Cell Bio Ch 4

enzymes function

catalyze covalent bond formation or breakage

structural proteins function

provide mechanical support to cells and tissues

transport proteins function

carry small molecules/ions

motor proteins function

generate movement in cells and tissues

storage proteins function

store amino acids or ions

signal proteins function

carry extracellular signals from cell to cell

receptor proteins function

detect signals and transmit them to cell’s response

transcription regulators function

machinery bind DNA to switch genes on or off

special purpose proteins function

highly variable

what are proteins made of

amino acids

order of amino acid sequence unique or diff for each protein

unique

linear sequence of amino acid considered

primary structure

the r group of amino acid determines

identity/chemical behavior

How many amino acids in polypeptide chain

20

how do polymers grow

the addition of a subunit onto oneend of the polymer chain via a
condensation reaction, where a molecule of water is lost for each subunit added

what holds amino acid in protein together

peptide bonds between carboxyl and amino group of adjacent amino acid

proteins are also known as polypeptides because

they made of peptide bonds

protein is made of

amino acids linked in polypeptide chain

directionality of protein synthesis is known as

N to C synthesis

20 common amino acids

polar and charged amino acids vs nonpolar amino acids

hydrophilic vs hydrophobic

polar side chains of polypeptide bond

partial charges can form hydrogen bonds

electrically charged side chains

charged side chains can form ionic and polar bonds

three types of non covalent bonds that help proteins fold

hydrogen bonds, electrostatic attractions, vanderwal attractions

Hydrophobic forces help proteins

fold into compact conformations

how is a hydrophobic core formed

Hydrophobic amino acid side chains cluster together in the
protein's interior, away from the surrounding water, forming a hydrophobic core

chaperone proteins do what

assist in folding the polypeptide chain (folding decreases conformation energy)

some chaperone proteins help with folding by forming

isolation chambers

primary vs secondary protein structure

amino acid sequence vs interactions between atoms of backbone (NO R GROUP INVOLVED)

tertiary structure

full 3d conformation primarily due to interactions between r groups of amino acids

quaternary structure

ASSOCIATION OF MULTIPLE POLYPEPTIDE CHAINS

what does it mean to say R group is not involved for secondary protein structure

hyd bonds involve ONLY the atoms of the backbone

N–H of every peptide bond is hydrogen-bonded to the C=O of a neighbouring peptide bond located _____ amino acids
away in the same chain.

FOUR

α-HELICES FORM CYLINDERS THAT CAN CROSS

LIPID BILAYERS

PROTEINS EMBEDDED IN THE CELL MEMBRANE OFTEN CONTAIN

SHORT ΑLPHA HELICES STRUCTURES (I.E. RECEPTORS, TRANSMEMBRANE PROTEINS, AND TRANSPORT PROTEINS)

THE R SIDE CHAINS THAT STICK OUT THE POLYPEPTIDE ARE (polar or nonpolar)

NON-POLAR (HYDROPHOBIC)

ALPHA HELICES CAN WRAP AROUND ONE ANOTHER TO FORM STIFF

COILED-COIL DOMAINS

the stiff coiled coil domains alpha helices form often make what type of proteins

ELONGATED ONES like keratin

Hydrogen bonds between N-H and to C=O happen between

BACKBONE atoms of adjacent strands (no r group involved)

separate regions of proteins are called

domains

WHY ARE THE ALPHA HELIX AND BETA SHEET SO COMMON IN PROTEIN STRUCTURE?

