Bio 303 Exam Iii

Front 1

Central Dogma

Back 1

DNA --> (transcription)
RNA --> (translation)
proteins!

Front 2

Attributes of genetic material

Back 2

1. Replication
2. Storage of info
3. Expression of info
4. Variation by mutation

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DNA is genetic info, except...

Back 3

in some viruses, which use RNA as genetic info

retroviruses: RNA>DNA>RNA>protein

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DNA Structure

Back 4

DNA is a polymer of millions of nucleotide bases

Front 5

4 Nucleotide Bases

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Purines: Adenine, Guanine
Pyrimidines: Thymine, Cytosine, Uracil
COMPLEMENTARY base pairs: A&T, G&C
*U replaces T in RNA

Front 6

Purines vs. Pyrimidines

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Purines have 2 rings, pyrimidines only have one

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Phosphate Groups are like...

Back 7

little batteries, they are ENERGETIC with directionality (not symmetric)

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Double Stranded DNA

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composed of two single strands of DNA linked by HYDROGEN BONDS between nucleotides

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Strands have directionality...

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-based on the way the phosphate group is linked to the deoxyribose sugar
-Double stranded DNA runs ANTI-PARALLEL
-wrap around each other = DOUBLE HELIX

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New nucleotides are only added at which end of the DNA molecule?

Back 10

3'

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DNA synthesis occurs from which end to which end?

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5' --> 3'

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# bonds between nucleotides

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A-T = TWO BONDS
G-C = THREE BONDS

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%GC/GC Content

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-mitochondrial DNA has lower %GC than most nuclear stretches of DNA
-%G WILL ALWAYS EQUAL %C

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Hydrogen bonds

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one = weak
many = STRONG

Front 15

Size of DNA

Back 15

~10 bases per turn of double helix
~3.4 angstroms per base
-have Major and Minor grooves

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Phosphodiester Linkage

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links 5'-phosphate group on the phosphate to the 3'-OH on the deoxyribose sugar

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Ribonucleic acid

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the ribose sugars have an extra -OH than the deoxyribose
*USUALLY SINGLE STRANDED

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Importance of DNA structure

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-double-stranded = backup always present
-structure makes replication easy

Front 19

A, B, Z DNA

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A DNA = 2.3 nm/turn of 11 bases
B DNA = 3.4 nm/turn of 10
Z DNA = left-handed

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Alternate Localized Structures of DNA

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ex: loops, hairpins - based on direct/inverted repeats, biologically important
ex: TACTCAT

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Each chromatid is...

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ONE DNA duplex (one cross)

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DNA Replication occurs...

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every time cells divide

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4 Steps in DNA Replication

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1. Strand Separation
2. Priming
3. Extension
4. Primer removal and gap closure

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1. STRAND SEPARATION

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Enzyme: DNA Helicase unzips helix
DNA Gyrase (at a distance)

-Single Strand Binding proteins (stabilize single strands)

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2. PRIMING

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Enzyme: Primase
*enzymes that carry out DNA synthesis cannot initiate synthesis, they require a PRIMER

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primer

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short RNA molecule synthesized by primase

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3. EXTENSION (DNA SYNTHESIS)

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Enzyme: DNA Polymerase III
-DNA synthesis begins at the end of primer
-DNA Gyrase releases tension
-synthesis occurs 5'-3'

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4. PRIMER REMOVAL

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Enzyme: DNA Polymerase I and Ligase
-DNA polymerase replaces the RNA primer with DNA
-Ligase seals cuts in the DNA backbone

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Semi-conservative DNA replication

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one old strand, one new strand

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What does DNA gyrase do?

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loosens DNA strands for helicase to pull apart, relieves TORSIONAL STRESS

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Directionality of DNA Replication

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DNA Replication beings at specific sites along the chromosomes, and moves in both directions (2 replication forks form an oval)

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Leading Strand

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continuous DNA replication

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Lagging Strand

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discontinuous DNA replication, when DNA is replicated to join the lagging strand, the stretches of DNA are separated by RNA primer

Front 34

What do single stranded binding proteins do?

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bind and stabilize single stranded DNA during DNA replication until the single stranded DNA can be used as a template for a new strand to bind to

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Replication near chromosome ends...

