much larger

2. eukaryotic genetic material is enclosed in a nucleus

3. eukaryotic cytoplasm is compartmentalized into a larger number of distinct organelles

Eukaryotic cells may be multicellular or unicellular

animal cell image

plant cell image

important functions of biological membranes

• selective uptake and export of ions and molecules

• cell compartmentalization

• protein sorting

• anchoring of the cytoskeleton

• production of energy intermediates such as ATP

• cell signaling

• cell and nuclear division

• adhesion of cells to each other and to the extracellular matrix

4 interacting parts of the eukaryotic cells

• nucleus

• cytosol

• endomembrane system

• semiautonomous organells

nucleus

• location of most genomes

• gene regulation

• organization and protection of chromosomes via nuclear matrix

cytosol

• coordination of responses to the environment

• coordination of metabolism

• synthesis of the proteome

• organization and movement via cytoskeleton and motor proteins

semiautonomous organells

Mitochondria

• synthesis of ATP

• synthesis and modification of other organic molecules

chloroplasts (plants and algae)

• photosynthesis

Endomembrane system

Nuclear envelope

• boundary that surrounds the nucleus

Endoplasmic reticulum

• protein secretion and sorting

• glycosylation

• lipid synthesis

• metabolic functions and accumulation of Ca²⁺

Golgi apparatus

• protein secretion and sorting

• glycosylation

lysosome/vacuoles

• degradation of organic molecules

• storage of organic molecules

• accumulation of water (plant vacuoles)

peroxisomes

• breakdown of toxic molecules such as H₂O₂

• breakdown and synthesis of organic molecules

Plasma membrane

• uptake and excretion of ions and molecules

• cell signaling

• cell adhesion

the nucleus controls protein production

• nucleus is composed of DNA and proteins = chromatin

• messenger RNA (mRNA) is synthesized in the nucleus and it matches the sequence of DNA

• mRNA carries the protein “recipe” through a nuclear pore to ribosomes, where the protein is synthesized

• assembly is ribosomes is happening in nucleolus

Endoplasmic reticulum

part of the endomembrane system; it is an extension of the nuclear envelope

The rough ER

• has bound ribosomes

• involved in synthesis and sorting of proteins, and glycosylation

• it is a membrane factory for the cell-it grows in place adding membrane proteins and phospholipids to its own membrane

The smooth ER

• lacks ribosomes

• function is detoxification, carbohydrate metabolism, calcium storage, and synthesis and modification of lipids

the Golgi apparatus

Golgi completes protein folding and further modifies products of the ER, sort an packages materials into transport vesicles.

from ER to Golgi and out…

lysosomes

• some transport vesicles leaving the Golgi carry enzymes that catalyze hydrolysis reactions

• they originate in the rough ER, Golgi apparatus usually detects these specific enzymes by recognizing a sugar attached to hem, then packages them into the vesicles that eventually become lysosomes

• Acid hydrolyses the break down macromolecules work best at low pH

Vacuoles

• Vacuoles are prominent organelles in plant cells, fungal cells, and certain proteins

• most plant cells lack lysosomes, cellular digestion occurs in large central vacuoles, which also helps regulate the size and water balance of plant cells

peroxisomes

• peroxisome catalyze a variety of chemical reactions

• in mammals, they breakdown toxins in cells of the liver

• contain enzymes that remove hydrogen atom from various substrates and transfer them to oxygen, producing hydrogen peroxide (during alcohol detoxification for example)

• catalase breaks down H₂O₂ yielding water as oxygen gas

mitochondria

• mitochondria extracts energy from food (sugars, lipids) to make ATP

• folds in the mitochondrial membrane are called Cristae

• these are the sites for the chemical reactions of cellular respiration- ENERGY extraction/ATP production