Biology exam 1 review

Exam review

Characteristics of living organisms

• Organized

• Sensitive and respond to stimuli

• Reproduce, grow and develop

• Regulation

• Maintain Homeostasis

• Process and use Energy

• Highly adapted to their environment

Living organisms

• organized into cells, tissues, organs, and organ systems

• sense and respond to: light, temperature, pressure

• reproduce sexually or binary fission

• regulate temperature, blood flow, oxygen

• maintain homeostasis: constant temperature, blood pressure, water, energy, pH

• convert chemical energy to mechanical energy

Levels of biological organization

• Atoms

• Molecules

• Macromolecules

• Organelles

• Cells

• Tissues

• Organs and organ systems

• Organisms, populations, and communities

• Ecosystems

• Biosphere

Dependent variable

What you measure in an experiment (Y-axis in a graph)

Independent variable

What you change in an experiment (X-axis in a graph)

Hypothesis

A testable explanation that predicts the relationship between variables

• A testable and falsifiable proposed explanation for an observable phenomenon or scientific question

Theory

A well-substantiated, comprehensive explanation of an aspect of the natural world that is supported by a vast body of repeated observation and experimentation

Matter

has a mass and occupies space (gas, liquid, solid)

Elements

A pure substance made of only one kind of atom that cannot be broken down into simpler substances by normal chemical reactions

• Have specific chemical properties

• Have specific physical properties

• Each element is designated by a unique chemical symbol:

• Are made of atoms

Most common elements in living organisms

CHON

• Make up about 96% to 99% of living matte

Protons

• Charge: +1

• Location: nucleus

• Mass: 1 amu

Electrons

• Charge: -1

• Location: orbitals around the nucleus

• Mass: 0 amu

Neutrons

• Charge: 0

• Location: nucleus

• Mass: 1 amu

Which subatomic particles exist in the nucleus of the atom

• Protons

• Neutrons

The difference between atomic mass and atomic number

• Atomic number: number of protons

• Atomic mass: protons + neutrons

What are Isotopes?

Different forms of the same chemical element that have the same number of protons (and electrons) but a different number of neutrons, which changes the atomic mass

What is an orbital and how many electrons in each orbital?

A specific 3D space around an atomic nucleus where an electron is most likely to be found

• s subshell: Contains 1 orbital and holds up to 2 electrons.

• p subshell: Contains 3 orbitals and holds up to 6 electrons total (2 per orbital).

• d subshell: Contains 5 orbitals and holds up to 10 electrons total (2 per orbital).

• f subshell: Contains 7 orbitals and holds up to 14 electrons total (2 per orbital).

What is the Bohr model?

An early simplified depiction of how sub-atomic particles are arranged within an atom

• Protons are located in nucleus and electrons in circular orbits around the nucleus

• Orbits: electron shells or energy levels

• a structural model of the atom stating that negatively charged electrons orbit a positively charged nucleus in distinct, circular paths called energy levels (or shells).

Reactants

The starting molecules that enter a chemical reaction and are transformed into products

• They are the inputs that undergo chemical bond breaking and rearrangement during metabolic processes

Products

The final molecules or substances formed as the result of an enzymatic or chemical reaction

In an atom what determines if two atoms will interact?

Electrons in outer shell (valence electrons)

• Valence electrons (the outer shell electrons) and their need to achieve a stable, full outer energy level determine if two atoms will interact

What can help you determine if a reaction is reversible or irreversible?

The direction of the arrows

• Double arrows: shows the reaction proceeds in both forward and reverse directions.

Non-polar Covalent bond

A type of chemical bond where two atoms share a pair of valence electrons equally because they have similar or identical electronegativities

• Equal sharing

• No partial charges

Ionic bond

A chemical link formed through the electrostatic attraction between oppositely charged ions caused by the complete transfer of electrons from one atom to another

• Cation: A positively charged ion formed by losing electrons (p+ > e-)

• Anion: A negatively charged ion formed by gaining electrons (e- > p+)

Polar covalent bond

A type of chemical bond where two atoms share valence electrons unequally because one atom has a higher electronegativity than the other

• Unequal Sharing

• This unequal pull creates uneven charge distribution across the molecule. The atom pulling harder gets a partial negative charge, while the other atom gets a partial positive charge