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Telomeres: 1) prevent chromosome shortening
2) prime DNA synthesis near ends

-telomerase lengthens telomeres/telomere loops

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Prokaryotic DNA Organization

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circular with one origin of replication, some DNA binding proteins but not as intense as histones

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Eukaryotic DNA Organization (highly organized, compact)

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1. Nucleosomes
2. Solenoid Fiber
3. Chromatin Fiber
4. Chromatid

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1. Nucleosomes

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DNA wrapped around proteins known as HISTONES

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2. Solenoid Fiber

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Coil of DNA + Histones

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3. Chromatin Fiber

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Coil of Solenoid fiber (coil of coils)

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4. Chromatid

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Chromatin Fibers arranged in loops (loops of coils of coils)

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B DNA Final Packing Ratio

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10,000-40,000:1

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Level of DNA condensation affects...

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DNA function --> more highly condensed, DNA is less accessible to proteins = less "active"

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Heterochomatin

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highly condensed DNA, INACTIVE
(less transcription)

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Euchromatin

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ACTIVE DNA

Front 46

Examples of heterochromatin

Back 46

Barr bodies = inactivated X chromosomes in females,
Also: centromeres, telomeres

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4 Components of CHROMOSOMES

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1. Centromeres
2. Telomeres
3. Genes
4. Repetitive DNA (junk DNA)

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1. Centromeres

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specific (middle, connecting) region of the chromosome, "handle" for chromosome movement

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2. Telomeres

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caps/ends of chromosomes, offer protection and aid in DNA replication

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3. Genes

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actual genetic information, code for proteins
*account for LESS THAN 5% of human DNA

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4. Repetitive DNA (junk DNA)

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-most of the genome
-different types of repeats = functional, tandem, repeated genes, transposable elements

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Functional DNA Repeats

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associated with centromeres and telomeres

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Tandem DNA Repeats

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repeats of 2-100 nucleotides; can cause diseases

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Transposable DNA Elements ("Selfish DNA")

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like molecular parasites, move from place to place within genome

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Alu family of elements...

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5% of human genome

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Genome

Back 56

all genes in an organism, each gene codes for a specific protein
~25,000 genes

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Three main types of RNA

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Messenger RNA (mRNA) carries genetic info
Ribosomal RNA (rRNA) part of ribosomes
Transfer RNA (tRNA) translate genetic info from mRNA to proteins

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Genes = proteins in two steps

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1. DNA transcription to RNA (both in the language of nucleotides)
2. RNA translation to protein (nucleotides --> amino acid sequence)

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Transcription

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-produces RNA using DNA template
-RNA product is complementary to one DNA strand
-RNA product identical to other DNA strand (except U instead of T)

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Location of RNA

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portable, unlike DNA, ex: mom provides RNA to an embryo

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Amplification of RNA

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one DNA copy of a gene can yield multiple RNA transcripts

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Regulation of RNA

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all genes are present in every cell, but not all genes are transcribed in every cell

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How transcription works?

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RNA polymerase synthesizes RNA 5' --> 3' using DNA as a template, 3 steps:
1. initiation
2. elongation
3. termination

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1. Initiation

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directed by gene promoter (specific DNA sequences at the beginning of genes) ex: TATA box, controls amount of transcription, euks have enhancers and silencers

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2. Elongation

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transcription continues by DNA polymerase

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3. Termination

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occurs at the end of genes, specific DNA sequences trigger termination

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RNA processing (euks only)

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Caps and tails added - protect 5' and 3' ends of molecules, introns removed/spliced out, exons spliced (alternating)

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Introns

Back 68

-99% of genes is intron sequences
-introns = JUNK
-spliced out after transcription

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Exons

Back 69

-exons = "good stuff"
-remains after alternate intron splicing
-part of the gene that will represent codons

Front 70

the FINAL sequence (info) is determined by...

