genetics exam 1

heredity

a transmission of properties from one generation to the next

genotype

heritable information that an individual possesses

phenotype

physical, observable traits that an individual possesses

central dogma

a concept of information flow in living cells

DNA

deoxyribonucleicacid; double-stranded, antiparallel molecule that carries genetic information for the development and functioning of an organism

RNA

ribonucleic acid; single-stranded; principle role is to act as a messenger between DNA and the synthesis of proteins; carries genetic information in some viruses

protein

a large molecule made up of amino acids whose sequence is determined by the DNA code within a gene

replication

the process of duplicating a strand of DNA

transcription

the process of going from DNA to RNA

translation

the process of going from RNA to proteins

prokaryote

a single-celled organism whose cells lack a nucleus and other organelles

eukaryote

an organism whose cells contain a nucleus within a membrane

transforming principle

a physical material that is transmissible and heritable

“Smooth” strain of S. pneumoniae

appears shiny and smooth due to a polysaccharide capsule that protects it from the host's immune system which makes it virulent.

“Rough” strain of S. pneumoniae

appears rough and lacks the polysaccharide capsule, making it non-virulent.

virulent organisms

those that are able to cause disease

non-virulent organisms

those that are not able to cause disease

bacteriophage

A virus that injects material inside of its host cell and uses the host cell’s components to many copies of itself. The host cell eventually lyses and the virus copies are released.

E. coli

an bacteria found in the lower intestine of warm-blooded organisms; used in the Hershey-Chase experiment

Griffith’s experiment and conclusions

The transforming principle: When a mouse was injected with a live smooth virulent of of Streptococcus pneumoniae, it developed pneumonia. When injected with heat-killed smooth strains and live rough strains, the mouse survived, but when both were combined, the mouse died, indicating transformation. This meant that the observable traits of Streptococcus pneumoniae are caused by a physical material that’s transmissible and heritable

Avery, McCarty, and McLoed’s experiment and conclusions

Demonstrated that DNA is the transforming principle. They isolated DNA from heat-killed smooth strains and showed that it could transform rough strains into smooth, confirming that DNA carries genetic information. Under the same process, proteins and RNA were not capable of the transformation from smooth to rough strains.

Hershey and Chase’s experiment and conclusions

Demonstrated that DNA, not protein, is the genetic material by using radioactive isotopes to label the protein and DNA components of a bacteriophage (virus that infects bacteria), then showing that only the labeled DNA entered the bacterial cell during infection.

ribose

pentose sugar (OH chemical group); RNA

2’-deoxyribose

pentose sugar (H chemical group); DNA

nitrogenous base

covalently attached to the 1’ carbon; include purines and pyrimidines

triphosphate

phosphate groups attached at the 5’ carbon; make attachments to other nucleotides via their 3’ carbon

hydrogen bonds

procures interaction between antiparallel strands through nitrogenous bases; relatively weak

What kinds of bonds are phosphodiester and hly

include phosphodiester and glycosidic bonds

phosphodiester bonds

connect phosphate group to 3’ carbon in next nucleotide to form the phosphate backbone

glycosidic bonds

connect nitrogenous base to 1’ carbon

purine

2-ring structure: 1 6-member ring, 1 5-member ring; adenine and guanine

pyrimidine

1-ring structure: always 6-member ring; thymine and cytosine

adenine

purine; forms 2 bonds

guanine

purine; forms 3 bonds

cytosine

pyrimidine; forms 3 bonds

thymine

pyrimidine; forms 2 bonds

sugar-phosphate backbone

phosphodiester bonds that link nucleotides together (3’ carbon and phosphate group at 5’ carbon")

A-DNA

right-handed structure seen in conditions of low humidity; short+wide with narrow, deep major group and a wide, shallow minor groove

B-DNA

nearly all natural DNA is right-handed B-DNA; wide major groove, narrow minor groove of similar depths

Z-DNA

left-handed with alternating purine and pyrimidine bases; major groove near surface of the helix

minor groove

some proteins bind here if they are small enough

major groove

some proteins (mostly large) bind here and can interact with nitrogenous bases

Chargaff’s rules

%A=%T

%G=%C

helix properties - 1 “rung”

involves 1 nucleotide’s base pair; 0.34 nm apart

helix properties - 1 complete turn

distance of 10 rungs (10 nucleotides); includes 1 major and 1 minor groove; length of 3.4 nm; strands are antiparallel

complementary

describes the bases on two strands; why one strand contains all info needed to produce a second strand

semiconservative

template hypothesis; DNA is copied to create two new DNA strands, each containing one old strand and one new strand

conservative

one copy is made of the old strands and the other is made of 2 new strands (conserves original strand)

dispersive

DNA replication model by which a new strand is made up of fragments from the old strand as well as newly synthesized fragments

