Bio 1110 Exam 1 (based on the book)

Principle 1: cells are the simplest units of life

• Organism: can be used to term all living things (maintain internal order seperate from teh environment)

Cell theory:

1. All living things are composed of one or more cell (unicellular: one cell and multicellular: multiple cells)

2. cells are the smallest units of life

3. new cells come from pre-existing cells by cell division

Principle 2: living organisms use energy and are composed of matter

The maintence of organization requires energy; therefore, all living things auire and use energy from their enviornment to maintain internal order.

• cellular respiration: the release of energy through chemical reations that breakdown energy-yielding nutrients.

• Metabolism: energy used to synthesis the components that make up individual cells and living organisms. involved in the breakdown and synthesis of cellular molecules.

• photosynthesis: plants, algae, and certain bacteria harness light energy to produce their own nutrients.

Principle 3: living organisms interact with their enviornment

• all organisms must respond and interact to changes in their enviornment an dother organisms they may encounter.

Ex: many species develop thicker coatsof fur to protect themselves in winter

principle 4: living organisms maintain homeostasis

• homeostasis: living organisms regulate their bodies to maintain relatively stable internal conditions

all organisms continually regulate their cellular metabolism so that nutrient molecules are used at an apptopriate rate and new cellular componenets are synthesized when they are needed.

princple 5: the genetic material provides a blueprint that allows organisms to grow, develop, and reporduce

• to sustain life from one generation to the next organisms must reproduce

• off spring tend to have very similar characteristics to their parents becuase all organisms contain genetic material composed of deoxyribonucleic acid (DNA), which provides a blueprint for the organization, development, and function of living things

• DNA is heritable so offspring get inherit DNA from their parents

Genes: are a segment of DNA that govern the characteristics, or traits of organisms. They are transcribed as mRNA or messanger RNA, in which they are then translated into a polypeptide ith a specific amino acid sequence.

protein: is composed of one or more polypepetides, and tehy are largly responsible for traits in living organisms.

genome: entire genetic makeup of an organism

principle 6: population of organisms evolve from one generationb to the next and are related by an evolutionary history

• Evolution or biological evoltion: heritable change in a population of organisms from generation to generation, which cause populations to be better adapted to the enviornment.

We also all share a common ancestry

principle 7: the structural features of living organisms determine their functions

• structure determines function pertians to all biological organisms

ex: webbed feet in ducks helps them swim

principle 8: New properties of life emerge from complex interactions

• Emergent properties: when individual componenets of an organism interact with each other or with the external enviornment to create novel structures and functions,

principle 9: biology is an experimental science

• biologist gather additional information to form a hypothesis, which is proposed explanation for a natural phenomenon, and then they run experiments to test teh validity.

principle 10: biology is a quantitative science

• biologist analyze data in a quantitative way and use mathematical apporches to make predictions

principle 11: biologists use models and simulations to test experimental predictions and convey their ideas

• Scientific model: is a conceptual, mathmatical,or physical depiction of a real world phenomeon

principle 12: biology affects our society

• the works of biologists have far-reaching effects on our society

ex: insulin

living organisms are studied at different levels of orgaization

molecules and macromolecules

atoms bond together to form molecules. many smaller molecules can bond together to form large polymers called macromolecules.

• Exapmles of macromolecules: carbohydrates, protiens, and nucleic acids

hypothesis vs. prediction

• Hypothesis: is a proposed explination fro a natural phenomenon.

Ex: maple tress drop their leaves in autumn becuas ethe shortened amount of daylight

• Prediction: expected outcomes that can be shown to be correct or incoorect. Should be testable (hypothesis can be shown to be consistent or inconsistent with data that are ibtained via experimentation.

also can be faslifiable: show to be incorrect by additional observations or experimentation

theory

is a broad explination of some aspect of the natural world that is substained by a large body of evidence.

two key attributes of a scientific theory

1. constistency with a vast amount of know data

2. the ability to make many correct predictions

hypothesis testing

1. observations are made regarding a natural phenomenon

2. these observations lead to a hypothesis that tries to explain the phenomenon. A useful hypothesus is one that is testable because it makes specific predictions

