UNIT 2/8 - Molecular Biology Flashcards
Define condensation reaction of the nucleotide
combination of nitrogenous base, pentose sugar, phosphoric acid to form a nucleotide (and two molecules of water)
State the role of proteins for the DNA
proteins make up more than 50% of chromosome
supporting and packaging role for DNA
List the functions of the nucleosomes
help in packaging of DNA during mitosis or meiosis by supercoiling
markers of particular genes, either to promote gene expression or silence a gene
Define a dehydration reaction
either a hydroxyl group from one molecule combines with a hydrogen atom from the other molecule, or two hydrogen atoms from one molecule combine with an oxygen atom on the other molecule. In either case, water is released, and the two molecules are joined together.
Explain why the hydrogen bonds can form between the atoms within the polypeptide backbone
the oxygen atoms have partially negative charge and the hydrogen atoms attached to nitrogen have partial positive charge
Distinguish fibrous and globular proteins and provide examples for both
fibrous - long and narrow shape, insoluble in water
e.g. collagen, keratin, myosin
globular - round shape, soluble in water
e.g. enzymes (catalase), some hormones - insulin, hemoglobin, immunoglobin
Give examples on how the distribution of non-polar and polar amino acids affect protein function and location
- controlling the position in plasma membranes - non-polar amino acids causing proteins to be embedded in membranes while polar amino acids causing portions of the proteins to protrude from the membrane
- creating hydrophilic channels through membranes - polar amino acids found inside membrane proteins and create a channel through which hydrophilic molecules can pass through
- specificity of active site in enzymes - if non-polar amino acids make up the active site of an enzyme it makes the active specific to non-polar substance and vice versa
Describe how on the example of the sickle-cell disease a slight change in primary structure can affect protein’s shape and ability to function
sickle-cell disease is an inherited blood disorders caused by the substitution of ONE amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin
therefore hydrophobic interactions between sickle-cell hemoglobin proteins lead to their aggregation into fiber and the capacity to carry oxygen is greatly reduced causing the patient anemia, damage nerves and organs, including kidneys, liver and spleen, and can be fatal
Define starch and distinguish its two types
is the stored form of sugars in plants and is made up of a mixture of two polysaccharides:
- amylose and amylopectin (polymers of glucose)
amylose - entirely unbranched chains of glucose monomers connected by 1-4 linkages
amylopectin - branched polysaccharide, most monomers connected by 1-4 linkages but some 1-6 occur periodically causing branched points
Distinguish and define main three polysaccharides
glycogen - storage carbohydrate formed from glucose in the liver, muscle cells and other cells (not in brain) when glucose is not immediately required for cellular respiration, hydrolysis releases glucose from it when the demand for sugar increases, extensively branched, composed of a-glucose linked together by both 1-4 linkages and 1-6 linkages (branching)
cellulose - manufactured in cells and laid down externally, in bundles of fibers, as the main component of the cell walls, linear molecule composed of β-glucose subunits (bound in a 1-4 arrangement)
starch (has its own flashcard lucky bastard)
Explain why are fatty acids such a high-density energy storage
metabolism of fatty acids in cell respiration skips glycolysis and instead Coenzyme A cuts off carbon atoms from the fatty acid in the link reaction and carries them to the Krebs cycle
therefore longer chains are a greater store of potential energy
List the roles of fats and oils in living things
- energy store and metabolic water source
- subcutaneous fat as a buoyancy aid and thermal insulation
- water-proofing of hair and feathers
- electrical insulation
- phospholipid bilayer is a major component of the plasma membrane
Compare and distinguish carbohydrates from lipids as an energy source
CARBOHYDRATE (glycogen)
- short-term energy storage
- more effect on osmotic pressure
- more readily digested- used for aerobic or anaerobic respiration.
- stores half as much ATP per gram
- water soluble as monomers/dimers - easier to transport
LIPID (triglyceride)
- long-term energy storage
- less effect on osmotic pressure.
- less easily digested - can only be used for aerobic respiration.
