Biochemistry Flashcards
Amino acids contain which two functional groups
amino group (-NH2) and carboxyl group (-COOH)
For all amino acids, the alpha carbon is chiral, except for ______
glycine
Central dogma is that ____ makes __________ which makes ___________
DNA, RNA, Protein
Reverse transcription is…
the flow of information from RNA to DNA via reverse transcriptase (generates cDNA from an RNA template), used for retroviruses
tRNA and rRNA are referred to as
ncRNA (noncoding RNA), they are not used in protein synthesis
Peptide bonds are formed by the nucleophilic addition-elimination reaction between
-the carboxyl group of one AA and the amino group of the other AA
There IS/IS NOT much rotation around a peptide bond
IS NOT
The amino ground at the end of a polypeptide is known as the
N Terminal
Breaking a peptide bond occurs through
Hydrolysis
Put a polypeptide chain in with a strong acid and some heat and you will get
The cleaved peptide bonds
Proteases are used in
cleaving peptide bonds in a very specific spot
Histidines pka is
6.5
If the pH is less than the pKA the AA will exist in a
protonated form
If the pH is more than the pKa, the AA will exist in a
deprotonated form
Glycine and Proline are known as ______ ______ _____
Alpha Helix Breakers
Antioxidants are found IN the cell, and therefore, the inner cell would favor a _____ environment
reducing (H’s are present)
What happens if you shoot plane polarized light at a chiral carbon?
It would rotate that light
Mirror image molecules that are not superimposable (cannot slide it over and have it be the same)
enantiomers
In an L-amino acid, the amino group is to which side of the chiral carbon in a fischer projection?
Left (L for left)
What form of amino acid is the only kind you will find in the human body?
L- Amino Acid
What is called when an amino acid is at a neutral state?
Isoelectric point
When a molecule has both a positive and a negative charge present, this is known as
a zwitterion
On average, what is the pKa of the amino group?
9
On average, what is the pKa of the carboxylic acid group?
2
Which amino acids have alkyl groups as side chains?
Glycine
Alanine
Valine
Methionine
Leucine
Isoleucine
Proline
*all nonpolar, hydrophobic
Which amino acids have aromatic groups as side chains?
Phenylalanine
Tryptophan
*all nonpolar, hydrophobic
Which amino acids have neutral side chains?
Serine
Threonine
Asparagine
Glutamine
Cysteine
Tyrosine
*all are polar, and these AA all contain a sulfur or oxygen atom which likes to hog the electrons to create a localized negative charge, but with a positive charge over the rest of the side chain, hence creating a neutral atom
Which amino acids are considered “Acidic”
Aspartic Acid
Glutamic Acid
- both are polar, hydrophilic, if they have donated their hydrogens, then they are aspartate and glutamate
Which amino acids are considered “basic”?
Histidine
Lysine
Arginine
*they all have nitrogen atoms, and nitrogen is a very willing proton acceptor, and therefore that is why these ones are basic
Amyloid is
clumps of misfolded proteins that can interfere with the neurons ability to send messages
The secondary structure of protein folding is determined by…
backbone structures (specifically Hydrogen bonds)
-think alpha helix and beta sheet
How does a tertiary protein structure remain intact and maintain conformational stability?
vanderwaals, hydrophobic packing and disulfide bridges
denaturation disrupts what structures of protein folding?
secondary, tertiary, and quartenary
This type of reaction is the breakdown of a single compound into two or more simpler substances
A decomposition reaction (i.e. AB = A + B)
What is the direction in which mRNA is read?
5’ —> 3’
A negative sense genome (CAN or CANNOT) be used directly for translation
Cannot (it must first be transcribed)
A bronsted lowry base is
a proton acceptor
a bronsted lowry acid is
a proton donor
a lewis base is
an electron pair donor
a lewis acid is
an electron pair acceptor
A right shift on the hemoglobin/oxygen saturation curve is signified with an (increased or decreased) Hb-O2 affinity?
decreased, marked by higher CO2 and higher acidity, and temperature. This shift is also consistent with higher levels of 2-3BPG, which allows the release of oxygen
weak acids (do/do not) readily give away their protons
do not, they stay mostly protonated
a strong acid will have a Ka > or < than 1?
> > 1
a weak acid will have a Ka < or > than 1?
«_space;1
This type of reaction is when an element undergoes both oxidationa nd reduction in the same reaction
Disproportionation
The greater the value of ( rate constant, k), the quicker the rate of reaction.
nickel tags are associated with which amino acid
histidine tags
Which amino acids are aromatic?
Tryptophan
Tyrosine
Phenylalanine
What are cytochrome p450 enzymes?
membrane bound proteins that enable oxidation reactions, also knonw as monooxygenase enzymes
When an electron moves to a higher energy state, a photon is …
absorbed
When an electron moves to a lower energy state, a photon is…
emitted
This chromatography technique is used to separate charged biomolecules (AA, proteins, nucleotides)
Ion Exchange Chromtography
In using Ion exchange chromatography, if the resin is postively charged, what charged proteins will bind, and what charged proteins will pass through
(-) proteins will bind, allowing (+) proteins to pass through
In size exclusion chomatography, which size molecules will pass through faster?
larger ones, since the small ones will go through the beads, whereas the large ones will go around.