3. experimentation is conducted to dtermin eif the predictions are correct

4. the data from the experiment are analyzed

5. the hypotheis is consideredd to be consistent with the data or it is rejected

well designed experiment

• many experiments need a control group (not subject to one particular variable) and an experimental group (sample has a variation that doesn’t occur in the control group)

• need a common form od analysis to determine if the data collected from the two groups is truly different

• Valid experiments are repeatable (obtained results over multiple occasions)

features of living organisms

1. living organisms use energy and are composed of matter

2. the structural features of living organisms determine their functions

3. genetic materical provides a blueprint that allows organisms to develop, grow, and reporduce

4. new properties of life emerge from complex interactions

5. biologists use models and simulations to test emerimental predictions and convey their ideas

subatomic particles in an atom

modeling of a nitrogen atom

main elements in all living organisms

oxygen, carbon, hydrogen, nitrogen

covalent bonds

in which atoms share a pair of electrons, can occur between atoms whose outer shells are not full.

electronegativity

is a measure of an atoms abitilty to attract electrons in a bond with another atom

hydrogen bond

ability of one molecule to lossely associate with another molecule through a weak interaction.

• form when a hydrogen atom in on epolar molecule becomes electrically attracted to an electronegative atom in another polar molecule.

cations vs. anions

• cations: ions with a net positive hcarge

• anions: ions with a net negative charge

ionic bond

when a cation bonds to an anion

solutes vs. solvents

• solutes: substances that dissolve in liquid

• solvents: the liquid that dissolves substances

for a substance to dissolve in water…

it must be eletrically attracted to the H₂O molecules

• the oxygen in water has a slight negative charge

• the hydrogen in water has a slight positive charge

hydrophilic vs. hydrophobic

• hydrophilic: “water loving” polar/ionic molecules that dissolve in water

• hydrophobic: “water fearing” nonpolar molecules that don’t dissolve in water

amphipathic

molecules that have both hydrophilic and hydrophobic reagions

• when mixed with water, long, amphipathic molecules may aggregate into spheres called micelles where the nonpolar ends move toward the interior and the polar/ionic ends facinging the exterior

heat of vaporization

heat required to vaporize 1 mol of any substance at its boiling point

heat of fusion

the amount of heat energy that must be withdrawn or released from a substance to cause it to change from the liquid to teh soild state.

specific heat

as the amount of heat energy required to raise the temperature of one gram of a substance by one degree celcius

heat capacity

the amount of heat energy required to raise the temperaute of an entire object other a particular amount of a substance

cohesion

the ability of like molecules to noncovalently bind to each other; the attraction of water molecules to each other

adhesion

ability of different molecules to be attracted to each other

• water can adhere to surfaces to which it can hydrogen bond such as paper towels.

surface tension

is a measuer of the attraction between molecules at the surface of a liquid.

• in the case of water, the attrictive force between hydrogen bonded water molecules at the interface between water an dair is what causes water to form droplets

pure water has the ability to dissociate to a very small extent into..

hydroxide ions (OH-) and hydgrogen ions (H+)

• [H+] [OH-] = [10^-7 M] [10^-7 M] = 10^-14 M

pH

the mathmatical expression of a solution’s hydgrogen ion (H+) concentration, defined as the negative logarithm to the base 10 of the H+ concentration

• pH= -log₁₀[H+]

orgainc molecules include:

lipids and macromolecules such as proteins, nuecleic acids, and some carbohydrates.

hydrocarbons

• molecules that are predominantly or entirely C-H and C-C bonds, and are hydrophobic

biologically important functional groups that bond to carbon

dehydration (condensation) reation

• two molecules from a covalent bond and become a single molecule, usually with the release of a small molecule of water.

hydrolysis reaction

• polymers are broken down into their constituent monomers

• water molecule is used to break, or lyse, the linkage that holds monomers together

Carbohydrates

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

• Function: simple carbohydrtes are metabolized to make ATP, which is used as a source of energy. Larger carbohydrates, called polysaccharides, 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.

• Ex: simple sugars, such as glucose; larger polysaccharides, such as glycogen, starch, and cellulose

Lipids

• Structure: lipids are nonpolar molecules that are primarily composed of carbon and hydrogen, with some oxygen.