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intron splicing

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Codon

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3 nucleotides --> 1 amino acid
-some codons code for more than on AA
-STOP codons terminate translation

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tRNA

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converts RNA --> proteins
-recognizes codons
-carries one amino acid

Front 73

Translation

Back 73

synthesis of proteins, follows mRNA directions, then uses tRNA, then ribosomes

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Ribosomes

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huge, multi-protein complexes, non-specific protein synthesis machines

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Three steps in translation

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1. initiation (AUG codon)
2. elongation
3. termination (STOP codon)

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mRNA

Back 76

carry genetic info from DNA to protein

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small ribosomal subunit

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FIRST component in translation to interact with mRNA

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tRNA

Back 78

RNA that translates specific words in the genetic code into amino acids of proteins

Front 79

Reading Frame

Back 79

a way of breaking a sequence of nucleotides in DNA or RNA into three letter codons

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Mutations

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Changes in DNA sequence: substitution, insertion, deletion

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Causes of mutation

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1. Spontaneous - error in DNA replication
2. Induced - by chemicals/radiation

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Protein importance

Back 82

-do most of work to be alive
-most abundant macromolecules in cells
-enzymes
-structural proteins - maintain shape/organization

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Silent Mutation

Back 83

no change in protein

Front 84

Missense Mutation

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changes one codon - amino acid difference

Front 85

Nonsense Mutation

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changes one codon - results in a premature STOP codon

Front 86

Frameshift Mutation

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insertion or deletion of nucleotide which alters the reading frame; affects "downstream" of mutation

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Misfolded proteins can cause...

Back 87

alzheimers, Mad Cow

Front 88

Genes are portable...

Back 88

genes from Organism A can be expressed in Organism B --> GMO products

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Mutations cause a chain of events...

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1. change in DNA sequence
2. change in RNA
3. change in amino acid
4. change in protein structure
5. alter/elimination of function

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Induction vs. Repression

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Lac Operon Induces gene expression

Tryptophan Operon Represses gene expression

Front 91

Protein motifs exist...

Back 91

to facilitate binding to DNA

Front 92

Polycistronic mRNA

Back 92

only found in prokaryotes

Front 93

Lactose Operon

Back 93

response to the presence of lactose as a carbon source, normally OFF but is INDUCED/ACTIVATED

Front 94

Tryptophan Operon

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response to the need for tryptophan, normally ON, but is REPRESSED when not needed

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Cis Element

Back 95

Operator/promoter

Front 96

Trans Element

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Repressor

Front 97

Allo-lactose

Back 97

metabolite of lactose, usually the inducer

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F' Factor

Back 98

-carry portions of regular bacterial chromosome
-maintained separately from chromosome
-construct essential "partial diploids" in genes
-only ONE per bacterial cell

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Conjugation Tube

Back 99

structure that can transfer F' factors from one bacterial cell to another

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Recipient

Back 100

bacterial cell that receives F' factor and therefore has two copies of genes

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Merozygote

Back 101

recipient cell that is now "partially diploid"

Front 102

Glucose

Back 102

preferred carbon source, if glucose is available (even if lactose is also present), the lac operon genes are not expressed

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CAP

Back 103

Catabolite Activating Protein, acts as a transcription factor

Front 104

cAMP

Back 104

cyclic AMP, "second messenger" used in biology

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When glucose is present...

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induction of the lac operon genes is NOT allowed

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Catabolite Repression

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mechanism for: when glucose is present, there is no need to metabolize lactose (or other non-glucose sugars)

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Lac promoter is weak/strong?

Back 107

WEAK

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PRESENCE OF GLUCOSE

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1. Increased glucose
2. Decreased cAMP
3. Decreased cAMP-CAP
4. Decreased cAMP-CAP-CAP binding site
5. Decreased lac promoter activity
6. Decreased expression of lac operon genes
7. Reduced gene expression

Front 109

Eukaryotic Gene Expression

Back 109

-more complex than prokaryotic

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Half-life of some mRNAs...

Back 110

is in minutes

Front 111

Chromatin...

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-loosened during mitosis/meiosis
-very packed
-needs to be remodeled to be transcribed
-remodeling moves histones

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GENE REGULATION

Back 112

1. Absence of lactose = regulator protein (repressor/trans element) binds to operator, inhibits transcription
2. Presence of lactose = some --> allolactose
3. Allolac binds to regulator protein, inactivates it
4. b/c the regulator can't bind to the operator, structural genes continue to be transcribed/transcripted

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Ends of eukaryotic DNA (not proks)

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5' cap structure, poly A tail

Front 114

siRNA, miRNA, RNAi

Back 114

molecular device/mechanism to inactivate expression of specific eukaryotic mRNAs

Front 115

Which are polymerases?

