IB Molecular Biology Flashcards
What is an organic compound?
An organic compound is a compound that contains carbon and is found in living things
What are exceptions to the organic compounds? (4)
CN, CO, CO2, CaC2
What are Carbohydrates and what are their functions?
- Most abundant organic compound found in nature, composed primarily of C,H and O atoms in a common ratio – (CH2O)n
- Principally function as a source of energy (and as a short-term energy storage option)
- Also important as a recognition molecule (e.g. glycoproteins) and as a structural component (part of DNA / RNA)
What are Lipids and what are their functions?
- Non-polar, hydrophobic molecules which may come in a variety of forms (simple, complex or derived)
- Lipids serve as a major component of cell membranes (phospholipids and cholesterol)
- They may be utilized as a long-term energy storage molecule (fats and oils)
- Also may function as a signaling molecule (steroids)
What are Nucleic acids and what are their functions?
- Genetic material of all cells and determines the inherited features of an organism
- DNA functions as a master code for protein assembly, while RNA plays an active role in the manufacturing of proteins
What are proteins and what are their functions?
- Make over 50% of the dry weight of cells; are composed of C, H, O and N atoms (some may include S)
- Major regulatory molecules involved in catalysis (all enzymes are proteins)
- May also function as structural molecules or play a role in cellular signaling (transduction pathways)
What are Carbohydrates composed of?
Carbohydrates are composed of monomers called monosaccharides
Catabolism
breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers
Anabolism
synthesis of complex molecules from simpler molecules, including the formation of macromolecules from monomers using condensation reactions
Metabolism
web of all enzyme-catalyzed reactions in a cell or organism
four biochemical groups
- carbohydrates
- lipids
- proteins
- nucleic acids
Why is life based on carbon
-it can form four covalent bonds; creates stable molecules
-allows for a diversity of molecules (bonds easily)
Not very reactive
Very small
What are the elements in living organisms
- hydrogen
- oxygen
- nitrogen
- phosphorous
- carbon
Monomers/Dimers/Polymers of Carbohydrates
monomer; monosaccharides
dimers; disaccharides
polymers; polysaccharides
Monomers/Dimers/Polymers of Lipids
monomers; glycerol, fatty acids, phosphate groups
dimers/polymers; triglycerides, phospholipids, steroids (FAT)
Monomers/Dimers/Polymers of Proteins
monomer; amino acids
dimer/polymer; polypeptides
Monomers/Dimers/Polymers of Nucleic Acids
monomer; nucleotide
What determines if a reaction occurs or not?
- identity of colliding molecules
- orientation of colliding molecules
- speed/kinetic energy of molecules
Why do cells use enzymes?
to increase the likelihood that a successful collision will lead to a useful reaction
What are enzymes?
protein molecules with a specific shape that a react can fit into at the active site
- act as catalysts
- increase rate of reaction
- lower activation energy
What explains the properties of water?
- dipolarity
- hydrogen bonding
What makes water so special?
its polar and hydrogen bonds form between them
Why is water polar?
due to the unequal sharing of electrons within the water molecule that makes oxygen slightly negative and hydrogen slightly positive
Cohesive properties of water
Cohesion: attraction of water molecules to other water molecules
- due to hydrogen bonds that form between water molecules due to polarity
explains;
- why water forms into droplets when it is spilt
- why water has a surface tension that allows for some animals to walk/run on it
- why water can move as a water column in the xylem
Thermal properties of water
- high latent heat of vaporization
- high specific heat capacity
explains;
- water can absorb a great deal of heat (good for chemical reactions)
- act as a coolant
Adhesive properties of water
Adhesion: is the formation of hydrogen bonds between the water molecules and F, N and O (attraction between unlike molecules)
explains;
why water sticks to the vascular tissue in plants (fight gravity!) and can be pulled up
Bonds formed during condensation reactions
- ester bond (triglycerides)
- glyosidic bond (maltose)
- peptide bond (amino acids)
Hydrophilic
- water loving
- polar substance
Hydrophobic
- water hating
- non polar substance
Monosaccharides (4)
- glucose
- fructose
- galactose
- ribose
Disaccharides (3)
- sucrose
- maltose
- lactose
Polysaccharides (3)
- starch
- cellulose
- glycogen
What is the role and structure of Cellulose
- major component of cell walls
- helps give rigidity support to plant parts such as roots, stems and leaves
Structural polysaccharide in plants
B-glucose
1:4 glyosidic bond
Unlike starch, cellulose is very strong and prevents cells from bursting when they take excess water
Consists of long chains of glucose molecules
What is the role and location of Glycogen
- animals stores excess glucose in this form
- stored in liver and muscle areas
What are the functions of Lipids
- long term storage of energy
- they are important components of the cell membrane
- they are used as a heat insulator
- can act as a shock absorber
What are the 3 main types of Lipid
- triglycerides (Fats + Oils)
- Phospholipids (components of cell membrane)
- Steroids (Cholesterol, progesterone, estrogen, testosterone)
What are Triglycerides composed of?
