カテゴリー 全て - carbohydrates - polysaccharides

によって Carl Mallet 2年前.

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Biochemistry

Carbohydrates are essential macromolecules with the primary role of providing energy and structural support in various organisms. They can exist as monosaccharides, like glucose and fructose, which are simple sugars serving as immediate energy sources.

Biochemistry

Biochemistry

Topic 5 - Cells and Organelles

Cell Structure and Functions
Plant-Only Organelles

Chloroplast

Found in Plants and Algae

Site of photosynthesis - the production of glucose using the sun’s energy

Contains stacks (called grana) of pancake-like structures (called thylakoids)

Inner and outer membrane

Contains pigments - especially chlorophyll

Green oval

Cell Wall

Found in Plant cells (also fungi and bacteria)

Structural support and protection

Rigid outer layer, composed of cellulose

Double Membrane-Bound Organelles

Mitochondrion

Releases energy from glucose

Site of aerobic respiration

Has its own DNA

Folded inner membrane (cristae)

Smooth outer membrane

Double-membrane bound

Single Membrane-Bound Organelles

Lysosome

In both Animal and Plant Cells

The digestive enzymes they possess are used to break down a variety of things, including the cell itself!

Membrane balls containing digestive enzymes

Vesicle/Vacuole

Plant cells tend to have one large vacuole, while animal cells will have a few smaller ones, if any

All cells have vesicles

Vacuoles tend to be larger, especially in plants, and are typically used for storage

Vesicles transport materials out of the cell and store materials inside the cell

Literally just membrane balls

Packaging and Transport Organelles

Golgi Body

Modifies proteins

Processes and packages proteins to be sent out of the cell

Stacks of flattened membrane sacs

Endoplastic Reticulum

In all eukaryotes

Transport of molecules within the cell

Rough - embedded with ribosomes

Smooth - no ribosomes attached

Network of tubes/membranes extending outwards from the nucleus to the membrane

Ribosomes

In all cells

Constructs proteins

Made of rRNA and protein

Freely floating in the cytoplasm or attached to the endoplasmic reticulum

Nucleus

Present in all cells in some form

Contains all instructions to govern cell function

DNA/RNA

Nucleolus

Production of ribosomes

Cluster of protein - RNA in the center of the nucleus

Nuclear Envelopment

Both in Animal & Plant Cells - not present in prokaryotic cells

Protect the genetic material inside the nucleus

Single bilayer surrounding the nucleus

Types of Cells
Eukaryote

Plant

Animal

Prokaryote

Cyanobacteria

Bacteria

Common Cell Structures
Cytoplasm
Genetic Material
Cell Theory
Cells only come from pre-existing cells
The cell is the smallest unit of life
All living things are composed of cells or cell products

Topic 4 - Enzymes

4.2 - Enzyme Function
Feedback Inhibition

Occurs when a product from one of the reaction inhibits a previous step

Can be competitive or non-competitive inhibition

Can take place when there is a series of enzyme catalyzed reactions, where a product from each reaction becomes part of the next reaction

Competitive Inhibition

The inhibitor molecule is similar in shape to the substrate, and can bind directly to the active site - substrate is now blocked from binding

Allosteric Regulation

An allosteric site on an enzyme is any site that is NOT the active site. It can be used as an on-off switch

If a cell wants the ability to turn on and off a particular enzyme. Allosteric regulation is one mechanism it can use.

More complex method of controlling enzyme activity

Factors Affecting Enzyme Activity

Enzyme Co-Factor

Substances other than the enzyme and substrate. Their job is to help activate the enzyme itself

Coenzymes, which are organic molecules. Their job is to transfer energy in the form of electrons

They include vitamins, and an important molecule we’ll see much more of later called NAD+

Metal ions, such as Ca2+, Zn2+ and Cu2+

pH

Certain enzymes are designed to function within a very narrow range of pH conditions

Temperature

Higher temperature can increase rate of reaction up until the point that it denatures the enzyme

Substrate concentration

The more substrate the there is, the higher the rate of reaction - up to a point

Enzyme Catalyzed Reaction

7 : The active site becomes available for another set of substrates

6 : Product is released

5 : Substrates are converted into new product, new bonds are formed

4 : Enzyme lowers EA

3 : Substrates are held in the active site through weak intermolecular forces like H-bonds

2 : Enzyme changes shape accordingly

1 : Substrates binds to the active site

4.1 - Enzymes
Why rely on enzymes?