This type of chromatography is related to how molecules will bind specifically to a binding partner (think: enzyme/substrate, antibody/antigen)
Affinity chromatography
A Nuclear localization signal/sequence is an amino acid sequence that …
tags a protein for transport into the nucleus
A signal sequence is a speciific amino acid sequence that …
directs proteins in translation to the rough ER & secretory pathway
Negative gene regulation controls the production of genes by
turning them off
The method of Flow Cytomtery is one where
single cells are stained for certain protein markers using specific antibodies (w/ flouresecene)- emitted light is measured, and we then can see cell size, and how many cells expres the protein markers
Immunohistochemistry is a lab technique that is used
uses an antibody to detect a specific protein and measure its expression
In Situ Hybridization is a lab technique that is used
to study gene expression in a tissue or embryo; this process can detect where transcripts are expressed
the average weight of an amino acid is
110 dA
cytochrome C (a component of the mitochrondria attached to the ETC) is often a driver of…
apoptosis
What is a Thymine Dimer?
When a Thymine base forms a covalent bond with another Thymine base d/t UV light damage. This can then lead to replication issues
Calcitonin is produced (location)
the thyroid gland
Though oxyocin is secreted by the pituitary gland, it is produced by the _____
hypothalamus
Surfactant helps to (increase/decrease) surface tension of alveoli
decrease the surface tension
During inhalation the diaphragm (contracts/relaxes)
contracts
During inhalation, the volume of the thoracic cavity (increases/decreases)
increases, therefore pressure decreases
W (watt) is =
Joules/second
V (volt) is =
Joule/ Coloumb
A (amp) is =
Coloumb/ second
____ is the term used to describe the total heat content of a system
Enthalpy
How does a dielectric impact capacitance in a circuit?
It partially decreases the net field created by the capacitor, and the potential difference across it
If the dielectric has a high permitivity
it INCREASES the capacitance for any given voltage
A dielectric interrupts a circuit, and can also be known as
an insulator
The total capacitance of capacitors in series is equal to the
sum of the inverse of the individual capacitors
The capacitance of a single parallel plate capacitor is directly proportional to the
surface area of the plates
The capacitance of a single parallel plate capacitor is inversely proportional to the
distance between the two plates
A dielectric can be inserted between two plates and is directly proportional to
the capacitance of the capacitor
Which of the following is NOT a strong acid?:
A) H2SO4
B) CH3COOH
C) HI
D) HBR
B) CH3COOH
Acetic Acid, a weak acid
A is sulfuric acid
C is hydroiodic acid
D is hydrobromic acid
List the Strong acids
“So I Brought No Clean Clothes”
“So”: Sulfuric Acid (H2SO4)
“I”: HydroIodic Acid (HI)
“Brought”: Hydrobromic Acif (HBr)
“No”: Nitric Acid (HNO3)
“Clean”: Hydrochloric Acid (HCl)
“Clothes”: Perchloric Acid (HCLO4)
Describe Pi Stacking interactions
A Non-covalent attraction that occurs between pi bonds of aromatic rings
How is secondary strucutre of protein held together?
Hydrogen bonds
(which create the alpha helix and beta pleated sheets)
How is tertiary structure of a protein held together?
Side Chain interaction, think hydrogen bonds or dipole interactions, van der waals, and disulfide bridges
How is primary structure of a protein held together?
Peptide bonds between amino acids
Which amino acid makes disulfide birdges?
Cysteine
The _______ variable is one that you are changing on purpose
independent
The ________ varibale is one that you are measuring the reponse of
dependent
Describe the TAID P Method for analyzing graphs/tables
T: Title
A: Axes
I: Independent Variables
D: Dependent Variables
P: Patterns
Which two amino acids are likely to initroduce kinks and flexibilty into peptide chains
Glycine, and proline
This technique can amplify small amounts of DNA, very useful in determining cellular mRNA levels
PCR (and RT-PCR)
This technique measures protein levels in a sample using antibodies
Western Blot
This technique measures DNA levels
Southern Blot
This technique measures RNA levels
Northern BlotT
This technique separates molecules on the basis of size/charge
Gel Electrophoresis
This technqiue separates denatured proteins on the basis of size
SDS-Page
This technique separates proteins in their native conformations that allows subunits to remain intact
Native gels
This technique is used to introduce genetic information into a plasmid for protein expression or genetic manipulation
Molecular Cloning
If two molecules have the same connectivity, they can/cannot be constitutional isomers
they cannot be
If molecules were _______, they have equal and opposite rotations (think +40, and -40)
enantiomers
A racemic mixture is 50% of one ______ and 50% of the other.
enationmer. This leads to a specific rotation of 0.
Conformational isomers will always have the same specific rotation becaues they are forms of the
same compound
________ differ in the magnitude of their specific rotations
diastereomers
The main function of the loop of henle is to
reabsorb water and NaCl
What occurs during prophase?
