Biochemistry Flashcards
Name the functional groups
Hydroxyl, carbonyl, carboxyl, amino, methyl, phosphate, sulfhydral
Name the functional groups associated with carbohydrates
Hydroxyl, carbonyl
Name the functional groups associated with proteins
Hydroxyl, carbonyl, amino, sulfhydryl
Name the functional groups associated with nucleic acids
Hydroxyl, carbonyl, amino, phosphate
Name the functional groups associated with lipids
Hydroxyl, carboxyl, phosphate
What is a macromolecule
Large, complex molecules usually composed of repeating units of smaller molecules covalently linked together
What is a monomer
One sub unit
What is a polymer
Several sub units (monomers) combined
What is a carbohydrate
A biological macromolecule that contains carbon, hydrogen and oxygen in a 1:2:1 ratio
Provide short or long term energy storage
What is a monosaccharide
A carbohydrate composed of between 3 and 7 carbon atoms
“Mono” means one, “saccharide” means sugar
Considered to be simple sugars such as glucose, fructose and galactose
Glucose, fructose and galactose are isomers
What is an isomer
One of two or more molecules with the same number and type of atoms, but different structural arrangements
What are the two equilibrium that sugars exist in
Cyclic (Haworth model) and acyclic (fisher projection)
What is a disaccharide
A carbohydrate composed of two monosaccharides joined by a glycosidic linkage
An example is sucrose, composed of glucose and fructose
What is a polysaccharide
A carbohydrate polymer composed of many monosaccharides joined together by covalent bonds
Explain starch
Responsible for energy storage in plants
Long chain of glucose subunits
Provide short term energy storage
Explain glycogen
Responsible for energy storage in animals
Animals and humans when consuming glucose break it down and convert it into glycogen where it is stored in the liver
Has a larger amount of branching than starch in order to pack more glucose units into a single cell
Too much glycogen can result in glycogen storage disease which is usually hereditary
Explain cellulose
Used by plants to build walls
Structural molecule as it protects and supports the plant
Only a few bacterial species produce the digestive chemicals to break it down, mammals and humans do not have the bacteria
Explain lipids
Lipids are hydrophobic
The presence of many energy rich C-H bonds makes lipids efficient energy storage molecules
Lipids provide long term energy storage, provide insulation, protects and cushion the organs
What are the four classes of lipids
Triglycerides, phospholipids, steroids, waxes
Explain triglycerides
Triglycerides are a lipid molecule composed of a glycerol molecule and three fatty acids linked by ester bonds
What is a fatty acid
A fatty acid is a hydrocarbon chain ending in a carboxyl group
What are unsaturated fatty acids
Fatty acids with double bonds
0 double bonds= saturated
1 double bond= monounsaturated
2+ double bonds= polyunsaturated
Explain saturated fats
No double bonds between carbon atoms
Fairly straight, pack tightly
Solid at room temperature
Explain unsaturated/polyunsaturated fats
One or more double bonds between carbon atoms
Cis double bonds cause kinks in molecules
Cannot pack tightly, trans double bonds don’t allow bending
Explain hydrogenation
Add hydrogen atoms to double bonds
For example, adding hydrogen atoms in vegetable oils to convert them to semi-solids like margarine
Explain trans fat
Trans fats are unsaturated fatty acids that are not commonly found in nature. The common unsaturated acids have a cis configuration of H’s attached to double bonds. Trans fatty acids have a trans configurations of H’s attached to double bonds
Cis- H’s go the same way
Trans- H’s go the opposite way
What are phospholipids
Lipids composed of a glycerol molecule bonded to 2 fatty acids and a phosphate groups with an R group
The head of the phospholipid molecule is polar, thus the head is hydrophilic while the tail is non-polar and hydrophobic
What is a phospholipid bilayer
A structure with hydrophilic heads of phospholipids directed towards the aqueous environment and hydrophobic tails directed toward the centre, interacting with each other
This keeps water out, allows the cell to be selective of what goes in and out
What is a micelle
A single layered barrier formed when phospholipids are added to water
Forms spheres, forms a single layer membrane with a hydrophobic interior
What are steroids
Lipids composed of four attached based rings
Explain cholesterol
A key component of cell membranes
High cholesterol can restrict blood flow. Cells convert cholesterol into compounds such as vitamin D and bile salts. Important for keeping cell membrane fluid, not rigid
Explain high density lipoprotein (HDL)
Aids in moving cholesterol through blood stream
Removes cholesterol by transporting to liver
Explain low density lipoprotein (LDL)
Deposits cholesterol onto vessel wall
Causes blockages
What are waxes
Lipids containing long chain fatty acids linked to alcohols or carbon rings
Hydrophobic, firm, pliable consistency, used as waterproof coating on plants and animals
What functions do proteins perform
Catalyze chemical reactions, provide structural support, transport substances in the body, enable organisms to move, regulate cellular processes, provide defence from disease
What is an amino acid
An amino acid is an organic molecule composed of a central carbon atom bonded to a hydrogen atom, an amino group, a carboxyl group and a R group
Explain the primary structure of a protein
The primary structure of a protein is the polypeptide chain formed by covalent peptide bonds
Explain the secondary structure of a protein