Hydrogen bond

A weak electrostatic attraction between a partially positive hydrogen atom and a partially negative atom—such as oxygen or nitrogen—on a neighboring molecule or another part of the same molecule

• Weak Individually, Strong Collectively

Van der Waals interactions

Weak, temporary attractions between molecules that happen when shifting electron clouds create tiny, fleeting partial charges

• weak interaction b/w molecules

Difference between single, double bond and triple bond

The number of shared electron pairs, which directly dictates their length and strength

• Single bond: shares 1 pair of electrons (2 total electrons), longest and weakest of the three

• Double bond: shares 2 pairs of electrons (4 total electrons)

• Triple bond: shares 3 pairs of electrons (6 total electrons), shortest and strongest type

What are the properties of water

1. Polarity and Hydrogen Bonding

2. Cohesion and Adhesion

3. High specific heat capacity

4. High Heat of Vaporization / Evaporative Cooling

5. Lower Density as a Solid (Floating Ice)

• As water freezes, hydrogen bonds lock molecules into an open, spaced-out crystalline lattice, making ice less dense than liquid water.

6. Water as a Universal Solvent

• Water's polarity allows it to surround and dissolve polar and ionic substances

Why water makes hydrogen bonds?

Oxygen is electronegative and pulls electrons towards itself (unequal sharing of electrons)

• This creates two poles: one negative in Oxygen side and one positive pole in H side

• One negative pole in one water molecule forms bond with a positive H atom on an adjacent water molecule:

Why do ions dissolve in water?

Because the polar water molecules form strong electrical attractions with the charged ions, pulling them apart from their crystal lattice

• The attractive force between polar water molecules and individual ions overcomes the electrostatic forces holding the ionic crystal lattice together

What does pH of a solution indicate?

The pH indicates the concentration of hydrogen ions (H+) in that solution, which tells you how acidic or basic it is

How are acidic solutions related to H+ ions?

The higher the concentration of H ions, the more acidic the solution is

How are basic solutions related to OH- ions?

The higher the concentration of OH ions, the more basic the solution is

What pHs are Acidic? Neutral? Basic?

• Acidc: pH < 7

• Neutral: pH = 7

• Basic (alkaline): pH > 7

What is the difference b/w pH 6 and 4? Which one is more acidic and by how much?

pH 4 is more acidic

• By 100 times

• The pH scale is a base-10 logarithmic scale, meaning each whole number step represents a tenfold (10x) change in hydrogen ion concentration

How do buffers work?

An aqueous solution that resists changes in pH when small amounts of acid or base are added

• Made of a pair consisting of a weak acid and its conjugate base (or a weak base and its conjugate acid

• Work by using one part of the pair to absorb added H+ and the other part to absorb added OH-

What is a functional group in a molecule?

A specific cluster of atoms attached to a carbon skeleton that gives an organic molecule its unique chemical properties and behavior

Carboxyl

A specific functional group with the formula -COOH, where a central carbon atom is double-bonded to an oxygen atom and single-bonded to a hydroxyl group (-OH)

Hydroxyl

A functional group consisting of a hydrogen atom covalently bonded to an oxygen atom

Amino group

A functional group made of a nitrogen atom bonded to two hydrogen atoms (-NH2)

Carbonyl

A functional group consisting of a carbon atom double-bonded to an oxygen atom (C=O)

Why are hydrogen bonds in biomolecules essential?

H bonds give molecules their functional 3-dimensional shape

• Denatured (unfolded with no H bonds) are not functional.

Four classes of macromolecules (biomolecules)

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Dehydration synthesis

A chemical reaction that joins smaller subunits (monomers) into larger chains (polymers) by removing a water molecule

Hydrolysis

A chemical reaction that uses a water molecule to break the covalent bond holding a large polymer together, splitting it into smaller monomers

• Water splits: A water molecule (H2O) breaks apart into a hydrogen ion (H+) and a hydroxyl group (OH-)

• Bonds attach: The hydrogen ion attaches to one of the separated monomers, and the hydroxyl group attaches to the other.

What are the monomers of carbohydrates?

