Biochemistry Flashcards
What is the pH of human blood?
What happens if it is below or above that pH?
- Optimal pH is 7.2 for human blood
- Acidic and basic blood would damage blood cells
What do buffers do?
Application in the body?
- Buffers minimize changes in pH by taking up or releasing H+ or OH- ions in solution
- Cells use buffers to regulate pH levels
Difference between dehydration synthesis and hydrolysis?
- Dehydration synthesis is anabolic (brings things together) with two subunits as reactants and one subunit as a product (+creation of H2O)
- Hydrolysis is catabolic (breaks apart) and the reverse reaction of dehydration synthesis, one reactant + water —> two subunits
What do carbohydrates contain?
What are they used for?
- Contain a 1:2:1 ratio of C:H:O as well as many hydroxyl and carbonyl groups
- Used for energy, building materials in cells, and cell-cell ID during metabolic processes
What do monosaccharides contain (number of carbons)?
Give examples of them.
- Contain between 3, 5 or 6 carbons (triose, pentose or hexose)
- E.g. glucose, fructose, and galactose
Define glucose:
Glucose: Blood sugar, used by cells in the body first for energy
Define fructose:
Fructose: fruit sugar, principle sugar in fruits
Define galactose:
Galactose: sugar found in milk
What is similar in all monosaccharides? What is different?
- All have same molecular formula
- Differ in 3D shape and arrangement of H and OH
- They are isomers
What are disaccharides?
Disaccharides: two monosaccharides that form a covalent bond (glycosidic bond) in a dehydration synthesis reaction
Formation of the three disaccharides:
Glucose + fructose —> sucrose
Glucose + glucose —> maltose
Glucose + galactose —> lactose
Define polysaccharides:
Complex carbohydrate composed of hundreds to several thousand monosaccharide subunits joined by glycosidic bonds
Examples of polysaccharides?
- Starch
- Glycogen
- Cellulose
- Chitin
Characteristics of starch?
- form of glucose storage in plants
- monomer is alpha glucose
- insoluble due to large size
- linear or branched
Characteristics of glycogen?
- stored in muscle/liver cells of humans and animals
- monomer is alpha glucose
- insoluble
- highly branched
Characteristics of cellulose
- primary structural unit in plants
- monomer is beta glucose
- H-bonding produced tight bundles called microfibrils
- linear
- humans cannot digest beta glucose
Characteristics of chitin?
- makes up exoskeletons of insects and crustaceans
- monomer is N-acetyl-glucosamine
- linear
Characteristics of lipids?
- non polar molecule made mostly of carbon and hydrogen
- made with CHO
- insoluble in water (soluble in non polar substances)
- stores energy, builds membranes/cell parts, chemical signalling, insulation and protecting organs
Four main categories of lipids?
1) fatty acids (saturated and unsaturated)
2) fats (saturated and unsaturated)
3) phospholipids
4) steroids
Characteristics of fatty acids:
- consists of singular hydrocarbon chain with a hydroxyl group at one end
- numbered evenly from 14-22
- no double bonds=saturated
- double bonds= unsaturated
Saturated vs unsaturated
Saturated: solid at room temperature, no double bonds, found in animals
Unsaturated: liquid at room temperature, double bonds, found in plants
Characteristics of fats
- fatty acid + glycerol
- 1-3 fatty acids per fat
- made through dehydration synthesis
- can be saturated or unsaturated
Characteristics of phospholipids
- make up cell membranes
- glycerol + 2 fatty acids + polar phosphate group
- ampipathic: polar head is hydrophilic and non polar tail is hydrophobic
Characteristics of steroids
- lipids that contain 4 fused hydrocarbon rings + several different functional groups
- cholesterol is building block for other steroids and is important in cell membrane
- sex hormones are also steroids (testosterone and progesterone)
Define proteins
Large molecules that consist of many amino acid subunits that are joined together by peptide bonds folded into a specific 3D shape
The shape of the protein depends on…
the sequence of amino acids that make up the protein
What are the four basic structures for proteins
Primary, secondary, tertiary and quaternary
What are amino acids made up of?
- amino group
- central carbon with hydrogen on top
- carboxyl group
- R group/side chain
What is a peptide?