Enzymes exhibit substrate specificity - so they only encourage reactions the cell wants

Enzymes are not consumed during the reaction, and are therefore reusable

Heat - for instance, will generally speed up reactions by getting particles to move around faster, increasing the chance that reactants will bump into each other

Strategies to Decrease Activation Energy

S - Straining Bonds

Enzyme pulls on intramolecular bonds causing strain, and making it more likely for them to break with lower input of energy

D - Direct Participation

Enzyme, well, participates directly in the reaction in some way

O - Orientation

Enzyme orients the substrate in such a way that it makes it more likely bonding sites come into contact with one another

M - Microenvironment

Enzyme creates a more suitable mini-environment for the reaction to occur

Energy profile

Endergonic Reaction

Typically Anabolic

Results in an “absorption” of energy

More energy in the products than in the reactants

Exergonic Reaction

Typically Catabolic

Results in an overall release of energy

More energy in the reactants than the products

Free energy - a measure of the energy available to do something

Role :is to speed up biological reactions by lowering activation energy (EA)

Activation energy : energy needed to be added before a reaction can proceed

Is a Biological Catalyst

Topic 3 - Macromolecules

3.8 - Nucleic Acids
Shape of DNA

Bases are joined together with hydrogen bonds

Formation of a Polymer

The bond created is called a phosphodiester bond

When two nucleotides join, the nitrogenous base is not involved. The phosphate group from one nucleotide binds to a hydroxyl group on the sugar of the second nucleotide

General Structure of Nucleotide (Nucleotide - Monomer which make up a Nucleic Acid)

3 Main Components

Phosphate Group

Pentose Sugar (5 carbons)

Ribose in RNA

Deoxyribose in DNA

Nitrogenous Base

Uracil (U)

Thymine (T)

Cytosine (C)

Guanine (G)

Adenine (A)

ATP (adenosine triphosphate) - stores potential energy in phosphate bonds, releases than energy when converted to ADP

RNA (ribonucleic acid) - translates DNA into protein

DNA (deoxyribonucleic acid) - stores and transmits genetic material

3.4 - Proteins
Protein Denaturation

Can be caused by heat, pH, salt, and mechanical agitation

Temporary - Heating up milk

Permanent - cooking an egg

Alternation of structure of a protein since function of a protein is dependent on its structure, denaturation ALSO disrupts its function.

Protein Structure

Quaternary Structure - Multiple folded polypeptides joining together (not all proteins reach this stage)

Will fold up in precisely the same way every time - specific interactions between side chains

Tertiary Structure - Folding of the polypeptide due to interactions between side chains - some proteins will stop here for their specific functionality

Will fold up in an extremely precise way every time

R-groups will become positively charged or negatively charged - attraction or repulsion between each other

Nonpolar amino acids will cluster together inwards whereas the polar ones will move outwards - to be close to the water (protects nonpolar from water)

Some R-groups give the amino acids the properties of being nonpolar therefore hydrophobic or to others polar properties therefore hydrophilic

Secondary Structure - hydrogen bonding of the peptide backbone (α-helix or β-pleated sheet)

Primary Structure - specific sequence of amino acids

Created in a watery environment
Amino Acids Structure

Categories

Linkage between NH bond and double bonded oxygen divides the amino acid groups

Polymer of Amino Acids - Polypeptide Chain

R- ground can make an amino acid

Subtacidic/negatively charged, alkaline/positively charged, or neutralopic

Polar and Non-Polar

20 amino acids - 8 are “essential” (our body cannot synthesize them) - we need to include them in our diet

Protein is a polymer - its monomers are amino acids

Functions

Acceleration of Chemical Reactions - Enzymes

Coordination and Regulation of Activities - Shape Changes

Movement Between Cells - Protein Channels

Cell Signaling - Insulin, Antibodies

Transport of Substances - Ion Channels

Structural Support - Connective Tissues

3.3 - Lipids
Phospholipid

Composition

One phosphate group

Makes the “head” polar and therefore hydrophilic.

Two fatty acids

The fatty acid “tail” is nonpolar and hydrophobic.

Resulting molecule is amphipathic - it is both partly hydrophilic and hydrophobic

Saturated vs Unsaturated Fatty Acids

Unsaturated Fatty Acids

Trans Fatty Acids

Acts like a solid saturated fat

Happens when one of the hydrogen atoms connected to the double-bonded carbons is not on the same sides as each other

Resulting in no repulsion between hydrogen atoms on top of the unsaturated fatty acid creating the bend

Modified Unsaturated Fatty Acids

NOT saturated by hydrogen atoms, because there is at least one double-bond between carbons