TRIGLYCERIDES;
tri: refers to 3 fatty acids chains
- glycerol
- fatty acids
What are Saturated fatty acids and where are they found?
if the bonds between carbon atoms are SINGLE
the fatty acids contain as much hydrogen as they possibly could
animal sources (red meats, milk, etc.)»_space;> FATS
What are Unsaturated fatty acids and where are they found?
UNSATURATED FATTY ACIDS
when the fatty acids contain 1 or more DOUBLE BONDS
contains less hydrogen atoms than it could (unfulfilled)
Plants (Oil)
can be polyunsatured or monoundsatured
What does CIS and TRANS unsaturated Fatty acids refer to and what are their roles and uses?
CIS:(can be poly)
same side C=C bond
when hydrogen atoms are on the same side with respect to the double bond
TRANS:(can be poly)
-when the hydrogen atoms are on the opposite side with respect to the double bond
CIS= Healthy Trans= unhealthy
cis-fatty acids cannot line next to each other, thats why the are lipid at room temperature
cis fatty acids are ‘slippery’ and will not clog arteries
Trans Fatty Acids
-hydrogenation of vegetable or fish oils
-modification of natural, healthy oils
-hydrogenation changes the shape of the oil
-trans fats are illegal
-turns it from liquid» solid
What are phospholipids?
these are modified triglycerides that have one fatty acid chain by a phosphate group
Scientific Evidence of trans unsaturated fats health risk
Coronary heart disease: arteries become blocked due to fatty deposits
High intake of trans fats
CHD: found in patients who take more cis unsaturated fatty acids
BMI formula
weight (kg)/[height (m)x height (m)]
How is energy stored in humans?
- storing glucose as glycogen in liver and muscle cells
- storing triglyceride lipids within adipose (fat) cells
What are the functions of proteins? (4)
- structural
- catalytic
- signaling
- immunological
What is Rubisco?
short hand name for enzyme that catalyzes the first reaction of carbon fixing reactions of photosynthesis
What is Insulin?
a protein hormone produced by the pancreas that results in a decrease of blood sugar levels and an increase of sugar inside body cells
What is Immunoglobin?
an antibody that recognizes an antigen as part of the immune response
What is Rhodopsin?
pigment found in eye retina for low light conditions
What is Collagen?
main protein component of connective tissue which is in skin, tendons and ligaments
What is Spider silk and what are its uses for spiders?
fibrous protein spun by spiders for webs, lines, nest building, hunting
How do the proteins differ from each other?
Length: different # of amino acids
Types: different types
Order: different order
Primary structure of protein
- linear sequence of AAs
- contains only peptide bonds
- in nature: proteins are almost never found in this structure because they fold to produce more complex molecules
Secondary structure of protein
- the polypeptide chain folds to form: alpha helix or beta pleated sheet
examples: keratin (alpha helix) and silk (beta pleated sheet) - these structures are held together by hydrogen bonds
Tertiary structure of protein
- alpha helix and beta pleated sheets fold into compact globules
- the structures are held together by: hydrogen bonds, ionic bonds and disulphide bonds
- example: enzymes
Quaternary structure of protein
- examples: hemoglobin, collagen, insulin
- held together by: hydrogen bonds, ionic bonds, disulphide bonds
Fibrous Proteins
Shape: Long and narrow
Role: Structural (strength and support)
Solubility: Generally insoluble in water
Sequence: Repetitive amino acid sequence
Stability: Less sensitive to change in heat and pH
Examples
Collagen, myosin, fibrin, actin, keratin, elastin
Globular Proteins
Shape: Rounded/spherical
Role: Functional (catalytic, transport, etc)
Solubility: Generally soluble in water
Sequence: Irregular amino acid sequence
Stability; More sensitive to change in heat, pH, etc
Examples:
Catalase, hemoglobin, lipase, insulin, immunoglobulin, DNA Polymerase,
Protome
All of the proteins produced by a cell, tissue or organ in a human
- as cells can differentiate they don’t have to produce the same proteins to have the same genome
How do Proteins Denature
- proteins can denature by heat and pH environment alteration (bonds broken and proteins get broken down into simpler forms/become inactive)
- each protein has an optimum temperature
Enzyme function
-Speed up reactions, acting as a catalyst
Long chain of amino acids (globular protein in tertiary structure)
Substrate»>enzyme»>product
Active site
A small region on the enzyme where the substrate binds to and the reaction takes place, enzymes are substrate specific
What are Catalysts?