Monosaccharides: the simplest type of carbohydrate and serves as a single-molecule building block for larger sugar structures

• Ex: glucose, fructose, galactose

Examples of sugar monomers

Called monosaccharides, which serve as the basic building blocks for more complex carbohydrates

Ex:

• Glucose

• Galactose

• Fructose

What is the difference between an aldose and ketose sugar?

The primary difference between an aldose and a ketose sugar is the position of the carbonyl group (C=O) within their carbon chain

• Aldose: Contains an aldehyde group (CHO) located at the very end (terminal carbon, usually Carbon 1) of the carbon chain

• Ketose: Contains a ketone group (C=O) located at an internal carbon (usually Carbon 2) within the carbon chain

What is the link between two sugar (monosaccharide) molecules called?

A glycosidic bond

• Covalent bond that joins a carbohydrate (sugar) molecule to another group or molecule, such as another monosaccharide

• Formed through dehydration synthesis

Common disaccharides

• Sucrose

• Lactose

• Maltose

• A carbohydrate molecule formed when two monosaccharide monomers join together through a covalent (glycosidic) bond

• Form via dehydration synthesis

Difference between branched and unbranched polysaccharides

Unbranched polysaccharides form a single, linear chain of monosaccharides, whereas branched polysaccharides feature side chains of monosaccharides branching off the main carbon backbone

Starch

A storage polysaccharide made of glucose monomers linked by α-1,4 and α-1,6 glycosidic bonds, serving as the primary energy storage molecule in plants

• Ex: potatoes, wheat, rice

Cellulose

A structural polysaccharide that makes up the tough cell walls surrounding plant cells, providing them with shape and rigidity

• Most abundant carbohydrate; insoluble

• Cows & sheep can digest it: cellulose- digesting bacteria

• Structural polysaccharide in plants

Glycogen

A highly branched polysaccharide polymer made of glucose monomers that animals use to store extra energy

• energy source in animal tissue

• Stored in liver & muscle cells

Different functions of lipids

• Long-term energy stores

• Insulation for plants and animals

• Building blocks for some hormones

• Component of cells membranes

Different types of lipids

• Fats

• Oils

• Waxes

• Phospholipids

• Steroids

Two components of fat and which one is hydrophobic:

A fat (triglyceride) molecule is made of glycerol and fatty acids, and the fatty acid tails are the hydrophobic components

• An isolated glycerol molecule is hydrophilic (water-loving), but when it is bound inside a fat molecule like a triglyceride, it behaves as part of a hydrophobic structure

What is the difference between saturated and unsaturated fatty acids?

Saturated fatty acids have only single carbon-carbon bonds and are full of hydrogen atoms, while unsaturated fatty acids have at least one double carbon-carbon bond which creates a bend or kink in the chain

What is a phospholipid; properties of the head and tail

A major type of lipid molecule that forms the primary building block of cell membranes

• Head: polar, negative charge, hydrophillic, faces outward towards aqueous environments

• Fatty acid tails: nonpolar, uncharged, hydrophobic, face inwards (away from water)

Why are phospholipids an amphipathic molecule?

Because they contain both a hydrophilic (water-loving) region and a hydrophobic (water-fearing) region within the exact same molecule

What are steroids and their function?

A type of lipid molecule characterized by a core chemical structure of four fused carbon rings (three six-sided and one five-sided)

• Membrane Fluidity (Cholesterol): Cholesterol embeds itself in animal cell plasma membranes. It acts as a fluidity buffer

• Cholesterol serves as the vital starting material or precursor used to synthesize important steroid hormones, including testosterone, estrogen, progesterone, and cortisol

• Cell Signaling and Gene Expression

Different functions of protein

• Regulatory functions

• Structural functions

• Protective functions

• Transport

• Enzymes

• Toxins

What are enzymes?

Proteins that work as catalysts (speed up reactions). Enzymes are very specific for one type of reaction and can be used repeatedly

• Specific enzyme for specific substrate

• Catalysts accelerate chemical reactions by lowering the activation energy required for the reaction to occur, without being consumed in the process.