- stores twice as much ATP per gram
- not water soluble (hydrophobic) - more difficult to transport
Define the term monosaccharides, state its general chemical formula and list examples
monomers of carbohydrates linked together by condensation reactions to form disaccharides and polysaccharides polymers,
small, sweet taste, water soluble
CnH2nOn
e.g. glucose, galactose, fructose
Define the term disaccharides and list examples
carbohydrates mase of two monosaccharides combined together in condensation reaction via glycosidic linkage
small enough to be soluble in water, transport form commonly
e.g. lactose, maltose, sucrose
Define the term polysaccharides and list examples
macromolecules polymers with a few hundred to a few thousand monosaccharides joined together in condensation reaction via glycosidic linkages
used for energy storage or cell structure, play a role in cell recognition
e.g. cellulose, glycogen, starch
State on what does the type of polymer formed depend on
monosaccharide subunits involved
Determine why is cellulose indigestible for most animals and state ones that have the ability to digest it
its composed of β-glucose and most animals lack the enzyme required to break it down
the misfits:
- Ruminants (e.g. cows) may digest cellulose due to the presence of helpful bacteria in a specialized stomach
- Chaecotrophs (e.g. rabbits) will re-ingest specialized feces that contain digested cellulose (broken down in the caecum)
Classify monosaccharides depending on the amount of carbon atoms
trioses - contain 3 carbons, formula C3H6O3
pentoses - contain 5 carbons, formula C5H10O5
hexoses - contain 6 carbons, formula C6H12O6
State another name for condensation reaction
dehydration synthesis reaction
State when does monosaccharides form rings
in aqueous solutions
Define what is glycosidic linkage
covalent bond between two subunits of polysaccharides formed by dehydration
Distinguish α-glucose from β-glucose
differ in placement of the hydroxyl group attached to number 1 carbon
(alpha has it down, beta up)
List reasons for why glucose is an especially important monosaccharide
in animals:
- glucose is transported to cells in blood plasma
- glucose is used as a respiratory substrate for cellular respiration or converted to glycogen (storage carbohydrate)
in plants:
- a first product of photosynthesis
Distinguish dehydration reaction from hydrolysis
dehydration - synthesizing a polymer
removes a water molecule forming a new bond
hydrolysis - breaks down a polymer
adds a water molecule, breaking a bond
Distinguish 3 most popular disaccharides and show their functions
lactose - produced in mammary glands, secreted into the milk as an important component in the diet of very young mammals(galactose + glucose)
sucrose - produced in green leaves from glucose and fructose, transported in plant in solution in the vascular bundles (glucose + fructose)
maltose - breakdown product in the hydrolysis of starch (glucose +glucose)
Define fatty acids
long hydrocarbon chains found in certain types of lipids (triglycerides and phospholipids), all have a hydroxyl group (-COOH), methyl group (CH3-) and chains of hydrocarbons (11-23 carbon long)
insoluble in water, soluble in organic solvents
List and define types of fatty acids
saturated fatty acids - are saturated with hydrogen (carbons carry as many hydrogen atoms as they can), found in animal products (butter, bacon, red meat), solid at room temp, straight AF = no double bonds, high density energy store=high CHD risk
monounsaturated fatty acids - one double bond, typically liquid at room temp, kinked
polyunsaturated fatty acids - have at least two double bonds in the carbon chain, come from plants, tend to be liquids in room temp, very kinked, bended
Define the term hydrogenation
complete or partial elimination of the double-bonds by adding hydrogen atoms
straightens out the natural bent of unsaturated fatty acids
present in many heavily processed fatty acids
Distinguish two distinct structural configurations of unsaturated fatty acids
cis - hydrogen atoms attached to carbon double bond on the same side, less CDH risk, oils at room temp
trans - unsaturated but linear structure, solid at room temp, hydrogen atoms attached to carbon double bond on opposite sides, ULTRRA HIGH CHD RISK
Characterize omega-3 fatty acids and explain their name origin
cis fatty acids, found in plant and fish oil = v healthy because -> reduce tendency to form blood clots and provide healthy plasma membranes around cardiac muscles
name: first carbon double bond is to be found at third carbon counting backwards from the omega end (methyl group)
Define triglyceride lipids
largest class of lipids and function primarily as long-term energy storage molecules (animals tend to store it as fats - solid, plants as oils - liquid)
consist of glycerol and three fatty acids formed in condensation reaction between fatty acids and glycerol fats in animal cells, oils, plant cells
What determines the overall characteristic of the triglyceride lipid
identity of the fatty acids
What characteristic bond occurs in triglycerides
ester linkage
State why being insoluble in water is beneficial for the fatty acids as human energy storage
they do not upset osmotic balance in the cells
Explain why are lipids such a good energy storage
they have 2x energy content per gramme than any other type of storage
because triglyceride lipids can by hydrolyzed into two carbon segments that can enter into cell respiration at a chemical sequence point and is v efficient for the production of ATP
Distinguish LDL from HDL
LDL - low density lipoproteins - carry cholesterol from the liver to the rest of the body - they raise blood cholesterol levels - increased by saturated and trans fats
HDL - high density lipoprotein - scavenge excess cholesterol and carry it back to the liver for disposal - lower blood cholesterol levels - increased by cis fats
Explain the health risk of high cholesterol
high cholesterol levels lead to hardening and narrowing of arteries (atherosclerosis)