Back 115

RNA polymerase, DNA polymerase, primase

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operon

Back 116

common approach to coordinated gene regulation in prokaryotes

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DNA polymerase is invovled in...

Back 117

extension, primer removal

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N-terminus

Back 118

first amino acid AFTER initial Met

Front 119

C-terminus

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first amino acid BEFORE STOP codon

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T/F: the 5'-->3' nature of nucleic acid synthesis requires a special mechanism to faithfully replicated telomeres (ends of chromosomes)

Back 120

TRUE

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T/F: Promoters generally mark the physical start of transcription in a gene.

Back 121

TRUE

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T/F: Every gene in the genome is transcribed in every cell in the body.

Back 122

FALSE

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T/F: Each amino acid has/is carried by only ONE specific tRNA.

Back 123

FALSE

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T/F: The transformation of an alpha-helix portion of a protein into a beta-sheet structure is unlikely to significantly alter the protein's structure/function.

Back 124

FALSE

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T/F: The final packing ratio of DNA in the human nucleus if about 10000-40000:1

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TRUE

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T/F: In eukaryotes, the lifetime of some mRNAs may be as short as a few minutes, while the lifetime of other mRNAs can be as long as months or years.

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TRUE

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Semi conservative DNA means...

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each newly formed duplex of DNA consists of one old strand and one new strand

Front 128

How to find the complementary strand of DNA 5' CGTA 3'

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1. Draw out complementary 3'>5'
(3' GCAT 5')
2. Reverse for answer
(5' TACG 3')

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The analysis of a properly formed double-strand DNA molecule would find...

Back 129

-%A = %T
-%purines = %pyrimidines
-total # hydrogen bonds is 2x(AT) + 3x(GC)

Front 130

What is expected from RNA base composition?

Back 130

A =/= U, G =/= C

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What ALL proceeds 5' --> 3'?

Back 131

1. DNA synthesis
2. RNA synthesis
3. mRNA translation

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Template strand

Back 132

Template for new DNA strand

Front 133

How to find the new RNA strand?

Back 133

Copy the new DNA strand EXACTLY but replace U's for T's.

If DNA 3'>5', and RNA is 5'>3' it will be reversed.

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Exons

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portions of a gene that are transcribed into RNA and translated into protein

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Introns

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portions of a gene that are transcribed into RNA but removed before translation

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An 82aa and a 56aa proteins have a lot in common - activity, one mutation ruins both, etc - WHY?

Back 136

The two proteins are probably from the same gene, but with different alternate INTRON splicing

Front 137

The human genome...

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~5% (25,000 genes)
-highly organized and packed into nucleus
-contains a number of families of highly repeated sequences

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Heterochromatin

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-can affect the expression of nearby genes
-genes, if present, are not expressed in heterochromatic regions

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Chromatin Remodeling

Back 139

-part of regulating eukaryotic gene expression
-involves the temporary repositioning and removal of histones from chromatin

Front 140

What components are involved in translation of mRNA transcripts into protein?

Back 140

mRNA, ribosomes, amino acids, tRNA

Front 141

Truths about Proteins

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1. first amino acid in a protein is METHIONINE
2. shape is dependent on amino acid sequence
3. prions = disease caused by change in shape of mature protein
4. binding of various compounds to a protein can cause its shape to change
5. Proceeds from N terminus - C terminus

Front 142

How could a missense mutation outside the actual proteins affect subunits?

Back 142

the single change in amino acid alters shape and therefore function, altering binding affinity

Front 143

How can one mutation located outside of any affected operons shut down all sugar metabolism operons?

Back 143

The mutation could cause CAP to be incorrectly synthesized so that it cannot bind to the CAP binding site, making the promoter inefficient in helping RNA polymerase transcribe/translate the genes necessary to break down sugars other than glucose.

Front 144

Normal base pairing in nucleic acids is stabilized by...

Back 144

Hydrogen bonds

Front 145

Factors than increase/decrease stability of mRNA...

Back 145

1. formation of small stretches of double stranded RNA on mRNA
2. presence of a 5' cap structure
3. presence of a 3' poly A tail