Molecular Genetics Flashcards by Michelle Estrada

branch of genetics that deals with the structure and function of genes at the molecular level

molecular genetics

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genetic material

DNA

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basic physical and functional unit of heredity

gene

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made up of DNA and and associated proteins, including positively charged histones and less positively charged non-histone proteins

chromatin

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fives types of histones

H1, H2A, H2B, H3, H4

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secondary structure of the chromatin made up of 6 nucleosomes

solenoid

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composed of a segment of DNA wrapped around 8 histone proteins (2 of each - H2A, H2B, H3, H4)

nucleosome

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connects adjacent nucleosomes (associated with H1)

spacer or linker DNA

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characteristics of genetic material

stable, replicable, translatable, mutable

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transformation principle of Griffith

virulent strain -> dead
avirulent/ heat-killed virulent strain - > alive
avirulent + heat-killed virulent strain -> dead
must be a transformation

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Avery: DNA as transforming principle

w/ protease -> transformation
w/ deoxyribonuclease -> no transformation
DNA must be the transforming principle

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Hershey-Chase experiment

T2 bacteriophage
P-labeled DNA transferred into bacterial cell
S-labeled proteins found in phage ghosts

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genetic material of 5 kingdoms of life + virus

ds-DNA - plants, animals, fungi, bacteria, archaeans

DNA/RNA or single-/double- - viruses

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differentiate DNA and RNA based on (1) nitrogenous base; (2) sugar present; (3) pentose sugars

(1) thymine vs. uracil
(2) deoxyribose vs. ribose
(3) no OH group on 2’-C vs. present OH group on 2’-C

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made up of sequences of nucleotides

nucleic acids

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building block of DNA/RNA

nucleotide

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components of a nucleotide

pentose sugar, phosphate group, N base

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differentiate pyrimidine vs. purine based on (1) no. of rings present, (2) ring structure, (3) covalent bond with sugar phosphate, (4) examples

(1) 6 vs. 9; (2) single vs. double; (3) N1 atom vs. N9 atom; (4) C, U, T vs. A, G

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N base + pentose sugar

nucleoside

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nucleoside + phosphate

nucleotide

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bond between sugar and phosphate

C2’, C3’, (primarily) C5’

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covalent bond joining nucleotides

phosphodiester bonds C3’ atom to C5’ (3’ to 5’ phosphodiester bond)

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joins the two chains of DNA/RNA between pairs of nucleotides

H-bonds

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number of bonds between (1) A-T, (2) G-C

(1) 2 H-bonds, (2) 3 H-bonds

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rule which states that a purine binds with a pyrimidine

Chargaff's rule

Watson-Crick model of DNA

ribbon-like strands = sugar-phosphate backbone horizontal rungs = N base pairs antiparallel strands complementary

A-DNA, B-DNA, vs. Z-DNA

(1) high salt/dehydration conditions (2) Watson and Crick's model; aqueous no salt conditions; biologically significant conformation (3) exist in some regions of chromosomes

describes the flow/transfer of genetic information within a biological system and is often stated as DNA makes RNA, RNA makes protein

central dogma

three general transfers

DNA replication, transcription, translation

special transfers that occur in some viruses

RNA replication, reverse transcription

DNA is copied into DNA; occurs at S phase of interphase

DNA replication

DNA information is copied into mRNA

transcription

synthesis of protein using mRNA

translation

replication of RNA from RNA by RNA replicase

RNA replication

synthesis of DNA using RNA

reverse transcription using reverse transcriptase

phenomenon in which a new of strand of DNA is made of a parental strand and a new strand

semi-conservative replication

breaks H-bonds between N-bases to cause unwinding of DNA strands

helicase

prevent rewinding of two strands by stabilizing them

single-strand binding proteins

catalyzes the synthesis of a short RNA primer for replication

primase

relaxes supercoiling by introducing single- or double- stranded cuts into the DNA molecule

