Molecular Biology Exam I

molecules

collection of atoms held together by covalent bonds

biology

the study of living things

polarity

the distribution of electric charge around a molecule, leading to areas of partial positive and negative charge

non-polar molecule

a molecule with even distribution of electric charge that does not have distinct positive or negative areas

hydrophobic

substances that do not mix well with water

hydrophilic

substances that like being near water, and can be dissolved in water

the charge of DNA

negative

why is DNA negative

it has phosphate groups which are negatively charged, and loses H ions in the watery environment in the cell leaving behind the negatively charged oxygen atoms

entropy

the measure of disorder or unavailable energy inside a system

second law of thermodynamics

the total entropy in an isolated system always increases over time, systems naturally move from order to disorder

DNA

composed of nucleotides, forms a double helix, deoxyribose sugar, carries genetic instructions used in the growth, development, functioning, and reproduction of all living organisms.

RNA

composed of nucleotides, forms a single strand, ribose sugar, carries out instructions coded in DNA to build proteins

four bases of DNA

Adenine, guanine, cytosine, thymine

four bases of RNA

adenine, uracil, guanine, cytosine

mRNA

used to carry information in the cell, information in translated into a protein

tRNA

used to turn mRNA sequence information into a distinct protein, it’s shape is important when loading amino acid onto tRNA

rRNA

ribosomal RNA, enzyme that builds proteins by binding to proteins to build ribosomes

replication

the process where an exact copy of DNA is formed, usually before cell division

transciption

the process where a cell copies a gene’s DNA sequence into a temporary message called messenger RNA, RNA polymerase unzips DNA and builds mRNA with base pairing

translation

when a cell uses the mRNA message to build a specific protein, ribosomes read the mRNA in groups of three called codons and matching amino acids are brought from tRNA and linked

the base pairings for DNA nucleotides

adenine to thymine, guanine to cytosine

the base pairings for RNA nucleotides

adenine to uracil, guanine to cytosine

purines

adenine, guanine: all have the same two-ring structure as purine

pyrimadines

thymine, cytosine, uracil: have the same ring structure as pyrimidine

protein

composed of amino acids, multiple functions such as contracting muscles, converting food into ATP/energy, fight microbial invaders, move oxygen in our blood

ribosomes

composed of RNA, assemble individual protein polymers

what determine protein function

protein structure

primary protein structure

sequence of a chain of amino acids

secondary protein structure

localized, repeating folding patterns of the protein backbone, form either an alpha-helix (spring-like coil) or beta-pleated sheet (folded, accordion-like tracks), held together by hydrogen bonds between nearby backbone pieces

alpha helix

forms cylindrical shape, hydrogen bonds of amide backbone hold it together, every 3rd or 4th amino acid sidechain will be angled in the same direction

tertiary protein structure

three-dimensional folding of a single protein chain and forms compact, rounded globular shapes, or long fibrous shapes, held together by interactions between amino acid side chains

quaternary structure

the arrangement and joining of multiple polypeptide chains, not all proteins have a quaternary structure

denaturation

when the chemical bonds holding the folded structure of protein are disrupted or the amino acids are changed

what causes denaturation

heat, pH levels, and chemicals

what is primary structure used for

genetic disease tracking, and evolutionary tracing

what is secondary structure used for

used when trying to understand the local mechanical stability of building blocks of a protein: biomaterial design, and predicting folds

what is tertiary structure used for

used in pharmaceutical drug design to develop a molecule that fits into the proteins pockets, and to understand protein function

what is quaternary structure used for

large-scale molecular cooperation: allosteric regulation or understanding how a protei managed complex tasks, and is studied to understand how massive multi-protein complexes

enzyme nomenclature

a standardized system used to name and classify biological catalysts based on the specific chemical reactions they facilitate

lysis buffers

a solution of soap or salts used to rupture cells, usually bacteries, along with mechanical agitation like sonification

how would mammalian cells be studied

specific organs are collected and put in a blender so they can be smashes and the material inside may be studied, sometimes protease inhibitors are added to prevent the cells from self destructing and destroying released material

centrifugation

spins a blended mixture at high speeds which forces the heavier parts to the bottom and leaving the lighter parts near the top.

differiential centrifugation

a liquid mixture of cells homogenized in a liquid buffer to release their internal parts occurs first, then the mixture goes is spun in a tube at increasingly higher speeds to separate specific parts of the cell

chromatography

a laboratory technique used to separate a mixture into its individual chemical parts

mobile phase (chromatography)

a moving fluid (liquid or gas) that carries the mixture

stationary phase (chromatography)

a fixed material (solid or liquid on a solid) that the mobile phase passes through or over; the material can be based on size, charge, specific binding interactions, and more.