Liquid at room temperature

Found in plant-based fats

Saturated Fatty Acids

Every carbon is bonded to the maximum number of hydrogen atoms

Saturated by hydrogen bonds

Usually solid at room temperature

Found in animal fats

4 Categories

Waxes

Combination of a fatty acid bound to an alcohol

Protection

Water Resistance

Steroids

Characterized by 4 carbon rings and varying functional groups

Growth

Cell response to the environment

Hormonal Signaling

Cell Membrane

Triglycerides

Composed of a glycerol molecule and 3 fatty acid chains

Insulation

Energy Storage

Composed of C, H , and O

Chains or Rings

3.2 - Carbohydrates
Isomers

Molecules with same chemical formula but different structures

Molecular Structure

Possess 1:2:1 ratio of C:H:O

𝝰-linkages and 𝞫-linkages

𝞫-linkages occur when the -OH groups are oriented in opposite directions

𝝰-linkages occur when -OH groups involved in reaction are oriented the same way - both up or both down

Structure and Function

Polysaccharides

Ex: Starch, Glycogen, Cellulose, Chitin

Chitin : Structural molecule in organisms like insects and crustaceans (exoskeleton strength)

Glycogen : Energy storage in animals (and fungi and bacteria). Highly branched chains of 𝛼-glucose

Starch : Energy storage molecule in plants. Straight and branched chains of 𝛼-glucose (Zigzaggy structure resulting in weak structural support)

Cellulose : Structural molecule in plants. Straight chains of 𝛽-glucose (Result in great structural molecule for plants). We can’t digest cellulose because we don't have the ability to break 𝛽-linkages.

Energy source, Structural support, cell to cell communication

Many monosaccharides

Disaccharides / Oligosaccharides

Formation of Disaccharides

Bonds between monosaccharides are called glycosidic linkages. Usually identify which carbon on each monosaccharide is involved

Ex: Maltose, Lactose

2-7 monosaccharides

Monosaccharides

Ex: Glucose, Fructose

Energy Source

One Subunit

3.1 - Building and Breaking Macromolecules
Building Macromolecules

Polymer

Long-chain molecule made up of repeated patterns of monomers

Examples - starch, proteins, DNA

Monomer

A small molecule

Examples - glucose, amino acids, nucleotides

Macromolecule - a molecule containing a very large number of atoms, such as a protein, nucleic acid, or synthetic polymer
2 Types of Biochemical Reactions

Catabolic Reactions

Break down larger molecules into smaller molecules - Polymers into Monomers

Releases Energy

Done through a hydrolysis reaction

Anabolic Reactions

Builds larger molecules out of smaller molecules - Polymers out of Monomers

They do so through dehydration synthesis

Topic 6 - The Cell Membrane and Transport Across Membranes

6.2 - Transport Across Membranes
Exocytosis

When the cell needs to release molecules that can’t pass through the membrane

Just the reverse of the three forms of endocytosis

“Cell spitting”

Receptor-Mediated Endocytosis

Very similar to phagocytosis, except it is prompted by molecules binding to specific receptors

Pinocytosis

Basically the same thing, except it’s used for the intake of fluid droplets

“Cell Drinking”

Phagocytosis

Particles are engulfed by a section of the membrane which pinches in to become a vesicle

“Cell Eating”

Bulk Transport

Used for molecules that simply can’t get through the membrane by any other means

Coupled Transporter

Two proteins working together

Antiporters

Example : a sodium-potassium pump

Move two different solutes in opposite directions

Active Transport

Usually requires a specific carrier protein

Molecules are moving UP the concentration gradient

From low concentration to high concentration

Requires Energy

In form of ATP

Aquaporins

Ex : Water reabsorption in the kidney

Proteins the allow for facilitated diffusion of water across the membrane

Types of Solutions

Isotonic

Same solute concentrations

Hypertonic

Higher relative solute concentration

Hypotonic

Lower relative solute concentration

Solution Terminology

Concentration Gradient

a gradual change in the concentration of solute from one area of the solvent to another

Solvent

the substance doing the dissolving

Solute

the substance being dissolved

Types of Movements

Active Transport (Requires Energy)

Coupled Transport

Protein Carriers

Passive Transport (Does not Require Energy)

Simple Diffusion

In the context of molecules moving across the cell membrane, this works for small, lipid soluble molecules, O2, and CO2

Movement of solute down a concentration gradient (from high to low)

Facilitated Diffusion

There is also facilitated diffusion with carrier proteins for larger molecules like amino acids, sugars, and small proteins

Since they cannot get through the phospholipid bilayer, they must pass through a protein channel instead.