They increase the rate of reaction without themselves being being used up.
Steps of enzymatic process (4)
- substrate enters active site
- enzyme-substrate complex is formed
- substrate is changed into a different chemical (product)
at the end of the reaction, the product leaves the active site - enzymes are never permanently modified, they can return into their original state, to be used over + over again
What are the two enzymatic reaction theories?
- Lock and key
- Induced Fit
Describe the Lock and Key Hypothesis
The substrate molecular shape is the exact match to the enzyme’s active site
the substrate fits perfectly into the enzyme’s active site, the way a key fits into a lock. Each substrate has a particular corresponding enzyme
Describe the Induced-Fit Hypothesis
The substrate binds to the enzyme’s active site
the once the enzyme changes shape to fit and hold the substrate
Once the substrate binds into distorted active site, the complex is formed. and makes or breaks substrate by force
What are the factors affecting enzyme activity
Temperature
-as temperature increases so does enzyme activity
this is because:
molecules move faster (most often substrate moves around, but enzyme can as well) causing more of a chance for the enzyme and the substrate to find each other and bind
Optimum temperature
when the activity of an enzyme is at its greatest (any point beyond that the activity declines because they begin to break)
SUBSTRATE CONCENTRATION
Denaturation
change in the shape of an enzyme, for example:
-an active enzyme is tridimensional
-when it is heated it loses shape because heat causes the enzyme to twist and bend, and the hydrogen bonds to break
-this affects its activity to recognize the substrate (because of the change in the shape of the active site
Stages of Denaturation
- Quaternary Structure lost = protein subunits are dissociated
- Tertiary structure lost = interaction between side chains of amino acids are lost (hydrogen bonds/ionic bonds)
- Binary Structure lost = proteins lose patterns such as alpha helix and beta pleated sheet and become random coil configurations
- Primary structure = the sequence of amino acids (peptide bonds) remains
How does a change in pH affect enzyme activity?
each enzyme has an optimum pH
-change in pH could result in change in the shape of the enzyme (new shape may not be active)
Optimum pH and location of: pepsin amylase lipase lactase
Pepsin - PH2 (Stomach
Amylase - PH7 (mouth, small intestine, pancreas)
Lipase - PH8 (small intestine)
Lactase - PH7 (small intestine)
Uses of immobilized enzymes
- used as catalysts in industry
- enzymes can be held in tiny pores on beads called calcium alginate (trapped there; immobilized) so enzymes can be recovered and reused in processes
-used in the production of lactose-free milk for lactose intolerant people (enzyme lactase is immobilized to break don’t lactose into glucose and galactose and digest it)
What is the role, and structure of DNA
deoxyribose nucleic acid, code for life and all the functions in a living organism
- a double stranded helix
- sugar phosphate backbone
- anti parallel
- nitrogen containing
- hydrogen bonding and phosphodiester bonds
- found in nucleus
- pentose sugar- deoxyribose
What are the nucleotide bases and their subdivisions?
PURINE:
- adenine
- guanine
PYRAMIDINE:
- thymine
- cytosine
- uracil (only in RNA)
What is RNAs role and function?
Single stranded
Ribose sugar
Uracil (GCUA)
Nucleic Acid
Found in nucleus and outside of it (can travel out)
Has pentose sugar
What is Semi conservative replication
Mechanism of DNA replication where two new copies of DNA are produced from an original DNA strand consisting of one of the original strands and one new strand
What are the 3 types of RNA?
