Exam One Flashcards
Relative size of eukaryotic and prokaryotic cell
Eukaryotic cells are 10x larger
6 Elements that make up life
CHNOPS
Strong chemical bonds
Covalent
Weak chemical bonds
Ionic bonds, hydrogen bonds, van der waals interactions, hydrophobic interactions
Electropositive means
low electron affinity
Electronegative means
high election affinity
Polar covalent bond definition
A bond with an unequal sharing of electrons which creates a dipole moment
Straight bonds are
stronger
Angled bonds are
weaker
H2O Hydrogen bonds well with
Other H2O molecules and polar molecules
Molecules that ____________ do not interact well with H2O
lack dipole moments
Molecules that have both hydrophobic and hydrophilic regions are called
Amphipathic
The interior of the lipid bilayer is made of
Van der Waals interactions
Covalent bonding results from
Filling electron orbitals
How many amino acids can exist as distinct L or D stereoisomers?
19 (glycine cannot)
Life uses L or D amino acids?
L
Acids are proton
Donors
Bases are proton
Acceptors
Degree of acidity or basicity is determined by measuring
[H+]
When pH is BELOW pKa, it is more likely to be ________
protonated
When pH is ABOVE pKa, it is more likely to be
deprotonated
Pyrimidines
Cytosine, Uracil, Thymine
Purines
Adenine, Guanine
Nucleoside consists of
Nitrogenous base and sugar
Nucleotide consists of
Nitrogenous base, sugar, and phosphate group
How do nucleotides link?
3’ OH links to 5’ C
Oligonucleotide length
<= 50 nucleotides
Polynucleotide length
> 50 nucleotides
Things responsible for DNA structure
- base pairing
- base stacking
- hydrophobic interactions of bases
- repulsion of negatively charged phosphate groups
Three conformations of DNA
B, A, Z
DNA strands are held together by
weak non-covalent interactions
Things that causes denaturing
- high temperature
- hydrogen bonding reagents (urea)
- methanol
- ph > 11
- decreased salt concentration
Purpose of gel electrophoresis
- identify size, topology, restriction pattern, purity, and concentration of DNA
- to separate a fragment of interest from a complex mixture of DNA fragments
Agarose gel has a broad separation range of
200bp to 50000bp
Acrylamide gel has a narrow separation range of
5bp to 500bp
Southern blot is a way of
finding a particular fragment in a mixture
Alanine abbrev
Ala
Alanine symbol
A
Arginine abbrev
Arg
Arginine symbol
R
Asparagine abbrev
Asn
Asparagine symbol
N
Aspartate abbrev
Asp
Aspartate symbol
D
Cysteine abbrev
Cys
Cysteine symbol
C
Glutamine abbrev
Gln
Glutamine symbol
Q
Glutamate abbrev
Glu
Glutamate symbol
E
Glycine abbrev
Gly
Glycine symbol
G
Histidine abbrev
His
Histidine symbol
H
Isoleucine abbrev
Ile
Isoleucine symbol
I
Leucine abbrev
Leu
Leucine symbol
L
Lysine abbrev
Lys
Lysine symbol
K
Methionine abbrev
Met
Methionine symbol
M
Phenylalanine abbrev
Phe
Phenylalanine symbol
F
Proline abbrev
Pro
Proline symbol
P
Serine abbrev
Ser
Serine symbol
S
Threonine abbrev
Thr
Threonine symbol
T
Tryptophan abbrev
Trp
Tryptophan symbol
W
Tyrosine abbrev
Tyr
Tyrosine symbol
Y
Valine abbrev
Val
Valine symbol
V
Nonpolar, Aliphatic R Group AAs
Glycine, Alanine, Valine, Proline, Leucine, Methionine, Isoleucine
Polar, Uncharged R Group AAs
Serine, Threonine, Cysteine, Asparagine, Glutamine
Polar, Negatively Charged R Group AAs
Aspartate, Glutamate
Polar, Positively Charged R Group AAs
Lysine, Arginine, Histidine
Nonpolar Aromatic R Group AAs
Phenylalanine, Tyrosine, Tryptophan
Is thyrotropin releasing hormone small or large?
Small (3 AAs)
Is Titin small or large?
Large
What is the average size of a polypeptide?
260 AAs (30 kDa)
Examples of protein chaperones
- GroE
- Peptidylproline isolmerases
- disulfide bond isomerases
Lk
Linking number
Tw
twist
Wr
Writhe
Linking number definition
total number of times DNA strands cross one another
Twist definition
number of helical turns
Writhe definiton
Number of times helix crosses itself
DNA gyrase is a special topoisomerase because it
introduces negative supercoils
Characteristics of type II topoisomerases
- ATP dependent
- passes both strands thru dsDNA
- covalent intermediate 5’ phosphate to tyrosine
- changes linking number by 2
Characteristics of type I topoisomerases
- ATP independent
- relaxes DNA
- makes ss breaks and passes one strand thru the other
- covalent intermediate 5’ phosphate to tyrosine
- changes linking number by 1
Chromatin refers to
DNA + Proteins
What histone proteins form the core?
H2A, H2B, H3, H4
H1 histones bind linker DNA to form
30 nm fibres
Histone N terminal ends stick out in order to
Stabilize the 30nm fibre
Histone Tails purpose
control overall chromosome structure and function
Acetylation and phosphorylation of histone trails promote
transcription of neighboring genes
What type of topoisomerase(s) do Eukaryotes have?
Type I and II
Helicase function
melts parental dsDNA, interacts with Pol III and primase
Single Stranded Binding Protein function
Binds ssDNA template, prevents reannealing
Primase function
Synthesizes RNA primers
DNA Pol III function
Synthesizes DNA starting at RNA primers
RNAse H function
Removes RNA primers
DNA Pol I function
Removes RNA primers and fills gap with DNA
DNA Ligase function
Seals nicks between Okazaki fragments
Proteins that bend DNA
- Integration Host Factor (IHF)
- Factor for Inversion Stimulation (FIS)
