biochem exam 4

Which of the following removes the RNA nucleotides from the primer and adds equivalent DNA nucleotides to the 3' end of Okazaki fragments?

DNA POL 1

Which of the following statements is true of chromatin?

Heterochromatin is highly condensed, whereas euchromatin is less compact.

Which of the following removes the RNA nucleotides from the primer and adds equivalent DNA nucleotides to the 3' end of Okazaki fragments?

DNA POL 1

Which of the following statements is true of chromatin?

Heterochromatin is highly condensed, whereas euchromatin is less compact.

Which of the following techniques could help a researcher inhibit the expression of a target gene?

RNAi

how many base pair codons do we have total

64

Shine-Dalgarno sequence is

upstream from AUG

A polysome could be best described as

an active site for protein biosynthesis

Identify the false statement regarding the control and secretion of insulin

High intracellular ATP opens the ATP-sensitive potassium ion channel.

DNA replication occurs ( ), while transcription and protein translation take place ( ), respectively

in the nucleus, in the nucleus and on ribosomes

Binding of high level of insulin molecules to their receptors will () - in regards to appetite

inhibit the production of appetite-stimulating neuropeptide Y and induce the production of appetite-suppressing -MSH

Insulin stimulates glucose uptake in

muscle and adipose where glucose is converted to glucose 6 phosphate

insulin in liver activates

glycogen synthase and inactivates glycogen phosphorylase, so that much of the glucose-6-phosphate is channeled into glycogen.

lipoprotein lipase breaks down

triglycerols in the lipoproteins to smaller fatty acids and monoglycerides that are transported into your tissues and either burned for fuel or re-assembled into triglycerides for storage

specialized pancreatic cells that secrete important hormones:

alpha- glucagon
beta cells- insulin
delta- somatostatin

somatostatin inhibits

insulin and glucagon

where are the alpha beta and delta cells found

the islets of Langerhans in pancreas

beta cells secrete what in response to increasing blood glucose levels

insulin

glucose enters what cells via what

enters beta cells via GLUT2
-glycolysis, ATP increases

ATP binds to

ATP gated K+ channels then K+ channels close depolarizing plasma membrane

the closing of K+ channels triggers opening of

Ca2+ voltage gated ion channels and theres an increase of Ca2+ in cytosol through exocytosis

maturation of insulin

-24 AA−long signal sequence targets proinsulin into the endoplasmic reticulum where the storage vesicles form
-formation of disulfide bonds occurs within storage vesicles
-Ca2+ activated proteases that cleave C-peptide from proinsulin
-tests of insulin levels measure C-peptide

1 glucose forms how many ATP

30-32

Ca2+ is also released from

endoplasmic reticulum in response to initial elevation of Ca2+ levels in cytosol

depolarizing the membrane

internal is less positive

process of fuel metabolism due to prolonged fasting or type 1

leads to CAC inhibition, ketone body formation, and eventual coma/death due to ketoacidosis
-glycolysis isn’t stimulated leading to muscle and fat breakdown, so the oxaloacetate produced is used to send glucose to your brain
-without oxalo staying in CAC it’s inhibits so the fat broken down remains acetyl coa and is used for ketone bodies which provide some fuel also for the brain but accumulate in your kidneys

Fuel Use Over Four Hours of Normal Human Metabolism

right after eating- glucose rises
-insulin stimulates glycolysis and glycogen synthesis
-two hours after eating blood glucose drops- glycogen secreted liver glycogen releases glucose
-four hours after eating more glucagon from pancreatic alpha cells, more TAG hydrolysis, FA becomes fuel for muscle and liver

two forms of diabetes

type 1- insufficient production of insulin:
-due to autoimmune destruction of B-cells
-develops early in life
-genetic
-ie insulin dependent or juvenile diabetes
type 2- insulin resistance
-worse type
-more common
-develops in late adulthood
-associated with obesity
-cells dont respond appropriately to insulin

diabetes symptoms

in both forms of diabetes, blood sugar becomes elevated
body tries to dilute glucose and this causes excessive urination and thirst

in type 1 diabetes fat breakdown is accelerated which leads to

high production of ketone bodies
this raises H+ and leads to ketoacidosis
Bicarbonate buffering system activated, leads to altered breathing
Breakdown of ketone body acetoacetate produces acetone, which is expelled via the breath
Untreated diabetes leads to dramatic weight loss