DNA gyrase/ DNA topoisomerase

catalyzes the synthesis of DNA molecules from the 5' to 3' direction

DNA pol III

provides the 3'OH group needed by DNA polymerase

RNA polymerase

replaces RNA primer with DNA nt

DNA pol I

formed by the opening of the origin of replication

replication fork

newly synthesized DNA, continuous DNA synthesis

leading strand

discontinuous DNA synthesis

lagging strand

fragments of small DNA present in the lagging strand

Okazaki fragments

origin of replication in E. coli with 9-mers and 13-mers

OriC

initiates unwinding of DNA helix in E. coli

DnaA

joins fragments of DNA nucleotides and seals nicks between discontinuously synthesized strands

DNA ligase

DNA polymerase holoenzyme

DNA pol III

subunit of DNA pol III responsible for nucleotide polymerization

alpha subunit

subunit of DNA pol III responsible for 3 to 5 exonuclease activity/proof-reading ability

epsilon subunit

sliding clamp structure of DNA pol III which prevents the core enzyme from falling off the template during polymerization

beta subunit

Why are more DNAs replicated in eukaryotes even if DNA replication in bacteria is 500 nt/second and only 15 nt/second in eukaryotes?

Eukaryotes have multiple replication bubbles per parent DNA

DNA pol involved in the repair of DNA damage due to external forces like UV light

DNA Pol II, IV, V

ends of the linear chromosomes of eukaryotes which preserves integrity and stability of a linear chromosome

telomeres

problem encountered during DNA replication at the telomere

gaps left by RNA pol at lagging strand template leaving a gap labeled '--b--'

solution to the problem of telomere shortening; ribonucleoprotein containing RNA as a guide for the attachment and a template for RT

telomerase

process by which information stored in the DNA is converted into instructions for making a functional product such as proteins/RNA

gene expression

two steps of gene expression

translation and transcription

DNA replication vs. RNA transcription

(1) only a small region of DNA is used as template in transcription (2) transcription makes use of RNA pol vs. DNA pol (3) transcription results in ssRNA

RNA which plays a role in translation; acts as temporary carrier of amino acids

transfer RNA

RNA which becomes part of a ribosome, the site of protein synthesis

ribosomal RNA

RNA which are protein-coding genes that are translated to proteins; template for protein synthesis

messenger RNA

regulatory mRNA

micro RNA

serves as the binding site of RNA polymerase in transcription

promoter sequence

recognizes the promoter and catalyzes the synthesis of RNA molecules

RNA pol

step of transcription which involves the insertion of a ribonucleotide at the start site

initiation

step of transcription where ribonucleotide complements are inserted

elongation

step of trasncription where transcribed RNA molecule is released

termination

formed when RNA pol binds to a promoter and the two strands of DNA detach from each other

replication bubble

untranscribed strand which has an identical sequence to the transcribed RNA

sense strand

serves as the template strand

anti-sense strand

subunits of RNA pol which provide the catalytic basis and active site for trancription

beta and beta'

subunit of RNA pol and has a regulatory role; recognizes promoters

sigma factor

How does termination of transcription occur in prokaryotes?

hairpin loop secondary structure, Rho protein

Bind to promoters of certain genes among eukaryotes; also known as reprogramming factors (can reprogram differentiated cell to become pluripotent)

transcription factors

basic building blocks of a protein

amino acids

may increase or decrease the level of expression of genes (includes silencers and enhancers)

regulatory elements

Silencers can bind transcription regulation factors known as _____.

repressors

primary RNA transcript produced at the end of transcription in eukaryotes

pre-mRNA

coding sequences

exons

non-coding sequences

introns

steps post-transcriptional RNA processing

5'-capping, 3'-polyadenylation, removal of introns and joining of exons

removes introns and joins exons; consists of small nuclear RNAs complexed with proteins to form small nuclear ribonucleoproteins

spliceosomes

types of RNA in bacteria vs. archaea. vs. eukarya

1 type vs. several types but not fully studied vs. 3 types

use of RNA pol I, II, III in eukaryotes

I - rRNA, II - mRNA, III - tRNA

consists of three nucleotides that specifies a particular amino acid

codon

Amino acids are linked together by ____.

peptide bonds

chain of amino acids

proteins

level of structure in proteins - sequence of amino acids

primary

level of structure in proteins - patterns of folding (alpha-helix and beta-pleated sheets)

secondary

level of structure in proteins - folding of the entire polypeptide into 3D

tertiary

level of structure in proteins - how different subunits are packed together to form overall structure of protein

quaternary