THE ATOMS NECESSARY FOR THE H-BONDS IN THESE
STRUCTURES ARE FOUND IN EVERY AMINO ACID (NOT
DEPENDENT UPON A PARTICULAR SIDE CHAIN)

Proteins that have similar aa sequence, and so similar shape, belong to the same

family

EACH DIFFERENT POLYPEPTIDE CHAIN IS CALLED A

SUBUNIT

REGIONS OF PROTIENS INVOLVED IN MOLECULAR INTERACTION ARE CALLED

BINDING SITES

HEMOGLOBIN

AN OXYGEN- CARRYING PROTEIN ABUNDANT IN RED BLOOD CELLS,

HEMOGLOBIN CONTAINS TWO COPIES OF WHAT GLOBINS

α-GLOBIN (GREEN) AND TWO COPIES OF β-GLOBIN (BLUE)

HOW MANY MOLECULES OF OXYGEN PER HEMOGLOBIN PROETIN

EACH OF THESE FOUR POLYPEPTIDE CHAINS CRADLES A MOLECULE OF HEME (RED ), WHERE OXYGEN (O2) IS BOUND. THUS, EACH HEMOGLOBIN PROTEIN CAN CARRY FOUR MOLECULES OF OXYGEN

try to answer

Normal hemoglobin (HbA) is more polar and soluble in water than the sickle cell hemoglobin (HbS) because HbA has glutamic acid which loves water and HbS has valine which hates water

4 ways proteins are modeled (BWRS)

backbone, wire, ribbon, space filling model

Single filamentous molecules are held together by

cross-link bonds

how do disulfide bonds stabilize protein conformation

by forming a strong, covalent cross-link between two cysteine amino acids, acting as a "staple" to hold different parts of a protein's structure together (only form OUTSIDE the cell)

why do disulfide bonds stabilize protein conformation outside the cell only

the cellular environment inside the cytoplasm is reducing, which prevents protein formation. Outside, the environment is oxidizing so that favors the creation of the disulfide bonds

THE SHAPE OF A PROTEIN IS SPECIFIED BY ITS

AMINO ACID SEQUENCE

PROTEINS FOLD INTO A CONFORMATION OF LOWEST ENERGY THROUGH WHAT TYPE OF BONDS

NON-COVALENT BONDS (HYDROGEN BONDS, ELECTROSTATIC ATTRACTION, VAN DER WALLS FORCES, AND HYDROPHOBIC FORCES

protein four levels of organization

primary, secondary, tertiary, quaternary

THE Α HELIX AND THE Β SHEET ARE COMMON FOLDING PATTERNS BECAUSE

BECAUSE THEY INVOLVE BACKBONE ATOMS

EXTRACELLULAR PROTEINS ARE OFTEN STABILIZED BY COVALENT CROSS-LINKAGES. ONE IMPORTANT CROSS-LINK IS THE

DISULFIDE BOND (S-S) THAT REINFORCE A PROTEIN (MOLECULAR STAPLER)

HOW DO PROTEINS WORK

BY BINDING TO ANOTHER MOLECULE

ligand

substance, such as an ion or molecule, that binds to a larger target molecule

how do ligands bind to larger molecule (type of bond)

through non covalent bonds of amino acid side chain

ENZYMES ARE GROUPED INTO FUNCTIONAL CLASSES BASED ON

THE CHEMICAL REACTIONS THEY CATALYZE AND EACH ARE HIGHLY SPECIFIC TO A CERTAIN SUBSTRATE

An enzyme’s performance depends on how rapidly it can process
its

substrate

what is v and km in relation to enzymes

v is rate of enzyme reaction and km is how tightly it binds

how are proteins controlled

feedback inhibition and positive regulation

feedback inhibition

a form of enzyme regulation whereby products prevent product formation

positive regulation

a mechanism, often an activator protein, that increases the frequency, rate, or extent of a biological process, such as gene expression

inhibitor vs activator

reduce vs increase activity of enzyme (neg vs pos regulation)

allosteric regulation inhibition example

REGULATORY MOLECULE BINDS TO AN
ENZYME SOMEPLACE OTHER THAN THE ACTIVE SITE

allosteric regulation activation example

more adp makes the enzyme in green more stabilized by keeping it closed on the substrate

two types of sites on an enzyme

regulatory and active

2 conformations of allosteric regulation

active vs inactive

protein localization

process by which proteins are precisely targeted to and maintained at specific locations within or outside a cell

