biochemistry quiz #2 review

what are proteins?

polymers made of amino acid monomers

Primary Structure

Polypeptide chain made up of amino acids, held together by peptide bonds

Secondary Structure

Folding or coiling of the amino acid chain into patterns like alpha-helix and beta pleated, results from H-bonding between amino acids in the polypeptide

Tertiary Structure

3D shape of a single protein molecule formed when secondary structures fold further due to interactions between the R groups of the amino acids (hydrophobic interactions, disulphide bridges, hydrophilic interactions, hydrogen bonds, ionic bonds)

Quaternary Structure

Arrangement of 2 or more polypeptide chains (subunits) that work together as one protein, each subunit has its own primary, secondary, and tertiary structure. They are held together by the same types of interactions as tertiary.

Polypeptide chain

A covalent bond that connects the amino group of one amino acid to the carboxyl group of another, forming a chain.

amino acid molecule

The building block of proteins, consisting of an amino group, a carboxyl group, a hydrogen atom, and an R-group

Active site

The specific region on an enzyme where a substrate binds and the chemical reaction occurs.

Substrate molecule

The reactant molecule that binds to an enzyme’s active site and is transformed during a chemical reaction.

Enzyme

A catalyst (usually a protein) that speeds up chemical reactions + makes it easier for the reaction to happen without being used. 

Imagine a reaction like pushing a ball over a hill, the enzyme makes the hill smaller, so the ball can get over it more easily.

activator

substances that allow enzymes to work better

Inhibitor

slows down or stops an enzyme from working

allosteric regulation

a process where a molecule, called an allosteric effector, binds to a site on a protein that is distinct from the active site, changing the protein's overall shape and its activity 

This binding can either enhance (activate) or decrease (inhibit) the protein's function

What is the "active site" of an enzyme?

A special pocket or groove on the enzyme with a unique shape, where the specific molecule it works on (the substrate) binds. It's like a lock that only a specific key (the substrate) can fit into.

What does it mean to "denature" an enzyme?

To destroy the enzyme's specific 3D shape, especially its active site. A denatured enzyme is like a bent key or a broken tool—it can no longer do its job because the substrate can't bind to it anymore.

What are the two main causes of enzyme denaturation?

• Extreme Heat: Causes the enzyme to vibrate and shake apart, unfolding it.

• Extreme pH: (Too acidic or too basic) Messes with the enzyme's internal charges, disrupting the bonds that hold its shape.

Uses of proteins in the body (add more?)

• Structural: forms hair, nails, muscles, is a component of cell membranes (lipid bilayer)

• Transportation: Helps move materials across cell membranes

• Help protect the body against viruses

• many hormones are made of proteins

Osmosis

Diffusion of water

Diffusion

movement of a substance from an area of high concentration to low concentration in order to achieve an equillibrium

why does the cell need oxygen?

• cellular respiration (access energy in glucose and store it in ATP molecules)

How/why does oxygen get through the cell membrane?

Via diffusion through spaces between the phospholipids in the cell membrane

• oxygen is nonpolar and so they can dissolve through the nonpolar bilayer (like dissolves like)

why does the cell need carbon dioxide?

part of cellular respiration and is exhaled from the body

how/why does CO2 get through the cell membrane?

• via diffusion to areas of low concentration

• small and nonpolar, so it can go through the nonpolar bilayer

• cell continually generates CO2 so there is a higher concentration within the cell than the interstitial fluid

why does the cell need glucose?

to produce ATP (energy)

how/why does glucose diffuse into the cell?

• travels by a GLUT transporter by facilitated diffusion

• once inside, glucose binds to an enzyme

• Bc glucose is polar, it can’t diffuse through the bilayer so it uses transport proteins to help it

why does the cell need potassium?

• helps the cell to maintain fluid balance and creates a small electrical charge which is needed for nerve signals and for muscles to contract

how/why does potassium diffuse into the cell?

• goes through a specific ion channel, active transport

• it is a charged ion, so it can’t pass through the nonpolar bilayer, therefore it needs special channels that allow it to pass through

why does the cell need sodium?

helps to send nerve signals, control muscle contractions, and maintain fluid balance

how/why does sodium get through the membrane?

• via protein pumps (active transport)

• the cell needs a low concentration of Na inside itself and a high concentration of K inside itself

• the protein pumps export Na and import K

• 2 K in for every 3 Na out

why does the cell need water?

• universal solvent, builds + breaks molecules via hydrolysis/condensation

• osmosis helps maintain cell volume

how/why does water get through the membrane?

• osmosis (diffusion of water)

• sometimes pass through the bilayer because the molecules are so small even tho it’s polar

• usually it goes through pores in the membrane called aquaporins

why does the cell need enzymes?

• catalysts (speed up chemical processes)

how/why do enzymes get through the membrane?

• exocytosis; sphere made up of the membrane surrounds the enzymes and then attaches to the membrane, releasing the contents outside the cell (can also import via endocytosis)

• enzymes are generally too large and polar to pass through the bilayer

• they are typically needed outside the cell

hypertonic

• higher concentration of non-diffusible solutes (lower water concentration) OUTSIDE the cell

• water diffuses out of the cell, causing it to shrink

• animal cell: cell shrinks (crenation)

• plant cell: vacuole shrinks, cell loses it shape (flaccid)

hypotonic

• lower concentration of non-diffusible (higher water concentration) OUTSIDE the cell

• water moves into the cell

• animal cell: cell expands and ruptures (lysis)

• plant cell: vacuole swells and pushes against cell wall (turgid)

isotonic

• equal concentration of non-diffusible solutes

• no net water movement

• cell stays the same

passive transport

diffusion + osmosis

concentration gradients

• natural movement of particles (high to low concentration

key points about diffusion

• molecules tend to slowly spread apart over time

• high to low concentration

• particle size, membrane permeability, and temperature all affect how quickly things diffuse

solute

stuff dissolving (salt)

solvent

thing doing the dissolving (water)

solution

solute + solvent

“like dissolves like”

if things are both polar/nonpolar they will dissolve each other

something polar can’t dissolve something nonpolar

what is osmosis

movement of water across a semi permeable membrane

what does selectively permeable mean

only certain substances can pass through

membrane is made of lipids, therefore polar/ionic cannot dissolve

linkage groups in phospholipids

• phosphate ester (head)

• ester linkages (tail)

• therefore: the head is polar and hydrophilic

• the tail is nonpolar and hydrophobic

active transport

• requires ATP (energy) goes from low to high concentration (AGAINST concentration gradient)

• endocytosis: pulls in large particles using cell membrane

• exocytosis: fusing membrane bound vesicles with cell membrane to help them leave the cell

• protein pumps: move small proteins/ions into or out of the cell

cholesterol

keeps the cell membrane at correct fluidity and communicates with other cells

proteins

make sure the right molecules get in and out of the cell they allow specific molecules through

How does temperature affect diffusion?

Higher temperatures increase particle movement, speeding up diffusion.

How does surface area affect diffusion?

it provides more space for particles to move across a membrane or through a medium

How does distance or thickness of the membrane affect diffusion?

A thinner membrane or shorter distance increases diffusion rate; a thicker membrane slows it down.

How does size of the particles affect diffusion?

Smaller particles diffuse faster than larger particles because they have less mass and can move more easily

How does permeability of the membrane affect diffusion?

A membrane's permeability directly dictates how easily molecules can diffuse across it: a more permeable membrane allows for faster diffusion, while a less permeable membrane slows diffusion