Biology Exam 1

identify the four components of amino acids and describe how amino acids are linked

an amino group, a carboxyl group, a hydrogen atom, and a variable R-group. Amino acids link together through dehydration synthesis, forming a covalent peptide bond between the carboxyl group of one amino acid and the amino group of

organize amino acids based on structural and functional properties

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predict whether the R group on an amino acid will interact with water and be changed or unchanged

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describe each of the four levels of protein structure and explain how each influences the proteins final size, shape, and chemical properties

The four levels of protein structure range from a simple linear chain to a complex multi-subunit assembly. Each level builds upon the previous one to determine the protein's overall size, three-dimensional shape, and specific chemical behavior through covalent bonds, localized folding, side-chain interactions, and subunit aggregation.

predict how changes to protein structure affect protein function

Protein function is entirely dictated by its structure, meaning any structural alteration can disrupt its biological activity. A genetic mutation in the primary sequence can alter foundational chemical properties and ruin downstream folding, while disruptions to secondary and tertiary structures—often caused by environmental stressors like heat or pH changes—can cause the protein to unfold or denature, destroying crucial active sites and mechanical strength.

compare which bonds are responsible for a proteins primary structure, secondary structure, tertiary structure, and quaternary structure.

Structural Level	Primary Bonding Type	Specific Bonds & Interactions Involved
Primary	Covalent Bonds	Peptide bonds linking the amino group of one amino acid to the carboxyl group of the next.
Secondary	Non-Covalent Bonds	Hydrogen bonds formed between the oxygen of the carbonyl groups and the hydrogen of the amino groups along the polypeptide backbone.
Tertiary	Both Covalent & Non-Covalent	Hydrophobic interactions (packing of nonpolar groups), hydrogen bonds, ionic bonds (salt bridges), and covalent disulfide bridges between amino acid side chains (R-groups).
Quaternary	Both Covalent & Non-Covalent	The same interactions as tertiary structure (hydrophobic packing, hydrogen bonds, ionic bonds, and occasionally disulfide bonds), but acting between separate polypeptide chains.

identify the chemical components of nucleic acid

carbon, hydrogen, nitrogen, oxygen, and phosphorus

define complementary base pairing and explain its connection to the DNA strands and how they’re antiparallel

adenine - thymine, cytosine - guanine

identify the components and describe the properties of the cell membrane

Its structure and behavior are best explained by the fluid mosaic model, which describes the membrane as a flexible, tapestry-like layout of various molecular pieces.

describe the fluid mosaic theory of the cell membrane

flexible, dynamic boundary that interacts with many molecules and lets certain molecules in when it can

how to predict how differences in phospholipid composition will affect their relative fluidity and permeability, and explain your reasoning

Tight packing makes the membrane more rigid and less permeable, while loose packing makes it more fluid and highly permeable.

define concentration and electrochemical gradients

A concentration gradient is the difference in the number of particles (solutes) per unit volume between two regions, typically separated by a cell membrane.

• How it works: If there is a high amount of glucose outside a cell and a low amount inside, a concentration gradient exists.

• Driving Force: This gradient drives chemical diffusion. Particles will naturally move from the area of high concentration to the area of low concentration until they are evenly distributed.

Electrochemical Gradient

An electrochemical gradient is a dual-force gradient that determines which way a charged particle (ion) will move across a membrane. It combines two distinct forces:

1. The Chemical Gradient (Concentration): The difference in the specific ion's concentration across the membrane.

2. The Electrical Gradient (Charge): The difference in total electrical charge across the membrane (also known as the membrane potential). Because the inside of a resting cell is typically negative compared to the outside, it attracts positively charged ions and repels negatively charged ones.

define passive and active transport and explain the role of channels, carriers, and pumps in transport

Passive transport moves substances down their concentration gradient without using energy, while active transport uses cellular energy (ATP) to pump substances against their gradient. Channels are open, selective tunnels that allow fast passive transport of ions and water molecules down their gradients. Carriers are shape-shifting proteins that bind specific molecules, like glucose, to ferry them across the membrane during either passive or active transport. Pumps are specialized carrier proteins that consume ATP to forcibly move ions against their gradients during active transport.

given a diagram of an electrochemical gradient, predict which direction a specified ion or molecule will cross a plasma membrane

To predict the direction a particle will move across a membrane from a diagram, first identify if it has a charge. For uncharged molecules, they move passively from high concentration to low concentration. For charged ions, combine the concentration force (high to low) and the electrical force (opposites attract, pulling positive ions toward the negative side). If these combined forces point in the same direction, the ion moves that way via passive transport. If a diagram shows an ion moving against this combined electrochemical pull, it represents active transport powered by a pump.

summarize cell theory

all organisms are made up of one or more cells

the cell is the basic structural and functional unit of life

all cells arise from pre-existing cells

prokaryotic v.s eukaryotic cells

dude yk this

plant v.s. animal cells

you know this too

summarize functions of major cell organelles and predict what would happen to a cell if a particular organelle or structure Las altered in some way

nucleus, mitochondria, ribosomes, rough ER, Golgi apparatus, the lysosomes would break down waste, old organelles, and foreign invaders

list the components of the endomembrane system

nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, plasma membranes, transport vesicles

how are proteins processed and packaged as they move from the ribosomes in the cytosol to their destination/secretion