- chain of amino acid subunits connected by peptide bonds
- peptide bonds link many amino acids into chains of subunits that make proteins
- peptide bond is a covalent bond that is formed by dehydration synthesis between NH2 of one + COOH of another
When is a peptide a polypeptide?
When there are more than 50 amino acids in the chain
Characteristics of primary structure
- unique linear sequence of amino acids
- ultimately determines shape and function of the protein
- endless combinations
- one alteration of animo acids changes protein
Characteristics of primary structure
- unique linear sequence of amino acids
- ultimately determines shape and function of the protein
- endless combinations
- one alteration of animo acids changes protein
Characteristics of secondary structure
- peptide chain will look like a helix or a fold
- due to H bonding between different parts of backbone
- beta pleated sheet
- alpha helix coil
Characteristics of tertiary structure
- now can be called protein
- shape due to large bonding reactions with R groups
- non polar will be hydrophobic and move towards middle of the molecule
- polar will form H bonds
- some will bond with S and create disulfide bridges
What’s good about disulfide bridges?
They are strong stabilizers for tertiary structures
What happens to proteins under extreme conditions?
Give examples of those conditions:
- protein will unfold causing denaturation (loss of structure and shape)
- e.g extreme temp and pH
Characteristics of quaternary structures:
- SOME proteins have more than 1 polypeptide chain
- interactions with 2 or more polypeptide chains make this structure
- for example hemoglobin is made up of four polypeptide chains
Define nucleic acids:
Polymers made up of many monomer subunits called nucleotides
What makes up a nucleotide?
- nitrogenous base
- 5 carbon shaped sugar
- 1-3 phosphate groups
What are the two types of nitrogenous bases? What nitrogen bases fall into each category?
Priymidine: single ringed structures (cytosine, thymine and uracil)
Purine: double ringed structures (adenine and guanine)
Which bases are found in doxyribonucleic acid
- Adenine
- Guanine
- Cytosine
- Thymine
Which bases are found in ribonucleic acid?
- Adenine
- Guanine
- Cytosine
- Uracil
What is the name for a chain of nucleotides?
Polynucleotide chains
What does 5’ and 3’ mean?
- five prime and three prime
- refers to way the carbon is oriented
Polynucleotide chain bonding:
- linked to next chain by bridging phosphate group between 5’ carbon of one sugar and 3’ carbon of another sugar
- alternating sugar and phosphate groups form backbone of nucleic acids chain
What is the name of the linkage between nucleotides?
Phosphodiester bond
Compare RNA and DNA
Each nucleotide in RNA and DNA are made up of a phosphate group, a nitrogenous base and a 5 carbon sugar
Contrast RNA and DNA
- ribose sugar (RNA) deoxyribose sugar (DNA)
- single stranded (RNA) double stranded (DNA)
- Uracil (RNA) Thymine (DNA)
Define enzyme
Proteins that act as a catalyst (speed up chemical reactions- reactants are consumed into products faster than if there were no catalysts involved)
What’s special about a catalyst in a reaction
Catalysts are not consumed into products a reaction so they can be used over and over again
What is unique about a catalyst
Each has a unique 3D shape, determines which enzyme catalyizes which reaction
How do enzymes speed up a reaction
For chemical reactions to move forward they must overcome an energy barrier (enzymes lower that barrier so that the reaction moves faster
What do enzymes bind to
Substrates: a substance recognized by an enzyme and bonded to it
What part of the enzyme does a substrate interact with
Active site: 3D pocket that matches the shape of the substrate in order for binding to occur
Induced fit model
Interaction happens between functions groups of the enzyme and the substrate causing the protein to change shape as the substrate enters the active site
Assumes active site is more flexible and changes in order to assist binding
Structure when substrate binds to enzyme:
Enzyme-substrate complex
How can you tell an enzyme based on written name alone
All enzymes have an ending of -ase
Lock and key model
An active site fits perfectly with a substrate and no changes are made during binding
Define cofactor and coenzyme
Cofactors: non protein group (usually metal) that binds precisely to an enzyme
Coenzyme: an organic molecule that acts as cofactor of an enzyme
Difference between cofactor and coenzyme
Cofactors are metal while coenzymes are organic molecules
Similarity between cofactor and coenzyme
Both help enzyme and substrate fit together
Enzyme inhibitors
Foreign agents that effect the enzymes ability to work (decrease their activity)
Competitive inhibition