The polypeptide chain begins to fold and interact with itself due to hydrogen bonding. It has been observed to form two possible orientations: an alpha helix and a beta pleated sheet
Explain the tertiary structure of a protein
This structure forms due to hydrophobic and hydrophilic interruptions within the cellular environment. Alpha helixes and beta sheets will fold and re-orient themselves so that:
Hydrophilic groups will direct towards the water
Hydrophobic groups will be directed towards the interior of the folded protein, to avoid interaction with water
Explain the quaternary structure of a protein
When the different tertiary structure group together and interact they form a large quaternary structure.This is the functional protein stage
Explain denaturation
Understood and conditions, proteins will unfold to do breaking of bonding interactions with R groups. For example changes in temperature, change in pH of the environment, exposure to harmful chemicals, high salt concentrations)
Protein can no longer function normally at this point
Explain nucleic acids
Biological macromolecule composed of nucleotide monomers. The two types are DNA and RNA
DNA is composed of nucleotides containing sugar deoxyribose
RNA is composed of nucleotides containing the sugar ribose
Explain DNA
Composed of four different types of nitrogenous bases: adenine, thymine, guanine and cytosine
Stores genetic information of an organism
H in DNA
Explain RNA
In RNA uracil is used in place of thymine
Participates in protein synthesis
OH in RNA
What is a nucleic acid composed of
A phosphate group, a sugar, a nitrogenous base
What is the monomer of a carbohydrate
Monosaccharide
What is the polymer of a carbohydrate
Polysaccharide
What are the bonds between the monomers of a carbohydrate
Glycosidic linkage
What is the monomer of a lipid
Glycerol and 3 fatty acid chains
What is the polymer of a lipid
Triglyceride
What are the bonds between the monomers of a lipid
Ester bonds
What is the monomer of a protein
Amino acids
What is the polymer of a protein
Polypeptides
What are the bonds between the monomers of a proteins
Peptide bonds
What is the monomer of a nucleic acid
Nucleotides
What is the polymer of a nucleic acid
Strands
What are the bonds between the monomers of a nucleic acid
Phosphodiester bonds
What is an acid
A substance that produces hydrogen ions when dissolved in water
What is a base
A substance that produces hydroxide ions when dissolved in water
pH scale
>7 = basic <7 = acidic 7 = neutral
What is the normal pH range of human blood
7.35 - 7.45, slightly alkaline
Define alkalosis
If the pH increases to 7.5
This could be the result of breathing too quickly at high altitudes, feeling anxious, too many antacids, the person can feel dizzy and agitated
Define acidosis
The pH falls between 7.1-7.3 and symptoms include disorientation and fatigue and can result from severe vomiting, brain damage, and kidney disease
Define buffer
A substance that minimizes changes in pH by donating or accepting hydrogen ions as needed
Buffers tend to exist as a pair of acids and bases
Define oxidation
The process involving the loss of electrons
Define reduction
The process involving the gain of electrons
Define redox reaction
The chemical reaction that involves the transfer of electrons from one substance to another
What is a condensation reaction
A chemical reaction that results in the formation of a covalent bond between two molecules with the production of a water molecule
What is a hydrolysis reaction
A chemical reaction that results in cleavage of a covalent bind with the addition of a water molecule
What are enzymes
Enzymes are catalysts- these are chemicals that speed up a chemical reaction without being used up in the process
The molecule that the enzyme acts on is called the substrate molecule
Enzymes are very specific to the substance which they bind
The site where the enzyme binds to the substrate is called the active site
When the two are attached, this creates the enzyme substrate complex
Enzymes can be inorganic (cofactors) or organic (coenzymes)
Why are enzymes important
Enzymes prepare substrates for reaction by changing the substrate, its environment or both in some way
Enzymes reduce the activation energy required for a reaction to begin, thus less energy is needed for reactions to occur
What is an inhibitor
Molecules that bind to the allosteric site or active site of an enzyme and causes a decrease in the activity of that enzyme
What is an allosteric site
A site on an enzyme that is not the active site
What is competitive inhibition
Interferes with the active site of the enzyme so substrate cannot bind
What is non-competitive inhibition
Changes the shape of the enzyme so it cannot bind to substrate
What is an activator
Molecules can also bind to an allosteric site
It is a molecule that keeps an enzyme active or causes an increase in the activity of that enzyme
What are the factors that affect enzyme activity
Temperature, pH, substrate concentration
Explain how temperature affect that activity of an enzyme
As temperature increases, so does the vibrational energy of each atom. This causes the intermolecular forces holding the protein together to break. This result in a denatured protein, thus the enzyme is non functioning
Explain how pH affects the activity of an enzyme
As pH changes, the enzymes amino acids R-groups gain or lose protons, which change their shape and thus activity
Explain how substrate concentration affects the activity of an enzyme
If there are more molecules present in a solution, there is a higher chance that one will interact with the enzyme. At a certain point (x), there are not enough enzyme molecules to catalyze all of the substrate molecules. The enzyme becomes the limiting factor