- mRNA
- rRNA
- tRNA
What are the replication theories? (3)
- Conservative: parental DNA is conserved
- Dispersive (fragmented) : mixture of old and new DNA within the same chromosome
- Semi conservative
mRNA function
messenger RNA. Copy of a gene, carries information to make a protein
rRNA function
ribosomal RNA, component of ribosomes. Large and small subunit
tRNA function
transfer RNA. Brings amino acids to ribosomes during protein synthesis, has a site for the AA to attach and an anticodon (determines which of the 20 AA’s is attached to the tRNA)
What Enzymes are used in replication? (4)
- DNA Helicase
- DNA Polymerase I
- DNA ligase
- Single-stranded binding protein:
DNA Helicases function
DNA Helicase: separates the two DNA strands before replication
Function of:
DNA Polymerase I
DNA Polymerase II
DNA Polymerase I:
Removes the primer and replaces it with DNA
DNA POLYERMASE II; Synthesized new strand by adding nucleotides onto the primer in a 5’ to 3’ direction
DNA Ligases function
DNA ligase: joins together short sections of the lagging strand (okazaki fragments)
Single-stranded binding proteins function
Single-stranded binding protein: keeps the separated DNA strands apart during replication`
What is Polymerase Chain Reaction
developed in 1970’s
- artificial DNA replication
- duplicates short segments of DNA
- scientists can produce large quantities of DNA this way for study
- used for forensics studies and paterntity testing
- Process consists of fluctuating temperatures
AEROBIC respiration equation
AEROBIC:
Normal form of respiration through breathing (muscular contraction)
Glucose + oxygen —–> carbon dioxide + water + energy (ATP)
C6H12O6 + 6O2——> 6CO2 + 6H2O + 36ATP
ANAEROBIC: respiration
ANAEROBIC:
When the body is getting no oxygen from breathing, so the cell creates energy just with glucose (inefficient)
In humans: glucose —–> Lactic Acid + Energy
C6H12O6—–> 2C3H6O3 + 2 ATP
alcoholic fermentation
- yeast
- produces ethanol, carbon dioxide
- use of fermentation in baking and alochol production
lactic acid fermentation
-organisms can respire without oxygen
-produce lactic acid by breaking down pyruvate
-e.g. during excersize
Lactic acid causes muscular fatigue and pain, forms crystals in the muscle tissue that makes the movement hard, toxic to body
OXYGEN DEBT: oxygen needed to break down lactic acid into carbon dioxide and water
PHOTOSYNTHESIS equation
CO2 + H2O ——–> O2 + C6H12O6
Photosynthesis is the production of carbon compounds in cells using light energy
Oxygen is produced from the photolysis of water (splitting of light)
what does chlorphyll do when hit by light (and why are plants green?)
- its a green pigment; reflects green light and absorbs all other wavelengths of the visible light spectrum (red and blue are absobved and used for photosynthesis)
LIMITING FACTORS OF PHOTOSYNTHESIS:
LIMITING FACTORS:
1. Temperature: has an optimum temperature, when it gets an higher, the rate goes down, as the plants begin to deteriorate
- Carbon Dioxide: reaches a max concentration, after there is no change in the rate
- Light Intensity: reaches a max intensity, after there is no change in the rate
What is the structure of Lactose?
Beta Glucose 1-4 Galactose
What is the structure of Maltose?
Alpha Glucose 1-4 Alpha Glucose
What is the structure of Sucrose?
Alpha Glucose 1-4 Fructose
What is the structure of Starch?
Alpha Glucose 1-4 Alpha Glucose chain
What is the structure of Cellulose?
Beta Glucose 1-4 Beta Glucose chain
Why is Cellulose indigestible by humans but digestible by cows?
Because it is composed of β-glucose, it is indigestible for most animals (lack the enzyme required to break it down), however, cows have special bacteria that allow them to break down cellulose
What are the two forms of Starch?
- amylose
- amylopectin
What is the structure of Glycogen?
It is composed of α-glucose subunits linked together by both 1-4 linkages and 1-6 linkages
What do LDLs do?
Low density lipoproteins (LDL) carry cholesterol from the liver to the rest of the body
What do HDLs do?