Different Types of Channels

Ligand-gated channels (open in response to certain chemical interactions)

Voltage-gated channels (open in response to electrical potential)

Ion channels (Na+ channels, K+ channels)

Osmosis

The semi-permeable membrane doesn’t allow the solute through, so the solvent - water - moves to balance out the concentrations instead

The movement of water, across a semipermeable membrane, down the concentration gradient

6.1 - Phospholipid Bilayer
Components

Glycolipids

Ex : ABO Blood markers

These play a role in maintaining stability of the membrane and in cellular recognition

A lipid molecule bound to a carbohydrate

Glycoproteins

Ex : Mucins, antibodies

Provides structural support, is involved in cell recognition, and plays a role in cell to cell interactions

The carbohydrate stick out of the cell

A carbohydrate bound to a membrane protein

Peripheral Membrane Proteins

Ex : Cytochrome C

These proteins are capable of moving around the cell membrane

Integral Membrane Proteins

Ex : Insulin receptors, ion channels

Are permanent and usually transmembrane

Cholesterol

At low temperatures, it increases fluidity

At high temperatures, it reduces fluidity

Regulates the fluidity of the membrane - serves as a kind of membrane lubricant

Phospholipids

Resulting membrane is impermeable to water-soluble molecules

Serve as the main component of the membrane, and create a barrier

Fluid Mosaic Model

Mosaic-like

Funtions of Membrane Proteins

Attachment and Recognition

Signal Triggering (eg. hormones)

Enzymatic activity

Transport of large molecules such as glucose across the membrane

The membrane is composed of many types of macromolecules

Fluidity

The phospholipids and proteins move laterally. The components are not static

Selective Permeability

Based on the size and solubility of the molecule and the availability of specific protein channels

Function

Regulates what can enter and exit the cell

Divides and protects the interior of the cell from the exterior

Topic 1 - Fundamental Chemistry

1.2 - Solubility and Intermolecular Bonding
Intermolecular Bond - Forces of attraction between molecules

3 Types of Intermolecular Bonds

Hydrogen Bond (Most Important)

Hydrogen Bonds in Water

Adhesion

Ability of water to form hydrogen bonds with other substances

Cohesion

Ability of water molecules to form hydrogen bonds with other water molecules

Interactions between 3 specific elements

Fluorine

Oxygen

Nitrogen

Strongest of the 3

Dipole-Dipole Interactions

Refers to forces of attraction between polar molecules

Stronger than London Dispersion Force

London Dispersion Force

Temporary forces attraction due to unequal distribution of electrons in a molecule at any given moment

Weakest of the 3

Hydrophobic Compounds (Water-Fearing)

Non-Polar Substance that will not Dissolve in Water

Hydrophilic Compounds (Water-Loving)

Polar Substance that Dissolves in Water (Soluble)

Solubility

Insoluble - Incapable to Dissolve

Soluble - Able to Dissolve (especially in water)

Polarity (Rule of Solubility)

Non-Polar Solutes Dissolve in Non-Polar Solvents

Polar Solutes Dissolve in Polar Solvents

1.1 - Atoms, Bonding, Polarity
Electronegativity Difference (of Elements)

Less than 0.5 - Non-Polar Covalent Bond

Equal Sharing of Electrons

Symmetry Needed

Between 0.5 and 1.7 - Polar Covalent Bond

Unequal Sharing of Electrons

Asymmetry Needed

Less than 1.7 - Covalent Bonding

Example : HCL - Hydrogen : 2.1, Chlorine : 3.0, Difference : 0.9

Greater than 1.7 - Ionic Bonding

Example : HF - Hydrogen : 2.1, Fluorine : 4.0, Difference : 1.9

Topic 2 - Functional Groups

Types of Functional Groups
Methyl

Needs to be branching off the longest hydrocarbon chain

Doesn’t change much about the initial molecule

Non-Polar

Additional carbon (and its 3 hydrogens) added to a hydrocarbon

Sulfhydryl/Thiol

Found in certain amino acids - Co-A

Rotten egg smell

Sulfur-hydrogen group attached to a carbon chain

Phosphate

Found in DNA, RNA

can be represented with the two hydrogens missing, in which case their respective oxygen atoms would be negatively charged

Amino

Found in Porteins

can become charged (positive)

Can Gain H (alkaline)

Nitrogen and two hydrogen form a (primary) amino group

Hydroxyl

Found in alcohols and carbohydrates

OH group bound to a carbon

Carboxyl

Found in Proteins

Can become charged

Can lose H (acidic)

Carbon double-bonded to an oxygen AND single-bonded to an oxygen-hydrogen (OH) group

Carbonyl

2 Categories of Carbonyls

Ketone

Carbonyl category sits on carbon that isn’t a terminal carbon

If both R-group represent carbons, the compound is a ketone

Aldehyde

Double Bonded oxygen is on the terminal carbon (End of the chain)

If one R-group is a hydrogen, the compound is an aldehyde

Found in Lipids

Polar

oxygen double bonded to a carbon

Functional Group - Specific group of atoms that can be added to a hydrocarbon to modify its chemical behavior
Chemical Behavior Changes

Can become more prone to certain types of bonds

Polarity

Influences Solubility

Hydrocarbon - organic compound consisting entirely of hydrogen and carbon atoms