• Function: lipids are a key part of cell membranes and function as hormones and in energy storage; in animals, they act as insulators and shock absorbers

• Ex: phospholipids, estrogen, testosterones, triglycerides

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.

• Functions: proteins play a key role in cell structure and carry out a diverse array of cellular functions; for example, there are proteins involved with gene expression and regulation, motor protiens, cell-signaling proteins, metabolic enzymes, structural proteins, and transporters

Nucleic acids

• Structure: a linear sequence of nucleotides; DNA is double stranded. RNA is single stranded but may have double stranded regions

• Function: DNA stores genetic information in units called genes. RNA is made using DNA as a template and provides access to that information

• Ex: DNA and RNA

what groups are found in certain carbohydrates?

• amino (-NH₂)

• sulfate (-SO₄^-4)

monosaccharides

• simplest carbohydrates

• most common contains 5 carbon, called pentose, or 6 carbon called hexos

• pentose: ribose and deoxyribose which are part of RNA and DNA molecules

• hexoses: galactose, glucose, and fractose (they have the same chemical formula but are arranged differently so they are isomers)

glucose importance in the cell

• very soluble in water and circulates in the bood or body fluids of animals, where it can be transported across cell membranes. Once inside the cell, glucose can be metabolized by enzymes into smaller molecules, thereby relesing energy

• this energy is then used to produce ATP, which, in turn, dircetly powers a variety of cellular processes

disaccharides (two sugars)

• monosaccharides linked together during dehydration reaction

• sucrose (composed of glucose and fructose) is the major transporter of sugar in plants

• fromed by glycosidic bond (dehydration reaction between two sugars)

polysaccharides

many monosaccharides are linked together to form long polymers

• starch: found in plant cells

• glycogen: present in certain types of animal cells

• cellulose: found in the cell walls of plant cells

• peptidoglycan: found in the cell walls of certain bacteria

• chitin: found in cells walls of fungi and the exoskeletons of arthopods

• glycosaminoglycans: found in the connective tissue and teh extracellular matrix in animals

solubility of polysaccharides

• starch and glycogen, the bonds form between carbons 1 and 4, and between 1 and 6. The high degree of branching in lycogen contributes to its solubility in animal tissues. This is because the extensive branching creates a more open structure, in which many hydrophilic -OH functional groups have access to water and can hydrogen bond with it.

• starch is less branched, making it less soluble

starch and glycogen are used to

store energy in the cells

• they cane be hydrolyzed to yield monosaccharides, which are metabolized to provide the energy to make ATP

• they are an effecient manes of storing energy for those times when a plant or an aminal cannot obtain sufficent energy from its enviornment.

cellulose, peptidoglycans, chitin, and glycosaminoglycan play a

structural role

• cellulose has a linear arrangement for carbon- carbon bonds and no branching which allows a vast number of hydgrogen bonds to form between plant cell walls.

• the hydrogen bonds from between -OH groups on carbon 3 and 6

• peptidoglycan: found in cell walls of certian bacteria; consist of sugars and amino acids.

• chintin is a tough polysaccharidee that forms the external skeleton of insects and crustanceans (lobster, shrimp) ad ell as the cell waslls of fungi

• glycosaminoglycans in the ECM and provides a structural framework in cells of animals

lipids definition

fatty acids or their derivatives that are poorly soluble in water

• triglycerides, phospholipids, steriods, and waxes

triglycerides (fat)

• consist of a glycerol molecule linked to three fatty acids .

• Glycerol is a three-carbon molecule with on e-OH group bonded to each carbon.

• a fatty acid is a chain of carbon and hydrogen atoms with a carboxyl group (-COOH) at one end

the fatty acids found in triglycerides and other lipids differ with regard to their…

lenght and the presence or absence of double bonds

saturated fatty acids

all carbons in the hydrocarbon chain are linked by single bonds (C-C). the term saturated indicates means that each carbon has a maximal number of attached hydrogens.

• monosaturated fatty acids contain one C=C double bond that introduces a kink into the linear shape

• polyunsaturated fatty acids contain two or more C=C double bonds

the hydrocarbon tain of a fatty acid does not

for a hydrogen bond with water and is very hydrophobic.

triglycerides are important for

storing energy

• they hydrolysis of triglycerides releases their fatty acids, which can be metabolized and provide energy to make ATP

phospholipids

• similar structure to triglycerides but have. athird -OH group of glycerol liked to a phosphate group instead of a fatty acid.