Proteins are synthesized and folded inside the Rough Endoplasmic Reticulum (RER), where they receive initial carbohydrate chains. A transport vesicle then carries the protein to the Golgi apparatus for final chemical modification, tagging, and sorting. Finally, the Golgi packages the finished protein into a vesicle that either delivers it to an internal organelle like a lysosome or fuses with the plasma membrane to release it via exocytosis.

describe the cytoskeleton

a dynamic network of protein filaments extending throughout the cytoplasm of all cells

compare and contrast the structure of microfilaments, intermediate filaments, and microtubules

Feature	Microfilaments (Actin Filaments)	Intermediate Filaments	Microtubules
Structure	Two intertwined strands of actin	Fibrous proteins coiled into thick cables (rope-like)	Hollow tubes made of protofilaments
Diameter	Thinnest (~7 nm)	Middle (~8–12 nm)	Thickest (~25 nm)
Protein Subunits	G-actin monomers	Varies (e.g., keratin, lamins, vimentin)	\(\alpha \)-tubulin and \(\beta \)-tubulin dimers
Dynamic Behavior	Highly dynamic (treadmilling, fast assembly/disassembly)	Very stable (permanent, structural)	Highly dynamic (dynamic instability)
Polarity	Polar (distinct plus and minus ends)	Non-polar	Polar (distinct plus and minus ends)
Primary Functions	Muscle contraction, cell movement (ameboid), pinching cells during division	Maintaining cell shape, anchoring the nucleus and organelles	Vesicle transport (highways), chromosome separation, cilia/flagella movement
Motor Protein Associations	Myosins	None	Kinesins and dyneins

describe the extracellular matrix

a complex, nonliving network of macromolecules secreted by cells into the surrounding extracellular space

summarize the structure and function of tight junctions, desmosomes, gap junctions, and plasmodesmata

Junction Type	Cell Type	Structure	Function
Tight Junctions	Animal	Interlocking membrane proteins	Waterproof seal preventing extracellular leaks
Desmosomes	Animal	Anchoring rivets bound to keratin	Mechanical strength preventing tissue tearing
Gap Junctions	Animal	Protein pores (connexons)	Rapid communication via shared ions and signals
Plasmodesmata	Plant	Membrane-lined wall channels	Cytoplasmic transport of water and nutrients

predict the outcome for a tissue if these connections are disrupted

• Disrupted Tight Junctions: The tissue becomes highly leaky, allowing fluids, toxins, and pathogens to seep unchecked between cells (e.g., causing leaky gut syndrome).

• Disrupted Desmosomes: The tissue tears and pulls apart under mechanical stress, leading to severe blistering or structural failure in organs like the skin and heart.

• Disrupted Gap Junctions: The tissue loses synchronized communication, stopping the rapid flow of ions and causing signaling failures like cardiac arrhythmias.

• Disrupted Plasmodesmata: Plant tissues experience stunted growth and starvation because cells can no longer share water, nutrients, or hormones.

ionic bonds

oppositely charged ions get put together

polar covalent bonds

a chemical bond where two atoms unequally share a pair of electrons

non polar covalent bonds

bond that forms when two atoms share electrons almost perfectly equally

dehydration synthesis

chemical reaction that joins two monomers into a polymer by removing a molecule of water (H2O)

Carbohydrates

made of Carbon, Hydrogen, and Oxygen

monosaccharides are polymerized into polysaccharides → dehydration synthesis

lipids

most are hydrophilic

made of hydrocarbon chains which are chemical structures made entirely of carbon and hydrogen atoms linked together by covalent bonds

saturated → no double bonds, solid @ room temp, stack easily

unsaturated → double bonds, liquid at room temp, kinks prevent stacking

central dogma of biology

DNA → RNA → Protein

amino acids

building blocks of polypeptides

polypeptides then form proteins

amino acids are bonded together by peptide bonds

have diverse functions due to a variety of r groups

r groups

if it is mainly carbons and hydrogens, it is generally hydrophobic, but if it has a -OH, -NH2, -COOH, or a charge, it is hydrophilic

proteins

shapes are central to functions

primary

the order in which amino acids are linked together

joined together by strong covalent peptide bonds

secondary

formed by hydrogen atoms within the backbone

can form alpha helices or beta sheets

tertiary

determined by interactions between r groups and between r groups and their enviornment

hydrophobic interactions → non polar r groups cluster away from water, usually towards the proteins interior

ionic interactions → attraction between oppositely charged r groups

hydrogen bonds → attractions between polar regions groups

disulfide bridges → covalent bonds formed between 2 cysteine r groups

quaternary

multiple polypeptides come together as subunits of a single functional protein (hemoglobin is an example)

Nucleic acids

provide info for our cells

deoxyribonucleic acid and ribonucleic acid

composed of nucleotides → sugar phosphate and nitrogenous base, subunits of DNA and RNA

bases of nucleic acids

cytosine - guanine (cars in the garage)

adenosine - thymine (apples in the tree

(RNA) adenosine - uracil (hey you (a u))

DNA

polymer of deoxyribonucleic acid

directionality runs 5’ → 3’ (path for reading and building genetic code

phosphodiester bond: between 5’ phosphate group and 3’ hydroxyl group

antiparallel double helix

held together by hydrogen bonds

active membrane transport

energy input

low → high concentration

• primary active transport

• secondary active transport

passive membrane transport

no energy

high → low concentration

• osmosis

• simple diffusion

• facilitated diffusion