- happens in active site
- “musical chairs”
- molecule resembling substrate binds causing competition for the active site
- substrate cannot bind to enzyme
Non competitive inhibition
- alters enzyme shape
- occurs in the allosteric site
- molecules binds at allosteric site causing the enzyme shape to change so that the substrate cannot bind to the enzyme
Allosteric regulation
Regulatory molecules naturally regulate enzyme activity by binding to allosteric site (inhibit or stimulate enzyme activity)
Allosteric activation
1) enzyme binds to allosteric site
2) binding activator converts enzyme to high affinity state
3) enzyme binds to substrate in high affinity state
Allosteric inhibition
1) enzyme binds to allosteric site
2) binding inhibitor converts enzyme to low affinity state
3) (changes shape so that’s substrate is released/others cannot bond)
Feedback inhibition
The regulation of a pathway by one of the products in the pathway (always stops the process at beginning “enzyme one” or rarely “enzyme two”)
Characteristics of the cell
All organisms we see around us are made up of cells
A cell is the smallest unit of living matter
Cell theory: cells come only from other prexisting cells and are capable of reproducting
Cell structure and function
A cell carries out all functions we associate with living things (growth and reproduction)
Particular functions are carried out by certain parts of a cell
All cells are surrounded by plasma membrane that separates the internal and external environment
Some cells (plant cells) are strengthened by the addition of a cell wall that protects cell membrane
Types of cells
Prokaryotic and eukaryotic
Prokaryotic cells
Lacy true nucleus and DNA consists of a single chromosome found in a region called the nucleoid
Eukaryotic cells
Have membrane nucleus that holds DNA within thread like structures called chromosomes
Has organelles that carry out specific functions depending on structure
Cell membrane
In both plants and animals
Regulates transport of materials entering and exiting the cell
Cell wall
Found in plant
Surrounds plasma membrane and provides strength and protection
Allows cells to develop turgor pressure
Cytoplasm
Found in both
All contents from cell membrane to the nucleus
Where organelles are able to operate
Cytosol refers to the fully fluid part of the cytoplasm
Vacuole
Found in both
Stores nutrients and water, also involved in removal of waste products
In plant cells involved in maintaining turgor pressure
Ribosome
Found in both
Protein synthesis
Golgi body
Found in both
Helps process and package proteins
Sugars and phosphate groups are added and shipped by vesicles out of the cell
Rough ER
Studded with ribosomes
Found in both
Transports proteins to smooth ER
Smooth ER
Found in both
Proteins stay in the smooth ER and act as enzymes to produce lipids and digest toxins, carbs and fats
Some proteins leave in vesicles and are transported to the golgi body
Central vacuole
Found in plant
Stores salts minerals nutrients proteins digests toxins etc
Most importantly plays a major structural role
Chloroplast
Found in plants
Produce energy through photosynthesis
Mitochondria
Found in both
Generates the chemical energy in form of ATP
Nucleus
Found in both
Stores cells DNA
Controls protein and enzyme synthesis
Nucleolus
Produce and assemble ribosomes
Nuclear membrane
Found in both
Acts as barrier that separates the nucleus from the rest of the cell
Controls what enters and exits the nucleus
Centrosome
Found in animals
Involved in the process of cell division
Organizes cell motility bonding and polarity in interphase, facilitates the organization of spindle fibre poles during mitosis
Lysosomes
Found in animals
Digestive system of the cell
Breaks down or digests macromolecules
Responds against foreign substances
Microtubles
Found in both
Involved in mitosis cell motility intracellular transport and help maintain cell shape
Nuclear pores
Found in both
Providence access to the nucleus
Regulate transport of proteins
Vesicle
Found in both
Move substances into and out of a cell
Storage of nutrients minerals and water
Digestion (lysosome peroxisome)
Membrane structure and function
Plasma membrane regulates the passage of molecules into and out of the cell and is made up of a bilayer of phospholipids
Fluid mosaic model
Widely accepted model of the cell surface membrane in which proteins are embedded and float freely within a bed of semi fluid lipids
Proteins in the membrane
Some proteins are involved in transport and attachment
Others are enzymes used in a variety of biochemical pathways
Small number of membrane proteins anchor cytoskeleton filaments to the membrane
Several lipid and protein components of some membranes have carb groups linked to them forming….