• small polar or charged nitrogen coniating molecule is attached to this phosphate.

• the glycerol, phosphate group, and charged molecule constitute a polar (hydrophilic) head and the two fatty acids from nonpolar (hydrophobic) tails

• in water, they form a phosophlipid bilayer with the polar heads interacting with water and the nonpolar tails facing inward

steroids

• have a distinctly different chemical structure than other lipids

• 4 fused rings of carbon atoms

• sterols: conatains an -OH group at a particular carbon. found in fungi, plants, and animals.

• cholesterol: found in cell membranes of animals, where it contributes to the membrane structure and function. in animal cells, synthesizes steroid hormones like estrogen and androgens.

waxes

• secreat onto the surface of leaves of plants and the cuticles of insects.

• all waxes contain one or more hydrocarbons and long structures that resemble a fatty acid attached by its carboxyl group to another long hydgrocarbon chain.

• most waxes are nonpolar and exclude water.

• also have structural element like honeycomb

proteins involved in gene expression and regulation

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

• Ex: RNA polymerase assists in synthesizing RNA from DNA

motor proteins

• initiate movement

• Ex: myosin provides the contractile force of muscle

defense proteins

• protect organisms against disease

• Ex: antibodies help destroy bacteria or viruses

metobolic enzymes

• increase rates of chemical reactions important in energy balance

• Ex: hexokinase is an enzyme involved in glucose metabolism

cell- signaling proteins

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

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

structural proteins

• support and strengthen structures

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

transporters

• mediate movement of solutes across membranes

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

proteins are polymers of…

amino acids

• all amino acids contain a carbon atom, called a-carbon, that is linked to an amino group (-NH₂) and a corboxyl group (-COOH).

what happens when amino acids dissolve in water at a neutral pH?

• the -NH₂ group acts as a base and accepts a hydrogen ion, becoming positivily charged

• the -COOH group acts as an acid and loses a hydrgoen ion and becomes negatively charged

amino acids found in proteins are distiguished by their

side chains

• the arrangement and chemical features of teh side chains cause proteins to fold and adopt their three-dimensional shapes

• certain amino acid chains may be critical in protein functions

Ex: amino acid side chains with specific regions of enzymes are essential for enzymes to catalyze chemical reactions

20 amino acids found in proteins

peptide bond

• a covalent bond that links amino acids in a polypeptide

polypeptide: a structural unit compose of linear sequence of amino acids

• a protein is a functional unit compose of one or more polypeptides that have folded or twisted into precise three- dimensional shapes

primary structure of proteins

• is the amino acid sequence of its polypeptides.

• determined by genes (they carry the information for the production of polypeptides with specific amino acid sequences)

• mutations withing genes can alter the amino acid sequence and affect teh proteins function

secondary structure of a protein

• folding (that can be irregular) in certain regions can have a repeating folding pattern (contribute great strenght)

• basic types are a helix and B pleated sheets

• a helix: a polypeptide backbone forms a repeating helical structure that is stabilized by hydrogen bonds alonbg the length of the backbone. occurs atr irregular intervals which cause the backbone to twist to a helix. the hydrogen linked to a nitrogen atom formation a hydrogen bond with an oxygen atom, which in turn is double bonded to a carbon atom.

• B pleated sheets regions of a polypeptide backbone lie parallel to each other. hydrogen bonds netween hydrogen linked nitrigen atom an a double bonded oxyegn form between these parallel regins. causes a repeating zigzag, or pleated, shape

tertiary structure of a protein

• the polypeptide from the seondary structure folds and refolds upon itself to assume a three-dimensional shape

• includes all secondary structures plus any other interactions involving amino acid side chains.

• final structure for some proteins

Quaternary structure of proteins

• proteins that consist of more than one polypeptide.