The chromatin condenses
What occurs during M Phase?
Chromsomes are segregated into two nuclei and metaphase, anaphase, and telophase occur
Cytokinesis (of the division of the cell membrane) yields
two daughter cells
It is possible to separate diastereomers or enantiomers?
Diastereomers (enantiomers cannot be separated from each other)
A Transverse (T) tubule is a channel formed within the sarcolemma that
brings the depolarized current nearer the sarcoplasmic reticulum (which then induces Ca2+ to be released
After Ca2+ is released in muscular contraction, then what occurs?
Ca2+ binds troponin, which then allows the actin and myosin filaments of the sarcomere to slide across each other (which shortens the sarcomere) inducing the muscle contraction
How does an enzyme function to lower the activation energy
They faciliate a more stable transition state, and this more stabilized state leads to a lower actvivation energy
How are parathyroid hormone and bone remodeling related?
low calcium stimulates PTH, which causes increased activity of osteroclasts
How does high amounts of calcium circulating affect hormone levels?
high calcium stimulates calcitonin, which causes decreased activity of osteoclasts
The boiling point is defined as the point at which the vapor pressure of a solution is equal to the
atmospheric pressure
What occurs during Beta-minus decay?
a neutron is converted to a proton as an electron is emitted
Mass spectrometry can be used to make clear…
the structure of a compound
Why does hydrogen bonding increase the boiling point of a compound?
It takes more energy to break the van der waals and hydrogen bond forces
Nitrogen, in its neutral state, has how many bonds/lone pairs?
3 bonds, and a lone pair of electrons
Oxygen, in its neutral state, has how many bonds/lone pairs?
2 bonds, and 2 lone pair of electrons
A stereocenter carbon means…
it must be sp3 hybridized and bonded to 4 different groups
τ = rFsin(θ) is the equation for
torque
Ka is the acid disassociation constant, and is found with the equation:
[H+][A−]/[HA]
The smaller the Pka value, the _____ the acid
stronger
1 µg is equal to
1 x 10-6 g
According to Newtons Third Law,
Every force has an equal and opposite force (think: when earth exerts a gravitational force on your body, your body is also exerting a gravitational foce on the earth)
N2 (diatomic Nitrogen) is what type of gas
an inert gas (also means a noble gas)- this means that it is not very reactive
Is C6H6 or CH a empirical formula?
CH (empirical formula is the lowest common denominator among the molecules at the correct ratios)
Power is measured in…
watts (W)
ACcording to Ohms Law, P=
IV or V^2/R
PCC could be used to
oxidize a primary alcohol to an aldehyde (and a secondary alcohol to a ketone)
LiAIH4 (a strong reducing agent) could redule a carboxylic acid to a
alcohol
Kinases and phosphorylases can be grouped into the broader enzyme category of
transferases
Referring to IR Spectroscopy, a carbonyl spike will be at what number?
1700, and it will be a sharp spike
Referring to IR Spectroscopy, an alcohol spike will be at what number?
3,000, and it will be broad
In the electron transport chain, electrons are passed from a species with a ____- positive reduction potential to a species with a _____-positive reduction potential
less-positive to more-positive
ΔG° < 0 corresponds to a Keq …
Keq > 1
In regard to light hitting water, how are the angle of reflection and the angle of incidence related?
They are always the same (angle of refraction will differ)
The more negative the RSE of an element (relative stabilization energy), the more/less stable the compound is
more stable (more negative RSE= more stable compound)
An electrolytic cell allows for this type of spontaneous reaction
redox
If all electrons of a molecule are paired, what is the resulting magnetic outcome of the molecule?
it is then “diamagnetic”, and the paired electrons will be repelled by the magnetic field
If electrons in a molecular orbital are left unpaired, what is the resulting magnetic outcome of the molecule?
it is then “paramagnetic”, and the unpaired electrons will be attracted to an external magnetic field
In Beta minus decay, the atomic number is _____ by 1
increased
In Beta plus decay, the atomic number is ______ by 1
decreased
In alpha decay, the atomic number is _____ by 2, and the atomic mass is _____ by 4
decreased, decreased (-2 neutrons, -2 protons)
In gamma decay, the atomic number is ____
unaffected
Electronegativity is the tendency of an atom to (attract / repel) electrons within a bond
attract electrons
Ionization energy is the energy that that is required to
remove an electron from an atom
L-DOPA is a precursor to …
catecholamines [dopamine, norepinephrine, epinephrine]
When two complementary single stranded strands bind together to form a double stranded molecule, this is known as
hybridization
How many arms of the chromosome does a double crossover event affect?
Just one of the arms
The Hardy- Weinberg equation is
AA + 2Aa + aa = 1
_________ structures are those structures that evolved independently to carry out the same function
analogous
________structures are those that have a similar evolutionary history, arising from the same source, even if they now have separate functions
Homologous
Sucrose, lactose, and maltose are _______
disaccharides
Galactose is a monosaccharide or a disaccharide?
monosaccharides
_____ is a term used in conditioning that refers to small steps being reinforced in order to achieve some larger behavior
Shaping