The monomer that makes proteins:

Amino acids

• Link together through covalent bonds called peptide bonds formed via dehydration synthesis (condensation reactions) to create polypeptide chains

The three main functional groups of amino acids:

• Amino group (-NH2)

• Carboxyl group (-COOH)

• R-group (Side chain): a unique chemical group that gives each specific amino acid its distinct size, charge, and function

What functional group in an amino acid gives the acid its chemical properties?

The variable side chain, also universally known as the R-group, is the functional group that gives each amino acid its unique chemical properties (such as being polar, nonpolar, hydrophobic, or hydrophilic)

R-groups can be:

• Nonpolar (hydrophobic)

• Polar

• Positive charged

• Negative charged

• Nonpolar aromatic (rings)

What bond links amino acids together?

Individual amino acids are linked together by covalent chemical bonds called peptide bonds

• Peptide bonds: a covalent chemical bond formed through dehydration synthesis that links two amino acids together to form the primary backbone of a protein

Denatured protein

A protein that has lost its normal three-dimensional shape and function because external stress disrupted its weaker internal bonds, while its primary amino acid sequence remained intact

• The strong covalent peptide bonds of the primary structure (the amino acid sequence) do not break

Protein structure/shape can change with altering primary structure due to:

• Changes in pH

• Changes in temperature

What are nucleic acids?

Large biological macromolecules that store, transmit, and express genetic information in living systems

Two types

• Deoxyribonucleic acid (DNA)

• Ribonucleic acid (RNA)

Where do you find DNA in eukaryotes?

• Nucleus

• Mitochondria

• Chloroplasts

What are the three components of DNA?

A DNA molecule is a polymer made of repeating smaller units called nucleotides, and each individual nucleotide consists of three main components:

1. A pentose (five-carbon) sugar molecule

2. Phosphate group

3. Nitrogenous base

The monomers of nucleic acids are

Nucleotides

What component of DNA makes the whole molecule negative?

The phosphate group in the sugar-phosphate backbone gives DNA its overall negative charge

• At normal cell pH, the oxygen atoms on the phosphate group carry a negative charge

Differences between DNA and RNA:

Sugars:

• DNA uses deoxyribose, which lacks one oxygen atom on the second carbon (2'-H)

• RNA uses ribose, which has a full hydroxyl group (-OH) on the second carbon

Nitrogenous Bases:

• DNA contains Adenine (A), Cytosine (C), Guanine (G), and Thymine (T)

• RNA contains uracil (U) instead of thymine

Number of Strands:

• DNA is typically double-stranded, forming an antiparallel double helix that protects genetic information

• RNA is typically single-stranded, allowing it to fold into various shapes for protein synthesis (such as mRNA, tRNA, and rRNA)

What weak bond keeps two strands of DNA bound to each other?

A hydrogen bond

• hydrogen bonds in DNA are located directly between the complementary nitrogenous base pairs on opposite strands

The central dogma of life

The one-way flow of genetic information inside a cell from DNA to RNA to protein

• DNA → RNA → Protein

Two main steps:

• Transcription

• Translation

• Retroviruses (like HIV) use reverse transcription to turn RNA back into DNA, which is a special transfer

What are the three parts of the cell theory?

1. Cells are basic units of life

2. All living organisms are made of cells

3. All cells come from pre-existing cells

What is an advantage of using a transmission or scanning electron microscope?

They provides a much higher magnification and resolution than a light microscope, allowing scientists to see tiny cell parts like ribosomes and internal membrane structures

• Transmission: show fine detail within cells

• Scanning: provide 3-D exterior views

What structures do ALL cells have in common?

1. Plasma membrane: separates the cell’s interior from the outside

2. Cytoplasm: inside of cell (cytosol) where organelles are found

3. DNA: the genetic material

4. Ribosomes: synthesize proteins

What is an advantage of using a light microscope?

It allows you to view living cells and whole organisms in real time

Define prokaryote and give an example

A unicellular organism that lacks a nucleus and other membrane-bound organelles

• Two domains: bacteria & archaea

• Ex: cyanobacteria, methanogens (archaea), Escherichia coli (E.coli)

The General features of prokaryotic cells are below. What is the function of each one?