Physiological Effects of Blood Glucose Levels

Blood glucose is normally determined after several hours of fasting
High fasting blood glucose level (126 or higher) is a warning sign for diabetes
Low fasting blood glucose level below 50 (in men) or 40 are warning signs of various hypoglycemic conditions
Blood glucose levels after meal (postprandial) are typically higher (up to 145 mg/100 mL is normal)

long term effects on elevated blood sugar

Compromises O2 delivery, especially in extremities (feet, etc.)
Increases risk of cardiovascular disease, renal failure, and damage to small blood vessels and nerves

adipose tissue releases

peptide hormones called adipokines which carry info about fuel stores to brain

hormones that control eating

alpha MSH suppresses appetite- eat less metabolize more
neuropeptide Y (NPY)- inceat more metabolize less

Both leptin and insulin are peptide hormones both trigger production of ( ) and act upon what cells

acts on anorexigenic neurosecretory cells to increase production of alpha MSH

Leptin and insulin also act on orexigenic neurosecretory cells to inhibit the release of

NPY

leptin

Stimulates production of anorexigenic (appetite-suppressing) hormones
Stimulates sympathetic nervous system
Triggers cascade that regulates gene expression
May be involved in hard-wiring of neuronal circuits during development

neuropeptide Y

orexigenic (appetite-stimulating) hormone
Sends signal to eat
Levels rise in starvation
Levels rise in ob/ob and db/db mice
Inhibited by leptin and insulin

alpha melanocyte stimulating hormone (a-MSH)

is an anorexigenic (appetite-suppressing) hormone
Sends signal to stop eating
Release is stimulated by leptin
Acting through melanocortin 1 receptor, α-MSH stimulates the production and release of melain, by melanocytes in skin and hair.

leptin increases transcription of gene yielding

a-MSH

what happens to leptin receptor when leptin binds

it dimerizes and JAK phosphorylates 2 Tyr in receptor dimer

after JAK is phosphorylated in the receptor dimer what happens

Receptor becomes docking site for STAT3, STAT5, STAT6 (Signal Tranducers and Activators of Transcription)
STATs are phosphorylated by the same JAK

once that STATs dimerize they

move the nucleus stimulate transcription of gene for precursor to anorexigenic a-MSH

JAK-STAT mechanism of leptin signal transduction

folic acid helps treat

stroke and heart attacks

high blood glucose levels cause hemoglobin to become

glycosylated

insulin also inhibits appetite by interacting with

hypothalamus

The orexigenic neurons have insulin receptors to Regulate

wakeful appetite

insulin binding to orexigenic neurons

Inhibits release of appetite-stimulating NPY
Stimulates appetite-suppressing a- MSH

there can be cross talk between

insulin and leptin pathways

Leptin makes liver and muscle more sensitive to

insulin
common 2nd messenger may enable leptin and insulin to trigger same downstream pathways

type 2 diabetes epidemic

90% of diabetes cases are type 2
300 million diagnosed cases world-wide and growing
Hallmark is resistance to insulin
Initially, the body responds by making more insulin
Over time, some individuals have to supplement with insulin

type 2 diabetes syndrome

Believed to affect 27% of adult U.S. population
Cluster of symptoms along with insulin resistance:
Abdominal obesity
High triglycerides (TAGs)
Low HDL Good high-density lipoprotein (HDL) cholesterol
They act as cholesterol scavengers, picking up excess cholesterol in your blood and taking it back to your liver where it's broken down. The higher your HDL level, the less "bad" cholesterol you'll have in your blood.
High blood pressure
Elevated blood glucose (but may not be full-blown diabetic)
Often includes other signs of inflammation

functions of nucleotides

Energy for metabolism (ATP)
Enzyme cofactors (NAD+)
Signal transduction (cAMP)

functions of nucleic acids

Storage of genetic info (DNA)
Transmission of genetic info (mRNA)
Processing of genetic information (ribonucleic acid enzymes)
Protein synthesis (tRNA and rRNA)

central dogma

replication - DNA- transcription- RNA- translation- protein

nucleotide=

nitrogenous bases
pentose
phosphate

nucleoside=

nitrogenous base
pentose

nucleobase=

nitrogenous base

pentose in nucleotides

beta-D-ribofuranose in RNA
beta-2-deoxy-D-ribofuranose in DNA

nucleobases

Derivatives of pyrimidine or purine
Nitrogen-containing heteroaromatic molecules
Planar or almost planar structures
Absorb UV light around 250–270 nm

pyrimidine bases

Cytosine is found in both DNA and RNA
Thymine is found only in DNA
Uracil is found only in RNA

purine bases

adenine
guanine

B-N-glycosidic bond

in nucleotides the pentose ring is attached to the nucleobase through this bond
bond is formed to position N1 in pyrimidines and to position N9 in purines
bond is stable toward hydrolysis especially in pyrimidines

how does B-N-glycosidic bond get cleaved

catalyzed by acid

nucleotide and nucleic acid nomenclature

what minor nucleoside (modification done after DNA synthesis) in DNA is common in eukaryotes, also found in bacteria