size-exclusion chromatography

liquid chromatography method that separates molecules molecules purely by their size and shape in solution, gel beads with holes the size of the molecule

affinity chromatography

liquid chromatography method that separates molecules based on their unique biological binding interactions with a specific ligand, and non-specific, unbound molecules pass through the column and are washed away, and the desired molecule is released by something that sticks to it

agarose gel electrophoresis

a standard laboratory technique used to separate DNA fragments by size by apply electricity, so the DNA moves from the negative side to the positive side

what is an amino acid composed of

an amine group, a carboxyl group, and an alpha carbon connected to an r-group sidechain.

r-group

appear on the alpha carbon in a amino acid, determine the structure and function of a protein based on which are present and their order

leucine

an amino acid monomer, in water will have a positive charge on the amine group and a negative charge on the carboxylic acid group

serine

an amino acid monomer, in water will have a positive charge on the amine group and a negative charge on the carboxylic acid group, also has a polar sidechain

alanine

an amino acid monomer, has a single methyl group side chain

where do hydrophobic side-chains of amino acids like to remain in a folded cytosolic protein

in the interior

anabolic metabolism/anabolism

building a large molecule from many small pieces, costs energy

catabolic metabolism/catabolism

breaking a large molecule down into small pieces, gives energy

amide bonds

holds together protein polymers when being constructed by ribosomes where the carboxylic acid function group and amine function group are replaced by an amide functional group

in reactions for peptide bond formation reactions will have ______ transitions states

unstable

enzymes

speed up reactions, usually proteins, have shapes and charge distributions that are complimentary to the unstable transition state of a reaction

protein misfolding

occurs when a protein chain fails to fold into its correct three-dimensional, functional shape; this can cause a loss in function, gain of a toxic function (aggregation), or infectious spreading of misfolding proteins.

in vitro factors that affect protein misfolding

temperature, pH, radiation, agitation, pressure, solvent

in vivo factors that affect protein misfolding

pathogenic mutation, oxidative stress, proteasome degradation, aging, over expression, impaired autophagy

major diseases linked to protein misfolding

alzheimer’s disease, parkinson’s diseas, cystic fibrosis, prion disease

cystic fibrosis

affects several organs with most severs symptoms from recessive mutation on the lung, affects a gene CTFR which is an ion channel that regulates osmotic pressure. where it causes these channel to not open

disulfide bonds

when the sulfur atoms of two cysteine amino acids form a covalent bond

phosphorylization

when a molecule binds to other phosphorus containing molecule, for proteins; kinases chemically attach a phosphate group onto a specific amino acid to active or deactivate the protein.

sds-page

separates proteins based on the molecular mass of

the unfolded, denatured protein coated in negatively-charged

soap molecules.

western blot

a laboratoru technique used to detect, analyze, and quantify specific protein within a comples mixture of tissue or cell extracts. combines gel electrophesis with highly specific antibody binding to hunt down one exact protein out of thousands

dimer

a macromolecular complex formed by two proteins chains (subunits) that bind tightly to one another.

homodimer

composed of two identical protein chains, encoded by the exact same gene

heterodimer

composed of two different protein chains, they have different amino acid sequences and are encoded by separate genes.

x-ray diffraction

generates visual data patterns using x-rays that will hit the electrons of the tightly packed, repeating molecules in the crystal, the light waves bounce offf and interfere with one another

primer

a short piece of nucleic acid

PCR

a polymerase chain reaction, a technique used for a particular stretch of DNA that rapidly amplifies it so it can leave a trace and be analyzed

DNA polymerse

extends existing strands of DNA

minor groove of DNA

the phosphate backbones is more accessible, the place where proteins that bind to any DNA sequence are most likely to bind and interact

major groove

the edges of the nucleobases are more accessible, proteins that bind to specific DNA sequences are most likely to interact with this groove

isotope labeling

a tachnique used to track the movement, transformation, or structural layout molecules by swapping out specific standard atoms for their isotopes

NMR spectroscopy

a technique used to determine the 3D structure, molecular formula, and chemical environment of molecules. It scans molecules in a dissolved test tube, by using intense magnetic fields and radio waves, which forces atomic nuclei to act like tiny radio transmitters that broadcast their location and chemical neighbors