Give an example of a buffer
In the human body, carbonic acid and hydrogen carbonate
If blood becomes to basic, carbon dioxide and water react to produce carbonic acid which dissociates into hydrogen carbonate and hydrogen ions and increases the acidity of the blood
Describe cytoplasm
The region of the cell that is contained within the cell membrane; Includes the cytosol, the organelles and other life supporting materials
Describe the nucleus
Contains DNA which stores and replicates the genetic information of the cell
Describe nucleoplasm
A thick fluid that fills the nucleus of a cell
Describe nuclear matrix
A filamentous Network of proteins that is found inside the nucleus and lines the inner nuclear membrane; serves to organize chromosomes
Describe nuclear envelope
A double membrane surrounding the nucleus of a cell
Describe nuclear pore complex
A group of proteins forming openings in the nuclear envelope
Describe nucleolus
A non-membrane-bound structure in the nucleus, contains RNA and proteins
Describe chromosome
A strand-like complex of nucleic acids and protein tightly bounded together; chromosomes contain the hereditary units known as genes
Describe chromatin
The non-condensed form of genetic material that predominates for most of the eukaryotic cell cycle. Chromatin represents the unfolded state of chromosomes
Describe rough endoplasmic reticulum
Studded with ribosomes, plays a key role in the initial synthesis of proteins
Describe smooth endoplasmic reticulum
Synthesizes lipids and lipid containing molecules
Describe ribosomes
I structure composed of RNA and proteins; and responsible for synthesis of polypeptides in the cytosol and on the surface of the rough ER
Describe lysosome
A membrane-bound vesicle containing enzymes that catalyze hydrolysis reaction thereby breaking down macromolecules
Describe Golgi apparatus
A stack of curved membrane sacs that packages, processes, sorts, and distributes proteins, lipids and other substances within the cell
Describe peroxisomes
A membrane-bound sac containing oxidative enzymes that break down excess fatty acid and hydrogen peroxide, and participate in the synthesis of bile acids and cholesterol
Describe vesicle
Small membrane bound sac that stores substances within a cell
Describe vacuole
Large membrane bound sac in plant cells and some other cells that store water, ions, macromolecules, sugars, amino acids
Describe chloroplast
An organelle in the cells of photosynthetic organisms, in which light energy from the sun is captured and stored in the form of high energy organic molecules such as glucose
Describe chlorophyll
Photosynthetic pigment; absorbs light energy as part of the process that converts carbon dioxide and water into energy rich organic molecules
Describe stroma
The fluid filled interior surrounding the grana in a chloroplast
Describe thylakoids
One of many interconnected sac-like membranous disks within the chloroplast, containing the molecules that absorb energy from the sun
Describe granum/grana
In a chloroplast, a structure made up of stacked thylakoids
Describe mitochondria
An organelle found in eukaryotic cells that supplies most of the cells ATP
Describe matrix
The fluid filled space in the inner membrane of the mitochondria
Describe cristae
Folds of the inner membrane of the mitochondria
Describe cytoskeleton
A network of protein fibers that extend throughout the cytosol, providing structure, shape, support and motility
Describe microtubules
Proteins that form hollow tubes. Maintain cell shape, facilitate movement of organelles, assist in cell division (spindle formation)
Describe intermediate filaments
Proteins coiled together into cables. Maintain cell shape, anchor some organelles, form the internal scaffolding of the nucleus
Describe microfilaments
Two strands of actin wound together. Maintain cell shape, involved in muscle contraction, assist in cell division (cleavage furrow)
Describe cilia
Numerous short appendages protruding from a cell; each cilium is composed of a microtubule-based shaft covered in an extension of the cell membrane; allow a cell to propel itself or to propel substances across the surface of the cell
Describe flagella
Long, thin appendages that allow cells to move themselves, or to move substances over their surface
Describe cell wall
A rigid layer surrounding plant, algae, fungal, bacteria and some archaea cells. Composed of proteins and/or carbohydrates; gives the cell its shape and structural support
Describe cell membrane
A thin structure composed of various macromolecules, that separates the inside of the cell from extracellular environment; controls the flow of substance in and out of the cell
Explain the surface area to volume ratio
The surface area to volume ratio is very important for a cell. As it grows, the cells volume becomes too large for the membrane to hold and the ratio decreases. It is fixed by cell division and folding of the organelles
Explain fluid in regards to the fluid mosaic model
Varies it shape due to weak intermolecular attractive forces, not covalent bonds
It is flexible
A small tear is quickly fixed by lipids rearranging themselves
Explain mosaic in regards to the fluid mosaic model
A variety of macromolecules make up the membrane inside and surface, such as proteins, glycoproteins and cholesterol’s
What are the three factors affecting fluidity
Temperature: change in state
Double bonds: create kinks and affects ability to pack tightly
Fatty acid tail length: more molecules increase intermolecular attraction
How does temperature affect fluidity
As temperature increases, molecules gain more energy and intermolecular forces break, fluidity increases.
