BIOS 3450 Midterm 1 Content (Ch.1-6)

nonpolar + hydrophobic

amino acid with no charge on side chain

central dogma

DNA —transcription—> RNA —translation—>protein

5’ to 3’

direction that DNA is read

N terminus to C terminus

direction that proteins are read

acdic and hydrophillic

negative charge on amino acid carboxylic side chain at pH=7

basic and hydrophillic

positive charge on amino acid side chain

peptide bonds

bonds that hold proteins and amino acids together

L amino acids

what amino acids are natural on earthy

chiral carbon

alpha carbon attached to four different groups

amino acid side chains

determine protein properties

L amino acids

form right hand helixes

hydrophobic amino acids

face towards the inside of an alpha helix

3.6

turns on alpha helixes occur every ___ amino acids

transmembrane helix

~ 20-25 continuous hydrophobic amino acids

amphipathic

has both hydrophobic and hydrophillic parts

amphipathic helix

heptad repeat of HPPHPPP

HPPHPPP

amphipathic alpha helix amino acid repeat

higher order assemblies (alpha helix)

two alpha helixes can wrap aroudn each other

beta sheet

forms when >=2 polypeptide chains line up side by side

tensile strength

beta sheets are good for ___ because of rigidity

antiparallel beta sheets

hydrogen bonds are parallel

parallel beta sheets

hydrogen bonds are diaganol

beta barel

higher order beta sheet structure that is rigid, amphipathic, and allows molecules to pass through

HPHPHPHP

beta barel amphipathic dyad repeat

tertiary structure

contains >=2 alpha helix and/or beta sheets together

disulfide bridge

forms when two cysteines are oxidized, often in proteins taht leave the cell because they’re very rigid, help to increase the stability of proteins

quaternary structure

a protein compoudn of several polypeptide chains (subunits)

globular protein

compact, spherical, water soluble, function, irregular amino acid sequences

fibrous protein

long, strand-like, water insoluble, structural, repetitive amino acid sequence

2

the number of hydrogen bonds A and T make

3

the number of hydrogen bonds C and G make

mRNA

RNA that codes for proteins

tRNA, rRNA

two types of noncoding RNA

40000

number of protein coding genes humans have

prokaryotes

bacteria and archaea cellular classification

eukaryotes

plant and animal cellular classification

archaea, bacteria, eukarya

three domains of life

phosphodiester bonds

bonds DNA along the backbone

hydrogen bonds

bond nucleotides together across the helix

glycosidic bonds

bond carbohydrates together

peptide bonds

bond proteins together and bond amino acids together

linear

DNA and proteins are ___ models

covalent bond

strong bond, nonmetal + nonmetal

noncovalent bond

weak, H-bonds, electrostatic interactions, hydrophobic forces, van der Waals forces

oxidation

loss of electrons

reduction

gain of electrons

enzymes

catalyze reactions by decreasing hte activation energy via stabilization of the transition site

allosteric

adopt two different conformations depending on if something is bonded to it or not

positive regulation

bonding of molecule to allosteric site allows process to take place

negative regulation

bonding of nmolecule to allosteric site prevents a process from taking place

Ser, Thr, Tyr

amino acids that can be phosphorylated

kinase

enzyme that ca phosphorylate another protein by taking a phosphate group from ATP and giving it to the protein

phosphatase

enzyme that removes phosphate group from a phosphorylated protein

Lys

amino acid that can have a methyl or acetyl group added to it

motor proteins

use energy from ATP or GTP hydrolysis to produce directional movement, converts chemical energy into mechanical work

intrinsically disordered regions (IDRs)

look like loops and allow for more elastic structure in proteins, lack a fixed structure

IDRs

regions of proteins most likely to be phosphorylated

IDRs (intrinsically disordered regions)

can tether intermediates in a large multi-protein complex

bacteria

do not splice mRNA

exon

coding sections of mRNA kept after splicing

introns

noncoding sections mRNA removed during splicing

46

number of chromosomes humans have

1%

% protein coding DNA sequences (in exons) in humans

~5000

number of human noncoding RNA genes

45%

% DNA transcribed in humans, only 1% of this becomes proteins

~20000

number of human genes that code for proteins

~50%

% of transposon in humans

transposon

high copy repetitive element, DNA sequences that is capable of inserting itself into a genome and moving along a DNA strand, some are capable of copying themselves

centromere, 2 telomere, replication origin

the there specialized sites chromosomes are required to have in order to produce a eukaryotic chromosome

histone proteins

protein that DNA wraps around in a chromatin to provide structure

euchromatin

less condensed sections of chromatin, generally associated with gene activity

heterochromatin

highly condensed sections of chromatin, often transcriptionally inactive

147

number of nucleotide pairs sufficient to wrap around histone 1.7 times

200

number of nucleotide pairs that nucleosomes repeat at (interval that they repeat at)

histone octamer

an H3-H4 tetramer with two H2A-H2B dimers

histone acetyl transferases (HATs)

an acetyl group added to a Lys on a histone

histone code hypoethsis

specific patterns of histone modifications acts as signals recognized by other proteins

reader complex

binds tightly only to a region of chromatin that contains several different histone marks that it recognizes

topologically associating domain (TADs)

regions where DNA sequences interact more frequently with each other than with sequences outside of the TAD

structural maintenance of chromosomes (SMC)

protein complexes play key roles in forming and maintaining these loops

mutations

changes in nucleotide sequences

gene duplication

creates copies that can diverge to new functions

exon shuffling

recombination of exons can create new genes with novel domain combinations

transposable elements

mobile DNA sequences can move and insert, altering gene expression or creating new genes

mutations, gene duplication, exon shuffling, transposable elements

mechanisms of genome evolution

compartive genomics

reveals conserved sequences (often function) and regions of rapid evolution

transforamtion, transduction, conjugation

methods of horizontal gene transfer in bacteria

transformation

the process in which a bound DNA molecule is fragmented on the surface of a recipient bacterial cell, with only one strand of each fragment entering the cell

transduction

the process by which a virus transfers genetic material from one bacterium to another

conjugation

the process by which one bacterium transfers genetic material to another through direct contact

semiconservative

DNA replication is…

conserved, new

each daughter DNA double helix is composed of one ___ and one ____ strand

antiparallel nature

what about DNA makes replication possible

helicase

unwinds DNA

DNA polymerase

replicates new DNA strands

leading strand

which DNA has continuous synthesis

5’ to 3’

direction of DNA synthesis

lagging strand

which DNA strand has discontinuous synthesis

okazaki fragment

short DNA fragments that are temporarily produced during DNA replication at the lagging-strand

DNA polymerase alpha, DNA polymerase epsilon, DNA polymerase delta

the DNA polymerases in eukaryotic cells