what can control protein function and localization

different post-translational modifications

Phosphorylation can control protein activity by causing

conformational change

what chemical group does phosphorylation add to a molecule and how

phosphorylation adds a phosphate group to a molecule via a covalent bond

how do gtp binding proteins form molecular switches

When GTP binds to the G protein, it activates the protein. The G protein remains active until GTP is hydrolyzed to GDP

atp hydrolysis allows for what

Atp hydrolysis allows motor proteins to produce directed movement in cells

The Catalytic Activities of Enzymes Are Often Regulated by Other Molecules called

inhibitors or activators

four types of enzyme regulation (AEPG)

allosteric, enzyme modification, phosphorylation, gtp binding

Allosteric regulation involves the binding of what to what

regulatory molecules (inhibitors or activators) to the enzyme. Involves enzyme conformational change

Enzyme modification has around how many types

> 100 type of modifications. Ex: Acetylation, Glycosylation, Ubiquitination. Most used: Phosphorylation, which Can Control Protein Activity by Causing a Conformational Change

Phosphorylation involves the addition of what to what

phosphate group (PO₃²⁻) to a Protein. This process is a reversible post-translational modification that changes the protein's shape, activity, and ability to bind other molecules, acting as a molecular switch.

GTP binding proteins, also known as G proteins, act as "molecular switches" because

When GTP binds to the G protein, it activates the protein. The G protein remains active until GTP is hydrolyzed to GDP

how to get proteins out of cells (four steps)

1. break them apart with high ultrasound frequency

2. use detergent to make holes in them

3. force cells through small holes

4. use plunger and tube to smash them up

homogenate vs supernatant vs pellet of centrifugation

homogenate is the mixture before centrifugation while supernatant is the less dense part of the mix and pellet is the more dense part

centrifugation vs ultracentrifugation

Centrifugation separates components of a mixture by spinning, while ultracentrifugation is a specialized form of centrifugation using much higher speeds to separate smaller, more delicate particles

differential centrifugation

a specific type of centrifugation that uses successive increases in centrifugal force to separate particles based primarily on their SIZE AND DENSITY

velocity sedimentation

centrifugation with a sucrose gradient to top separate cellular components based on size and their sedimentation rates

equilibrium sedimentation/density gradient centrifugation

Allows you to isolate different cellular components based on their buoyant density

velocity sedimentation vs equilibrium sedimentation biology

separates molecules based on how fast they move (their sedimentation rate) through a solution in a centrifugal field vs. separates molecules based on their buoyant density. Centrifugation continues until molecules stop moving and settle at a certain point where their density equals that of the surrounding gradient.

protein column chromatography

uses resin-filled columns to separate and purify proteins from complex mixtures based on their unique properties, such as size, charge, and specific binding affinities

3 types of chromatography (GAI)

gel, affinity, ion

ion exchange chromatography

separates proteins by charge. beads have charges and oppositely charged proteins stick, while same-charged proteins flow through

gel chromatography

separates proteins by size. Beads have pores, and small molecules get trapped in pores (move slower). Large molecules can’t enter pores (move faster)

affinity chromatography

separates proteins by specific binding. Beads have a molecule (e.g., antibody or substrate) that binds only the target protein. Other proteins wash away. Bound protein is then released by pH change or salt

gel electrophoresis

uses an electric current to separate macromolecules like DNA, RNA, or proteins based on their size and electrical charge

isoelectric focusing

separates proteins based on isoelectric point where they are at a pH with no net charge and will thus not move in an electric field

two dimensional gel electrophoresis

separates complex protein mixtures into thousands of distinct "spots" on a single gel by first separating proteins by their isoelectric point (charge) and then by their molecular weight (size)

how to identify a protein with mass spec steps (CCPC)

1. Cut the protein from a gel.

2. Chop it into small pieces (peptides) with an enzyme.

3. Put peptides into a mass spectrometer → it measures their sizes (mass/charge).

4. Compare sizes with a database.

5. Match found = protein identified.

what are antibodies

proteins that bind very tightly to their targets (antigens)