DNA polymerase I

removes primer; also capable of DNA synthesis to replace primers

also has 3’ to 5’ exonuclease activity that enables reparations of mistakes

DNA polymerase III

responsible for most DNA synthesis; works from 5’ to 3’ starting at primer

also has 3’ to 5’ exonuclease activity that enables reparations of mistakes

template strand

single-strand DNA

primer

short, single-stranded RNA that acts as a starting point for DNA synthesis

initiator protein

opens of (melts) DNA as a step to creating a template strand

origin of replication

the location where initiator proteins perform; typically A-T rich as they are weaker (only 2 H-bonds)

helicase

responsible for unwinding DNA to create the template; work in opposite directions of the origin of replication

primase

responsible for synthesizing a short RNA primer (antiparallel to template)

ligase

connects fragments by ligating DNA at “nicks” of phosphodiester bonds from removal of primers

topoisomerase

relaxes supercoils caused by replication fork

telomerase

extends 3’ end to preserve the ends of a chromosome

1. removes RNA primer

2. adds an extension to the template strand

3. new RNA primer produced

4. extra DNA added

3’ to 5’ exonuclease activity

1. locate mismatch

2. remove 3’ nucleotide

3. add new OH, then new nucleotide

performed by DNA polymerase I and III

replication fork

a very active area where DNA replication processes take place

leading strand

5’ to 3’; synthesis occurs continuously

lagging strand

3’ to 5’; synthesis is discontinuous

Okazaki fragments

the result of synthesis occurring discontinuously on the lagging strand

DNA “nicks”

gaps of missing phosphodiester bonds resulting from the removal of RNA primers on fragmented lagging strands

DNA super-coiling

double helix twisted in space about its own axis; caused by the replication fork

proof-reading

action taken place in 3’ to 5’ direction by DNA Pol 1 and DNA Pol III

replisome

the complex of replication proteins that form at the replication fork; moves as a unit along the DNA

Meselson and Stahl’s experiment and conclusions

confirmed that DNA replicated through semi-conservative model; used heavier 15N isotope of E. coli DNA as well as a natural light 14N DNA media to measure how much of the 15N was in the sample after each replication

Kornberg’s experiment and conclusions

determined that the components necessary for DNA replication were the template, primer, DNA nucleotides (dNTPs) and DNA polymerase I

What components are needed for DNA replication in vitro?

• template

• primer

• DNA nucleotides (dNTPs)

• DNA polymerase + Mg2+ to increase efficiency of DNA pol

DNA replication in living cells

be familiar with replication fork and DNA synthesis on both strands

replication bubble

locally denatured segment of DNA

coding strand

sequence directly matches produced RNA

mRNAs

messenger RNAs that code for proteins; aka coding RNAs

tRNAs

transfer RNA; serves as a link between mRNA and growing chain of amino acids that make up a protein

rRNAs

ribosomal RNA; non-coding; acts as a catalyst to carry out protein synthesis

non-coding RNA

includes rRNA and tRNA as well as RNAs used for splicing / processing

RNA polymerase

capable of initiating new RNA chains (no primer needed)

RNA nucleotides

uracil, guanine, cytosine, adenine

uracil

RNA contains uracil in place of thymine; can form two bonds with A and G

GU “wobble” base-pairing

occurs due to 2 bonds with G instead of 3 (like in a typical GC pairing)

stem-loop RNA / hairpin

structure in RNA that forms when complementary sequences on the same strand pair up

initiation of transcription in prokaryotes

1. formation of closed promoter complex

2. conversion of closed to open promoter complex

3. polymerizing the first 10 nucleotides while polymerase remains at promoter

4. promoter clearance (transcript becomes long enough to form a stable hybrid with template strand

elongation

after the first nucleotide, there is processive addition at growing 3’ end of RNA

termination in prokaryotes

two methods: Rho-independent, Rho-dependent

promoter region

the DNA sequence located upstream of a gene (-35 box); typically TA rich (weaker); helps RNA pol transcribe a gene

terminator

a section of nucleic acid that signals the end of the transcription process

upstream

numbers decrease (-35,-10 boxes)

downstream

numbers increase

the +1 position

where the 1st nucleotide is transcribed

sigma factor

a protein; the sign post for RNA pol to initiate transcription

-10 box

part of the promoter located at base pair -10; where RNA pol begins to unwind DNA

-35 box

part of the promoter located at base pair -35; collaborates with Sigma factor to recruit RNA pol holoenzyme

open promoter

a DNA-RNA polymerase complex that’s partially unwound in preparation for transcription

closed promoter

when RNA pol has bound itself to DNA that is still double-stranded

rho-dependent

when a rho protein binds to RNA, RNA pol dissociates from DNA and transcription ends

rho-independent

when a hairpin forms, RNA pol dissociates from DNA and transcription ends

base-pairing in RNA-RNA duplexes

NOT predictable