Glycolipds and glycoproteins (involved in cell recognition and cell-cell interactions)
Glycolipids
May account for characteristics such as specific blood groups and why patients system sometimes rejects an organ transplant (glycocalyx)
What is the plasma membrane responsible for
Outer cell membrane responsible for regulating substances moving in and out of the cell
Contents of phospholipids in membrane
Contains 2 fatty acid trails usually linked to glycerol, phosphate group and an compound such as choline
What happens when there is irregular fluidity
If there is too much fluid too many molecules can diffuse and if there is not enough fluid too few molecules can diffuse
Factors that affect fluidity
Temperature and composition of the lipid molecules (presence of double bonds-increases fluidity)
Cholesterol role in fluidity
Important to maintain membrane stability to be not too fluid or not too ridged
Two types of membrane proteins
Proteins associated with membranes are integral proteins or peripheral proteins
Integral proteins
Embedded in membrane
Stabilization of membrane and keep them in place by linking with cytoskeleton
Peripheral protein
Stabilization of membrane and keep them in place by linking with cytoskeleton of the cell
Four categories of membrane proteins
Transport
Enzymatic activity
Triggering signals
Attachment and recognition
Transport
Shape shifting may allow some membrane proteins to shuttle molecules from one side of the membrane to the other
Enzyme activity
Proteins associated with respiration and photosynthesis are enzymes
Triggering signals
Membrane proteins may bind to be specific chemicals such as hormones, binding to these chemical triggers changes in the inner surface of membrane starting a cascade of events within the cell
Attachment and recognition
Surface proteins can recognize elements of disease causing microbes that may try to invade cells triggering an immune response
Moment of molecules across the plasma membrane
The plasma membrane is considered to be selectively permeable (special mechanisms regulate the passage of most molecules in and out of the cell)
Simple diffusion definition
Movement of a substance across a membrane with out the need to expend chemical energy
Characteristics of simple diffusion
Spontaneous and require concentration gradient (net movement of a substance from [high] to [low]
Rate of diffusion depends on the concentration difference
Very few molecules will diffuse across the plasma membrane
What molecule can diffuse across the plasma membrane and what is that process called
Water
Osmosis: the diffusion of water across a concentration gradient
Osmosis
Water molecules move from an area of [high free water] to [low free water]
Has bound water and free water
Define bound water
Bonded to solutes not free to cross the membrane
Define free water
Not bonded to a solute, free to cross the membrane
Facilitated diffusion
Transport of ions and polar molecules through a membrane via protein complexes
Carrier proteins help biological molecules that are unable to diffuse across the plasma membrane
*still moving from [high] to [low] without using energy
Active transport
AKA primary active transport
Molecules are using carrier proteins to go against the concentration gradient from [high] to [low] requiring energy in the form of ATP
What are protein carries often called
Pumps
One type of pump that is active in cells is the sodium potassium pump which is importanr for the transmission of nerve impulses
Secondary active transport
Uses the concentration gradient of an ion, established by a primary pump as its energy source (facilitated by symport and anitport)
Symport annd antiport
Symport regulates two molecules going the same direction while antiport regulates two molecules going opposite directions (both together are cotransport)
What is the largest molecule that can be transported across the cellular membrane
Via passive or active transport the molecules can be up to the size of amino acids or glucose
How do larger molecules transport
Transported by other mechanisms called endocytosis and exocytosis
Define exocytosis
Secretory edibles move through the cytosine and contact the plasma membrane, vesicle fuses with plasma membrane and contents of the vesicle are released
Define endocytosis
There are three types of depending on what is being taken in by the cell
1) phagocytosis- white blood cell taking in bacteria
2) pinocytosis- bulk transport and isn’t selective
3) receptor mediated endocytosis which is highly selective