Ex: hemoglobin (made of 4 protein subunits)

factor that detemine protein structure

• hydrogen bond: large number of weak hydrogen bonds collectively produce a strong force that promotes protein folding and stability

• ionic bonds and other polar interactions: positively chared side chains may bind to negatively charged side chains via ionic bonds

• hydtophobic effect: the nonpolar or hydrophobic amino acids are found in the center of teh protein, minimizing contact with water

• van der walls dispersion forces: atoms within a molecule haev temporary attractions for each other if they are an optimal distance apart (tertiary and quaternary structure)

• disulfide bridges: the side chain (-SH) of cystine can react with an -SH group of another cysteune side chain to form a covalent bond. can occur within or between polypeptides.

nucleic acids

• macromolecules that are responsible for the storage expression, and trasmission of genetic information.

• DNA: store genetic information

• RNA: decode the information in the DNA to instruct for linking a specific sequence of amino acids to form a polypeptide

three components of a nucleiotide (Monomers in the polymers of DNA and RNA)

• a phosphate group

• a pentose sugar (deoxyribose or ribose)

• a single or double ring of carbon and nitrogen atoms known as a base

DNA

• contains 5 carbon sugar deoxyribose

• Purine bases: Adenine (A) and Guanine (G) haev fused double rings of carbon and nitrogen atoms

• Pyrimidine bases: Cytosine (C) and Thymine (T) have a single ring structure

• double helix two strands of nucleotides coiled around each other (heald by hydrogen bonds)

• A pairs with T and G pairs with C

RNA

• consists of a single strand of nucleotides

• sugar in each nucleotide is ribose

• Thymine (T) base is replaced by Uracil (U)

Other forms of RNA:

• messanger RNA (mRNA)

• ribosomal RNA (rRNA)

• transfer RNA (tRNA)

to understand the origin of life, we can veiw the process as occurring in 4 overlapping stages:

• Stage 1: necleotides and amino acids were produced prior to the existence of cells

• Stage 2: nucleotides became polymerized to form RNA and/or DNA, and amino acids became polymerized to form proteins

• Stage 3: polymers bacame enclosed in membranes

• stage 4: by a process of chemical selection, polymers enclsoed in membranes acquired properties that are associated with living cells.

RNA importance as the first macromolecule

1. RNA have the ability to store information in its nucleotide base sequence

2. due to base pairing, its nucleotide sequence has the capacity for self-replication

3. RNA can preform a varirty of catalytic functions. the results of mayn experiments have shown that some RNA molecules function as ribozymes- RNA molecules that catlyze chemical reaction

cells structures are primarily determined by four factors:

1. Matter: found in all living things composed of atoms, molecules, and macromolecules.

2. Energy: neede to produce molecules and macromolecules to carry out cellular functions

3. Organization: all living cells have the ability to build and maintain their internal organization. Normally by protein-protein interactions that create intticate cell structure and faciliate processes in which proteins interact in a consistent series of steps.

4. Information: all living things have genomes, entire complement of genetic material, and its material is passed. from cell to cell (parent to offspring) and contain information on how to produce proteins.

prokaryotic cells

• have a simple structure

• lack a membrane enclosed nucleus

• two categories: bacteria and archaea

• bacteria cells typically include: Plasma membrane, cytoplasm, nucleoid, ribosomes, cell wall, glycocalyx, pili, and flagella.

plasma membrane

a bilayer of phospholipids and embedded proteins that forms a barrier between the cell and its external enviornment

cytoplasm

the region of the cell contained withing the plasma membrane

nucleoid

the location of the genetic material (DNA). The nucleoid is not a membrane-bound compartment

ribosomes

cell comeponents involved in polypeptide synthesis

cell wall

a relatively rigid structure that supports and protects teh plasma membrane and sytoplasm. The cell-wall composition varies widely among prokaryotic cells but commonly includes peptides and carbohydrates. The cell wall, which is relatively porous, allows most nutrients in teh enviornment to reach the plasma membrane

glycocalyx

an outer viscous covering curronding many species opf bacteria. It traps water and helps protect bacteria from drying out. Certain strands of bacteria that invade animals bodies produce a very thick, gelatinous glycocalyx called a capsule that may help the avoid being destroyed by the animal’s immune system or may aid in teh attachment to cels surfaces

pili (singular, pilus)

hairlike projections that allow cells to attach to surfaces anf to each other

flagella (singluar; flagellum)

long appendages that provide prokaryotic cells with a way to move, called motility