Thus, as temperature increases, so does fluidity. As temperature decreases, so does fluidity
How do double bonds affect fluidity
A double bond in the fatty acid tail creates bends or kinks in the chain. The more kinks a chain has, the lower its ability to pack tightly. Less tightly packed molecules have lower intermolecular interactions and therefore higher fluidity.
Thus, more double bonds, lower intermolecular forces, higher fluidity. Less double bonds, higher intermolecular forces, lower fluidity
How does tail length affect fluidity
The longer a fatty acid tail is, the more C/H atoms there are compared to a shorter tail. Intermolecular forces increase as the number of atoms increase
Thus, as chain length increases, fluidity decreases. As chain length decreases, fluidity increases
What are the two types of protein associated with the cell membrane
Integral and peripheral
Explain integral proteins
Integral membrane proteins are embedded, with hydrophobic ends within the membrane
Explain peripheral proteins
Per for a membrane proteins are loosely bound to the surface
What is passive transport
The movement of ions or molecules across a cell membrane from a region of higher concentration to a region of lower concentration, without the input of energy
What is diffusion
The net movement of ions or molecules from an area of higher concentration to an area of lower concentration
What affects diffusion
Molecule size- larger molecules are difficult to transport
Molecule polarity- highly polar molecules have difficulty passing through
Molecule or ion charge- cannot generally pass through a lipid bilayer
What is osmosis
The movement of water from an area of higher concentration to an area of lower concentration, across a semi permeable membrane
Water moves in and out of a cell, along their concentration gradient until their concentrations on both sides of the membranes are equal
What are the three types of osmosis solutions
Hypertonic: solute in the solution is higher than inside the cell
Hypotonic: solute in the solution is lower than inside the cell
Isotonic: both solutions have the solute concentration
Define lysis
In a hypotonic solution the osmotic pressure inside the cell is so great that it bursts
What is facilitated diffusion
The transport of ions or molecules across a membrane by means of a membrane protein along the concentration gradient for that ion or molecule
What is a channel protein
Forms a channel across a cell membrane, which allows specific ions or molecules to cross the membrane along the concentration gradient
What are carrier proteins
Binds to specific molecules, transport them across the membrane, and then release them on the other side. Thus, the proteins carry the molecules across
What is active transport
The transport of a solute across a membrane against its gradient
Occurs with the aid of ATP
With the aid of water, ATP undergoes hydrolysis to create ADP which releases energy for the cell
Explain primary active transport
The sodium – potassium pump transports sodium ions out of the cell while transporting potassium ions into the cell
- Three sodium ions bind to the ion pump in the cell membrane and hydrolyzed
- Three sodium’s are released outside the cell
- The potassium ions bind from outside the cell
- Phosphate is released and the pump switched and two potassium’s ions are released into the cytosol
Explain secondary active transport
Uses an electrochemical gradient as a source of energy to transport molecules or ions across a cell membrane
What is an electrochemical gradient
A result of a build up of positive or negative charges
Explain secondary active transport
- Hydrogen binds to the protein
- ATP undergoes hydrolysis to produce ADP
- Hydrogen is transported to the extracellular environment
- Hydrogen binds to the protein as well as sucrose
- Hydrogen ions provide energy to transport sucrose against its chemical gradient
What is endocytosis
Process by which a cell engulfs material by folding the cell membrane around it and then pinching off to form a vesicle inside the cell
Phagocytosis- involves solid particles
Pinocytosis- involves liquid particles
What are receptor-mediated endocytosis
Use of receptor proteins on a portion of a cell that bind with specific molecules outside the cell
Explain exocytosis
Transport method in which you back your fuses with the cell membrane and releases its contents outside the cell
This is important in plants to construct cell walls
In animal cells provides a mechanism for secreting and releasing many hormones, neurotransmitters, digestive enzymes and other substances
What is a concentration gradient
A difference in concentration between one side of a membrane and the other