High density lipoproteins (HDL) scavenge excess cholesterol and carry it back to the liver for disposal
Role of Hemoglobin
A protein found in red blood cells that is responsible for the transport of oxygen
Role of Cytochrome
A group of proteins located in the mitochondria and involved in the electron transport chain
Role of Actin
Thin filaments involved in the contraction of muscle fibers
Role of Myosin
Thick filaments involved in the contraction of muscle fibers
Role of Glucagon
Protein produced by the pancreas that triggers an increase in blood glucose levels
What are the roles of proteins in a cell? (7)
Structure – e.g. collagen, spider silk Hormones – e.g. insulin, glucagon Immunity – e.g. immunoglobulins Transport – e.g. hemoglobin Sensation – e.g. rhodopsin Movement – e.g. actin, myosin Enzymes – e.g. Rubisco, catalase
SHITs ME
Why can water dissolve polar substances?
The polar attraction of large quantities of water molecules can sufficiently weaken intramolecular forces (such as ionic bonds) and result in the dissociation of the atoms
The slightly charged regions of the water molecule surround atoms of opposing charge, forming dispersive hydration shells
What determines the primary structure of a protein?
The order of the amino acid sequence is called the primary structure and determines the way the chain will fold
Into which two configurations will amino acid sequences fold into?
- Alpha helices occur when the amino acid sequence folds into a coil / spiral arrangement
- Beta-pleated sheets occur when the amino acid sequence adopts a directionally-oriented staggered strand conformation
Both α-helices and β-pleated sheets result from hydrogen bonds forming between non-adjacent amine and carboxyl groups
What is Proteome?
The proteome is the totality of proteins expressed within a cell, tissue or organism at a certain time
Discuss and explain the uses of enzymes in industrial processes (8)
Enzymes are biological catalyst proteins which speed up the rate of reactions by lowering the amount of activation energy needed for a reaction to begin by providing an alternative pathway. As enzymes lower the amount of activation energy needed, introducing enzymes into an industrial process can allow for lower energy consumption and thus reducing costs. Such an example may be paper production as enzymes assist in the pulping of wood but also the production of biofuel by converting carbohydrates into ethanol which is then used as fuel.. Food production such as beer makes use of enzymes as well as fruit juice production, which relies on pectinase to increase juice yield. The production of lactose free milk is critical for organisms affected by lactose intolerant and relies on the enzyme lactase attached to static beads in order to break down lactose into glucose and galactose, safe for lactose intolerant organisms to consume. Enzymes may also be used for the production of textiles, a popular example is polishing clothes. Another property of enzymes is gene splicing, allowing genetic modification in biotechnology. In medicine the measure of certain enzyme levels in saliva, urine, blood or certain tissues allows us to identify damage or certain diseases in organisms and even pregnancy.
Distinguish between DNA and RNA
DNA | RNA
Deoxyribose sugar | Ribose sugar
ATGC | AUGC
Double strand | Single strand
Outline PCR
The polymerase chain reaction (PCR) is an artificial method of replicating DNA under laboratory conditions
The PCR technique is used to amplify large quantities of a specific sequence of DNA from an initial minute sample
Each reaction doubles the amount of DNA – a standard PCR sequence of 30 cycles creates over 1 billion copies (230)
The reaction occurs in a thermal cycler and uses variations in temperature to control the replication process via three steps:
Denaturation – DNA sample is heated (~90ºC) to separate the two strands
Annealing – Sample is cooled (~55ºC) to allow primers to anneal (primers designate sequence to be copied)
Elongation – Sample is heated to the optimal temperature for a heat-tolerant polymerase (Taq) to function (~75ºC)
Taq polymerase is an enzyme isolated from the thermophilic bacterium Thermus aquaticus
As this enzyme’s optimal temperature is ~75ºC, it is able to function at the high temperatures used in PCR without denaturing
Taq polymerase extends the nucleotide chain from the primers – therefore primers are used to select the sequence to be copie
Role of lipids in the body
Storage of energy for long-term use (e.g. triglycerides)
Hormonal roles (e.g. steroids such as oestrogen and testosterone)
Insulation – both thermal (triglycerides) and electrical (sphingolipids)
Protection of internal organs (e.g. triglycerides and waxes)
Structural components of cells (e.g. phospholipids and cholesterol)
Mnemonic: SHIPS