5-Methylcytosine

what minor nucleoside (modification done after DNA synthesis) in DNA is common in bacteria, but not found in eukaryotes

N6-Methyladenosine

epigenetic marker

Way to mark own DNA so that cells can degrade foreign DNA (prokaryotes)
Way to mark which genes should be active (eukaryotes)
Could the environment turn genes on and off in an inheritable manner?
Foreign DNAs (not methylated) that are introduced into the cell are degraded by sequence-specific restriction enzymes and cleaved

DNA can be methylated in

epigenetic

hydrogen bonding between what base pairs is easier to break and why

AT because it has 2 H bonds while CG has 3 bonds

mRNA - messenger RNA

Is synthesized using DNA template
Contains ribose instead of deoxyribose
Contains uracil instead of thymine
One mRNA may code for more than one protein
Together with transfer RNA (tRNA) transfers genetic information from DNA to proteins

gene expression control in Eukaryote-

Monocistronic- one promotor controls expression of one gene

gene expression control in prokaryotes-

polycistronic- one promotoer controls several genes

Palindromic sequences can form

hairpins and cruciforms

Different strands are read like

a palindrome read in reverse

same strands are read like

mirror- they repeat

When only a single DNA (or RNA) strand is involved, the structure is called

a hairpin

Tm of DNA

heat denaturation of DNA
it depends on pH and ionic strength and on the size and base composition of the DNA.
Tm= 50% of DNA becoming single stranded

factors that affect DNA denaturation

The midpoint of melting (Tm) depends on base composition
High CG increases Tm

Tm depends on DNA length
Longer DNA has higher Tm
Important for short DNA

Tm depends on pH and ionic strength
High salt increases Tm

what bases melt at a lower temp

AT

increase C and G nucleotides what happens to Tm graph

the temp increases
linear

Molecular Mechanisms of Oxidative and Chemical Mutagenesis

Oxidative damage
Hydroxylation of guanine
Mitochondrial DNA is most susceptible

Chemical alkylation
Methylation of guanine

Cells have mechanisms to correct most of these modifications

alkylating agent

chemical agents that cause DNA damage
S-adenosylmethionine
nitrogen mustard
dimethylsulfate
dimethylnitrosamine

which alkylating agent acts enzymatically

S-adenosylmethionine

molecular mechanisms of radiation induced mutagenesis

UV light induces dimerization of pyrimidines; this may be the main mechanism for skin cancers.

Ionizing radiation (X-rays and y-rays) causes ring opening and strand breaking .
These are difficult to fix.

Cells can repair some of these modifications, but others cause mutations. Accumulation of mutations is linked to aging and carcinogenesis.

deamination is removal of

NH group

depurination is removal of

prune group through hydrolysis

process by which DNA gets unwound from histones

acetylation

start codon

AUG (RNA)

stop codon

UAA UAG UGA (RNA)

what other amino acid only has one codon - and what is the code

Trp - UGG

bacteria also contains extra chromosomal double stranded circular

plasmids about 2000-10000 base pairs

E. coli

4,639,675 DNA 1 chromosome about 4400 genes

true or false: circular plasmids can be swapped easily in bacteria

true

what is one way bacteria can acquired antibiotic resistance

plasmid exchange

eukaryote DNA is in

multiple discrete chromosomes

composition of human genome

-only a small fraction (1.5%) of the total genome encodes for proteins
-Some DNA regions directly participate in the regulation of gene expression (promoters, termination signals, etc.)
-Some DNA encodes for small regulatory RNA with poorly understood functions
-Some DNA may be junk (pieces of unwanted genes, remnants of viral infections

exons

are expressed sequences (translated into amino acid sequence)
Exons account for only 1.5% of human DNA!

introns

are regions of genes that are transcribed but not translated
They do not encode polypeptide sequence

introns are removed after

transcription and the exon mRNA sequences are spliced together and creates “mature transcripts”

transposons are

sequences that can move within genome