• Nucleoid: houses and organizes the cell's circular DNA molecule without a surrounding membrane

• Cell wall: rigid outer layer that maintains cell shape, provides structural support, and prevents the cell from bursting from osmotic pressure in hypotonic environments

• Ribosomes: synthesize proteins by translating messenger RNA (mRNA) sequences into polypeptide chains

• Flagella: locomotion, enabling single-celled organisms to swim and actively navigate their liquid environments

What are the two main differences between eukaryotic and prokaryotic organisms

The presence of a membrane-bound nucleus and membrane-bound organelles in eukaryotes, both of which prokaryotes lack

What molecule is the cell membrane composed of?

The cell membrane Is primarily composed of phospholipids arranged in a double layer called a phospholipid bilayer

What are some of the functions of membrane proteins?

Membrane proteins perform six major functions vital for cell survival and communication:

1. Transport

2. Enzymatic Activity

3. Signal Transduction

4. Cell-Cell Recognition

5. Intercellular Joining

6. Attachment to the Cytoskeleton and Extracellular Matrix (ECM)

Membrane proteins

Proteins embedded in or attached to the phospholipid bilayer of a cell membrane. They act as gatekeepers, helping the cell transport materials, receive signals, and speed up chemical reactions

Prokaryotic organisms are found in which two domains of life?

• Bacteria

• Archaea

How many layers make up the cell membrane?

The cell membrane is made up of two layers of phospholipids, known as a phospholipid bilayer

• Outer Layer: The polar, hydrophilic (water-loving) phosphate heads face outward toward the aqueous extracellular fluid.

• Inner Layer: The polar heads face inward toward the cytoplasm.

• Core: The non-polar, hydrophobic (water-fearing) fatty acid tails point inward, meeting in the middle away from water

What part of the cell membrane is hydrophilic?

What part of the cell membrane is hydrophilic?

• Location: The hydrophilic (water-loving) heads face outward. They contact the watery fluid inside (cytoplasm) and outside (extracellular fluid) the cell.

What part of the cell membrane is hydrophobic?

The hydrophobic (water-fearing) part of the cell membrane consists of the nonpolar fatty acid tails of the phospholipid

• Location: The two fatty acid tails point inward, meeting in the interior of the phospholipid bilayer to form a nonpolar core away from cellular water

• Function: This hydrophobic interior acts as a selective barrier. It lets small, nonpolar molecules (like CO2 and O2) pass through easily, but blocks ions and large polar molecules (like glucose)

Eukaryotic organisms are found in which domain of life?

Eukaryotic organisms are found in the domain Eukarya

Characteristics of Domain Eukarya

• Nucleus: Cells store their DNA inside a distinct, membrane-bound nucleus.

• Organelles: Cells contain membrane-bound structures like mitochondria and the endoplasmic reticulum.

• Kingdoms: This domain includes four major groups: Protista, Fungi, Plantae, and Animalia

Organelle

A specialized sub-cellular structure that performs a specific job inside a cell, much like an organ does in the body

What is the function of the nucleus?

The primary function of the cell nucleus is to store, protect, and manage the cell's genetic information (DNA), serving as the control center for eukaryotic cells

How does the nucleus interact with other organelles?

• The Nucleus, Endoplasmic Reticulum, and Golgi Interact to Secrete Substances

What makes the rough ER "rough?"

Because its cytoplasmic surface is studded with bound ribosomes

What is made at the rough ER?

The rough ER synthesizes and processes secretory proteins, membrane-bound proteins, and phospholipids

• Proteins

What is made at the smooth ER?

Lipids (such as phospholipids and cholesterol) and steroid hormones

What is the function of the Golgi apparatus?

To modify, sort, and package proteins and lipids for transport to different locations inside or outside the cell

• Lipids or proteins within vesicles are sorted, packaged, and tagged to send to the right place

What is the function of lysosomes?

Membrane-bound organelles that use hydrolytic enzymes to break down waste, foreign material, and old cell parts

• Lysosomes in animal cells contain digestive enzymes

• The enzymes breakdown biomolecules and old organelles

Correlation between Lysosomes, Vacuoles, and Peroxisomes

Lysosomes, Vacuoles, and Peroxisomes Are Cellular Digestion Centers

• all membrane-bound sacs inside cells that handle metabolic waste, breakdown, and storage