because LDL particles will form deposits in the walls of the arteries and their accumulation leads to the development of atherosclerotic plaques that restrict blood flow and therefore leading to coronary heart disease (CDH) if the coronary arteries become blocked
State the formula for Body mass index
BMI=mass in kg/ (height in m)^2
State general functions of lipids in cell
- Storage of energy for long-term use (e.g. triglycerides)
- Hormonal roles (e.g. steroids such as estrogen 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)
Define how polypeptides are formed
synthesized from naturally occurring 20 amino acids, each from a specific gene in a condensation redaction at ribosomes
each has its own amino acid sequence and three-dimensional shape and carries out a specific function
List common elements of the basic amino acid structure
- central carbon atom (alpha carbon)
- amine group (NH2)
- carboxylic acid group (COOH)
- hydrogen atom (H)
- variable side chain (R)
Name 2 amino acids that are modified variants found only in certain organisms
- selenocysteine
- pyrrolysine
Define a peptide bond
a covalent bond between amino acids (the amino group and the carboxyl group) formed by dehydration reactions
AMINE GROUP LOSES HYDROGEN ATOM
CARBOXYLIC ACID LOOSES HYDROXYL OH
Define a polypeptide
polymer of amino acids linked by peptide bonds, with single c-terminal end and t-terminal end
if capable of carrying out its function its synonymous with protein
Define the R amino acid group and state its other name
variable group
group differentiating amino acids by different bonding location around the central carbon atom
Define an amino acid
organic molecule with both an amino group and a carboxyl group
List specific examples of proteins and their functions
rubisco - enzyme catalyzing the first reaction of the carbon-fixing reactions of the photosynthesis
insulin - hormone produced by the pancreas that results in a decrease of blood sugar levels and an increase of sugar body cells
immunoglobulin - antibody that recognizes an antigens as part of the immune response
rhodopsin - pigment found in the retina of the eye that is particularly useful in low light conditions
collagen - main protein component of the connective tissue, which is abundant in skin, tendons and ligaments
spider silk - fibrous protein spun by spiders for making webs, drop lines, nest building etc.
State what happens to amino acids in aqueous solutions (like cytoplasm or blood plasma)
amine and carboxyl group gets ionized, which does not alter the covalent bonding but makes the functional groups look different because each amine group has gained a hydrogen ion and each hydroxyl group has lost one
List the non-polar amino acids
- glycine
- alanine
- valine
- cysteine
- proline
- leucine
- isoleucine
- methionine
- tryptophan
- phenylalanine
List the +charge amino acids
- lysine
- arginine
- histidine
List the polar amino acids
- serine
- threonine
- tyrosine
- asparagine
- glutamine
List the -charge amino acids
- aspartic acid
- glutamic acid
Define the polypeptide backbone
repeating sequence of atoms with extending side chains of the amino acid
Define the term protein
biologically functional molecule made up of one or more polypeptides, each folded and coiled into 3D structure,
an organic substance consisting of covalently bonded amino acids and ready to carry out its function
Characterize the primary protein structure
the sequence and number of amino acids within the protein, determined by the base sequence of the gene, dictates secondary and tertiary structure due to the chemical nature of the backbone and R group
Characterize the secondary protein structure
repetitive shapes of either a helix or a pleated sheet, stabilized by the hydrogen bonds between groups in the main chains of a polypeptide
e.g. beta-pleated = spider silk, alpha-helix = myosin
- 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 happens when there is no secondary structure in the polypeptide
it will form a random coil
Characterize the tertiary protein structure
three-dimensional conformation of a polypeptide, caused by interactions between the amino acids when polypeptide folds up after translation
bonds present: hydrogen, van der Waals forces, disuphide bridges, ionic
e.g. enzymes
Characterize the quaternary protein structure
two or more polypeptide chain combined together to make a single functional protein
e.g. hemoglobin, insulin, collagen
Alternatively, proteins may have a quaternary structure if they include inorganic prosthetic groups as part of their structure
Not all proteins will have a quaternary structure – many proteins consist of a single polypeptide chain
Justify hemoglobin’s quaternary protein structure
- Hemoglobin is composed of four polypeptide chains (two alpha chains and two beta chains)
- It is also composed of iron-containing haeme groups (prosthetic groups responsible for binding oxygen)
Define the prosthetic group
non-polypeptide structure found in some proteins (conjugated proteins), often play an important role in enzyme catalysis
e.g. carbohydrate in glycoproteins
Define protein denaturation
structural change, unraveling and loss of proteins native shape due to pH, salt, temperature alterations
IS PERMANENT
will alter proteins activity
Determine why temperature higher than physiological optimum causes proteins to loose their structure and function
the stress is put on the intra-molecular bonds and therefore the primary structure remains intact but hydrogen bonds not really
but if covalent bonds remain intact the protein will return to its normal shape in normal temp
same happens in abnormal pH because of extra charge
Explain why amino acids are called zwitterions
bc they are neutral molecules possessing both negatively and positively charged regions
Define the term proteome
totality of proteins expressed within a cell, tissue, organism at a certain time
State why the proteome is always significantly larger than the number of genes
Gene sequences may be alternatively spliced following transcription to generate multiple protein variants from a single gene
Proteins may be modified (e.g. glycosylated, phosphorylated, etc.) following translation to promote further variations
